Spatial transcriptomics (10x Genomics Visium ) of mouse brain from a spatial object recognition training experiment

Dataset Overview

GSE201610: 10x Genomics Visium spatial transcriptomics of mouse brain from a spatial object recognition (SOR) training experiment

Analyses Performed

Unsupervised Spatial Clustering (Single Sample: HC1)

• Method: PCA + K-means clustering (k=12)

• Output: 12 spatial clusters with anatomically-defined regions

• Key Finding: Successfully identified oligodendrocytes, neurons, choroid plexus, ependymal cells, and stromal regions with canonical marker genes

Pan-Sample Clustering (All 6 Samples)

• Method: Quality filtering → SCTransform → Louvain clustering (resolution 0.5)

• Retention: 10,839 spots (66% of 16,451 total)

• Output: 18 anatomically coherent spatial regions

• Marker Genes: 16,743 significantly differentially expressed genes across regions

Condition Comparison: HC vs SOR (Proportional Analysis)

• Comparison: Home-cage Control (n=3) vs SOR-trained (n=3)

• Key Findings:

  • Thalamus: 11.7% (HC) vs 11.2% (SOR) — minimal change

  • Midbrain: 12.2% (HC) vs 9.4% (SOR) — −2.8% in SOR (dopaminergic/serotonergic circuits)

  • Hypothalamus (Oxt+): 9.1% (HC) vs 10.5% (SOR) — +1.4% in SOR

  • Mixed Cortical: 1.6% (HC) vs 4.0% (SOR) — +2.4% in SOR (potential learning plasticity)

  • Overall: Anatomical architecture highly conserved across conditions

Meninges/Vasculature Spatial Localization (HC1 vs SOR1)

• Markers Used: Col1a2, Dcn, Vtn, Col1a1, Col3a1

• HC1 Results: 83 meningeal spots (3.12% of tissue), concentrated at periphery

• SOR1 Results: 71 meningeal spots (2.78% of tissue)

• Key Finding: Meningeal/vascular compartment is structurally preserved between conditions

Key Biological Insights

1. Intact Brain Architecture: Unsupervised clustering faithfully recapitulates known mouse brain anatomy with clear demarcation of major structures (thalamus, midbrain, cortex, hypothalamus, white matter, choroid plexus)

2. Training-Induced Compositional Shifts:

   • Midbrain reduction in SOR suggests potential modulation of dopaminergic/serotonergic circuits

   • Cortical increase in SOR may reflect learning-associated plasticity

   • Overall effect sizes are modest (<3% absolute change), requiring larger cohorts for statistical validation

3. Preserved Stromal/Vascular Compartment: Meningeal and vascular structures remain structurally similar between HC and SOR conditions

Recommended Follow-Up Analyses

• Reference-based deconvolution: Apply RCTD or Cell2location with Allen Brain Atlas scRNA-seq for higher cell type resolution

• Statistical testing: Formal compositional data analysis (ALDEx2, scCODA) for differential abundance

• Spatial differential expression: Identify genes with condition-dependent expression within specific brain regions

• Pathway enrichment: Characterize functional programs in regions showing compositional shifts

• Larger sample size: Current n=3 per group limits statistical power; recommend n≥5 for robust conclusions