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A genomic barcoding scheme called two-layer DNA seqFISH+ enables the simultaneous mapping of more than 100,000 loci and has been used to identify cell-type-specific subnuclear compartments in the mouse brain.

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.

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.

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.

Adipogenesis is important for white adipose tissue function. Here the authors identify the transcription factor PATZ1 as a regulator of adipogenesis and adipocyte maintenance, and report that adipose-tissue specific loss of PATZ1 leads to reduced fat mass and larger adipocytes in mice.

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.

Extracellular anisotropic stresses trigger fibroblast transition into myofibroblasts by the mechanical self-reinforcement of cell–extracellular matrix interactions.

Drug target identification is a crucial step in drug development. Here, the authors introduce a Bayesian machine learning framework that integrates multiple data types to predict the targets of small molecules, enabling identification of a new set of microtubule inhibitors and the target of the anti-cancer molecule ONC201.

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.

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

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.

Tiled amplicon sequencing is an essential tool for tracking the spread and evolution of pathogens, including SARS-CoV-2, however existing methods for tiled amplicon design require slow and costly downstream manual optimization. Here the authors present Olivar, a first step towards fully automated, variant-aware design of tiled amplicons for pathogen genomes.

Durable clinical benefit observed in recurrent ovarian cancer patients treated with combination pembrolizumab, cyclophosphamide and bevacizumab are associated with increased T and B cell clusters, distinct microbial patterns, and altered metabolism.

Spatially segregated rRNA processing dictates nucleolar morphology and drives outward progression of pre-ribosomal RNA through nucleolar phases.

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.

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.

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.

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.

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.

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.

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.

Two simple and efficient methods for RNA circularization and a complementary Cas9 deimmunization method enhance a broad range of applications in genome and cell engineering.

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.

Analyses of hippocampal AMPA receptor–auxiliary subunit complexes provide insights into the predominant assemblies and organization of the AMPA receptor, TARP-γ8 and CNIH2/SynDIG4 and explain the mechanism of inhibition of a clinically relevant, brain-region-specific allosteric inhibitor.

Identifying biomarkers associated with risk of severe COVID-19 disease could inform clinical management. Here, the authors identify a long noncoding RNA associated with severe disease using data from three European countries, and validate their finding in data from Canada.

Adenosine deaminases acting on RNA (ADARs) impact diverse cellular processes. Here the authors chart time-course RNA editing profiles in human organs from fetal to adult stages to shed light on the role of ADARs in cell-fate specification.

This study looks at the diurnal temperature fluctuations in Kolkata through a model that tests the influence of rooftop photovoltaic solar panels on urban surface energy budgets, near-surface meteorological fields, urban boundary layer dynamics and sea breeze circulations. It found that panels heat cities during the day (up to 1.5 °C) but cool them at night (up to 0.6 °C).

To address an evidence gap for the efficacy of hypertension therapy using dual drug combinations in patients of South Asian origin, a randomized clinical trial conducted in India found that three types of dual drug combinations, each administered in a single pill, had similarly large effects on reducing blood pressure.

This study considers how urban heat islands are affected by rural regions neighboring cities, which may be a source of cooling for city centers. An analysis of 30 Chinese cities from 2000 to 2020 makes advances in defining urban–rural boundaries and specifying the importance of maintaining diverse, rich, dense rural land cover to mitigate urban heat.

During tomato fruit ripening, bitter and toxic steroidal glycoalkaloids (SGAs) are converted to nonbitter and less toxic forms, but proposed acylating enzyme in pathway remain unknown. Here, authors report BAHD-type acyltransferase that catalyze acylation step in biosynthesis of non-bitter SGAs in tomato.

In mice, sympathetic nerves associated with female mammary glands control the secretion of thermogenesis-controlling factors by epithelial cells in the adipocyte niche, revealing sex-specific differences in adipose thermogenesis.

Kim et al. show that NAD⁺ kinase 2 serves as a source of mitochondrial NADPH to support mitochondrial fatty acid synthesis, protein lipoylation and mitochondrial oxidative metabolism.

Steroidal glycoalkaloids (SGAs) accumulate in Solanum, but their hydroxylating enzymes are unknown. Here, the authors report 2-OXOGLUTARATE DEPENDENT DIOXYGENASE enzymes that catalyze the committed hydroxylation steps in the biosynthesis of leptinine insecticidal compounds in wild potato or non-bitter SGAs in cultivated tomato.

From 1980 to 2018, the levels of total and non-high-density lipoprotein cholesterol increased in low- and middle-income countries, especially in east and southeast Asia, and decreased in high-income western countries, especially those in northwestern Europe, and in central and eastern Europe.

Osteolytic lesions (OL) are frequent in multiple myeloma (MM), but are poorly understood. Here, the authors characterise OLs in MM patient samples using single-cell RNA-seq, revealing genes that are specifically regulated in OL compared to random bone marrow aspirates and that reflect the response to induction therapy.

A free-standing two-dimensional sheet composed solely of Mo atoms shows metallic character, with an electrical conductivity of ~940 S m⁻¹.

Early vertebrate genomes were shaped by multiple whole-genome duplication (WGD) events of debated timings. Here the authors’ reconstruction of ancestral genomes using the probabilistic macrosynteny model supports a WGD shared by all vertebrates and a gnathostome-specific WGD, and reveals evidence of a cyclostome-specific genome triplication.

From his early years as a medical student at Harvard University to his job as the director of the HIV/AIDS unit at the World Health Organization (WHO), Jim Yong Kim has worked toward building health care systems to provide care for poor people on a global scale. In the late 1980s, Kim worked with a team of doctors from the Cambridge, Massachusetts–based nonprofit Partners in Health to upend conventional wisdom on treatment for drug-resistant tuberculosis in the shantytowns of Lima, Peru. The team's campaign brought the price of tuberculosis drugs down about 90%. Kim, a physician who also has a doctorate in medical anthropology, says that the success helped overturn the notion that the disease could not be treated in such a poor setting. While at the WHO, he turned his attention to AIDS. In 2003, amid much skepticism, his team launched the global '3 by 5' campaign, an ambitious movement aimed at providing antiretroviral drugs to 3 million people worldwide by 2005. Today, Kim leads the François-Xavier Bagnoud Center for Health and Human Rights at the Harvard School of Public Health, where he oversees programs to address health issues plaguing poor childrenóespecially those afflicted with AIDS. Kim discussed the current state of universal AIDS treatment and the role of biomedical research in promoting social justice with Prashant Nair.

During aging, the ability of skeletal muscle to repair itself declines, in part due to a decrease in muscle stem cells. Here, the authors report that muscle stem cells that accumulate mitochondrial damage fuse with existing muscle fibers in a manner that depends on the induction of Scinderin.

Federated ML (FL) provides an alternative to train accurate and generalizable ML models, by only sharing numerical model updates. Here, the authors present the largest FL study to-date to generate an automatic tumor boundary detector for glioblastoma.