Long non‐coding RNA‐regulated alternative splicing modulates key cancer pathway in lung adenocarcinoma

Long non-coding RNAs (lncRNAs) are RNA transcripts that typically do not code for protein and are longer than 200 nucleotides.1 In recent years, their list of functions has increased, and they play critical roles in regulating transcription and post-transcriptional events. LncRNAs exhibit tissue- or cell-specific expression patterns and can interact with DNA, RNA, and proteins. In recent years, lncRNAs have emerged as oncogenes and tumour suppressors in various cancers, which can highly impact tumour progression and treatment efficacy. Although the effect of lncRNAs on the efficacy of drugs in cancer has been demonstrated, many questions remain related to drug resistance, such as how alternative splicing (AS) could affect treatment responses. Post-transcription, AS removes introns from nascent RNAs to generate mature RNAs.2 LncRNAs can modulate AS by interacting with splicing factors to produce non-protein-coding splice variants. Splicing factors are trans-acting factors that bind to cis-acting elements and alter the recruitment or recognition of spliceosome components at splicing sites, thereby regulating AS.2 However, AS is necessary for many developmental processes, including embryonic and pediatric liver development, and abnormal AS can produce disease-specific transcripts that support disease progression.3 Abnormal splicing in diseases typically yields splice variants lacking exons or containing unwanted remnants of exons, all of which impact the generation of canonical functional transcripts and eventually aid in advancing disease progression. LncRNAs could also be crucial in regulating epithelial-to-mesenchymal transition (EMT), a critical process commonly observed in tumours. This process allows epithelial cells to undergo molecular and biochemical changes resulting in a mesenchymal phenotype. LncRNAs’ diverse involvement in AS has been shown to impact the efficacy of cancer treatments and mediate acquired resistance to specific targeted therapies. A recent study by Chen et al. demonstrated the impact of lncRNA BC009639 (BC) on lung adenocarcinoma (LUAD) progression and its role in AS of inositol monophosphate domain containing 1 (IMPAD1) (Figure 1).4 BC was positively associated with growth, invasion, metastasis, and resistance to ‘epidermal growth factor receptor tyrosine kinase inhibitors (EGFR-TKIs)’. The sequence of BC is partially complementary to the 3′ untranslated region of IMPAD1 mRNA, which prompted the investigation of the relationship between BC and IMPAD1 in LUAD. BC overexpression in lung cancer cell lines resulted in the differential expression of IMPAD1 splice variants. The non-protein-coding IMPAD1-203 variant expression was increased mainly, while protein-coding IMPAD1-201 variant expression decreased. BC interacts with heterogeneous nuclear ribonucleoprotein K (hnRNPK), a part of the pre-mRNA-binding group of proteins (hnRNPs), to mediate IMPAD1 alternative splicing, resulting in IMPAD1-203 production and EMT activation in vitro as E-Cadherin expression was decreased, and Slug was elevated. Intriguingly, hnRNPK expression levels were high in gefitinib-resistant lung cancer cell lines, which is noteworthy as gefitinib is an EGFR-TKI typically used to treat non-small cell lung cancers (NSCLCs). BC overexpression also identified nucleolin (NCL) as a critical player in IMPAD1 splicing, suggesting that NCL is necessary for BC to form a splicing complex with IMPAD1 transcripts. The impacts of BC overexpression can be observed in the clinical outcomes of patients with LUAD, as shorter survival in EGFR-TKI-treated patients was associated with high BC expression. Studies of lncRNA effects across different cancer types have shown a common trend with regard to tumourigenesis. For example, the lncRNA metastasis-associated lung adenocarcinoma transcript 1 (MALAT1) has been demonstrated to support ovarian cancer progression by modulating splicing factor RNA binding Fox-1 homolog 2 (RBFOX2)-mediated AS, which exhibited a decrease in the activity of kinesin family member 1B (KIF1B), a pro-apoptotic tumour suppressor gene.5 Similarly, research on lncRNA H19 suggests that it regulates the metastasis of colorectal cancer cells by binding to splicing factor hnRNPA2B1, thus stimulating EMT processes downstream.6 Examining the roles of lncRNAs in cancer also involves recognizing differential expression patterns between cancer types and stages. Several lncRNAs, including Hox transcript antisense RNA (HOTAIR) and non-coding RNA activated by DNA damage (NORAD), have been identified as promising biomarkers in the prognosis of esophageal cancer due to their elevated expression levels.7 HOTAIR is well-known for being oncogenic, and its high expression in several cancer types is related to chemotherapy resistance.8 Determining the prognosis associated with the up- or down-regulation of each lncRNA would greatly benefit precision medicine, as it would facilitate the customization of treatment plans and thereby enhance the effectiveness of treatment plans to help reduce tumour recurrence. In addition, utilizing lncRNAs to develop biomarkers in the clinical setting would also be non-invasive, as they are detectable in blood, plasma, and saliva.9 Developing such non-invasive screening/monitoring techniques may likely contribute to increasing equality in access to cancer treatment and survivor care in underserved, low-access and/or health professional shortage areas. The increasing number of lncRNAs that have been investigated for their possible contribution to cancer progression highlights the necessity of continued interrogations of lncRNA function in developing new treatments. A comprehensive analysis of AS across over 8000 cancer patient samples has revealed that tumour samples have up to 30% more AS events than normal samples,10 further implicating the involvement of these events in carcinogenesis. In addition, there are many possibilities for applying our knowledge about lncRNAs to clinical settings due to having a multitude of functions across a wide range of diseases. Ultimately, future applications to predict drug resistance in different cancers based on their functional roles and expression levels of lncRNAs will significantly improve targeted therapies for cancer patients and enhance their quality of life. The authors would like to thank members of the Gadad lab for their careful review and helpful suggestions on this work. S.S.G. is a CPRIT scholar in cancer research and is supported by a first-time faculty recruitment award from the Cancer Prevention and Research Institute of Texas (CPRIT; RR170020). S.S.G. is also supported by the NIH 1RO1AI175837-01, Lizanell and Colbert Coldwell Foundation, The Edward N. and Margaret G. Marsh Foundation, and The American Cancer Society (RSG-22-170-01-RMC) grants. The authors declare that they have no known competing financial interests or personal relationships that could have appeared to influence the work reported in this paper.