Cancer cells are known to undergo metabolic reprogramming, such as glycolysis and glutamine addiction, to sustain rapid proliferation and metastasis. It remains undefined whether long noncoding RNAs (lncRNA) coordinate the metabolic switch in pancreatic cancer. Here we identify a nuclear-enriched antisense lncRNA of glutaminase (GLS-AS) as a critical regulator involved in pancreatic cancer metabolism. GLS-AS was downregulated in pancreatic cancer tissues compared with noncancerous peritumor tissues. Depletion of GLS-AS promoted proliferation and invasion of pancreatic cancer cells both in vitro and in xenograft tumors of nude mice. GLS-AS inhibited GLS expression at the posttranscriptional level via formation of double stranded RNA with GLS pre-mRNA through ADAR/Dicer-dependent RNA interference. GLS-AS expression was transcriptionally downregulated by nutrient stress–induced Myc. Conversely, GLS-AS decreased Myc expression by impairing the GLS-mediated stability of Myc protein. These results imply a reciprocal feedback loop wherein Myc and GLS-AS regulate GLS overexpression during nutrient stress. Ectopic overexpression of GLS-AS inhibited proliferation and invasion of pancreatic cancer cells by repressing the Myc/GLS pathway. Moreover, expression of GLS-AS and GLS was inversely correlated in clinical samples of pancreatic cancer, while low expression of GLS-AS was associated with poor clinical outcomes. Collectively, our study implicates a novel lncRNA-mediated Myc/GLS pathway, which may serve as a metabolic target for pancreatic cancer therapy, and advances our understanding of the coupling role of lncRNA in nutrition stress and tumorigenesis.
Significance: These findings show that lncRNA GLS-AS mediates a feedback loop of Myc and GLS, providing a potential therapeutic target for metabolic reprogramming in pancreatic cancer.
See related commentary by Mafra and Dias, p. 1302
Recent studies have shown that cancer cells exhibit metabolic dependencies to distinguish them from normal tissues. One of these addictions is “Warburg effect” that cancer cells tend to take advantage of glucose via “aerobic glycolysis” pathway, even in the presence of oxygen (1). As an outcome, the pyruvate generated via the aerobic glycolysis is converted to lactic acid, but not acetyl-CoA. To compensate for the insufficient citric acid cycle, cancer cells often activate glutamine metabolism (2). Therefore, markedly aggravated glucose and glutamine depletion may happen in tumor cells as there are inadequacies between vascular supply and metabolic requirement (3). Such a situation is especially distinct in pancreatic cancer, where glucose and glutamine metabolism is reprogrammed by oncogenic Kras to support cancer cell growth (4–6). Therefore, the metabolic characteristics and distinct hypovascular of pancreatic cancer would lead to a dramatic nutrients stress especially caused by glucose and glutamine depletion (7). In fact, such a paradoxical condition affords pathway to rapidly produce the energy and metabolites required for cancer cells' proliferation, which makes it correlatively resistant to metabolic stress including hypoxia and nutrient deprivation (8). Data from Yun and colleagues suggest that glucose deprivation can drive the acquisition of Kras pathway mutations (9), which commonly occurs in pancreatic cancer. The results suggested that glucose deprivation increases VEGF mRNA stability, which might facilitate tumor angiogenesis (10). Furthermore, results from Dejure and colleagues showed glutamine deprivation only halted the proliferation of colon cancer cells, but not killed them (11). Notably, nutrient deprivation has been correlated with poor patient survival, suggesting that instead of killing the tumor, the scarcity of nutrients can make the cancer cell stronger (12). Therefore, it is crucial to investigate the mechanisms that are required to accommodate nutrient stresses as an alternative strategy for the therapeutic treatment of pancreatic cancer.
Long noncoding RNAs (lncRNA) are a major class of transcripts, longer than 200 nt, and lack protein-coding potential. Accumulating evidence suggests that lncRNAs are dysregulated in cancers and involved in the development of cancers (13). Specifically, recent results have demonstrated a link between lncRNAs and altered metabolism in cancers. A study reported that a glucose starvation–induced lncRNA-NBR2 reciprocally activates AMPK pathway in response to energy stress (14). LncRNA-UCA1 promotes glycolysis in bladder cancer cells by activating the cascade of mTOR-STAT3/miR143-HK2 (15). Results from Ellis and colleagues suggested that insulin/IGF signaling–repressed lncRNA-CRNDE promotes aerobic glycolysis of cancer cells (16). LncRNA-ANRIL is upregulated in nasopharyngeal carcinoma and promotes cancer progression via increasing glucose uptake for glycolysis (17). In addition, lncR-UCA1 was found to reduce ROS production, and promoted mitochondrial glutaminolysis in human bladder cancer (18). Nevertheless, the specific lncRNAs, which couple nutrient stress and pancreatic cancer, have not been elucidated yet. In this study, we endeavored to discover a nutrient stress–responsive lncRNA that is involved in the pancreatic cancer progression.
Glutaminase (GLS) is a phosphate-activated amidohydrolase that catalyzes the hydrolysis of glutamine to glutamate and ammonia to support metabolism homeostasis, bioenergetics, and nitrogen balance (19). Recent studies have revealed GLS is commonly overexpressed in numerous malignant tumors and acts as an oncogene to support cancer growth (20, 21). It is noted that GLS is increased in breast cancers compared with surrounding nontumor tissues and positively correlates to the tumor grade (20). Moreover, GLS couples glutaminolysis of the TCA cycle with elevated glucose uptake and consequently the growth of prostate cancer cells (21). Meanwhile, knockdown of GLS significantly blocked the growth and invasive activity of various cancer cells (22). Results from Chakrabarti and colleagues demonstrated that GLS is highly upregulated in pancreatic cancer, thereby targeting glutamine metabolism and sensitizing pancreatic cancer cells to PARP-driven metabolic catastrophe (23). In previous study, we discovered a cluster of dysregulated lncRNAs in pancreatic cancer (24). Coincidently, one of the significantly downregulated lncRNA, AK123493, is an antisense lncRNA of glutaminase (GLS). Therefore, it draws our attention whether a nuclear-enriched antisense lncRNA of glutaminase (GLS-AS) might be involved in the GLS-mediated metabolism of pancreatic cancer.
Materials and Methods
Patients and specimens
The clinical tissues were obtained from Pancreatic Disease Institute of Union Hospital from May 2016 to March 2017. We randomly selected 30 pairs of pancreatic cancer and corresponding nontumor tissues from patients without chemotherapy or radiotherapy before operation. Procedures performed on those patients included pancreatectomy or palliative surgery including I125 seed implantation as well as gastroenterostomy and choledochojejunostomy according to the National Comprehensive Cancer Network (NCCN 2012) guideline for pancreatic cancer. The samples were obtained from surgical resection of patients or biopsy of the palliative surgery patients. The study was conducted in accordance with the Declaration of Helsinki. All samples were collected with the written informed consent of the patients, and the study was approved by the local Research Ethics Committee at the Academic Medical Center of Huazhong University of Science and Technology (Wuhan, China).
BxPC-3 and PANC-1 cells were obtained from ATCC. They were tested and authenticated for genotypes by DNA fingerprinting within 6 months. Cells were cultured in 5% CO2 at 37°C and grown in complete medium, which was composed of 90% RPMI1640 (Gibco), 10% FBS (Gibco), 100 U/mL penicillin, and 100 mg/mL streptomycin. To build nutrition deprivation model, we incubated cells with complete medium without glutamine [Glutamine (−)] or complete medium with 1 mmol/L glucose [Glucose (−)]. RPMI1640 having no glutamine or glucose was purchased from Gibco.
To detect GLS-AS and GLS pre-mRNAs, we purchased a kit named FISH Tag RNA Multicolor Kit from Invitrogen to perform FISH. The probe synthesis, labeling, and purification procedures were performed according to the manufacturer's instructions. The probe-identified GLS pre-mRNA (Probe1) was labeled with green fluorescence, and the GLS-AS probe (Probe2) was labeled with red fluorescence. Cells were fixed in formaldehyde, permeabilized by Triton X-100, and then hybridization was carried out using labeled probes in a moist chamber at 42°C overnight. If necessary, the GLS protein immunofluorescence was conducted after all the FISH procedures were completed.
RNA-binding protein immunoprecipitation
To detect RNA–protein binding complexes, RNA-binding protein immunoprecipitation (RIP) assays were performed according to the instructions of RNA-Binding Protein Immunoprecipitation Kit (Magna RIP, Millipore). First, the cells were lysed in lysis buffer containing protease inhibitor cocktail and RNase inhibitor. Magnetic beads were preincubated with an anti-ADAR1 antibody or anti-Dicer for 30 minutes at room temperature, and lysates were immunoprecipitated with bead-bound antibody at 4°C overnight. Then immobilized magnetic bead–bound antibody–protein complexes were obtained, washed off unbound materials, RNA purified from RNA–protein complexes, and then analyzed by qPCR.
We purchased a DIG RNA Labeling Kit (Roche) to perform Northern blot analysis for GLS-AS. First, we prepared GLS-AS–specific DNA template containing T7 promoter sequences from RT-PCR and the DNA template was purified. Then, the DIG-labeled RNA probes were produced according to the kit instructions with the DNA template. DIG-labeled probes were used for hybridization to nylon membrane–blotted total RNA. The hybridized probes were detected with anti-digoxigenin-AP, and then were visualized with the chemiluminescence substrate CSPD. The signals were also captured by ChemiDocTm XRS Molecular Imager system (Bio-Rad).
For coimmunoprecipitation (co-IP) analysis, anti-ADAR1, anti-Dicer, or normal mouse/rabbit IgG were used as the primary antibodies, and then the antibody–protein complex was incubated with Protein A/G PLUS-Agarose (Santa Cruz Biotechnology). The agarose–antibody–protein complex was collected and then analyzed by Western blot.
The PCR primers are indicated in Supplementary Table S1. We conducted chromatin immunoprecipitation (ChIP) assays using EZ-ChIPTM Chromatin Immunoprecipitation Kit (Millipore). All the procedures were performed according to the manufacturer's instructions. Rabbit anti-Myc (Cell Signaling Technology), anti-RNA polymerase II antibodies (Abcam), and corresponding rabbit-IgG (Cell Signaling Technology) were used as controls. The bound DNA fragments were amplified by PCR reactions, and then PCR products were analyzed by gel electrophoresis on 2% agarose gel. The PCR primers used were listed in Supplementary Table S2.
Luciferase activity assay
For GLS-AS promoter activity analysis, BxPC-3 cells were transfected with pGL3 vector wild-type or mutant GLS-AS promoter with firefly luciferase plasmid while a plasmid pRL-TK carrying Renilla luciferase was used as internal reference. To confirm the nutrition deprivation impact on GLS-AS promoter activity, cells were cultured under glutamine or glucose deprivation for 24 or 48 hours. To investigate the relationship between Myc protein and GLS-AS promoter activity, siMyc or the control siNC was cotransfected into the BxPC-3 cells containing luciferase plasmid. The reporter activity was measured using a luciferase assay kit (Promega) and plotted after normalizing with respect to Renilla luciferase activity. Firefly luciferase activity was normalized to the corresponding Renilla luciferase activity. The data are represented as mean ± SD of three independent experiments.
Biotin-RNA pull-down assay
The full or partial length of intron-17 of GLS gene sequences was amplified by PCR with SP6/T7-containing primer and then transcribed by MAXIscript SP6/T7 Transcription Kit (Thermo Fisher Scientific). The synthetic RNA was biotin-labeled with Pierce RNA 3′ End Desthiobiotinylation Kit (Thermo Fisher Scientific). The biotin-labeled RNAs were incubated with cell lysis individually and the target complexes were precipitated by streptavidin-coupled Dynabeads (Invitrogen). Finally, Northern blot analysis identified whether GLS-AS was pulled down or not.
RNA pull-down by MS2-GST
We constructed a plasmid expressing GLS-AS tagged with MS2 hairpin loops (GLS-AS-MS2), a plasmid expressing MS2-GST-NSL fusion protein, and a plasmid only expressing MS2 (MS2) RNA as control. Pancreatic cancer cells in the test and control groups were transfected with GLS-AS-MS2 and MS2, respectively, along with MS2-GST-NSL fusion protein. After the cotransfection for 48 hours, cells were harvested and then RNA pull-down assay was conducted as described previously (25). The purified proteins were analyzed by Western blot analysis while RNAs were detected with Northern blot.
Lentivirus containing specific DNA sequences was transfected into BxPC-3 and PANC-1 cells. Five-week-old BALB/c male nude mice were bought from HFK Bio-Technology Co. To assess tumor growth in vivo, 100 μL RPMI1640 medium without FBS containing 4 × 106 cells was suspended and then planted subcutaneously into the nude mice (each group has 6 mice). Tumor volumes were measured every 4 days according to the formula V = 0.5 × L (length) × W2 (width). Mice were sacrificed at 3 weeks after cell inoculation. Solid tumor tissues were removed and weighed. To investigate tumor metastasis in vivo, mice were injected with 1 × 104 tumor cells through the tail vein; visible metastases on liver were counted and then confirmed by hematoxylin and eosin–stained slides after 3 weeks. Care and handling of the mice were approved by the Institutional Animal Care and Use Committee of Tongji Medical College, Huazhong University of Science and Technology (Wuhan, China).
All results were presented as means ± SD. Comparisons between two groups were performed with Student t test. The correlation between GLS-AS and GLS mRNA or GLS and Myc mRNA was revealed by Pearson correlation analysis. The expression of GLS-AS and the clinical characteristics were analyzed by χ2 test, while the log-rank test was conducted to survey pancreatic cancer patient survival. Difference was regarded to be significant at *, P < 0.05 and **, P < 0.01.
