Gastineau, S. | bioRxiv Science

bioRxiv2026

Routine FFPE sections support clinically compatible single-nucleus transcriptomics across six human cancer types

Tumor cellular composition--including malignant cell states, immune populations, and stromal populations--is increasingly recognized as a determinant of therapeutic response and resistance to anti-cancer agents, yet comprehensive cellular profiling remains largely confined to research settings. Here, we present a clinically compatible sample-to-report workflow for tumor composition profiling from routine formalin-fixed paraffin-embedded (FFPE) clinical specimens. By combining low-input single-nucleus RNA sequencing with foundation model- based automated cell annotation, this workflow enables prospective sample-by-sample analysis without dedicated research material or cohort-based processing. Across 116 clinical specimens representing six cancer types, we generated reproducible measurements of cellular composition and cell-type-specific gene expression, demonstrated high technical reproducibility, and showed concordance with pathological assessment of immune infiltration. The workflow was similarly applicable to archival FFPE material and ultra-low-input biopsy specimens. Together, these findings establish a practical framework for routine single-cell profiling from standard pathology specimens and open the perspective of prospective evaluation of cellular composition as a clinical biomarker in precision oncology.

cancer biology↗

bioRxiv2025

Identification of a shared persistence program in triple-negative breast cancer across treatments and patients

Acquisition of resistance to anti-cancer therapies is a multistep process, which initiates with the survival of drug persister cells. Understanding the mechanisms driving the emergence of persister cells remains challenging, primarily because of their limited accessibility in patients. Here, using mouse models to isolate persister cells from patient tumors, we determine the identity features of persister cells from eight patients with triple-negative breast cancer (TNBC). Combining over 80 transcriptome studies, we reveal hallmarks of the persister state across patient models and treatment modalities: high expression of basal keratins together with activation of a stress response and inflammation pathways. Patient-derived persister cells are transcriptionally plastic and return to a common treatment-naive like state upon relapse, regardless of the treatment they have been exposed to. Leveraging gene regulatory networks, we identify AP-1, NFKB and IRF/STAT as the key drivers of this hallmark persister state. As a proof of concept, we show that FOSL1 - an AP-1 member - is sufficient to drive cells to the persister state by binding enhancers and reprogramming the transcriptome of cancer cells. On the contrary, cancer cells without FOSL1 have a decreased ability to reach the persister state. By defining hallmarks of drug persistence to multiple therapies of the standard of care, our study provides a resource to design novel combination therapeutic strategies to limit resistance.

cancer biology↗