LINC01963 promotes pancreatic ductal adenocarcinoma proliferation via METTL3/IGF2BP2 axis-mediated m⁶A modification of c-Myc

TL;DR

This study shows how a long noncoding RNA called LINC01963 helps pancreatic cancer grow by stabilizing a key protein called c-Myc through specific molecular interactions.

Contribution

The study identifies LINC01963 as a novel regulator of c-Myc stability via the METTL3/IGF2BP2 axis in pancreatic cancer.

Findings

LINC01963 knockdown reduces PDAC cell proliferation and tumor growth.

LINC01963 stabilizes c-Myc mRNA by enhancing m⁶A modification and forming a complex with IGF2BP2.

High LINC01963 expression correlates with poor prognosis in PDAC patients.

Abstract

C-Myc overexpression is an important molecular hallmark of pancreatic ductal adenocarcinoma (PDAC), but directly targeting c-Myc is extremely challenging. Identifying key upstream factors involved in c-Myc overexpression provides promising indirect targets for c-Myc.

Public transcriptomic and clinical datasets, including TCGA, GEO, were integrated to identify c-Myc-associated long noncoding RNAs in PDAC, with LINC01963 selected for further investigation. The functional roles of LINC01963 were validated using human PDAC cell lines and in vivo proliferation models. The molecular mechanisms underlying c-Myc regulation by LINC01963 were explored using RNA pull-down, RIP-seq, RIP-qPCR, Co-IP, mass spectrometry, ubiquitination assays, truncation and site-directed mutagenesis analyses, and dual-luciferase reporter assays. Survival associations were evaluated using Kaplan–Meier analysis and Cox proportional hazards regression.

Here, the long noncoding RNAs (lncRNAs) highly expressed in PDAC and significantly correlated with c-Myc expression were identified using RNA sequencing datasets. Among them, LINC01963 was found to interact with c-Myc, as confirmed by RNA pull-down and RIP-qPCR assays. Furthermore, high LINC01963 expression was correlated with poor PDAC prognosis, and functional studies demonstrated that its knockdown inhibited PDAC cell proliferation and xenograft tumor growth. Mechanistic studies identified LINC01963 as a key regulator of c-Myc stability, consequently affecting cell cycle through the c-Myc/p21-related signaling pathways. Further investigation revealed that LINC01963 enhanced N6-methyladenosine (m⁶A) modification of c-Myc mRNA by protecting methyltransferase-like 3 (METTL3) protein from KDM1B-mediated K48-linked ubiquitination and proteasomal degradation. Intriguingly, LINC01963 also stabilized c-Myc mRNA by facilitating the formation of a ternary complex with insulin-like growth factor 2 mRNA-binding protein 2 (IGF2BP2) and m⁶A-modified c-Myc.

Our study reveals that LINC01963 promotes PDAC tumorigenesis through METTL3/IGF2BP2 axis-coordinated regulation of c-Myc, suggesting a new strategy for indirectly targeting c-Myc.

The online version contains supplementary material available at 10.1186/s13046-026-03650-5.

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