AK123493.1, a nuclear accumulated antisense lncRNA of GLS (GLS-AS), is downregulated in pancreatic cancer
The microarray analysis showed AK123493.1 was decreased in the pancreatic cancer tissues compared with noncancerous peritumoral (NP) tissues (Fig. 1A). GLS-AS is an intronic antisense lncRNA embedded within intron-17 of the corresponding sense gene GLS (Fig. 1B). In addition, the Northern blot validated the expression of GLS-AS in BxPC-3 and PANC-1 cells using the RNA probe (Fig. 1C). Moreover, the expression levels of GLS-AS in BxPC-3 and PANC-1 cells were lower than that in the normal human pancreatic duct epithelial cells (HPDE; Fig. 1D). To validate the signal specificity, Northern blot analysis was conducted after the cells were transfected with siGLS-AS. As shown in Fig. 1E, siGLS-AS significantly decreased the expression of GLS-AS. Furthermore, the Northern blot results showed that GLS-AS was obviously lower in pancreatic cancer tissues compared with NP (Fig. 1F). Meanwhile, the FISH assay showed that GLS-AS is mainly accumulated in the nucleus (Fig. 1G), implying GLS-AS may predominantly function in the nucleus. Similarly, separation of nuclear extract and the cytoplasmic fraction showed that GLS-AS retained in the nucleus (Fig. 1H). Both Coding Potential Assessment Tool (26) and Coding Potential Calculator (27) predicted GLS-AS is a noncoding RNA. Furthermore, we blocked new RNA synthesis with RNA polymerase II (Pol II) inhibitor α-amanitin (50 μmol/L) in BxPC-3 cells and measured the expression of GLS-AS by qPCR relative to time 0. After treating with α-amanitin, the expression of GLS-AS was significantly decreased, while the 18s mRNA, which is transcribed by Pol I, was not affected. These results indicate that the transcription of GLS-AS is proceeded in a Pol II–dependent manner (Fig. 1I). We further validated the GLS-AS expression level in pancreatic cancer tissues and paired NP tissues by qPCR. Results showed that GLS-AS expression in pancreatic cancer was significantly lower than that in NP (Fig. 1J). In addition, the low expression of GLS-AS was associated with large tumor size, lymph node invasion, remote metastasis (Supplementary Table S1), and short overall survival time (Fig. 1K).
Low expression of GLS-AS facilitates proliferation and invasion of pancreatic cancer cells
To understand the roles of GLS-AS downregulation in pancreatic cancer progression, we depleted GLS-AS expression with siRNA (siGLS-AS) in pancreatic cancer cells (Fig. 2A; Supplementary Fig. S1A). After downregulation of GLS-AS, the proliferation and colony formation of PANC-1 (Fig. 2B and C) and BxPC-3 cells (Supplementary Fig. S1B and S1C) were significantly enforced. Meanwhile, transwell and wound-healing assays further revealed an enhanced invasion and migration ability in GLS-AS–depleted PANC-1(Fig. 2D and E) and BxPC-3 cells (Supplementary Fig. S1D and S1E). To further confirm whether reduced GLS-AS affects pancreatic cancer progression in vivo, PANC-1 and BxPC-3 cells were stably transfected with lentivirus containing siGLS-AS (LV-siGLS-AS) or siNC (LV-NC) transplanted subcutaneously into the mouse, respectively. Compared with LV-NC group, the PANC-1 tumors in the LV-siGLS-AS group were larger and heavier (Fig. 2F), with more visible liver and lung metastases (Fig. 2G and H). Similarly, the proliferation and metastasis of BxPC-3 tumor with LV-siGLS-AS were also enhanced (Supplementary Fig. S1F–S1H). These results indicate that the dysregulated GLS-AS expression might contribute to pancreatic cancer development.
GLS is the critical target of GLS-AS to exert function in pancreatic cancer
Because GLS-AS is an antisense lncRNA of GLS, we further investigated whether GLS is a functional target of GLS-AS. Coincidently, knockdown of GLS-AS apparently increased the GLS expression both in mRNA and protein levels in both PANC-1 (Fig. 3A) and BxPC-3 cells (Supplementary Fig. S2A). Coincidently, transfection with a plasmid containing GLS-AS sequence (GLS-AS) obviously decreased GLS expression both in mRNA and protein levels of PANC-1 and BxPC-3 cells (Fig. 3B; Supplementary Fig. S2B). Subsequently, co-staining fluorescence of GLS-AS transcription and GLS protein further validated GLS was negatively regulated by GLS-AS in PANC-1 and BxPC-3 cells (Fig. 3C; Supplementary Fig. S2C). In agreement, the costaining fluorescence assay further showed a decreased GLS-AS accompanied with increased GLS protein expression in pancreatic cancer tissue compared with NP tissue (Fig. 3D). Meanwhile, Western blot analysis further validated the downregulation of GLS protein in pancreatic cancer tissues compared with NP tissues (Supplementary Fig. S2D). Meanwhile, depletion of GLS with siGLS remarkable inhibited proliferation, colony formation, invasion, and migration ability of PANC-1 and BxPC-3 cells, which was reinforced by siGLS-AS (Supplementary Fig. S3A–S3J). Thus, these data implied that the GLS would be a critical target for dysregulated GLS-AS to exert its biological function in pancreatic cancer.
GLS-AS inhibits GLS expression in posttranscriptional level by ADAR1/Dicer-dependent RNA interference
To further identify whether GLS-AS regulates GLS transcription, BxPC-3 or PANC-1 cells were transfected with pGL3 plasmid containing GLS putative promoter region. As shown in Supplementary Fig. S4A and S4B, the luciferase reporter assay showed neither knockdown nor overexpression of GLS-AS and did not change the GLS promoter activity, which implied that GLS-AS did not regulate GLS expression at the transcriptional level.
