The research, led by Tülay Karakulak and Abdullah Kahraman of the Swiss Institute of Bioinformatics and their collaborators, including Holger Moch of the University Hospital Zurich and Christian von Mering of the University of Zurich, drew on an extraordinary wealth of data. The team analysed bulk RNA sequencing from 1,117 cancer patients with metastatic melanoma, ovarian cancer, or acute myeloid leukemia (AML), combining samples from the Tumor Profiler (TuPro) Project, a multi-omics clinical study based in Zurich, with data from The Cancer Genome Atlas (TCGA). To determine what a ‘normal’ splicing pattern looks like, they compared the tumour samples against 818 healthy tissue samples from the Genotype-Tissue Expression (GTEx) project, using skin, ovary, and blood samples as the appropriate reference tissues. For each gene in each sample, the researchers identified the Most Dominant Transcript, the isoform that is expressed at the highest level, and then looked for cases where the dominant isoform in a cancer sample differed from the dominant isoform in healthy tissue. These cancer-specific dominant transcripts, abbreviated cMDTs, are the molecular fingerprints of isoform switching.

The scale of what they found is striking. Across the three cancer types, the team identified 6,114 unique cancer-associated dominant transcripts arising from 4,151 genes. Of these, 1,707 encode transmembrane proteins, a particularly important class because many diagnostic assays and targeted therapies act on proteins embedded in the cell membrane. Most of these switches were rare, patient-specific events: 41 percent of the cMDTs were detected in only a single sample, and the majority appeared in fewer than 10 percent of samples within a cohort. Yet 526 of the switches were found in more than 30 percent of samples in at least one cancer cohort, and 131 of those involved transmembrane proteins. Metastatic epithelial ovarian cancer and metastatic melanoma showed the highest numbers of switching events, while AML showed the fewest, confirming earlier observations that splicing aberrations differ markedly between cancer types. The researchers also found that samples in which a spliceosome gene, encoding a component of the splicing machinery itself, had undergone a dominant-transcript switch carried significantly more cMDTs than other samples, whereas mutations in spliceosome genes without a switch did not produce the same effect. This suggests that functional disruption of the splicing machinery, rather than mutation alone, drives large-scale splicing chaos in tumours.

Among the most frequent switches was one involving the cytoskeletal gene ADD3, or adducin 3. In ovarian cancer, a longer isoform of ADD3 that includes an extra exon was the dominant transcript in 82 percent of metastatic TuPro samples and 91.3 percent of TCGA samples. Previous work in lung cancer has shown that inclusion of this exon, exon 14, is associated with poor prognosis, likely because downregulation of the RNA-binding protein QKI-5, which normally prevents that exon from being included, promotes cell proliferation. Another notable example in ovarian cancer concerned SLC44A2, the gene encoding the choline transporter-like protein CTL2. Healthy ovarian tissue predominantly produces a 704-amino-acid version called CTL2-P1, whereas ovarian tumours frequently switch to a slightly longer variant, CTL2-P2, which uses a different starting exon and carries a distinct N-terminal region. Crucially, only the CTL2-P2 variant has detectable choline transport activity. Because aberrant choline metabolism is known to fuel cancer progression, targeting this isoform switch could offer a therapeutic angle in ovarian cancer, and the team noted that nearly 8 percent of TCGA ovarian samples also carry amplifications of the SLC44A2 gene.

In melanoma, the spotlight fell on PDCD6, a gene involved in programmed cell death. The dominant isoform in healthy skin encodes a protein with five EF-hand domains, structural motifs that bind calcium and mediate interactions with other proteins. The cancer-specific isoform retains only two of these domains, which likely cripples its ability to interact with binding partners such as DAPk1, which promotes apoptosis, and VEGFR-2, through which PDCD6 inhibits angiogenesis. In other words, the tumour appears to be splicing away the very machinery that would help kill it. In AML, the team identified a switch to the longest isoform of USP34, a ubiquitin-specific peptidase whose overexpression has been linked to tumour growth in pancreatic cancer and laryngeal carcinoma. And in a striking ovarian cancer finding, the tumour suppressor TP53 itself showed isoform switching in 20 samples, with 18 samples expressing a 261-amino-acid variant known as Δ133p53α. This isoform lacks both transactivation domains, a proline-rich domain, and part of the DNA-binding domain, and according to the team’s interaction database it cannot bind critical partners including MDM2, MDM4, POLR2E, and EP300, fundamentally altering the behaviour of one of the most studied proteins in all of cancer biology.

