Genomics Papers of the Week

Through integrative analysis of time-resolved single-cell RNA sequencing in murine synovium and spatial transcriptomics of human OA tissues, we identified a pathogenic CD74 macrophage subset that expands in OA and localizes at the synovial-cartilage interface.

We investigated whether DDR1-mediated mechanosensation links arterial stiffness to vascular smooth muscle cell (SMC)-endothelial paracrine communication in CKD-related atherosclerosis.

We introduce cutting-edge single-cell epigenomic mapping technologies, their bone tissue-specific adaptations, and analytical frameworks for multi-omics data integration.

A combined in vivo, multi-omics and in vitro mechanistic study was conducted.

We demonstrate that ACKR1+ ECs promote fibrosis through two distinct mechanisms.

Formalin-fixed paraffin-embedded (FFPE) tissue-compatible spatial transcriptomics (ST) is transforming biology and histopathology, but achieving high sensitivity, genome-wide coverage, single-cell resolution, and researcher accessibility remains challenging. To address these challenges, we here present a dendrimeric DNA coordinate barcoding design for FFPE tissue-adapted spatial RNA sequencing (Decoder-FFPE-seq) by integrating RNA-to-DNA probe conversion with blotting-assisted barcoding.

In C. elegans, Zg I extended lifespan, improved locomotor and physiological fitness, reduced age-associated biomarkers, and enhanced oxidative stress resistance.

Cell-cell communication and spatial ligand-receptor analyses identify enhanced predicted MIF-CD74/CD44 interactions in B-cell-associated regions adjacent to cartilage.

Our study reveals a mechanistic link between Th2 inflammation and SG ferroptosis via IL-4-TRIM15-GPX4-ubiquitination signaling, thus offering new insights into SG dysfunction and skin barrier impairment in AD.

Here, we combined high-resolution spatial transcriptomics with single-cell multiomics to profile human embryos from Carnegie stages 15 to 23, capturing the codevelopmental dynamics of the urogenital system.

We have developed a multimodal spatial transcriptomics approach that enables the definition of transcriptional programs with subcellular resolution, somatic CAG repeat lengths, and eight other pathology markers, including HTT inclusions, in every cell of intact brain sections.

We performed region-stratified single-cell RNA sequencing across the adult body and mapped cell types and gene expression at single-cell resolution using spatial transcriptomics.

Here we use genetic multiplexing to generate population-scale single-nucleus chromatin accessibility (single-nucleus assay for transposase-accessible chromatin using sequencing (snATAC-seq)) and transcriptome (single-nucleus RNA sequencing (snRNA-seq)) maps across 287 frozen human skeletal muscle biopsies.

The drastic CAF and stromal compartment reduction observed indicated a fibroblast depletion rather than a fibroblast polarization shift.CONCLUSIONWhile our final clinical cohort does not allow assessment of the treatment effect, this study demonstrated that targeting TGF-β in patients can disrupt the tumor stroma within a short time frame.

In this Review, we dissect the multifaceted roles of CAFs, from their promotion of cancer cell proliferation, invasion and angiogenesis through secreted factors and extensive extracellular matrix (ECM) remodeling, to their profound influence on the immune landscape.

This work highlights the need for more nuanced examination of the similarities and distinctions in the associations between PTSD and alcohol consumption versus AUD.

To investigate IMNM pathogenesis, we applied spatial transcriptomics on myositis muscle biopsies and integrated the results with published single-nucleus transcriptomic data. This combined approach enabled analysis of gene expression with spatial localisation in the muscle.