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Discovery proteomics offers deep insights but is currently not applied clinically in diagnostics. Here, the authors present ADAPT-MS, a flexible machine learning framework that enables fast, personalized diagnostic and prognostic decisions directly from proteome-wide data.

Computer vision coupled with gene expression shed light on the collective organizational patterning of glioma stem cells, which correlates with glioma stem cell phenotypes

During SARS-CoV-2 infection caspase-8 fuels harmful inflammation independent of apoptosis. Genetic loss of caspase-8 reduces cytokine levels, lowers viral load and mitigates disease severity, revealing non-apoptotic caspase-8 as a key driver of severe COVID-19.

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.

The development of superior and cost-effective catalysts for the oxygen reduction and evolution reactions is pivotal for the future hydrogen economy. Now a series of Ru-modified Li₂MnO₃ catalysts have been designed to optimize the electronic structure and achieve a high performance in both oxygen reduction and evolution reactions, as demonstrated in practical anion exchange membrane fuel cell and water electrolyser tests.

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.

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.

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.

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.

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.

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.

ZrO₂ is known to be a very poor glass former, namely an extremely fragile liquid, while its high melting temperature impedes a mechanistic understanding. Here, Kohara et al. show the absence of intermediate-range ordering beyond the correlation between oxide polyhedron units in ZrO₂upon melting.

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.

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.

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.

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.

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.

Knowledge of the transcriptional programs of human kidney cell populations at homeostasis is limited. Here, the authors show sex-based differences in gene expression of kidney parenchymal cells and examine the complexity of kidney-resident immune cells using single cell RNA sequencing of healthy living kidney donors.

Metallic surface states on CoO₂ and Pd terminated surfaces due to electronic reconstruction have been observed in the CoO₂-based delafossites. In contrast, here the authors report an interesting insulating state on the CrO₂ terminated surface of PdCrO₂ due to charge-disproportionation.

Spectroscopic studies and theoretical calculations of the electrocatalytic oxygen evolution reaction establish that reaction rates depend on the amount of charge stored in the electrocatalyst, and not on the applied potential.

Electrocatalytic water oxidation is key in energy storage technologies, but deeper mechanistic understanding is still required. Grimaud et al. show that surface oxygen atoms in a model oxide catalyst act as electrophilic centres for reactions and observe drastic reconstruction of the catalyst surface.

Developing durable catalysts for the acidic oxygen evolution reaction is crucial for proton exchange membrane water electrolyzers. Here, the authors report incorporating high-entropy atoms (Co, Ni, Cu, Mn, Sm) into RuO₂ via annealing, achieving stable operation at 1 A cm⁻² and 50 °C for 1500 h.

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.

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.

PROTACs induce degradation by bridging a target protein and E3 ubiquitin ligase. Here, authors show that protein interface frustration correlates with cooperativity, offering a structural metric to prioritize PROTAC candidates prior to synthesis.

In colorectal cancer (CRC), finding loci associated with risk may give insight into disease aetiology. Here, the authors report a genome-wide association analysis in Europeans of 34,627 CRC cases and 71,379 controls, and find 31 new risk loci and 17 new risk SNPs at previously reported loci.

Improving materials for energy devices relates to an optimisation of their surfaces. Here authors show that surface modification with ultrathin oxide layers allows for a tailoring of the surface dipole and the work function of mixed ionic and electronic conducting oxides.

Whole-genome sequencing, transcriptome-wide association and fine-mapping analyses in over 7,000 individuals with critical COVID-19 are used to identify 16 independent variants that are associated with severe illness in COVID-19.

The development of the all solid-state battery requires the formation of stable solid/solid interfaces between different battery components. Here the authors tailor the composition to form both electrolyte and anode from the same novel family of perovskites with shared crystal chemistry.

Comprehensive elucidation of metal-support interactions is important for controlling and improving their performances in a range of pertinent technologies. Here, the authors reveal how subsurface defects influence the adhesion and wetting of a metal on the surface of a metal oxide.

Ammonia is industrially synthesized through an established process based on iron or ruthenium transition metal catalysts, although the quest for alternative and more sustainable processes is still ongoing. Here, the authors show that potassium hydride confined between graphene layers can reduce dinitrogen and catalyse ammonia synthesis under mild conditions.

Association analysis identifies 65 new breast cancer risk loci, predicts target genes for known risk loci and demonstrates a strong overlap with somatic driver genes in breast tumours.

While Ru-based electrocatalysts are among the most active for acidic water oxidation, they suffer from severe deactivation. Now, Yuen Wu, Wei-Xue Li and co-workers report a core–shell Ru₁–Pt₃Cu catalyst with surface-dispersed Ru atoms for a highly active and stable oxygen evolution reaction in acid electrolyte.

MoS₂ single layers spontaneously undergo a slow oxygen substitution reaction under ambient conditions giving rise to solid-solution-type 2D molybdenum oxy-sulfide crystals. The oxygen substitution sites of the 2D MoS_2−xO_x crystals act as efficient single-atom catalytic centres for the hydrogen evolution reaction.

A novel antiviral targeting the SARS-CoV-2 PLpro protease shows strong efficacy in a mouse model, preventing lung pathology and reducing brain dysfunction. The study provides proof-of-principle that PLpro inhibition may be a viable strategy for preventing and treating long COVID.

Control of ion diffusion is instrumental in understanding the behavior and structural transformations of transition metal oxides. Here, the authors use in-situ TEM to reveal the atomic-scale evolution of the topotactic phase transition in BM-SFO triggered by the migration of oxygen ions under an external stimulus.

Fungal infections are severely underestimated as a cause of mortality, and alternative drugs are urgently needed. Here, Schaefer et al. show that a synthetic polymer mimicking defensins shows different, but synergistic activity with known antifungals.

Saloner et al. used large-scale cerebrospinal fluid proteomics to uncover molecular signatures in frontotemporal dementia, revealing RNA splicing and synaptic protein candidate markers for genetic and sporadic disease progression.

Analysis of whole-genome sequencing data across 2,658 tumors spanning 38 cancer types shows that chromothripsis is pervasive, with a frequency of more than 50% in several cancer types, contributing to oncogene amplification, gene inactivation and cancer genome evolution.