Search

As the throughput of single-cell RNA-seq studies increases, there is a need for tools that can make the data analysis steps more streamlined and convenient. Here, the authors develop UniverSC, a tool that unifies single-cell RNA-seq analysis workflows and also facilitates their use for non-experts.

Transcriptomic and clinical data analyses from multiple cohorts of patients with cancer receiving immunotherapy find that PD-1 blockade potentiates tumor-specific IgG1 plasma cell responses that complement cellular immunity and contribute to clinical benefit.

Here, by integrating faecal metabolomics, metagenomics, and habitual dietary data of two large human cohorts, the authors show that faecal metabolites reflect diet and gut microbiome interactions, predict dietary patterns, and indicate cardiovascular risk, offering insights for diet-based health interventions.

The balance between cell proliferation and cell cycle arrest is essential for liver regeneration. Here the authors report the emergence of partially reprogrammed hepatocytes persisting in plastic states during liver tissue injury, which are resistant to proliferation thereby limiting overgrowth and tumorigenesis.

Chromothripsis (CT) is a type of genome instability which is prevalent in medulloblastoma with germline TP53 mutations (Li-Fraumeni syndrome, LFS). Here the authors combine single-cell genomic and transcriptomic analyses to reveal the clonal heterogeneity and functional consequences of CT in LFS medulloblastoma.

Germ layer specification during zygotic genome activation is regulated by chromatin state. Here, the authors use single-cell multiome profiling in Drosophila to show that H3K27me3 and H3K27ac at cis-regulatory elements control cell type-specific gene expression and developmental progression.

Boccella, Yu and colleagues reveal that the transmembrane protein ANTXR1 regulates post-infarction fibrotic remodeling, and its inhibition blocks collagen turnover and improves heart function.

Transcriptomic and proteomic profiling of blood samples from individuals with COVID-19 reveals immune cell and hematopoietic progenitor cell alterations that are differentially associated with disease severity.

The implications of early telencephalic development in cortical disorders remain elusive. Here, the authors define risk gene dynamics and perturbation effects in neural stem cells, revealing vulnerability phases during early human corticogenesis.

Multiplexed error-robust fluorescence in situ hybridization (MERFISH) together with deep-learning-based nucleus segmentation enabled the construction of a highly detailed and informative spatially resolved single-cell atlas of human fetal cortical development.

Coupling microbial metagenomics with machine learning enables prediction of donor strain engraftment after fecal microbiota transplantation (FMT) for a range of diseases, and may help tailor design of FMT to optimize microbial engraftment and achieve clinical outcomes.

Neuroimmune communication in Alzheimer’s disease (AD) is poorly understood. Here, the authors show that CD103–CD8+ resident memory T cells induce neurotoxicity and neuroinflammation in AD via the granzyme K–PAR-1 axis.

Toghani, Gupte et al. identify semaphorin 4A as a cell-extrinsic factor that protects myeloid-biased hematopoietic stem cells from inflammaging, mainly produced by their progeny—neutrophils—and acting via a negative feedback loop.

Dalit, Tan and colleagues provide a multiomic profile of T follicular helper (T_FH) cells responses to diverse pathogens, revealing a blueprint for transcriptional flexibility and new tools to interrogate T_FH heterogeneity in mice and humans.

A study using a mouse solid tumour model suggests that adjusting the dosing frequency of the PI3Kδ inhibitor AMG319 in the treatment of human cancers could decrease tumour growth with fewer adverse effects.

The sensitivity of mesothelioma to the treatment of immune checkpoint blockade remains elusive. Here this group reports a double blind, placebo-controlled, randomized phase III trial of PD1 inhibitor (Nivolumab) on 332 patients with relapsed mesothelioma, and to uncover determinants of efficacy.

Human primary and metastatic tumors harbor CD4⁺ T_reg cells that can suppress antitumor immune responses. Bonnal et al. identify an intratumoral type 1 T_reg-like CD4⁺ T cell subset that expresses the transcription factor EOMES, granzyme K and CHI3L2. This EOMES⁺ T cell subset correlates with disease progression but is responsive to PD-1 checkpoint blockade immunotherapy.

Panzer and colleagues show that the integrated stress response pathway regulates cytokine translation in CD4⁺ T_RM cells during homeostasis and inflammation.

