Search

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.

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.

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.

Aggregating similar single cells into metacells is a common heuristic for sparse data, but risks mixing dissimilar cells. Here, authors present mcRigor, which detects and filters heterogeneous metacells, optimizes metacell partitioning, and improves reliability in single-cell omics studies.

The latent HIV-1 reservoir is the key obstacle for curing HIV-1 infection, but the timepoint at which the HIV-1 reservoir is established is currently unclear. Here, Whitney et al. show in non-human primates that the SIV reservoir in CD4⁺ T cells is seeded within the first 2 days after infection.

Alcohol use disorder and drinks per week both have been studied genetically and have different correlations with psychiatric diseases. Here the authors integrate multi-omics data to identify unique and shared variants, genes and pathways for alcohol use disorder and drinks per week.

A soft mesh microelectrode array can seamlessly integrate in developing brains, enabling long-term, stable mapping of how single-neuron activity and population dynamics emerge and evolve during brain development.

Inbreeding depression has been observed in many different species, but in humans a systematic analysis has been difficult so far. Here, analysing more than 1.3 million individuals, the authors show that a genomic inbreeding coefficient (FROH) is associated with disadvantageous outcomes in 32 out of 100 traits tested.

Hundreds of genetic loci associated with age at menopause, combined with experimental evidence in mice, highlight mechanisms of reproductive ageing across the lifespan.

Head and neck squamous cell carcinoma (HNSCC) frequency and risk factors vary considerably across regions and ancestries. Here, the authors conduct a multi-ancestry genome-wide association study and fine mapping study of HNSCC subsites in cohorts from multiple continents, finding susceptibility and protective loci, gene-environment interactions, and gene variants related to immune response.

Jayavelu, Samaha et al., apply machine learning models on hospital admission data, including antibody titers and viral load, to identify patients at high risk for Long COVID. Low antibody levels, high viral loads, chronic diseases, and female sex are key predictors, supporting early, targeted interventions.

A genome-wide association study meta-analysis combined with multiomics data of osteoarthritis identifies 700 effector genes as well as biological processes with a convergent involvement of multiple effector genes; 10% of these genes express the target of approved drugs.

Antibody and antibody-avidity assays relying on near-infrared-fluorescence amplification by nanostructured plasmonic gold substrates accurately quantify antibodies to SARS-CoV-2 and to common viruses in human serum and saliva.

The hypersensitivity of sulfide solid-state electrolytes to moisture are not compatible with today’s manufacturing infrastructure. Here, authors present a reversible surface modification strategy using 1-undecanethiol, that enables the processability of sulfide SSEs under humid ambient air.

Mission improbable.

Analysis of the phase 3 PRODROME trial reveals that treatment with ubrogepant during the prodromal phase of migraine may ameliorate common prodromal symptoms, with improvements as early as 1 hour after dose administration.

In the phase 3 CEPHEUS trial, patients with transplant-ineligible or transplant-deferred newly diagnosed multiple myeloma were treated with subcutaneous daratumumab plus bortezomib, lenalidomide and dexamethasone (D-VRd), which led to a significantly deeper and more durable increase in minimal residual disease responses compared with the control arm of VRd.

Data from over 700,000 individuals reveal the identity of 83 sequence variants that affect human height, implicating new candidate genes and pathways as being involved in growth.

Polygenic risk scores can help identify individuals at higher risk of type 2 diabetes. Here, the authors characterise a multi-ancestry score across nearly 900,000 people, showing that its predictive value depends on demographic and clinical context and extends to related traits and complications.

Exome-wide analysis identifies rare and low-frequency coding variants associated with body mass index. Gene-based meta-analysis and functional studies implicate 13 genes, eight of which are novel, and neuronal pathways as factors in human obesity.

Cells use clathrin-mediated endocytosis to internalize biomolecular cargo. The authors demonstrate that the Epsin1 protein ensures uptake of ubiquitylated cargo through ubiquitin-dependent regulation of the stability of endocytic protein networks.

Hydrogel materials have emerged as versatile platforms for biomedical applications. Here this group reports an mRNA lipid nanoparticle-incorporated microgel matrix for immune cell recruitment/antigen expression and presentation/cellular interaction thereby eliciting antitumor efficacy with a single dose.