The co-RNA FISH assay disclosed both GLS-AS and GLS pre-mRNA hybridized in the same nuclear foci of PANC-1 cells (Fig. 4A), which indicates the formation of dsRNA. To further validate the direct interaction between GLS-AS and GLS pre-mRNA in PANC-1 cells, the RNA–RNA pull-down assay was performed with biotin-labeled full or partial length deletion of intron-17 transcripts (Fig. 4B). As GLS-AS is an antisense lncRNA of GLS pre-mRNA, we further presumed GLS-AS might regulate the stability of GLS pre-mRNA. To evaluate the stability of GLS pre-mRNA, pancreatic cancer cells were treated with amanitin (50 μmol/L). The expression of GLS pre-mRNA was measured by qPCR at the separated time point. Compared with time 0, the stability was dramatically enhanced by siGLS-AS, but impaired by GLS-AS overexpression in PANC-1 cells (Fig. 4C and D). Research had demonstrated that adenosine deaminases acting on RNA (ADAR1) are involved in RNA interference of dsRNA by formation of ADAR1/Dicer heterodimer complexes, a member protein of RNA-induced silencing complex (RISC; ref. 28). Meanwhile, the co-IP analysis validated the binding between ADAR1 and Dicer protein in PANC-1 cells (Fig. 4E; Supplementary Fig. S5A). To confirm whether the ADAR1/Dicer proteins physically bound to GLS-AS/GLS pre-mRNA dsRNA or not, we performed RNA immunoprecipitation (RNA-IP) assays in PANC-1 cells. Compared with the IgG-bound sample, the ADAR1 or Dicer antibody–bound complex showed significantly high enrichment of GLS-AS and GLS pre-mRNA in PANC-1 cells (Fig. 4F; Supplementary Fig. S5B). Thus, we wondered whether the GLS-AS and GLS pre-mRNA are regulated by ADAR1/Dicer-mediated RNA silencing. Both siADAR1 and siDicer increased the expression of GLS-AS, GLS pre-mRNA, and protein, were remarkably increased in PANC-1 cells (Fig. 4G; Supplementary Fig. S5C), reduced the enrichment of GLS-AS and GLS pre-mRNA in protein (ADAR1/Dicer)–antibody-bound complex in PANC-1 cells (Fig. 4H; Supplementary Fig. S5D), as well as strengthened the stability of GLS pre-mRNA in PANC-1 cells (Fig. 4I; Supplementary Fig. S5E). Meanwhile, the enrichment of GLS pre-mRNA was reduced by siGLS-AS, but upregulated by GLS-AS overexpression, both by anti-ADAR1 (Fig. 4J and K) and anti-Dicer (Supplementary Fig. S5F and S5G) in PANC-1 cells. In addition, both siADAR1 (Fig. 4L) and siDicer (Supplementary Fig. S5H) could rescue the expression of GLS mRNA and protein in PANC-1 cells, which was inhibited by GLS-AS overexpression. Furthermore, MS2-tagged RNA affinity purification analysis was performed to further confirm GLS-AS, GLS-pre-mRNA, and ADAR1/Dicer can form a complex in PANC-1 cells (Fig. 4M). Simultaneously, the experiments described above were also conducted in BxPC-3 cells. Results of BxPC-3 cells also confirmed an interaction between GLS-pre-mRNA and GLS-AS (Supplementary Fig. S6A and S6B), which could regulate the stability of GLS-pre-mRNA (Supplementary Fig. S6C and S6D). Moreover, results further displayed that ADAR1 is required for the regulation of GLS-AS on GLS expression in BxPC-3 cells (Supplementary Fig. S6E–S6M). In addition, results also validated that Dicer is necessary for the ADAR1/Dicer-mediated regulation of GLS-AS on GLS expression in BxPC-3 cells (Supplementary Fig. S7A–S7H). Supplementary Figure S8 is a schematic diagram of MS2-tagged RNA affinity purification analysis.
Nutrient stress is responsible for downregulation of GLS-AS in pancreatic cancer
We further investigated whether the GLS-AS downregulation in pancreatic cancer is attributed to metabolism stress including hypoxia, acidity, or depletion of glucose and glutamine. Interestingly, GLS-AS was obviously decreased during depletion of glucose or glutamine, but without significant alteration in BxPC-3 and PANC-1 cells during hypoxia or acidity (Fig. 5A). Moreover, qPCR and FISH assays demonstrated a time-dependent GLS-AS downregulation during glutamine or glucose deprivation (Fig. 5B–D). Coincident with the GLS-AS downregulation, both GLS mRNA and protein expression were elevated during glutamine or glucose deprivation in a time-dependent manner (Fig. 5E). Nevertheless, the expression of ADAR1 and Dicer showed no obvious change during glutamine or glucose deprivation in PANC-1 (Supplementary Fig. S9A–S9C) and BxPC-3 cells (Supplementary Fig. S9D–S9F), which further confirmed the critical function of GLS-AS in the regulation of GLS during nutrient stress. Thus, these results imply dysregulation of GLS-AS/GLS pathway in pancreatic cancer might, at least partially, be attributed to the nutrient stress including glucose or glutamine depletion.
