Spatial transcriptomics lacks standardized metrics for evaluating imaging-based in situ hybridization technologies across sites. In this study, we generated the Spatial Touchstone (ST) dataset from six tissue types across several global sites with centralized sectioning, analyzed on both Xenium and CosMx platforms. These platforms were selected for their widespread use and distinct chemistries. We assessed reproducibility, sensitivity, dynamic ranges, signal-to-noise ratio, false discovery rates, cell type annotation and congruence with single-cell profiling. This study offers ST standardized operating procedures (STSOPs) and an open-source software, SpatialQM, enabling evaluation of samples across all technical metrics and direct imputation of cell annotations. The generated imaging-based spatial transcriptomics data repository comprises 254 spatial profiles, incorporating both public and newly generated ST datasets in a web-based application, which enables analysis and comparison of user data against an extensive collection of imaging-based datasets. Finally, we establish best practices and metrics to evaluate and integrate imaging-based multi-omics data from single cells into spatial transcriptomics to spatial proteomics.

Gene regulation is orchestrated by the co-binding of proteins along chromosome-length chromatin fibers within single cells, yet the heterogeneity of this occupancy between haplotypes and cells remains poorly resolved in diploid organisms. Here we present Deaminase-Assisted single-molecule chromatin Fiber sequencing (DAF-seq), which enables single-molecule footprinting at near-nucleotide resolution while synchronously profiling single-molecule chromatin states and DNA sequence. DAF-seq illuminates cooperative protein occupancy at individual regulatory elements and resolves the functional impact of somatic variants and rare chromatin epialleles. Single-cell DAF-seq (scDAF-seq) generates chromosome-length protein co-occupancy maps across 99% of each individual cell's mappable genome. scDAF-seq uncovers extensive chromatin plasticity both within and between single diploid cells, with chromatin actuation diverging by 61% between haplotypes within a cell, and 63% between cells. Moreover, we find that regulatory elements are preferentially co-actuated along the same fiber in a distance-dependent manner that mirrors cohesin-mediated loops. Overall, DAF-seq enables the characterization of protein occupancy across entire chromosomes with single-nucleotide, single-molecule, single-haplotype and single-cell precision.

Cell-free nucleic acid (cfNA) liquid biopsy offers a versatile, noninvasive alternative to needle biopsy procedures for the diagnosis or surveillance of a broad range of diseases and physiological conditions. Although these noninvasive molecular measurements enable diagnostic biomarker discovery, they often lack the cellular resolution afforded by invasive needle biopsy. Cell type-specific changes frequently form the basis of disease and contribute to the molecular changes observed in a cfNA liquid biopsy. Recent experimental and computational advances in cfNA detection, alongside detailed molecular definitions across cell types of the human body from single-cell transcriptomic data, can enable cell type inference. In this Review, we delineate the respective strengths of cell-free DNA and cell-free RNA relative to the diagnostic use case. We then describe computational frameworks to infer cell type contributions in cfNA and the distinct opportunity afforded by single-cell transcriptomic data. Finally, we highlight current applications, future directions, and outstanding questions related to this paradigm in cfNA liquid biopsy.

Understanding the molecular anatomy and neural connectivity of the brain requires imaging technologies that can map the three-dimensional nanoscale distribution of specific proteins in the context of brain ultrastructure. Light and electron microscopy visualize either specific labels or anatomical ultrastructure but combining molecular specificity with anatomical context is challenging. Here we present pan-expansion microscopy of tissue (pan-ExM-t), an all-optical imaging method that combines ~16-24-fold linear expansion with fluorescent pan-stainings of proteins and lipids (providing electron microscopy-like ultrastructural context) and immunolabeling (for molecular imaging). We demonstrate the versatility of this approach by imaging synaptic and cell-specific antibodies in the ultrastructural three-dimensional context of presynaptic and postsynaptic densities, neuropil nanoarchitecture and cellular organelles in dissociated neuron cultures, and mouse brain tissue sections. Furthermore, we demonstrate tracing of neuronal circuitry from pan-ExM-t image volumes, suggesting that any laboratory with access to a confocal microscope can now localize specific molecules within nanoscale cellular and circuit contexts.

The efficacy of antimicrobial peptides (AMPs) is limited by challenges of delivery and potency. We enhance AMP performance in the lung by converting AMPs to a peptibody format that fuses AMPs with fragment crystallizable domains to activate innate immunity and cathelin domains for infection-responsive activation, with their mRNA constructs delivered by anti-inflammatory lipid nanoparticles. The highest-scoring design outperforms antibiotic therapy approved by the US Food and Drug Administration in multidrug-resistant pneumonia models, eradicating representative MDR bacteria while mitigating inflammation.