Identifying these switches at the RNA level is one thing; proving that the altered proteins are actually made is another. To do this, the researchers turned to data-independent acquisition mass spectrometry from matched TuPro protein samples, developing a three-tiered evidence system. Class I evidence comes from peptides unique to the cancer-specific isoform, the strongest possible proof that the switched protein is translated. Class II evidence uses peptides found on the cancer isoform and other non-canonical isoforms but absent from the normal dominant transcript. Class III evidence, the weakest tier, relies on differential expression patterns of multiple peptides between samples with and without the switch. Together, these approaches validated 12.1 percent of the more than 33,000 identified cMDTs, one of the highest detection rates reported to date. The validated switches included the ADD3 long isoform, detected with a specific peptide in 45 percent of matched ovarian cancer proteomics samples, and a long isoform of ATP2B4, a calcium-transporting enzyme implicated in apoptotic resistance in pancreatic cancer, found in 77.5 percent of matched samples. Importantly, a search of normal ovary proteomics data in the PaxDB database found no trace of the ADD3 cancer-specific peptide, underscoring its potential as a tumour-specific marker.

Perhaps the most consequential part of the study concerns what these switched proteins can no longer do. The team built an updated version of their CanIsoNet database, mapping nearly 100,000 protein isoforms onto the latest STRING protein interaction network and the 3did database of domain-domain interactions. Among 1,652 cMDTs with domain interaction information, 906 had lost all interactions with their protein partners, while only 718 retained all of them. A vivid example is TRAPPC5, a subunit of a vesicle-transporting complex that shuttles cargo from the endoplasmic reticulum to the Golgi. In melanoma, a truncated 121-amino-acid isoform of TRAPPC5 was the dominant transcript in up to two-thirds of samples, compared with a 188-amino-acid version in healthy tissue, and the shortened protein loses every one of its native interaction partners, including clinically annotated proteins. High expression of this truncated isoform was associated with lower survival in TCGA data, whereas expression of the normal isoforms had no survival impact, marking it as a candidate biomarker for melanoma.

The implications for drug treatment may be even more significant. The researchers constructed a new database, called IsoDrug, that links protein isoforms to the small molecules and drugs that bind them, drawing on structural data from more than 8,600 entries in the Protein Data Bank. Of the 641 cMDTs with drug interaction information, whose canonical counterparts are targets of 166 drugs, 56 percent had lost the binding residues needed to interact with their potential drug targets. Among tyrosine kinase inhibitors, the workhorse drugs of precision oncology, the team found 15 cancer-specific isoforms whose canonical versions bind one of 11 TKI compounds. The most frequent was a 154-amino-acid isoform of PDGFRA, expressed predominantly in melanoma samples, which lacks the entire tyrosine kinase domain that the drug sunitinib targets. A similar case is EPHB4, a receptor overexpressed in ovarian cancer, whose cancer-specific isoform retains only the ligand-binding domain and has lost the complete kinase domain targeted by inhibitors. Patients whose tumours predominantly express these truncated isoforms would likely derive no benefit from the corresponding drugs, even if the gene itself appears amplified or mutated on standard genomic tests.

The authors are careful to note the limitations of their work. Many of the single-sample switches could reflect technical variability rather than true biology, and the short-read sequencing they used cannot capture full-length transcripts as precisely as emerging long-read methods would. They also defined cancer-specific switches strictly within each tissue context, meaning some of these isoforms may exist in other healthy tissues. Still, the path forward is clear: the team highlights isoform-specific peptides from ADD3, ATP2B4, and PARP14 as prime candidates for liquid biopsy tests that could detect cancer or guide therapy decisions from a simple blood sample, and they call for drug-screening experiments in patient-derived cell cultures to confirm the predicted losses of drug binding. What emerges from this study is a compelling message for oncology: reading a tumour’s genome is no longer enough. To understand what a cancer is truly capable of, and which drugs it will resist, clinicians and researchers must also read the tumour’s RNA, exon by exon, and ask not just which genes are active, but which versions of their proteins the cancer has chosen to build.

Subject of Research: Alternative splicing isoform switches and their effects on protein and drug interactions in melanoma, ovarian cancer, and acute myeloid leukemia

Article Title: Switches in alternatively spliced isoforms impact protein and drug interactions in melanoma, ovarian cancer, and acute myeloid leukemia

Article References: Karakulak, T., Tumor Profiler Consortium, Aebersold, R., Ak, M., Al-Quaddoomi, F. S., Albert, S. I., Albinus, J., Alborelli, I., Andani, S., Attinger, P.-O., Bacac, M., Baciu-Drăgan, M.-A., Baumhoer, D., Beck-Schimmer, B., Beerenwinkel, N., Beisel, C., Bernasconi, L., Bertolini, A., Bodenmiller, B., … Kahraman, A. (2026). Switches in alternatively spliced isoforms impact protein and drug interactions in melanoma, ovarian cancer, and acute myeloid leukemia. British Journal of Cancer. https://doi.org/10.1038/s41416-026-03638-0

Image Credits: AI Generated

DOI: 10.1038/s41416-026-03638-0

Keywords: alternative splicing, isoform switching, melanoma, ovarian cancer, acute myeloid leukemia, biomarkers, drug resistance, proteomics, spliceosome, TP53, PDGFRA, transmembrane proteins