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A cross-organ, multi-omics U-shaped relationship between sleep duration and biological ageing clocks highlights the potential of sleep optimization to promote healthy ageing, lower disease risk and extend longevity.

HELIX is a deep learning framework for modeling tissue- and context-specific RNA splicing and isoform usage, prioritizing splicing-altering genetic variants and their functional effects from bulk and single-cell RNA sequencing data.

Cepharanthine is a secondary metabolite isolated from Stephania with a variety of medicinal properties. Here, the authors assembled three Stephania genomes, propose cepharanthine biosynthetic pathway, and assess the antiviral potential of cepharanthine-related metabolites.

Oral tolerance is an important feature of gut immune homeostasis but how it is maintained is not fully known. Here authors show in a mouse model that dietary nucleic acids activate the MAVS and STING pathways, which leads to an increased abundance of natural intraepithelial lymphocytes, producing soluble factors that maintain tolerance.

Birds uniquely exhibit high expression of constitutively active GCGR in white adipose tissue (WAT) enhancing lipid metabolism, WAT browning, and weight loss in mice. A naturally occurring human GCGRH339R mutation mimics this avian-like metabolism, suggesting therapeutic potential for obesity

Developing photocatalysts from earth-abundant materials is crucial for sustainable solar hydrogen production, yet challenges in efficiency and stability persist. Here, the authors report that the topological semimetal cobalt triarsenide functions as an active and durable platform for this reaction.

Here the authors use genetic mutations to alter TCR signal strength and clonal selection of exhausted CD8⁺ T cells. They implicate CARD11 signaling as a sensor of this TCR signal strength and as a regulator of antitumor function in exhausted T cells that might be targeted to enhance cancer immunotherapies.

APOL9a/b proteins coat mouse intestinal bacteria with high specificity, and genetic abolition of ceramide-1-phosphate synthesis pathways in the symbiote Bacteroides thetaiotaomicron significantly decreases this binding of APOL9a/b to the bacterium.

The lymphatic system is essential for maintaining homeostasis of our body. Understanding the impact of environmental factors on the lymphatic system and regulating its condition are therefore crucial. We developed a microfluidic device culturing functional skin barrier and lymphatic vessel monolayer. A deep-learning algorithm was employed to validate the pro-lymphangiogenic character of a natural substance Lymphanax™, an extract of Panax Ginseng root. We foresee this platform functioning as a valuable research tool for the pharmaceutical and cosmetic industries, replacing the need for animal models.

The authors present evidence based on satellite observations that the local cooling effect of potential forestation in Europe has intensified over the past two decades, driven by the reduced winter snow cover and declining summer soil moisture under global warming.

Fas signalling induces apoptosis of activated T cells to maintain immune homeostasis. Here the authors show that Fas also induces PKC-β activation to promote NF-κB-mediated T_H9 cell differentiation, while p38 activation by PKC-β antagonizes this effect, thereby supporting a synergy between p38 inhibitor and Fas for T_H9 differentiation.

Hepatic expression of constitutively active glucagon receptor may have contributed to the glucose and lipid metabolism and the high metabolic rates that enabled the evolution of flight in birds.

The advantage of living in cities compared with rural areas with respect to height and BMI in children and adolescents has generally become smaller globally from 1990 to 2020, except in sub-Saharan Africa.

Antibody-dependent enhancement (ADE) is an important safety concern for vaccine development against dengue virus (DENV) and the antigenically related Zika virus (ZIKV). Gao and colleagues designed a ZIKV vaccine that induced sterilizing immunity and fetal protection in mice challenged with ZIKV and did not induce ADE following subsequent DENV infection.

Humans that reach high altitude soon after the first ascent show faster adaptation to hypoxia. Songet al. show that this adaptive response relies on decreased red blood cell uptake of plasma adenosine due to reduced levels of nucleoside transporter ENT1 resulting from coordinated adenosine generation by ectonucleotidase CD73 and activation of A2B receptors.

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.

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.

The mechanisms underlying the nonclassical growth of penta-twinned gold nanocrystals remain unclear. Here, the authors elucidate the atomic-level processes that drive size-dependent and twin configuration-related aggregation phenomena.

Insulating molecular layers on the basal plane of 2D perovskite is a major bottleneck for charge injection that limiting device performance. Here, the authors show that plane-contacted graphene functions as a low barrier and gate-tunable contact to overcome this limitation.

ImmuScope, a weakly supervised deep learning model capable of analysing multi- and single-allelic data, is introduced, facilitating interpretable neoantigen discovery and immune escape analysis.

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.

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.

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.

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.

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 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.

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.

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.

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.

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.

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.

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.

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.

The authors provide observational evidence that the biophysical cooling or warming effect of potential tree restoration is 4–5 times stronger for space-measured land surface temperature than for the more policy-relevant near-surface air temperature.

This study shows a self-powered deep-sea current measurement system using a triboelectric nanogenerator (TENG) that measures currents from 0.02 to 6.69 m/s and withstands over 45 MPa pressure. Successful operation at 4531 m depth in the South China Sea is demonstrated.

Pilcher et al. present a single-cell transcriptomics-based immune atlas of participants with newly diagnosed multiple myeloma, reporting on the association of cell types, gene expression and intercellular interactions with disease progression phenotypes.

Analysis of mitochondrial genomes (mtDNA) by using whole-genome sequencing data from 2,658 cancer samples across 38 cancer types identifies hypermutated mtDNA cases, frequent somatic nuclear transfer of mtDNA and high variability of mtDNA copy number in many cancers.

This overview of the ENCODE project outlines the data accumulated so far, revealing that 80% of the human genome now has at least one biochemical function assigned to it; the newly identified functional elements should aid the interpretation of results of genome-wide association studies, as many correspond to sites of association with human disease.