4/ This TE atlas uncovers novel signatures within immune compartments, offering new avenues for cellular taxonomy and understanding TE biology in health and disease.

3/ Applied to human PBMCs, it quantifies locus‑specific TE expression, which was previously hidden in standard scRNA‑seq pipelines

The surprising finding? TE activity signatures distinctly mark cell types and subsets—sometimes even more sharply than conventional mRNA markers

2/ A major challenge with scRNA-seq is the low per-cell read depth - instead of having 30M reads to inform the model, we are lucky if we get 30K! To overcome this, we developed "pooling modes", where we can borrow strength from other cells to help reassign ambiguous reads.

Importantly, HERV-based subtypes predict prognosis.

Clusters enriched for plasma cell-like signatures had the poorest survival — a finding invisible in gene-only classifications.

6/

In DLBCL, we identified 7 distinct HERV-driven subtypes, refining the traditional 3-subtype COO model.

Some "unclassified" DLBCLs actually fit into new HERV-defined groups — with distinct survival outcomes! 📉📈

5/

Findings:

- Healthy B-cells show dynamic HERV activity during differentiation.
- Lymphomas retain HERV signatures from their cell of origin (COO).
- BL subtypes cluster by EBV status better with HERVs than with genes!

4/

We created the first locus-specific map of HERV activity in:
- Healthy B cells (Naïve, Memory, Germinal Center subtypes)
- Diffuse large B-cell lymphoma (DLBCL)
- Follicular lymphoma (FL)
- Burkitt lymphoma (BL)
🎯 Using RNAseq + #Telescope quantification.

3/

Endogenous retroelements (EREs), like HERVs, make up ~8% of the human genome. Their expression is often overlooked — but we found they hold key information about B-cell identity, both in healthy germinal centers and in malignancy!

2/

At the DC #standupforscience today.

The question was “Why are you here?” She came up with this on her own! (I helped her with the spelling)

So proud of her! #standupforscience2025
@standupforscience.bsky.social