New genetic driver found for rare small intestinal cancers

A signaling system known as the Wnt pathway plays a central role in how cells in the intestine grow, divide, and renew themselves. Decades of research have shown that disruption of this pathway is a defining feature of many intestinal cancers. In particular, mutations in the APC gene-which normally acts as a brake disrupting Wnt signaling-are widely recognized as a key initiating event in colorectal tumors.

Although cancer of the small intestine follows a similar developmental sequence, it is a rare disease, accounting for only 3% of all gastrointestinal cancers. Interestingly, while APC mutations are found in about 90% of small intestinal adenomas (benign), they appear in fewer than 30% of small intestinal adenocarcinomas (malignant form). This discrepancy has long raised an important question: What else is driving tumor formation and cancer progression in these cases?

In a recent study, a research team led by Professor Shigeki Sekine and Professor Toshiro Sato from Keio University School of Medicine, Japan, set out to address this knowledge gap. Their paper, co-authored by Associate Professor Masayuki Fujii and Assistant Professor Naoko Abeto from the same institute, will be published in Nature Genetics journal on June 12, 2026. The study identifies recurrent mutations in a gene with no prior known link to cancer as an alternative driver of small intestine tumorigenesis.

The team began by examining a morphologically distinct set of small intestinal adenomas taken from three patients. These adenomas were protruding rather than flat, with branched glands and unusual structural features. By sequencing the protein-coding regions of the genome in these tumors, the researchers found recurrent deletions in a specific part of a gene called COPA. This gene encodes a component of the coatomer complex, which is involved in transporting proteins between the Golgi apparatus and the endoplasmic reticulum.

To validate this finding, the team screened a broader cohort of small intestinal adenoma and adenocarcinoma cases and identified similar COPA mutations in a fraction of them. Notably, none of these cases carried mutations in APC or other known Wnt pathway genes, confirming that COPA mutations represent a genuinely independent route to tumorigenesis. "Scientists have exhaustively hunted down genes responsible for cancer, so this was a shocking new find," says Dr. Fujii.

To understand the functional consequences of these COPA mutations, the team grew small intestinal organoids (3D miniaturized and simplified version of an organ produced in the laboratory) from patient-derived tumor tissue and separately used gene editing tools to introduce the same COPA mutations into healthy small intestinal organoids. Both approaches converged at the same result: COPA mutations activate the Wnt pathway in a way that bypasses the normal requirement for R-spondin and Noggin, two key proteins that act as essential amplifiers of Wnt signaling.

This work has important implications for how small intestinal tumors are classified and diagnosed. Compared to colon cancer, the different subtypes of small intestinal adenomas have been difficult to categorize, in part due to their rarity. "The current discovery could inform catalogues like the WHO classification of digestive system tumors, which doctors widely use to identify tumor types in patients," explains Dr. Fujii.

Moreover, the findings help explain the previously unresolved gap between the high frequency of APC mutations in small intestinal adenomas and their relative scarcity in adenocarcinomas, suggesting that multiple atypical biological paths drive malignancy in these tissues, with COPA-driven tumorigenesis representing one of them. The researchers hope that further research on COPA mutations may help in development of new diagnostic and treatment strategies for intestinal cancers in patients without APC mutations, potentially improving outcomes in this challenging disease.

Source:

Keio University Global Research Institute

Journal reference: