Account of the Saez-Rodriguez lab at EMBL-EBI and Heidelberg University. We integrate #omics data with mechanistic molecular knowledge into #opensource #ML methods
Website: https://saezlab.org/
GitHub: https://github.com/saezlab/
Saez-Rodriguez Group
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Our alumna Sophia Müller-Dott was honored with the MTZ Award for Systems Medicine for her PhD work. Congratulations, Sophia! 🎉 A special thanks to Monika and Thomas Zimmermann from the MTZ Foundation for their enduring support of Systems Medicine. 🙌
When mapped onto an external longitudinal blood transcriptomic cohort, these programs predicted future flare risk and highlighted candidate blood protein biomarkers detectable by proteomics.
Together, this links systemic immune programs measured in blood to local tissue pathology in lupus nephritis.
We see our patient map as a reference where SLE or other autoimmune cohorts can be analyzed.
GitHub: github.com/saezlab/meta...
These programs revealed a rewiring of immune coordination during disease activation, including changes in cell-to-cell interactions and in how transcriptional “tasks” are allocated across immune cell types.
Using a new spatial transcriptomic cohort of lupus nephritis kidney biopsies, generated in collaboration with Michael T. Eadon’s team, we found that blood-derived programs were enriched in immune-infiltrated glomerular regions in lupus patients but not in healthy samples.
Led by José Linares Blanco, supervision from @juliosaezrod.bsky.social and @ricoramirez.bsky.social, contributions from @psl-schaefer.bsky.social, Leoni Zimmermann, Ricardo Melo Ferreira, Daniel Toro Dominguez, Pedro Carmona Saez, @tanevski.bsky.social, Marta E. Alarcon Riquelme and Michael T. Eadon
Why?
SLE is clinically and molecularly heterogeneous, but patient stratification often relies on gene expression signatures that miss multicellular context.
We wanted to ask how immune cell types act together across patients, disease activity and tissue pathology.
First, using two independent single-cell PBMC cohorts, we inferred patient-level transcriptomic immune programs that capture both SLE-vs-health differences and heterogeneity within SLE.
This month we welcome Ajita Shree as a postdoctoral researcher, who will be working on computational methods for cell–cell communication 🎉.
Ajita has a background in developing deep generative models for single-cell & spatial transcriptomics.
