Characterization of a Novel Long Noncoding RNA, SCAL1, Induced by Cigarette Smoke and Elevated in Lung Cancer Cell Lines

Abstract

The incidence of lung diseases and cancer caused by cigarette smoke is increasing. The molecular mechanisms of gene regulation induced by cigarette smoke that ultimately lead to cancer remain unclear. This report describes a novel long noncoding RNA (lncRNA) that is induced by cigarette smoke extract (CSE) both in vitro and in vivo and is elevated in numerous lung cancer cell lines. We have termed this lncRNA the smoke and cancer-associated lncRNA-1 (SCAL1). This lncRNA is located in chromosome 5, and initial sequencing analysis reveals a transcript with four exons and three introns. The expression of SCAL1 is regulated transcriptionally by nuclear factor erythroid 2-related factor (NRF2), as determined by the small, interfering RNA (siRNA) knockdown of NRF2 and kelch-like ECH-associated protein 1 (KEAP1). A nuclear factor erythroid-derived 2 (NF-E2) motif was identified in the promoter region that shows binding to NRF2 after its activation. Functionally, the siRNA knockdown of SCAL1 in human bronchial epithelial cells shows a significant potentiation of cytotoxicity induced by CSE in vitro. Altogether, these results identify a novel and intriguing new noncoding RNA that may act downstream of NRF2 to regulate gene expression and mediate oxidative stress protection in airway epithelial cells.Keywords: lincRNA; cancer; smoke; NRF2; epigenetics Recent advances in sequencing technology have revealed that significant numbers of noncoding RNAs are expressed and have significant functions in regulating gene expression. Noncoding RNAs have been classified according to size as either microRNAs (less than 200 base pairs) to long noncoding RNAs (greater than 200 base pairs; lncRNAs). LncRNAs have been further subdivided, based on their location relative to coding genes. Native antisense transcripts overlap with coding genes, intronic lncRNAs are expressed from the introns of coding genes, and long intergenic noncoding RNAs (lincRNAs) are found in the genome between coding genes (1). Unlike micro-RNAs, lncRNAs are much less well characterized, and how they function in biology and gene regulation remains an active area of investigation.Using gain and loss of function approaches, the function of individual lncRNAs are gradually being elucidated. X-inactive specific transcript (XIST), one of the earliest identified lncRNAs, plays an essential role in sex-specific imprinting by epigenetically silencing one of the two X chromosomes in female zygotes through the recruitment of polycomb repressor complexes (PRC2) (2). Other lncRNAs, such as HOX antisense intergenic RNA (HOTAIR) and P21-associated ncRNA DNA damage activated (PANDA), have also been found to regulate the chromatin state through their effects on the PRC2 complex (3, 4). Beyond its novelty in regulating important biological functions through epigenetic mechanisms, emerging evidence suggests that lncRNAs are associated with and may cause diseases such as cancer. Abnormal expressions of lncRNAs have been associated with cancers of the lung and breast (5, 6). Specific lnc...

The lncRNA XIST exhibits oncogenic properties via regulation of miR-449a and Bcl-2 in human non-small cell lung cancer

“…Recent studies have indicated that the type and number of lncRNAs vary greatly among species, tissues and cells [7][8][9] , and these macromolecules are biologically functional and associated with the development, progression and treatment response of various diseases, including cancer [10] . Previous studies have shown that MALAT1 [11] , HOTAIR, H19 [12] , the lncRNA GAS6-AS1 [13] and SCAL1 [14] are associated with the development and progression of lung cancer. However, the functional mechanism of lncRNAs remains largely unknown.…”

Pan-cancer transcriptome analysis reveals long noncoding RNAs with conserved function

“…Our results also build upon the recent finding of signaling pathway activation by an external stimulus such as oxidative stress and cigarette smoke, thereby altering lncRNA expression. For example, smoke and cancer-associated lncRNA-1 56 was recently shown to act downstream of nuclear factor erythroid 2-related factor (NRF2) and mediate oxidative stress in lung cancer. Similarly we also observed an NRF2 motif upstream of onco-lncRNA-3, which was found to have elevated expression in KEAP1 mutant patients in LUAD.…”

Transcriptome sequencing reveals altered long intergenic non-coding RNAs in lung cancer

“…The 111 LCALs include a lncRNA known to play a role in lung cancer (SCAL1 [16]), cancer-associated lncRNAs not previously implicated in lung cancer (CCAT1 [29], ESC-CAL-1 [30], LINC00261 [31], linc-UBC1 [32], UCA1 [33], ENST00000547963 [34], and PART-1 [35]), a lncRNA implicated in a lethal lung developmental disorder (FENDRR [36]), and three previously unannotated lncRNAs. Interestingly, the remaining 99 lncRNAs were previously annotated in normal human tissues but not implicated in human disease.…”

“…The most well-characterized lncRNA reported in lung cancer is MALAT1 (metastasis-associated lung adenocarcinoma transcript 1), which is associated with high metastatic potential and poor patient prognosis in non-small cell lung cancer patients with and without metastatic tumors [9,13]. More recent studies have found that the intronic non-coding RNA (ncRNA) lncRNA-LET plays a role in the regulation of hypoxia-mediated metastasis in squamous cell lung carcinoma [14], intronic ncRNA AK126698 confers resistance to cisplatin by targeting the Wnt pathway [15], and the lncRNA SCAL1 (smoke and cancer-associated lncRNA-1) is associated with tobacco-induced lung cancer [16]. These individual studies demonstrate the growing importance of lncRNAs in lung cancer while highlighting the need to systematically identify lncRNAs altered in lung cancer.…”