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Age is a risk factor for SARS-CoV-2 infection and severe disease. Here the authors perform DNA methylation analyses in whole blood from COVID-19 patients using established epigenetic clocks and telomere length estimators, and describing correlations between epigenetic aging and the risk of SARS-CoV-2 infection and severe disease.

Most genetic risk variants for brain disorders lie in non-coding regions and are difficult to interpret. Here, the authors develop BASIC, a method integrating bulk and single-cell eQTLs, to reveal cell-type-specific effects and improve gene discovery and disease colocalization.

This work introduces BraDiPho, an open-access resource of interactive 3D human brain models, integrating layer-by-layer dissections with tractography, cortical parcellations, and tools for multimodal white matter anatomical studies.

Multiancestry genome-wide association analyses identify new risk loci for stroke and stroke subtypes. Fine mapping and bioinformatics analyses of these risk loci point to mechanisms not previously implicated in stroke pathophysiology.

Nature Biotechnology’s annual survey highlights academic start ups that are, among other things, correcting misfolded or disordered proteins, creating second-generation GPCR agonists, building a new gene delivery platform and mining cancer genomes for novel targets.

A genome-wide study by the Long COVID Host Genetics Initiative identifies an association between the FOXP4 locus and long COVID, implicating altered lung function in its pathophysiology.

During the Last Ice Age, Neanderthals used a small cave in the Iberian Peninsula to accumulate the crania of large ungulates (bison, aurochs, red deer and rhinoceroses), some associated with small hearths. This seems to have been a symbolic practice.

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.

KDM4C regulates cathepsin L-mediated histone H3 N-terminal tail clipping through grainyhead-like 2 (GRHL2) methylation in breast cancer. This link between the cellular redox state and chromatin remodeling might represent a therapeutic target in KDM4C-amplified tumors.

Disparities in risk and outcomes of pediatric acute lymphoblastic leukemia (ALL) are apparent between different ancestries. Here the authors identify genetic variants with African ancestry-specific risks for developing pediatric B-cell ALL that are also linked to greater 5-year mortality risk.

DNA methylation is an epigenetic mark that plays a critical role in many biological processes. Here, we describe the development of SAM-DNMT3A a tool for induction of genome wide DNA methylation. Using SAM-DNMT3A we show that DNA methylation is a unique vulnerability in ER+ breast cancer.

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.

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.

Closely related plant species can have drastically different abundances of transposable elements. Now it is shown that the genome of Arabis alpina has experienced a striking expansion of retrotransposons, probably shaped by reduced DNA methylation.

Paul Pharoah and colleagues report the results of a large genome-wide association study of ovarian cancer. They identify new susceptibility loci for different epithelial ovarian cancer histotypes and use integrated analyses of genes and regulatory features at each locus to predict candidate susceptibility genes, including OBFC1.

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.

Two side-by-side papers report that H3K27me3 deposited by polycomb repressive complex 2 represents an epigenetic barrier that restricts naive human pluripotent cell differentiation into alternative lineages including trophoblasts.

In vivo experiments and clinical cohort analyses show that hypoxia-inducible factor 2 (HIF2)-induced parathyroid hormone-related protein (PTHrP) expression contributes to cachexia in the context of renal cell carcinoma (RCC). The pathway can be targeted by HIF2 inhibitors, including belzutifan, which may reduce cachexia in patients with RCC.

Zamboni et al. reveal how enhancers encode cell-type-specific responses to CNS injury. By combining multiomic profiling, deep learning and in vivo screening, they uncover injury-responsive enhancer logic and enable targeting of reactive astrocytes.

The majority of human genes can produce multiple isoforms, but studying their functional relevance requires tools to target specific isoforms. Here, the authors develop a CRISPR-based exon-exon junction-targeting strategy to achieve isoform-specific RNA knockdown.

A new version of nanorate DNA sequencing, with an error rate lower than five errors per billion base pairs and compatible with whole-exome and targeted capture, enables epidemiological-scale studies of somatic mutation and selection and the generation of high-resolution selection maps across coding and non-coding sites for many genes.

Pitulescu et al. and Hasan et al. show that Dll4–Notch signalling in endothelial tip cells regulates angiogenesis through control of artery formation, linking sprouting angiogenesis and artery formation.

Cancer liver metastases can be encapsulated by a fibrotic stroma. Here the authors use digital pathology to generate spatial growth pattern maps of colorectal cancer liver metastasis and show that prognosis depends on the degree of fibrotic encapsulation.

Here, the authors perform large trans-ancestry fine-mapping analyses identifying large numbers of association signals and putative target genes for colorectal cancer risk, advancing our understanding of the genetic and biological basis of this 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.

Telomere-to-telomere assemblies of two mouse inbred strains, C57BL/6J and CAST/EiJ, offer improvements over the current mouse reference genome by adding telomere and centromere sequences that lead to insights into variability in telomere and centromere sizes and organization, and the discovery of 225 and 355 new genes for C57BL/6J and CAST/EiJ, respectively.

