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Spatial Transcriptomics

All articles tagged with #spatial transcriptomics

SPACER AI Decodes Spatial Rules for Immune Cell Recruitment in Tumors and Hearts
science-and-technology6 days ago

SPACER AI Decodes Spatial Rules for Immune Cell Recruitment in Tumors and Hearts

A new interpretable AI framework called SPACER decodes gene-level rules governing how immune cells are recruited to specific tissue locations. Tested across 37 datasets, it outperforms existing methods by 4-21 times. Key findings link tumor mucins to T-cell exclusion and checkpoint inhibitor resistance, identify local antigen presentation as the primary driver of T-cell engagement, and reveal CD4+ T cells as the main effectors in severe checkpoint inhibitor-induced myocarditis.

via Nature|
#immunotherapy#myocarditis#science-and-technology
New Deep Learning Method VIMA Identifies Disease-Specific Spatial Patterns in Tissues
science-and-technology13 days ago

New Deep Learning Method VIMA Identifies Disease-Specific Spatial Patterns in Tissues

Researchers have introduced VIMA, a new computational method that uses deep learning to analyze spatial molecular data in tissues. By creating numerical 'fingerprints' for small tissue patches, VIMA identifies disease-associated structures without requiring manual cell segmentation or discrete clustering. Tested on rheumatoid arthritis, ulcerative colitis, and dementia datasets, the tool successfully recapitulated known biology and revealed new spatial features, outperforming existing methods in detecting case-control differences.

via Nature|
#bioinformatics#diagnostics#machine-learning
Microenvironment steers human kidney cell fate: insights from spatial single-cell mapping
science2 months ago

Microenvironment steers human kidney cell fate: insights from spatial single-cell mapping

A spatially resolved atlas combining single-cell RNA sequencing and spatial transcriptomics across fetal human kidneys (over 700k cells) shows that local microenvironments guide nephron cell fate, with an early but plastic decision between renal corpuscle and tubular lineages and evidence that some proximal-tubule–like cells can convert to PECs. The study links tissue location and signaling to fate decisions, identifying IGF2 as a locally acting cue promoting NPC renewal and early nephron differentiation, validated by mouse explant experiments and human organoid assays, and proposes a microenvironment-aware revision of nephrogenesis.

via Nature|
#cell-fate#igf2-signaling#kidney-development
Spatial atlas reveals how human organs begin to form after gastrulation
science4 months ago

Spatial atlas reveals how human organs begin to form after gastrulation

Pan et al. create a comprehensive spatiotemporal atlas of gene expression in 13 human embryos from Carnegie stage 12 to 23 using Stereo-seq and snRNA-seq, mapping 50 organs and 198 substructures, revealing context-specific regulatory networks and tissue identities, uncovering new gene functions in cardiac and brain development, and providing a public resource to visualize the embryonic transcriptional landscape and allelic expression dynamics across development.

via Nature|
#embryogenesis#organogenesis#science
TNBC’s heterogeneity mapped: four cancer archetypes and eight tissue ecotypes forecast chemo response
health5 months ago

TNBC’s heterogeneity mapped: four cancer archetypes and eight tissue ecotypes forecast chemo response

A large single‑cell and spatial transcriptomics study of pretreatment TNBC identifies four cancer-cell archetypes and eight ecotypes defined by cancer cells and the tumor microenvironment, reveals macrophage and interferon‑related programs linked to better neoadjuvant chemotherapy response, and provides cell-state– and gene-based classifiers (including a 13‑gene panel) to predict pathological complete response, offering new insight into TNBC heterogeneity and potential immune targets such as LAG3 and HAVCR2.

via Nature|
#health#neoadjuvant-chemotherapy#single-cell-sequencing
Scar-Driven Fibrosis Emerges as Target for Treatment-Resistant Rheumatoid Arthritis
health5 months ago

Scar-Driven Fibrosis Emerges as Target for Treatment-Resistant Rheumatoid Arthritis