GLS-AS is transcriptionally regulated by Myc under glucose and glutamine deprivation
Myc is a multifunctional transcription factor that is deregulated in many human cancers and impacts cell proliferation, metabolism, and stress responses (29). Specifically, DNA sequence analysis showed GLS-AS promoter region contains potential binding sites for Myc (Fig. 6A); therefore, we presumed GLS-AS might be transcriptionally controlled by Myc. As expected, the chromatin immunoprecipitation (ChIP) assay verified only site 4 locating from −358 to −353 bp on the GLS-AS promoter area could bind to Myc, but not sites 1–3 (Fig. 6B). To further confirm the transcriptional activity of the putative GLS-AS promoter sequence, basic pGL3 plasmid and pGL3 plasmid containing GLS-AS promoter was transfected into BxPC-3 and PANC-1 cells. The luciferase reporter assay showed the luciferase intensity was enhanced in pGL3-GLS-AS promoter–transfected cells (Fig. 6C), which was further downregulated by siPol II (Fig. 6D). In addition, ChIP analysis revealed that Pol II could also bind to the binding site of Myc on GLS-AS promoter (Fig. 6E). Furthermore, GLS-AS promoter sequence containing wild-type (WT) or mutant site 4 (MUT) was transfected into pancreatic cancer cells. Results showed luciferase activity from the WT was markedly repressed by Myc overexpression, but increased after depletion of Myc (Fig. 6F). Coincidently, siMyc substantially increased GLS-AS expression, but decreased GLS expression (Fig. 6G). These results indicate that GLS-AS is transcriptionally inhibited by Myc, which consequently increases GLS expression.
Furthermore, both glucose and glutamine deprivation elevated Myc expression in BxPC-3 and PANC-1 cells (Supplementary Fig. S10A). Specifically, the ChIP assay demonstrated that the enrichment of GLS-AS promoter by Myc antibody was remarkably increased during glucose and glutamine deprivation (Supplementary Fig. S10B). In addition, the decreased activity of GLS-AS promoter was noted during glucose or glutamine deprivation (Supplementary Fig. S10C). Moreover, knockdown of Myc could increase GLS-AS expression in glutamine or glucose deprivation stress, coupled with GLS downregulation (Supplementary Fig. S10D). Furthermore, Myc-induced upregulation of GLS protein levels can be inhibited by GLS-AS overexpression under glutamine or glucose deprivation (Supplementary Fig. S10E). Together, these results display that the downregulation of GLS-AS in pancreatic cancer might be attributed to energy stress through Myc-dependent regulation.
GLS mediates a reciprocal feedback between GLS-AS and Myc
The results demonstrated that GLS silencing mediates downregulation of Myc protein in glioma cells (30). Moreover, results from Andrew and colleagues showed that GLS inhibitor, CB-839, markedly reduced the protein levels of Myc in multiple myeloma, acute lymphocytic leukemia, and non-Hodgkin's lymphoma (31). Therefore, we wonder whether Myc can be regulated by GLS-AS/GLS pathway. Interestingly, GLS knockdown and GLS-AS overexpression significantly inhibited Myc expression at the protein level (Fig. 7A), but not at the mRNA level (Supplementary Fig. S11A and S11B) in BxPC-3 and PANC-1 cells, which indicates that GLS might regulate Myc expression at posttranscriptional level. To evaluate whether GLS affects stability of Myc protein, Myc protein was measured in the presence of cycloheximide, which blocks de novo protein synthesis. The results showed the stability of Myc protein was decreased by GLS knockdown or GLS-AS overexpression in BxPC-3 and PANC-1 cells (Fig. 7B and C). Besides, the proteasome inhibitor MG132 could rescue Myc protein level from the depression effect of GLS downregulation or GLS-AS ectopic expression in BxPC-3 and PANC-1 cells (Fig. 7D). During the glutamine or glucose deprivation, both GLS knockdown and GLS-AS overexpression obviously inhibited the nutrient stress–induced Myc and GLS expression (Fig. 7E). Furthermore, the GLS-AS depletion–induced Myc expression was inhibited by siGLS (Fig. 7F) in nutrition-deprived condition. All of these results imply that GLS-AS might regulate Myc expression at a protein level in the proteasome pathway in a GLS-dependent manner.
GLS-AS is conversely correlated with Myc and GLS expression in pancreatic cancer
In accordance with the in vitro and in vivo results, the clinical samples of pancreatic cancer demonstrated an increased expression of GLS mRNA, which was conversely correlated with GLS-AS (Supplementary Fig. S12A and S12B). In addition, Myc mRNA was upregulated in pancreatic cancer tissues and associated with GLS mRNA expression (Supplementary Fig. S12C and S12D). Meanwhile, IHC analysis validated the overexpression of Myc and GLS in pancreatic cancer tissues (Supplementary Fig. S12E). However, analysis of pancreatic cancer database (QCMG and TCGA) by cBioPortal revealed that the Pearson correlation value of Myc and GLS mRNA is only −0.007 and −0.049 (32, 33), respectively (Supplementary Fig. S12F and S12G). Similarly, although a positive correlation between Myc and GLS was shown in prostate cancer tissues (34), the similar correlation was not seen in breast tumors, and c-Jun was shown to drive GLS expression (35). Therefore, these different results indicate that the Myc–GLS correlation is not universal in human tumors, but exists more strongly in a specific subgroup of tumor samples. Also a possibility, there are multiple mechanisms involved in GLS mRNA regulation causing this complex and diverse scenario.