Despite frequent AKT/mTOR pathway activation in patient’s rhabdomyosarcoma (RMS), success of AKT inhibitors in the clinical has been limited. Here, using RMS patient-derived models, the authors demonstrate that the efficacy of the AKT inhibitor, ipatasertib, is in part due to its off-target effects on PRKG1, identifying PRKG1 as a potential biomarker for ipatasertib response.

Bovine fibroblast cell line generation without genetic modification is characterized. A technoeconomic analysis demonstrates the potential for price-competitive, scaled-up cultivated beef production.

Kim and colleagues perform a phase 2 clinical trial (ELM-2) of odronextamab monotherapy in patients with relapsed/refractory diffuse large B cell lymphoma and report on the primary analyses of the efficacy and safety profile.

Hutchinson-Gilford progeria syndrome is a genetic disease where an aberrant form of Lamin A disrupts chromatin by interfering with lamina associated domains. Here, the authors present the SAMMY-seq, a method for genome-wide characterization of heterochromatin dynamics and detect early stage alterations of heterochromatin structure in progeria primary fibroblasts, accompained by Polycomb dysfunctions.

Although topologically associating domains (TADs) have been extensively investigated, it is not clear to what extent DNA sequence contributes to their formation. Here the authors develop software to identify high-resolution TAD boundaries and reveal their relationship to underlying DNA motifs.

Pioneer neurons extend their axons to provide a track for follower neurons to follow, whether these neurons differ in other ways has not been clear. Here they show that pioneer and follower neurons are transcriptionally distinct and that RA signaling is required for pioneer axon targeting.

TFE3-fusions are known to drive both epithelial and mesenchymal renal tumors. Here, the authors generate a transgenic mouse model of renal tumorigenesis expressing the human SFPQ-TFE3 fusion, showing that the fusion regulates mTORC1 activity and induces lineage plasticity.

Integration of snATAC-seq and snRNA-seq data from brains of individuals with major depressive disorder identifies chromatin accessibility alterations and functional enrichment of risk variants in deep-layer excitatory neurons. Gray matter microglia in these individuals show decreased accessibility at sites bound by regulators of immune homeostasis.

Here the authors apply machine learning approaches to Alzheimer’s genetics, confirm known associations and suggest novel risk loci. These methods demonstrate predictive power comparable to traditional approaches, while also offering potential new insights beyond standard genetic analyses.

CREB-regulated transcriptional coactivators (CRTCs) have an important role in modulating transcription in a context-dependent manner. Here the authors dissect the role of CRTC-1 in worm lifespan and show that the CRTC-1 transcriptional domain ensures longevity under specific histone marks.

Analysis of 4,041 single-nucleotide variants (SNVs) linked to 13 cancers performed in primary human cell types identifies 380 potentially regulatory SNVs and their putative target genes. Editing one SNV, rs10411210, revealed that the risk allele increases RHPN2 expression and stimulus-responsive RhoA activation.

Scarfò, Randolph et al. perform transcriptomic analysis of 28- to 32-day human embryos and identify CD32 as a marker of haemogenic endothelial cells (HECs), thus providing a strategy to isolate HECs from human embryos and pluripotent stem cell cultures.

This protocol covers a package for running statistical testing on the temporal dynamics of neural activity data obtained from various functional neural recording modalities.

Genome-wide association analyses of 41,917 bipolar disorder cases and 371,549 controls of European ancestry provide new insights into the etiology of this disorder and identify novel therapeutic leads and potential opportunities for drug repurposing.

Common genetic variants associated with plasma lipids have been extensively studied for a better understanding of common diseases. Here, the authors use whole-genome sequencing of 16,324 individuals to analyze rare variant associations and to determine their monogenic and polygenic contribution to lipid traits.

Here the authors elucidate how epigenetic regulation influences the regulatory impact of transposable elements in the human genome using cellular models of the neurodegenerative disease XDP, which is caused by an SVA insertion at the TAF1 locus.

Patients with different small round cell sarcoma (SRCS) often receive the same treatment regimen but for some SRCS subtypes, response to chemotherapy is poor and targeted treatment options are limited. Here, the authors establish a biobank of paediatric patient-derived SRCS tumoroids and perform drug screening, identifying MCL inhibition as a potential therapeutic strategy in CIC::DUX4 sarcomas.

Spatial organization of the Trypanosoma cruzi genome and how it affects gene expression.

MORC2, a chromatin remodeler involved in epigenetic silencing and DNA repair, is linked to cancer and neurological disorders when dysregulated. Here, the authors show that MORC2 binds DNA at multiple sites, clamps onto it, and induces compaction, a process regulated by its phosphorylation.

Genome-wide association meta-analysis of AAA identifies 121 independent risk loci and highlights potential therapeutic targets such as proprotein convertase, subtilisin/kexin-type 9 (PCSK9).

Surface acoustic waves have previously been used, in conjunction with electric currents and assisting magnetic fields, to manipulate magnetization. Here, Rivelles, Yanes, and coauthors succeed in driving magnetic domain walls solely with surface acoustic waves, an important milestone in acoustically controlled spintronic devices.’

Transcription factors shape cell identity, but mapping their genomic targets remains challenging. Here the authors present DynaTag, a modified CUT&Tag method for profiling TF occupancy in bulk and single cells, and apply it to assess changes in TF activity in SCLC tumours following chemotherapy.

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.