The role of long non-coding RNAs in mediating chemoresistance by modulating autophagy in cancer

ABSTRACT

Cancer is a complex process in which protein-coding and non-coding genes play essential roles. Long noncoding RNAs (lncRNAs), as a subclass of noncoding genes, are implicated in various cancer processes including growth, proliferation, metastasis, and angiogenesis. Due to presence in body fluids such as blood and urine, lncRNAs have become novel biomarkers in cancer detection, diagnosis, progression, and therapy response. Remarkably, increasing evidence has verified that lncRNAs play essential roles in chemoresistance by targeting different signalling pathways. Autophagy, a highly conserved process in response to environmental stresses such as starvation and hypoxia, plays a paradoxical role in inducing resistance or sensitivity to chemotherapy agents. In this regard, we reviewed chemoresistance, the role of lncRNAs in cancer, and the role of lncRNAs in chemoresistance by modulating autophagy.

KEYWORDS:

• Cancer
• LncRNAs
• metastasis
• chemoresistance
• autophagy

1. Introduction

Cancer is the first or second leading cause of morbidity and mortality among noncommunicable diseases (NCDs) in the world [1]. Due to the rapid growth of the population and ageing problem, cancer mortality rate is increasing [2]. Although chemotherapy is one of the effective treatments in cancer, resistance to chemotherapy challenges the clinical outcome of cancer treatment and leads to cancer relapse, metastasis, and the main barrier in response to treatment [3]. Therefore, understanding chemoresistance mechanisms are very crucial.

Non-coding RNAs (ncRNAs), RNA transcripts which are not translated into proteins, regulate many physiological and pathological processes and pathways and are classified into two groups according to their molecular size: small non-coding RNAs (sncRNAs), ≤200 nucleotides, and long non-coding RNAs (lncRNAs), ≥200 nucleotides [4]. Various classes of ncRNAs have been identified, including microRNAs (miRNAs), PIWI–interacting RNAs (piRNAs), circular RNAs (circRNAs), small nucleolar RNA (snRNA), and lncRNAs [5]. It has been demonstrated that lncRNAs are aberrantly expressed or dysfunctioned in various diseases, such as cancer. Thus, in this paper, we will discuss about roles of lncRNAs in cancer, resistance to chemotherapy, and targeting autophagy in chemoresistance.

2. Chemoresistance in cancer

Despite the great achievements in cancer therapy during the last decade, resistance of cancer cells to classical chemotherapy agents and radiotherapy continue to be a major problem in cancer treatment [6]. Based on the time of resistance development, drug resistance in cancer cells can be grouped intrinsic and acquired resistance [7]. Both occur due to genomic mutations in the cancer cells and/or to epigenetic alterations [8]. Intrinsic resistance or innate resistance exists before administration of therapies owing to the pre-existing genetic mutations that reduce tumour cells’ responsiveness to therapeutic agents, tumour heterogeneity, and activation of pathways against anticancer drugs. On the other hand, acquired resistance refers to gradual reduction efficacy of anticancer drug during treatment which can be a result of alteration in expression levels of anticancer drug targets, activation of new proto-oncogenes, and changes in tumour microenvironment (TME) [7]. Therefore, understanding the molecular mechanisms of resistance to chemotherapy helps in finding novel therapeutic strategies for cancer therapy. According to various studies, we review the molecular mechanisms of chemoresistance in cancer cells.

2.1. Drug efflux

The major reason for chemoresistance is decreased intracellular accumulation of chemotherapy agents owing to the activation of drug efflux mechanisms, including ATP binding cassette (ABC) family transporters [9]. ABC family transporters are transmembrane proteins that translocate different substrates across cellular membranes coupling with ATP hydrolysis [10]. There are 48 genes for ABC transporters in the human genome which are classified into seven subfamilies (ABCA-ABCG) [11]. Among them, 13 transporters are highly involved in the multidrug resistance (MDR) to cancer chemotherapy, including multidrug resistance proteins (MRPs/ABCCs), P− gp (MDR1/ABCB1), and breast cancer resistance protein (BCRP/ABCG2) [12].

P-glycoprotein (p-gp), a 170 kDa protein, transports a variety of substrates and is able to detoxificate cytotoxic drug via efflux in cancer cells [11]. It has been demonstrated that P-gp upregulated in different kinds of cancers, including neuroblastomas, leukaemia, breast, and ovarian cancers [13]. Multidrug resistance-associated protein 1 (MRP1) or ABCC1 also pumps out a broad range of anticancer drugs and its overexpression and association with resistance has been reported in different cancers, including breast, lung, and prostate cancers [14–16]. Furthermore, ABCG2 is the main drug efflux transporter in breast cancer and associated with resistance to chemotherapeutic agents [7]. It has been demonstrated that ABCG2 overexpressed in many other cancers, such as leukaemia and lung cancer [17,18].