A Nature Immunology study using spatial transcriptomics reveals that persistent scar formation (fibrosis) and disrupted fibroblast–endothelial signaling in RA joints may drive treatment resistance even when inflammation is controlled, pointing to a new fibrosis-focused therapeutic target for patients who don’t respond to standard therapies.

via SciTechDaily|
#fibroblasts#fibrosis#health
B cell–driven Diabetic Kidney Disease uncovered by a high-resolution spatial atlas
science5 months ago

B cell–driven Diabetic Kidney Disease uncovered by a high-resolution spatial atlas

Researchers built a cross-platform spatial atlas of diabetic kidney disease using CosMx and Xenium, integrated with snRNA-seq to define 11 tissue niches and injury microenvironments. They identify a B cell–predominant immune microenvironment that defines a DKD subset with faster kidney function decline, and develop tissue biomarkers plus a plasma protein panel that improve risk prediction beyond clinical models; findings validated in UK Biobank and supported by plasma proteomics, highlighting biomarker-guided B cell–targeted DKD trials.

via Nature|
#b-cells#biomarkers#diabetic-kidney-disease
Live-donor atlas maps healthy liver zonation and early steatosis dynamics
science6 months ago

Live-donor atlas maps healthy liver zonation and early steatosis dynamics

Researchers built a high‑resolution spatial atlas of the healthy human liver from live donors, integrating Visium, MERFISH and single-nucleus RNA‑seq to map hepatocyte zonation along the porto–central axis and compare with adjacent diseased tissue. They validate distinct pericentral and periportal programs, reveal early steatosis signatures such as reduced nuclear-encoded mitochondrial genes with compensatory mitochondria-encoded transcripts, and extend analyses to other mammals. The atlas provides a healthy-liver baseline to advance biology and disease research.

via Nature|
#live-donors#liver#science
Skin’s cellular map reveals TNF-driven immune–fibroblast networks in SALT-like neighborhoods
science7 months ago

Skin’s cellular map reveals TNF-driven immune–fibroblast networks in SALT-like neighborhoods

Researchers generated an organ-wide, MERFISH-based single-cell spatial atlas of about 1.2 million cells from normal adult human skin, spanning 15 body sites and 22 donors, resolving 45 cell types and 10 multicellular neighborhoods. They highlight a perivascular neighborhood reminiscent of skin-associated lymphoid tissue (SALT) where TNF coordinates immune–fibroblast crosstalk, with CCL19+ fibroblasts proximal to vessels playing a central role. By integrating MERFISH with scRNA-seq and Visium data, they map site-specific cellular compositions, neighborhood dynamics, and ligand–receptor signaling, and show pan-disease immune alterations in the perivascular niche across skin conditions. An interactive web tool is provided to explore these data, underscoring spatial organization as a key driver of skin biology and disease.

via Nature|
#salt#science#single-cell-atlas
Developmental cell states drive heterogeneity in supratentorial ependymomas
science7 months ago

Developmental cell states drive heterogeneity in supratentorial ependymomas

A multidimensional study integrating single-cell and spatial transcriptomics with live-cell imaging reveals two progenitor-like states—neuroepithelial-like and embryonic-like—and diverse spatial architectures in supratentorial ependymomas. Brain-resident cells can shift tumor cells toward neuronal-like, migratory phenotypes, highlighting developmental origins of heterogeneity and suggesting potential therapeutic angles.

via Nature|
#ependymoma#science#single-cell-rna-seq
Mapping the Developing Human Heart to Understand Congenital Defects
science11 months ago

Mapping the Developing Human Heart to Understand Congenital Defects

This study provides a detailed spatiotemporal map of gene expression and cellular dynamics during early human heart development, analyzing over 69,000 tissue spots and nearly 77,000 cells across 36 hearts, revealing diverse cell types, specialized conduction system components, and the formation of cardiac innervation and valves, thereby advancing understanding of human cardiogenesis.

via Nature|
#cardiogenesis#cellular-dynamics#human-heart-development