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This study uses single-nucleus RNA sequencing to analyze lung tissue from 141 individuals with chronic obstructive pulmonary disease. Distinct patterns of spatially resolved changes in cell composition and cell states that correlate with clinical features are highlighted.

By incorporating spatial and social networks, this study captures the real-world spread of electric vehicle adoption across communities more accurately and highlights the substantial uncertainties in long-term adoption forecasts.

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.

Wang, Chu, Chen, Wei and colleagues discover a subset of tumour-associated macrophages expressing SLC2A1 whose spatial proximity to CD8⁺ T cells drives resistance to anti-PD-L1 treatment in non-small-cell lung cancer.

Environmental justice and drinking water in the US: Higher proportions of Hispanic/Latino, American Indian/Alaskan Native, and non-Hispanic Black residents were associated with higher public water arsenic and uranium at the county-level, findings differed by region.

Drug combination discovery remains slow and challenging. Here, the authors introduce Combocat, an open-source framework that combines acoustic liquid handling protocols with machine learning to achieve ultrahigh-throughput drug combination screening; as proof of concept, they use Combocat to screen 9,045 drug combinations in a neuroblastoma cell line.

Microbial mutualists could affect plant population persistence under climate change. Here the authors show that fungal endophytes contribute to the population persistence of a grass species by ameliorating drought stress but are more likely to disappear locally under climate variability.

The identification of top spatially variable genes is a key step in the analysis of spatially-resolved transcriptomics data. Here, the authors develop a scalable method based on nearest-neighbor Gaussian processes and evaluate performance compared to existing and baseline methods.

Individuals with schizophrenia show reduced structural similarity in temporal, cingulate, and insular lobes, especially those with worse cognition and symptoms, affecting late maturing association areas with low metabolism and high neurotransmission.

Decadal-scale observations reveal that plant diversity stabilizes ecosystem productivity over time. Phylogenetic diversity is the key driver of long-term stability, whereas plant height shapes short-term productivity dynamics.

Luppi et al. identify transcriptomic and connectomic controllers of information integration and its breakdown induced by anaesthesia in humans, macaques, marmosets and mice.

Building data is needed for assessing progress towards urban Sustainable Development Goals. An international team of scientists studies the spatial distribution of buildings in all cities globally and unveils their uneven coverage in OpenStreetMap.

The emerging field of imaging-by-sequencing aims to perform spatial biological analyses by molecular interactions. Here, authors used previously undiscovered spatial networks within Slide-tags data to reconstruct cell positions and capture biological information comparable to the original method.

Cardiomyocytes are the dominant initiators of a type I interferon response in the infarct borderzone.

Combining high-resolution mapping of foliar and herbivore faecal sodium concentrations across Africa, the authors show that plant-derived sodium availability constrains megaherbivore densities at a continental scale.

This study shows that fire-derived pyrogenic carbon constitutes a substantial share of soil carbon in African savannas, with clay-rich soils in drier regions storing the most, highlighting fire’s key role in shaping the savanna carbon cycle at regional scales.

Social behaviours such as altruism and spite are widespread in nature but the conditions that promote their evolution remain elusive. Here, Débarreet al. derive a model that captures general conditions for the evolution of social behaviour, which reveals the critical role of the scale of competition.

Newly developed mouse models that enable cell-specific analyses of proteostasis dynamics across the lifespan of the mice reveal key aspects of neuronal proteostasis with ageing.

HippoMaps provides an open-source resource for studying the human hippocampus at different scales and with different modalities such as histology, fMRI, structural MRI and EEG.

Albumin selectively inhibits Mucorales growth through the release of bound free fatty acids.

Single-cell RNA sequencing and assay for transposase-accessible chromatin using sequencing profiling of human retinal samples from diverse ancestries create an epitranscriptomic atlas characterizing over 130 cell types. Integration with genome-wide association study and expression quantitative trait loci data provides further insights into gene regulation and disease etiology.

Giotto Suite provides a comprehensive, flexible and scalable platform for technology-agnostic spatial omics analysis using R.

uMAIA is an analytical framework designed to enable the construction of metabolic atlases at high resolution using mass spectrometry imaging data.

Ritter et al. present a spatial transcriptomics and deep learning-based approach named NePSTA (neuropathology spatial transcriptomic analysis) and leverage it to improve neuropathological diagnostics and enhance central nervous system tumor subtype classification.

Machine-learning algorithms trained on 25,000 geolocated soil samples are used to create high-resolution global maps of mycorrhizal fungi, revealing that less than 10% of their biodiversity hotspots are in protected areas.

Spapros is a probe set selection pipeline for targeted spatial transcriptomics that optimizes for both transcriptional and within-cell type variation.

The authors incorporate mechanistic information about lizard physiological responses to heat into predictions of trait variation across time and space, finding that the range of functional traits is more constrained in locations where the local climate strongly selects for thermal performance.

A predictive model of soil microbiome composition is tested against community surveys from across the United States, showing an increase in predictability with spatial scale when using both functional and taxonomic groups.

This study presents a global map of predicted insect mitochondrial genetic diversity from cytochrome c oxidase subunit 1 sequences. From over 2 million mtDNA sequences, they find a negative quadratic latitudinal gradient in genetic diversity evenness, peaking in the subtropics and correlating with hot, stable environments.

Here, Schuldt et al. collate data from two long-term grassland and forest biodiversity experiments to ask how plant diversity facets affect the diversity of higher trophic levels. The results show that positive effects of plant diversity on consumer diversity are mediated by plant structural and functional diversity, and vary across ecosystems and trophic levels.

Analysis of species distribution models in a pan-African database comprising chronometrically dated archaeological sites over the past 120,000 years shows major expansion in the human niche from 70 ka, driven by adaptation to diverse habitats.

APOGEE 2 is a machine-learning tool for assessing the fragility of the mitochondrial genome, evaluating genetic variant pathogenicity and ultimately enhancing our understanding of the clinical heterogeneity of mitochondrial genetic diseases.

How macroscale connectivity relates to regional micro-architecture is poorly understood. Here, the authors annotate brain networks with microarchitectural attributes, finding that the interplay between connection patterns and biological annotations shape regional functional specialization.

Here, the authors examine the mechanisms behind cheatgrass’s successful invasion of North American ecosystems. Their genetic analyses and common garden experiments demonstrate that multiple introductions and migrations facilitated cheatgrass local adaptation.

Whole-slide images (WSI) and digital pathology are valuable approaches for the analysis of tumours and their microenvironments. Here, the authors present scMTOP, a framework to characterise tumour ecosystems and intercellular relationships at the single-cell level from WSIs, which they apply to breast cancer samples.

The drivers of genetic diversity (GD) are poorly understood at the global scale. Here the authors show, for terrestrial mammals, that within-species GD covaries with phylogenetic diversity and is higher in locations with more stable past climates. They also interpolate GD for data-poor locations such as the tropics.

The role of developmental pathways in medulloblastoma tumours (MB) with sonic hedgehog (SHH) activation remains to be explored. Here, the authors perform multi-omic analysis and characterise the key transcriptomic and metabolic patterns of highly differentiated cells in SHH MBs.

Spatial visualization of metabolites in tissues via mass spectrometry imaging can be prone to user perception bias. Here, the authors report the computational framework moleculaR that introduces probabilistic data-dependent molecular mapping of nonrandom spatial patterns of metabolite signals.