Transposons are repetitive DNA sequences that are hard to identify and map accurately. TEtrimmer automates key manual steps, enabling faster and more reliable annotation of transposable elements in any genome.

A deep learning system able to identify the most common skin conditions may help clinicians in making more accurate diagnoses in routine clinical practice

The goals, resources and design of the NHLBI Trans-Omics for Precision Medicine (TOPMed) programme are described, and analyses of rare variants detected in the first 53,831 samples provide insights into mutational processes and recent human evolutionary history.

A live-attenuated COVID vaccine could enrich the current vaccine portfolio. Here, Liu et al. engineer a live-attenuated SARS-CoV-2 vaccine candidate by deleting four viral accessory genes and show immunogenicity and protection in mice and hamsters.

Olfactory deficits occur early in Alzheimer’s disease (AD). Here, the authors identify that loss of locus coeruleus axons in the olfactory bulb underlies impaired olfaction in an AD mouse model and provide translational evidence for similar deficits in humans.

Cropland area—and associated carbon dioxide emissions—in 110 studied countries is 6% higher than it would be without declines in agricultural productivity caused by climate change, according to a comparison of models with and without climate impacts.

Caloric restriction improves Alzheimer’s Disease outcomes in mice, but this diet not only reduces calories, but imposes a prolonged fast between meals. Here, the authors show this fast is essential to improve Alzheimer’s pathology and cognition.

Analysis of 97,691 high-coverage human blood DNA-derived whole-genome sequences enabled simultaneous identification of germline and somatic mutations that predispose individuals to clonal expansion of haematopoietic stem cells, indicating that both inherited and acquired mutations are linked to age-related cancers and coronary heart disease.

Spatially resolved images of M87 obtained at a wavelength of 3.5 mm in 2018 show a ring-like accretion structure, the inner (outer) edge of which connects the black hole (jet).

Repeated vaccination is needed to maintain high levels of SARS-CoV-2 immunity in vulnerable populations, but there is concern that it could lead to immune exhaustion. Here, the authors assess the evidence for immune exhaustion following multiple SARS-CoV-2 vaccination three vulnerable population cohorts in Canada.

A clinical study of women with abnormal breast mammograms establishes a workflow to evaluate the capability of breast photoacoustic computed tomography in the classification, monitoring and segmentation of lesions.

Together with a companion paper, the generation of a transcriptomic atlas for the mouse lemur and analyses of example cell types establish this animal as a molecularly tractable primate model organism.

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.

Therapeutic checkpoint for acute myeloid leukemia requires further investigations. The authors here identify ST2⁺ Treg cells facilitate AML growth by inducing CD8⁺ T cell depletion and exhaustion, while targeting ST2 by antibodies depletes ST2⁺ Treg cells and improves AML prognosis.

The SARS-CoV-2 variant expressing spike(D641G) shows increased infectivity in human lung epithelial cells and in hamster and primary human upper airway tissues, but is more susceptible to neutralization by antibodies raised against SARS-CoV-2.

The contribution of genetic factors to the tumour immune microenvironment (TIME) remains to be investigated. Here, the authors suggest the role of TIME eQTLs for target genes involved in reversing immune suppressive features.

Genome engineering in bacteria remains a complex multistep process. Here, the authors developed make-or-break Prime Editing, a precise method for genetic modification in Streptococcus pneumoniae that enables high-throughput and scalable genome editing.

Global aquatic foods are a key source of nutrition, but how their production is influenced by anthropogenic environmental changes is not well known. The vulnerability of global blue food systems to main environmental stressors and the related spatial impacts across blue food nations are now quantified.

Safely opening university campuses has been a major challenge during the COVID-19 pandemic. Here, the authors describe a program of public health measures employed at a university in the United States which, combined with other non-pharmaceutical interventions, allowed the university to stay open in fall 2020 with limited evidence of transmission.

Widespread grassland degradation poses major societal and environmental challenges. Here, the authors propose multiple targeted interventions as a crucial strategy for simultaneously enhancing grassland ecosystem services and improving their equitability.

A data-efficient deep learning model developed to predict ground-state and photophysical properties of molecules and nanomaterials by learning many-body Green’s functions achieves an accuracy surpassing the state-of-the-art density functional theory calculations.