Stadler, R. | bioRxiv Science

bioRxiv2026

Cell-type-resolved spatial proteogenomics from matched genome and proteome of the same cells

The genome and proteome of the same cells are rarely measured together, which is especially consequential in cancer, where somatic mutations vary across clones and drive disease. We show that a single standard proteomics extraction tip can retain peptides on-tip after digestion while genomic DNA passes into the normally discarded flowthrough. Combined with Deep Visual Proteomics, flowthrough co-isolation enables cell-type-resolved spatial proteogenomics from archival FFPE tissue, demonstrated in melanoma.

biochemistry↗

bioRxiv2023

Long-read Sequencing Shows Complex Structural Variants in Tumor-stage Mycosis Fungoides

Mycosis fungoides is the most common cutaneous T-cell lymphoma. Recurrent copy-number variations are the main unifying mutations in this disease, but to date, a comprehensive analysis of occurrence and type of structural variants responsible for these copy-number variations remains elusive. In this study, we used Oxford Nanopore Technologies long-read sequencing to elucidate the highly rearranged genomic landscape of five mycosis fungoides samples. We show the occurrence of multiple classes of simple and complex SV and analyze the extend of tumor suppressor gene deletion by complex SVs. Furthermore, leveraging long-read data, we inferred the genomic structure of a chromothripsis event. Our findings highlight the potential of long-read sequencing as a powerful tool for comprehensive genomic analysis in mycosis fungoides.

genomics↗