GLS-AS may be a vital therapeutic target for pancreatic cancer treatment
To further validate the function of GLS-AS in pancreatic cancer development, BxPC-3 and PANC-1 cells were transfected with GLS-AS overexpression plasmid (GLS-AS) or empty vector (vector), respectively. GLS-AS overexpression effectively inhibited proliferation as well as invasion and migration ability of BxPC-3 and PANC-1 cells (Supplementary Fig. S13A–S13D). To further validate the function of GLS-AS in vivo, we transfected PANC-1 and BxPC-3 cells with a lentivirus containing GLS-AS (LV-GLS-AS) or the control (LV-vector). Then the transfected cells were transplanted subcutaneously into the nude mouse to investigate the tumor growth and metastasis. Results showed that PANC-1 tumors of LV-GLS-AS group were smaller and lighter than LV-vector group (Supplementary Fig. S14A). Moreover, the number of liver and lung metastases in the LV-GLS-AS group was considerably less than that in the LV-vector group (Supplementary Fig. S14B and S14C). Furthermore, the tumor with LV-GLS-AS displayed higher GLS-AS expression, coupled with lower expression of GLS mRNA (Supplementary Fig. S14D and S14E). Implanted BxPC-3 cells transfected with LV-GLS-AS also demonstrated impaired proliferation and metastasis in nude mice (Supplementary Fig. S15A–S15E). Together, these results suggest GLS-AS may be a novel metabolic target for therapeutic treatment of pancreatic cancer.
Recently, accumulative researches have revealed that lncRNAs play key roles in modulating various aspects of cancer cellular properties, including proliferation, survival, migration, genomic stability, and metabolism (36). Remarkably, aberrant expression of lncRNAs is identified in pancreatic cancer; whether the function of lncRNAs coupling the metabolism and tumorigenesis is far from elucidated (37). In our current research, we discovered a novel lncRNA GLS-AS was significantly downregulated in pancreatic cancer and associated with worse clinical outcomes. In addition, the downregulation of GLS-AS dramatically enhanced proliferation and invasion of pancreatic cancer cells both in vitro and in vivo. Therefore, these results intensively indicate that GLS-AS might function as an inhibitor in the progression of pancreatic cancer.
Antisense lncRNAs are a cluster of lncRNAs transcribed from the opposite DNA strand compared with sense transcripts (38, 39). Recent findings have shown that antisense lncRNA can regulate the expression of sense gene by acting as epigenetic regulators of gene expression and chromatin remodeling. The antisense transcript for β-secretase-1 (BACE1-AS) is elevated in Alzheimer's disease, which increases BACE1 mRNA stability and generates additional amyloid-β through a posttranscriptional feed-forward mechanism (40). Antisense Uchl1 increases UCHL1 protein synthesis at a posttranscriptional level through an embedded SINEB2 repeat (41). In this study, both GLS mRNA and protein expression were inhibited or increased by GLS-AS overexpression or downregulation. Moreover, GLS knockdown significantly decreased proliferation and invasion of pancreatic cancer cells, which was promoted by downregulation of GLS-AS. Furthermore, the clinical samples demonstrated a reversed correlation between GLS-AS and GLS expression. Therefore, our findings indicate GLS is a critical target for GLS-AS exerting inhibition effects on pancreatic cancer.
ADAR is a family of enzymes with double stranded RNA (dsRNA)-binding domains that converts adenosine residues into inosine (A-to-I RNA editing) specifically in dsRNA (28, 42). To date, three ADAR gene family members (ADAR1–3) have been discovered in mammals (43). ADAR1 differentiates its functions in RNA editing and RNAi by formation of either ADAR1/ADAR1 homodimer or heterodimer complexes with Dicer (28). Results showed that PCA3, an antisense intronic lncRNA of PRUNE2, forms a dsRNA that undergoes ADAR-dependent RNA editing to downregulate PRUNE2 level (44). However, genome-wide screening has revealed numerous RNA editing sites within inverted Alu repeats in introns and untranslated regions (43). ADAR1 promotes pre-miRNA cleavage and siRNA process by forming a Dicer/ADAR1 complex (28). Meanwhile, the FISH assay showed a colocalization of GLS-AS and GLS pre-mRNA. Moreover, we found that GLS-AS did not affect transcription of GLS, but impaired the stability of GLS pre-mRNA. Moreover, RIP assay further identified both ADAR and Dicer could bind to GLS-AS and GLS pre-mRNA simultaneously. Nevertheless, downregulation of ADAR1 or Dicer increased GLS expression, and also rescued the GLS-AS–induced inhibition of GLS. Therefore, these results intensively imply that GLS-AS inhibits GLS expression at a posttranscriptional level via ADAR1/Dicer-dependent RNA interference.
