Biology subjects

Koshkina, M. K.

Publications and source records attributed to Koshkina, M. K..

3 recordsLinked to original sources

bioRxiv2026

Oncogenic fusions induce an extensive cancer-restricted cryptic proteome in Ewing sarcoma

How tumors generate a cryptic "dark" proteome absent from healthy tissues, and whether it can be reversibly activated, remains unclear. In Ewing sarcoma, all tumors are driven by EWSR1::ETS fusions, making it a tractable model to study dark proteome activation. Integrating matched transcriptomes, translatomes and proteomes from 48 patient tumors with long-read RNA sequencing, single-cell Ribo-seq, proteomics and immunopeptidomics in cell line models, we show that EWSR1::FLI1 acts as a reversible switch recurrently inducing hundreds of cancer-specific neoproteins. Many arise from canonical coding regions via intragenic transcription start sites, generating truncated or out-of-frame neoproteins. We uncover a fusion-dependent increase in ribosomal readthrough into poly(A) tails, generating a stable 80-amino-acid TRPM4 neoprotein that, despite lacking a stop codon, is the most abundant tumor-specific microprotein across patients. Proteomic, immunopeptidomic, and immunofluorescence analyses validate neoproteins as tumor-restricted antigens, revealing a therapeutically actionable cancer dark proteome controlled by one oncogenic fusion.

cancer biology↗

bioRxiv2026

An alignment-last approach enables rapid transcriptomic biomarker discovery in large cohorts

Canonical transcriptomic analysis requires committing from the outset to a reference genome or transcriptome, which imposes a predefined feature set, usually annotated genes or isoforms. Alignment and annotation dilute the signal through feature-level aggregation, discard any sequence absent from the reference, and require reprocessing the entire dataset for each new question (mutations, fusions, transposable elements). Here, we introduce the alignment-last paradigm, in which the read becomes the unit of comparison across samples, and alignment is deferred to annotate only the relevant sequences. Querying the merome, a reference-free cohort k-mer index, with just a handful of reads (about 0.01% of a sample's) reveals the cohort's transcriptomic structure in bulk and single-cell data. At single-cell resolution, these reads outperform genes for cell classification and rediscover, without supervision, a transposable-element signature (VL30) of exhausted T cells. Finally, unsupervised read-level differential analysis recovers established lncRNA biomarkers; uncovers new prognostic transposable-element reads in adrenocortical carcinoma and sarcomas; and extracts signals even from reads that fail to align.

bioinformatics↗

bioRxiv2026

Specific killing of Ewing sarcoma by TCR-T cells targeting public neogene-encoded antigens

EWSR1::FLI1, the oncogenic chimeric transcription factor driving Ewing sarcoma (EwS)induces expression of exquisitely EwS-specific neogenes (Ew_NGs) through neomorphic binding and transcription activation at GGAA microsatellites in genomic regions that are silent in normal tissues. We show that peptides encoded by Ew_NGs are presented on HLA-I complexes on EwS cells. The cytokine secretion of CD8+ T cells specific for Ew_NG-encoded HLA-I-bound peptides is activated by all HLA-I-matched EwS cells but not by non-EwS cells. These T cells kill EwS cells in an HLA-I restricted manner. This cytotoxicity is dependent on the expression of EWSR1::FLI1 and of the corresponding Ew_NG. It can be reproduced by transduction of the TCR into donor T cells (TCR-T) which kill EwS cells in vivo. Moreover, we show that neither off target nor allogeneic activation are observed with TCR-T thus paving the way for cell therapy in relapsed/resistant EwS patients for which therapeutic options are very limited. Statement of significanceThe chimeric transcription factor EWSR1::FLI1 generates tumor-specific neogenes encoding neoantigen presented by the HLA-I molecules of Ewing cells. Neoantigen-specific CD8+ T-cell clones and engineered TCR-T cells can selectively recognize and kill EwS tumor cells in vitro and in vivo.

immunology↗