NEK2 Drives Trastuzumab Resistance in Gastric Cancer Through m6A Control of FN1

Trastuzumab, the monoclonal antibody that targets HER2, has transformed the treatment of HER2-positive gastric cancer, yet resistance to the drug remains one of the most stubborn obstacles in clinical oncology. Now a team of researchers in China has uncovered a molecular circuit that helps gastric cancer cells shrug off the antibody, and their findings point to a previously underappreciated role for RNA chemistry in drug resistance. The study, published in Molecular Biology Reports, identifies the kinase NEK2 as a central driver of trastuzumab resistance through its control of a chemical tag on messenger RNA known as N6-methyladenosine, or m6A.

The research, led by Zengchao Shen and colleagues at Lishui Municipal Central Hospital, The Fifth Affiliated Hospital of Wenzhou Medical University, began with a deceptively simple experimental strategy. The team took NCI-N87 gastric cancer cells, which are normally killed by trastuzumab, and exposed them stepwise to increasing concentrations of the drug over an extended period. What emerged were NCI-N87/TR cells, a resistant line that could survive doses of trastuzumab that would annihilate the parental population. These resistant cells became the model for dissecting exactly what had changed at the molecular level to allow survival.

When the researchers compared gene expression between resistant and parental cells, one protein stood out dramatically: NEK2, a serine-threonine kinase best known for its role in centrosome separation during mitosis. NEK2 was markedly upregulated in the trastuzumab-resistant cells, consistent with a growing body of evidence implicating the kinase in cancer progression and therapeutic resistance across multiple tumor types. Previous work has linked NEK2 to proliferation, migration, and drug resistance in gastric cancer through pathways including AKT signaling, ERK/MAPK signaling, and regulation of histone methylation, but its involvement in trastuzumab resistance had never been established.

To test whether NEK2 was merely a bystander or an active participant in resistance, the team used genetic silencing to knock down NEK2 expression in the resistant cells. The results were striking. With NEK2 silenced, cell viability dropped, DNA replication as measured by EdU incorporation declined, and apoptosis increased, indicating that the cells had lost much of their ability to withstand trastuzumab. Conversely, when the researchers forced NEK2 overexpression in parental cells, the cells became more resistant to the drug. The supplementary data confirmed this in a second gastric cancer line, SNU-216, where NEK2 overexpression shifted the dose-response curve and increased survival at trastuzumab concentrations that would normally be lethal.

Having established that NEK2 drives resistance, the team turned to the question of how a mitotic kinase could influence a cell’s response to an antibody that targets a cell-surface receptor. The answer, it turns out, lies in the emerging field of epitranscriptomics, the study of chemical modifications to RNA. The researchers found that NEK2 promotes the expression of fibronectin 1, or FN1, an extracellular matrix protein that has been repeatedly associated with gastric cancer progression and with resistance to various therapies. FN1 activates PI3K/AKT signaling, a pro-survival pathway that helps cells resist apoptosis, and exogenous FN1 partially rescued the resistance lost when NEK2 was knocked down.

But the mechanism went deeper than simple transcriptional regulation. Using RNA immunoprecipitation, MeRIP-qPCR, and dual-luciferase reporter assays, the team discovered that FN1 messenger RNA carries a specific m6A modification at nucleotide 5882, and that this modification is deposited by WTAP, a well-known m6A methyltransferase component. Once the methyl group is in place, the reader protein YTHDF1 recognizes the modified RNA and enhances its stability and translation, boosting FN1 protein production. In other words, NEK2 does not directly increase FN1 transcription; instead, it orchestrates a chain of RNA-level events that keeps FN1 messenger RNA alive longer and translated more efficiently.

The epitranscriptomic circuit proved functionally significant. When the researchers overexpressed either WTAP or YTHDF1 in cells where NEK2 had been silenced, FN1 expression returned, AKT phosphorylation was restored, and trastuzumab resistance came back. This rescue experiment demonstrated that the WTAP/YTHDF1 axis is not merely correlated with resistance but is causally responsible for it, acting downstream of NEK2. The finding places NEK2 at the top of a signaling hierarchy that flows through RNA methylation machinery to control a key extracellular matrix protein and, ultimately, the survival pathway that protects gastric cancer cells from trastuzumab.

The implications for clinical practice are considerable. Trastuzumab resistance in HER2-positive gastric cancer has been attributed to a variety of mechanisms, including HER2 loss, activation of alternative signaling pathways such as Wnt/beta-catenin and STAT3, and changes in the tumor microenvironment. The new study adds a fundamentally different layer to this picture, suggesting that the chemical modification state of messenger RNA can determine whether a tumor responds to targeted therapy. Because m6A modification is reversible and the enzymes involved are drug-targetable, the WTAP/YTHDF1/FN1 axis represents a potential vulnerability that could be exploited pharmacologically.

NEK2 itself has attracted growing interest as a therapeutic target. Recent reviews have catalogued a range of NEK2 inhibitors under development as antitumor agents, and studies in pancreatic cancer, multiple myeloma, and hepatocellular carcinoma have shown that blocking NEK2 can sensitize tumors to other treatments, including immune checkpoint inhibitors and proteasome inhibitors. The current findings suggest that combining NEK2 inhibition with trastuzumab, or targeting the downstream m6A machinery, could be a rational strategy to overcome resistance in gastric cancer patients whose tumors have stopped responding to HER2-directed therapy.

As with any cell-line study, the findings will need validation in patient tumors and animal models before they can inform treatment decisions. The researchers note that their work was conducted in established gastric cancer cell lines, and the datasets used in the study are available from the corresponding author on reasonable request. Nevertheless, the identification of a specific m6A site on FN1 messenger RNA, at a defined nucleotide position, and the demonstration that this single chemical mark can influence a clinically important drug response, represent a compelling example of how RNA modifications are moving from the bench to the forefront of cancer medicine. For patients with HER2-positive gastric cancer facing the prospect of trastuzumab failure, the study offers a molecular explanation for resistance and a set of new targets that may one day restore the effectiveness of one of oncology’s most important targeted therapies.

Subject of Research: Molecular Biology

Article Title: NEK2 promotes trastuzumab resistance in gastric cancer through WTAP/YTHDF1-dependent m6A regulation of FN1

Article References: Shen, Z., Zheng, J., Chen, Y., Liu, J., Li, M., & Shi, H. (2026). NEK2 promotes trastuzumab resistance in gastric cancer through WTAP/YTHDF1-dependent m6A regulation of FN1. Molecular Biology Reports, 53(1), Article 1738. https://doi.org/10.1007/s11033-026-12927-z

Image Credits: AI Generated

DOI: 10.1007/s11033-026-12927-z

Keywords: gastric cancer, trastuzumab resistance, NEK2, m6A modification, FN1, PI3K/AKT signaling, promotes, trastuzumab, resistance, gastric, cancer, WTAP