Catecholaminergic transmitters are critical signalling effectors known to be released by sympathetic nerves and adrenomedullary endocrine cells in response to physiological stress. In this paper, the authors demonstrate a uniquely distributed group of catecholaminergic cardiomyocytes with key regulatory roles in cardiac excitation conduction.

Here, the authors show how in β-thalassemia, a perturbed bone marrow microenvironment leads to altered hematopoiesis. Reduced TGFβ reduces autophagy levels, in turn reducing dormancy and priming of haematopoietic stem cells and multipotent progenitors towards erythroid lineage.

Songbirds have extensive germline–soma genome differences due to developmental elimination of a germline-specific chromosome (GRC). Here, the authors show that the GRC contains dozens of expressed developmental genes, some of which have been on the GRC since the ancestor of all songbirds.

Long-read single-cell RNA sequencing is capable of detecting isoform-level gene expression and genomic alterations such as mutations and gene fusions, thereby providing cell-specific genotype-phenotype information. Here, the authors use long-read scRNA-seq on metastatic ovarian cancer samples and detect cell-type specific isoforms and gene fusions that may otherwise be misclassified in short-read data.

Transcriptomic analysis following epidural electrical stimulation of the lumbar spinal cord during neurorehabilitation in mice identifies a population of neurons that orchestrates the restoration of walking following paralysis.

A genome-wide association study of mosaic loss of chromosome Y (LOY) in UK Biobank participants identifies 156 genetic determinants of LOY, showing that LOY is associated with cancer and non-haematological health outcomes.

Proteome-wide measurements of dose–response curves for 144 drugs reveal drug mechanisms of action.

Haltalli et al. show that Plasmodium berghei infection induces interferon release, and affects haematopoietic stem cell proliferation and function, as well as osteoblasts and vascular integrity, in the bone marrow niche.

Dual spatial gene expression assay in tissues with chronic lung infection by Mycobacterium abscessus paves the way for the simultaneous detection of host and bacterial transcriptomes in pathological tissues.

Authors utilise a murine model of infection to provide mechanistic insight into how antimicrobial therapy may be a predisposing risk factor for hospital-acquired pneumonia. They show that antibiotic-induced microbiota perturbations compromise inflammatory monocytes and thereby impair antibacterial defence.

During pregnancy, maternal cells are transferred to the fetus, where they can reach the developing brain. In this study, the authors demonstrate that these maternal cells play an important role in neurodevelopment.

Aging is associated with the formation of focal white matter lesions and atrophy. The authors discovered a role for CD8⁺ T cells in driving white matter-specific interferon responses in microglia and oligodendrocytes, leading to oligodendrocyte loss.

In hepatocellular carcinoma driven by non-alcoholic steatohepatitis, aberrant T cell activation and impaired immune surveillance seem to make hepatocellular carcinoma less responsive to anti-PD1 or anti-PDL1 immunotherapy.

The epithelial mesenchymal transition (EMT) is important in the metastatic spread of cancer cells. Here, the authors show that the EMT transcription factor, ZEB1, can modify estrogen receptor α during EMT and facilitate the migration of breast cancer cells to the bone

Government spending for COVID-19 recovery could have enhanced society’s resilience to environmental shocks, but it is unclear whether this was adequately reflected in policies. A study now sheds light on this issue by applying a fiscal policy taxonomy for climate change adaptation and resilience to policies across different countries.

The molecular mechanisms ensuring the specialized structure of small intestinal villus tip blood vessels are incompletely understood. Here the authors show that ADAMTS18⁺ telocytes maintain a “just-right” level and location of VEGFA signaling on intestinal villus blood vessels, thereby ensuring the presence of endothelial fenestrae for nutrient absorption, while avoiding excessive leakiness and destabilization of villus tip epithelial structures.

While EGFR-targeted therapies have clinical benefit, drug-resistant brain metastases present a major obstacle. Here, the authors identify a genetic signature in brain metastatic lesions associated with osimertinib resistance and find RhoA to have an important role in the resulting phenotype.

The involvement of age-related myelin damage in Alzheimer’s disease is unclear. Kedia et al. show that T cell-mediated microglia activation triggers a response against myelinating oligodendrocytes contributing to neurodegenerative diseases with amyloidosis.

Many sub-Saharan countries are failing to include climate information in long-term development planning. Ensuring climate-resilient development requires a step change in how medium- to long-term climate information is produced, communicated and utilized in sub-Saharan Africa and elsewhere.