Long Noncoding RNA NIHCOLE Promotes Ligation Efficiency of DNA Double-Strand Breaks in Hepatocellular Carcinoma

Abstract

Long noncoding RNAs (lncRNA) are emerging as key players in cancer as parts of poorly understood molecular mechanisms. Here, we investigated lncRNAs that play a role in hepatocellular carcinoma (HCC) and identified NIHCOLE, a novel lncRNA induced in HCC with oncogenic potential and a role in the ligation efficiency of DNA double-stranded breaks (DSB). NIHCOLE expression was associated with poor prognosis and survival of HCC patients. Depletion of NIHCOLE from HCC cells led to impaired proliferation and increased apoptosis. NIHCOLE deficiency led to accumulation of DNA damage due to a specific decrease in the activity of the nonhomologous end-joining (NHEJ) pathway of DSB repair. DNA damage induction in NIHCOLE-depleted cells further decreased HCC cell growth. NIHCOLE was associated with DSB markers and recruited several molecules of the Ku70/Ku80 heterodimer. Further, NIHCOLE putative structural domains supported stable multimeric complexes formed by several NHEJ factors including Ku70/80, APLF, XRCC4, and DNA ligase IV. NHEJ reconstitution assays showed that NIHCOLE promoted the ligation efficiency of blunt-ended DSBs. Collectively, these data show that NIHCOLE serves as a scaffold and facilitator of NHEJ machinery and confers an advantage to HCC cells, which could be exploited as a targetable vulnerability. Significance: This study characterizes the role of lncRNA NIHCOLE in DNA repair and cellular fitness in HCC, thus implicating it as a therapeutic target. See related commentary by Barcena-Varela and Lujambio, p. 4899

Home and Away: The Role of Non-Coding RNA in Intracellular and Intercellular DNA Damage Response

“…A similar scaffolding role was suggested for NIHCOLE, whereby its interaction with Ku80 promotes the formation of multimeric NHEJ complexes to increase ligation efficiency [26]. However, in contrast to the role of LINP1 in long-range synapsis [27], NIHCOLE is implicated in short-range synapsis [26]. While long-range synaptic complexes can provide the initial tethering of the DNA ends, it is the short-range synaptic complex that catalyses their precise alignment and ligation [38], distinguishing the functions of the two scaffolding lncRNAs.…”

“…Single-molecule assays utilising molecular forceps to imitate DSBs showed LINP1 to be even more effective than PAXX at bridging DNA ends [27], thus highlighting the increasing importance of studying RNA molecules as key drivers of DNA repair. A similar scaffolding role was suggested for NIHCOLE, whereby its interaction with Ku80 promotes the formation of multimeric NHEJ complexes to increase ligation efficiency [26]. However, in contrast to the role of LINP1 in long-range synapsis [27], NIHCOLE is implicated in short-range synapsis [26].…”

“…While long-range synaptic complexes can provide the initial tethering of the DNA ends, it is the short-range synaptic complex that catalyses their precise alignment and ligation [38], distinguishing the functions of the two scaffolding lncRNAs. Furthermore, single-molecule atomic force microscopy revealed hyper-stoichiometric clustering of NIHCOLE and Ku80, such that around three molecules of NIHCOLE could recruit 14 Ku80 molecules, proposing a potential role for NIHCOLE in promoting phase separation as a means to drive NHEJ via "repair hubs" [26]. Another lncRNA, LRIK, was also found to interact with the Ku70-Ku80 heterodimer.…”

“…NHEJ offers a rapid but low fidelity means of repairing a DSB via the binding of the Ku70-Ku80 heterodimer to the DNA ends at the break site, facilitating the recruitment of end-processing factors such as LIG4, which can resolve the DSB by means of the direct ligation of the DNA ends [2]. Many lncRNA species have recently been identified as enhancers of NHEJ efficiency, including LINP1 [23], LRIK [24], lnc-RI [25], and NIHCOLE [26], discussed below. These and other examples have been summarised in Table 1 to convey the diversity of lncRNA contributions to DDR.…”

Expression changes of serum LINC00941 and LINC00514 in HBV infection‐related liver diseases and their potential application values

“… 18 , 19 Unfried et al reported that the expression of NIHCOLE was related to the poor prognosis and survival of patients with HCC, and the inhibition of NIHCOLE expression in HCC cells may lead to limited cell proliferation and increased apoptosis rate through the accumulation of DNA damage. 20 Research by Peng et al showed that the expression of LINC00511 was higher in HCC tissues, and the mechanism study revealed that the invasion pseudopodia and exosomal secretion induced by LINC00511 were involved in tumor progression. 21 Yin et al found that LINC01133 expression in HCC tissues was elevated, and can predict the poor prognosis of HCC patients; in‐vitro studies showed that overexpression of LINC01133 can promote the proliferation and aggressive phenotype of HCC cells, and promote tumor growth and lung metastasis in vivo, while knockdown LINC01133 had the opposite effect.…”