Research on cell therapy for spinal cord injury has yet to achieve sufficient functional recovery. Previous studies in the field grafted oligodendrocyte progenitors, nonspinal neural stem cells or primary spinal neural progenitors. Here we sought to improve functional outcomes by grafting clinically compatible spinal cord neural stem cells derived from human embryonic stem cells (H9-scNSCs). H9-scNSCs significantly improved functional outcomes on a skilled hand task 9.2-fold (P = 2.5 × 10) in hemisected subjects compared with lesioned controls, achieving a fine object retrieval success of 53.4 ± 19.2%, and 2.9-fold (P = 6.3 × 10) superior to controls in hemicontused subjects. Recovery correlated with rehabilitation effort. Grafts extended up to hundreds of thousands of new axons into host circuits up to 39 mm below the injury, forming synapses with host circuitry. Lesion fill was substantially higher and differentiated cell-fate distributions were much closer to that of the normal spinal cord than in previous studies using primary spinal cord cells, likely enabling the observed superior functional outcomes.

Transcriptional regulators play key roles in plant growth, development and environmental responses; however, understanding how their regulatory activity is encoded at the protein level has been hindered by a lack of multiplexed large-scale methods to characterize protein libraries in planta. Here we present enrichment of nuclear trans-elements reporter assay in plants with sequencing (ENTRAP-seq), a high-throughput method that introduces protein-coding libraries into plant cells to drive a nuclear magnetic sorting-based reporter, enabling multiplexed measurement of regulatory activity from thousands of protein variants. Using ENTRAP-seq and machine learning, we screen 1,495 plant viruses and identify hundreds of putative transcriptional regulatory domains found in structural proteins and enzymes not associated with gene regulation. In addition, we combine ENTRAP-seq with machine-guided design to engineer the activity of a plant transcription factor in a semirational fashion. Our findings demonstrate how scalable protein function assays deployed in planta will enable the characterization of natural and synthetic coding diversity in plants.

Metagenomic sequencing and metabolomics of fecal matter have revealed the impact of the gut microbiome on health and disease. In addition to microbiota, feces also contain shed or exfoliated host epithelial, secretory and immune cells, but RNA profiling of these cells is challenging owing to degradation and cross-contamination. Here we introduce exfoliome sequencing (Foli-seq) to profile fecal exfoliated eukaryotic messenger RNAs (feRNAs) originating from the upper and lower gastrointestinal regions and show that this 'fecal exfoliome' harbors stable RNAs that reflect intestinal and immune function. By selectively amplifying targeted transcripts, Foli-seq demonstrates robust, accurate, sensitive and quantitative measurement of feRNAs. In murine colitis models, feRNA reveals temporal processes of epithelial damage, immune response and intestinal recovery specific to different types of gut inflammation. Simultaneous exfoliome and microbiome profiling uncovers a dense host-microbe interaction network. Moreover, we demonstrate stratification of patients with inflammatory bowel disease into subgroups that correlate with disease severity. Fecal Foli-seq is a noninvasive strategy to longitudinally study the gut and profile its health.

Light-sheet microscopy is ideal for imaging large and cleared tissues, but achieving a high isotropic resolution for a centimeter-sized sample is limited by slow and often aberrated, axially scanned light sheets. Here, we introduce a compact, high-speed light-sheet fluorescence microscope achieving 850 nm isotropic resolution across cleared samples up to 1 cm³ and refractive indices ranging from 1.33 to 1.56. Using off-the-shelf optics, we combine an air objective and a meniscus lens with an axially swept light sheet to achieve diffraction-limited resolution and aberration correction. The effective field of view is increased by twofold by correcting the field curvature of the light sheet using a concave mirror in the remote focusing unit. Adapting the light sheet's motion with a closed-loop feedback enhances the imaging speed by tenfold, reaching 100 frames per second while maintaining resolution and field of view. We benchmark the system performance across scales, from subcellular structure up to centimeter scale, using various clearing methods.

Several approaches exist to silence genes, but few tools are available to activate individual mRNAs for translation inside cells. Guiding ribosomes to specific start codons without altering the original sequence remains a formidable task. Here we design capped trans-RNAs capable of directing ribosomes to specific initiation sites on individual mRNAs when the trans-cap is positioned near the target start codon. Structural and biochemical data suggest that the capped trans-RNA facilitates ribosome loading and scanning on the target mRNA through a synergistic mechanism involving alternative cap recognition. The trans-RNA also acts independently of the cap on the target mRNA, enabling translation of circular RNAs lacking internal ribosome entry sites. We apply trans-RNAs in vivo to achieve programmable alternative translation of endogenous genes in mouse liver. Finally, we provide the evidence for the existence of natural transcripts that, similarly to exogenous trans-RNAs, activate translation of endogenous mRNAs.