Recent research showed that a part of lncRNA was dysregulated in cancer due to nutrient stress including glucose deprivation, hypoxia, and so on (14, 24, 45, 46). Therefore, we further investigated whether the GLS-AS downregulation is attributed to nutrient stress including deprivation of glucose and glutamine, hypoxia, and acidity. Interestingly, only deprivation of glutamine and glucose dramatically decreased GLS-AS expression, but increased GLS expression. Nevertheless, overexpression of GLS-AS dramatically inhibited the survival and invasion of pancreatic cancer cells in nutrient stress. These results imply the dysregulated GLS-AS/GLS pathway is an adaption to nutrient stress and is required for the pancreatic cancer progression.
We further explored the mechanism for downregulation of GLS-AS during nutrient stress. The Myc oncogene is a “master regulator,” which controls glucose and glutamine metabolism to maintain growth and proliferation of cancer cells (47). Research demonstrated deprivation of glucose or glutamine dramatically elevated Myc expression and further activated serine biosynthesis pathway (48). Results from Wu and colleagues also showed glucose deprivation upregulates Myc protein in BxPC-3 and PANC-1 cells (49). Meanwhile, a study demonstrated that Myc-induced mouse liver tumors significantly increase both glucose and glutamine catabolism with GLS upregulation (50). Results indicated that Myc is a dual-function transcription factor that may activate or repress coding or noncoding RNA expression. Hart and colleagues showed that 534 lncRNAs were either up- or downregulated in response to Myc overexpression in P493-6 human B cells (51). Zhang and colleagues showed that a Myc-induced lncRNA-MIF inhibits aerobic glycolysis and tumorigenesis (52). On the contrary, Gao and colleagues reported that Myc transcriptionally represses miR-23a and miR-23b, resulting in greater expression of their target protein, GLS (34). Interestingly, the bioinformatics analysis demonstrated a putative Myc-binding site in the promoter area of GLS-AS gene. Moreover, the ChIP and luciferase reporter assays verified the binding and transcriptional inhibition of Myc on GLS-AS promoter. Coincidently, Myc knockdown significantly increased GLS-AS expression, but inhibited GLS expression. In addition, the deprivation of glucose and glutamine dramatically induced Myc expression and its transcriptional inhibition on GLS-AS. Consistently, our data showed knockdown of Myc dramatically increased GLS-AS expression during nutrient stress. Furthermore, Myc expression was increased and reversely correlated with GLS expression in pancreatic cancer. Therefore, these data indicate that GLS-AS might be transcriptionally inhibited by Myc, leading to GLS upregulation in response to nutrient deprivation. Different from a recent study that reported that GLS expression was regulated by miR-23a/b in lymphoma cells and PC3 prostate cancer cells (34), we found a lncRNA-dependent regulation of GLS expression in pancreatic cancer cells.
Interestingly, recent results reminded a potential feedback between Myc and GLS. As elevated GLS activity is under regulatory control of Myc (50, 53), research observed that knockdown of GLS decreased Myc protein expression in glioma cells (30). Recently, Madlen and colleagues demonstrated that glutamine depletion with GLS inhibitor is reflected by rapid loss of Myc protein, which is dependent on proteasomal activity (54). Similarly, our results showed that downregulation of GLS dramatically inhibited Myc protein expression by impairing its stability. Coincidently, the Myc protein during nutrient stress was also inhibited by GLS-AS overexpression. In addition, siGLS-AS dramatically increased Myc expression, but decreased by siMyc. Therefore, our data provide further evidence for a reciprocal feedback of Myc and GLS-AS, which regulates GLS expression at a posttranscriptional level during nutrient deprivation. Given the regulatory mechanism for Myc is complex, the precise mechanism for the regulation of GLS on Myc protein stability needs investigation in the further research.
In summary, our study implicates a nutrient stress–repressed lncRNA GLS-AS is involved in the progression of pancreatic cancer through mediating reciprocal feedback of Myc and GLS. Furthermore, our findings suggest that the Myc/GLS-AS/GLS axis may be promising molecular targets for the nutrient-restricted treatment of pancreatic cancer.
Disclosure of Potential Conflicts of Interest
No potential conflicts of interest were disclosed.
Conception and design: G. Zhao
Development of methodology: S.-J. Deng, H.-Y. Chen, Z. Zeng, C. He
Acquisition of data (provided animals, acquired and managed patients, provided facilities, etc.): S. Zhu, Z. Ye, M.-L. Liu, K. Huang
Analysis and interpretation of data (e.g., statistical analysis, biostatistics, computational analysis): S. Deng, J.-X. Zhong, F.-Y. Xu, Q. Li, Y. Liu
Writing, review, and/or revision of the manuscript: G. Zhao
Administrative, technical, or material support (i.e., reporting or organizing data, constructing databases): C. Wang
Study supervision: G. Zhao
This study was supported from the National Science Foundation Committee (NSFC) of China (grant nos: 81372666, 81672406, and 81872030 to G. Zhao).
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