iiinova — where your digital self keeps evolving

Linda Kvastad @kvastad.bsky.social · 27/08/2026

We’re excited to share this resource with the community! Many thanks to all our co-authors and collaborators 🙏 📄 Preprint: doi.org/10.64898/202... 🗂️ Dataset: datarepository.kth.se/records/stbw... 🔬 Interactive viewer: pbt.serve.scilifelab.se

doi.org

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Linda Kvastad @kvastad.bsky.social · 27/08/2026

Some relapse-associated putative clones showed preferential localization to vascular niches, suggesting a potential role for specialized microenvironments in tumor regrowth during relapse.

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Linda Kvastad @kvastad.bsky.social · 27/08/2026

We also used spatially inferred copy-number alterations to identify relapse-associated putative tumor clones and investigate where they are located within the tumor tissue. This allowed us to connect putative clonal alterations with the spatial organization of the tumor ecosystem.

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Linda Kvastad @kvastad.bsky.social · 27/08/2026

Across tumor sections, we identified 2–4 recurrent spatial archetypes reflecting distinct biological programs. Some of these spatial programs mirrored developmental lineages — including oligodendrocyte-lineage programs in pilocytic astrocytomas.

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Linda Kvastad @kvastad.bsky.social · 27/08/2026

We’re excited to share our new preprint: Spatial mapping of pediatric brain tumors across diagnoses and relapses A spatial transcriptomic atlas of 59 tumor sections from 19 patients, spanning nine major and rare diagnoses, including seven relapses, 🧵 Highlights:

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Linda Kvastad @kvastad.bsky.social · 22/05/2025

💊 Spatial coexpression of disease genes in enriched structures suggests a new avenue: → Spatially informed drug repurposing strategies.

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Linda Kvastad @kvastad.bsky.social · 22/05/2025

🧠 Top Alzheimer’s genes, identified with STEAM, were enriched among upregulated DEGs in specific cell types—Microglia showing the strongest signal.

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Linda Kvastad @kvastad.bsky.social · 22/05/2025

In sc/snRNAseq from brain we found enrichment for Alzheimer’s pointing towards immune and barrier dysfunction. Here using a sliding window approach to enrichment, scanning through the ranked gene list of genetically associated genes.

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Linda Kvastad @kvastad.bsky.social · 22/05/2025

In the pancreas, we saw reorganization of disease-relevant cell types for type 1 diabetes—implicating both endocrine & exocrine compartments.

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Linda Kvastad @kvastad.bsky.social · 22/05/2025

In developing human spinal cord, we found anterior horn disorder enriched in ventral horn grey matter— this pattern was consistent across multiple developmental time points.

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Linda Kvastad @kvastad.bsky.social · 22/05/2025

Chronic kidney disease → Enrichment in proximal tubule & glomerulus. 🔄 These two structures are known to engage in crosstalk: damage to one can affect the other.

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Linda Kvastad @kvastad.bsky.social · 22/05/2025

🫀 Coronary artery disease → Enrichment in heart vessels.

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Linda Kvastad @kvastad.bsky.social · 22/05/2025

📊 Up to 20% of trait-tissue pairs show structure-specific enrichment — reinforcing the power of spatial resolution.

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Linda Kvastad @kvastad.bsky.social · 22/05/2025

🧮 For ranked gene lists, STEAM uses a sliding window to compare signal vs. null distribution — finding sets of top enriched genes. 💡 We used @opentargets.org for curated gene lists with genetic associations.

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Linda Kvastad @kvastad.bsky.social · 22/05/2025

🔬 Study scale: • 8 organs • 31 spatial datasets • 32 human diseases • 152 trait-tissue pairs • 2 brain sc/snRNA-seq datasets

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Linda Kvastad @kvastad.bsky.social · 22/05/2025

🚀 New method: Identify putative causal tissue structures and cell types for complex traits using your Seurat object + a ranked gene list. 🧰 Our tool: the upcoming R package STEAM.

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Linda Kvastad @kvastad.bsky.social · 22/05/2025

Recently presented our work on how spatial transcriptomics + genetics can reveal putative causal tissue structures for complex traits. 📄 Preprint: doi.org/10.1101/2025... #spatialbiology #genomics #genetics @lifesciences-ge.bsky.social

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Reposted by Linda Kvastad

Tuuli Lappalainen @tuuliel.bsky.social · 05/05/2025

New preprint! My (now former) postdoc @kvastad.bsky.social led this integration of GWAS and spatial transcriptomics (ST) data to identify tissue structures with enrichment of disease-implicated genes = likely causal drivers of disease biology. www.biorxiv.org/content/10.1...

biorxiv.org

Spatial transcriptomics and genetically implicated genes identify putative causal tissue structures for complex traits

Spatially resolved transcriptomics is transforming our understanding of cellular and molecular diversity of tissues. Here, to identify tissue structures that are enriched for putatively causal disease...

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