2.2. Changes in the activity of oncogenes and tumour suppressor genes

Although oncogenes are genes with oncogenic potential, their overexpression can lead to resistance to chemotherapy and poor outcome. For example, overexpression of growth factor receptors activate phosphatidylinositol 3-kinas (PI3 K)/Akt/NF-κB axis which upregulates the transcription of anti-apoptotic genes [8]. Overexpression of Akt in cisplatin or mitoxantrone-treated non-small-cell lung carcinoma (NSCLC) cells lead to delay in the activation of p53 and upregulation of anti-apoptotic Bcl-xL, resulting in chemoresistance [3]. Furthermore, Sun et al. revealed that bladder cancer cells with resistance to cisplatin show rapid tumorigenesis, more aggressiveness, EMT, and drug resistance through NF-κB activation [19].

Besides induction of positive signals for growth, tumour cells also are able to suppress inhibitors of proliferation. It has been reported that 53BP1 loss in colorectal cancer cells induces chemoresistance to 5-fluorouracil (5-FU) via inhibiting the ATM-CHK2-P53 pathway [20]. Zhang et al. found that the accumulation of p53 mutant Arg282Trp mediates resistance to cisplatin through binding to ERP29 promoter and upregulating its expression [21]. Furthermore, Lakshmanan et al. reported that MUC16 regulates TSPYL5 via the JAK2/STAT3/GR axis and induces resistance to gemcitabine and cisplatin by p53 downregulation in lung cancer cell [22].

2.3. DNA repair

Many chemotherapy agents, such as cisplatin and 5-FU, kill cancer cells by interacting with DNA and inducing DNA damage. As a general response, DNA damages activate a DNA damage response (DDR) results in an interruption of DNA synthesis, an arrest of the cell cycle, and activation of repair pathways [23]. These pathways have a vital role in the maintenance of cellular genomic integrity, whereas genomic instability is known as cancer hallmark [24]. Thus, DDR mechanisms in affected cells with anticancer drugs may reduce the efficacy of the drugs, leading to chemoresistance [25]. It has been shown that genes involved in DDR, such as FANCG, FEN1, RAAD23B, are overexpressed in human colon cancer cells resistance to 5-FU [26,27]. Li et al. found that the downregulation of ERCC1 or XPF, endonucleases in nucleotide excision repair system, is associated with increased sensitivity to cisplatin in both tumour tissues and cell lines [28]. Furthermore, high expression of O6-alkylguanine DNA alkyltransferase (MGMT) leads to resistance to alkylating agents [29]. Augustine et al. reported that resistance to temozolomide (TMZ) is associated with MGMT upregulation in melanoma [30].

2.4. Apoptosis pathways

Apoptosis or programmed cell death is a complex process that affects a wide range of genes, leading to remove abnormal or unwanted cells for maintaining the stability of organism. In the apoptosis pathway, proteins play either anti-apoptosis or pro-apoptosis roles [31]. Thus, resisting cell death and pro-apoptotic signals is another hallmark of cancer and most of the chemotherapy agents kill cancer cells via inducing apoptosis. Understanding the mechanisms by which cancer cells escape apoptosis is used to design novel therapeutic agents [8]. For example, designing BH3 mimetics to antagonizing Bcl-2 proteins [32], reactivating the p53 pathway either by activation of TRAIL death receptor [33] or with inhibiting Mdm2, or with directly interacting of molecules with p53 [34].

2.5. Epithelial-mesenchymal transition (EMT)

EMT is a complex and reversible process in which epithelial cells lose their characteristics and gain mesenchymal properties, leading to the cytoskeleton remodelling and initiation of tumour cells migration and metastasis [35]. During the process, epithelial cells lose E-cadherin, as an epithelial adhesion molecule, and acquire mesenchymal markers such as fibronectin and/or vimentin [36]. Research findings have revealed the role of EMT and EMT inducing transcriptional factors, including Snail, Twist, Slug, Zeb1, and Zeb2, in therapy resistance. For example, Zheng et al. found that EMT induces resistance to chemotherapy in pancreatic cancer. They showed that knocking out EMT transcription factor, Twist1 and Snail1 enhances sensitivity to gemcitabine in the mouse model of pancreatic adenocarcinoma [37]. Kim et al. demonstrated that 5-FU-resistant colon cancer cells show morphological changes relative to parental cells, including an increase in fibronectin, Twist, Zeb1, and Zeb2 [38]. Furthermore, EMT transcription factors promote chemoresistance by inducing the expression of ABC transporters [39–41] and the knocking down of EMT transcription factors sensitizes cancer cells to chemotherapy agents via suppressing drug efflux [42–44].

2.6. Tumour microenvironment

Tumours are complex of malignant cells and various types of cells, such as fibroblasts, immune-inflammatory cells, adipose cells, neuroendocrine cells, vascular networks, as well as extracellular matrix (ECM) which create the tumour microenvironment (TME) [45]. The dynamic interaction among components of TME leads to tumour initiation, growth, migration, and development of chemoresistance [46]. One of the TME factors contributes to drug resistance is physical and biochemical barriers which limit penetration of drugs into solid tumours [47]. Hypoxia and limited accessibility of cells to oxygen which arises from uncontrolled growth of cancer cells leads to upregulation of hypoxia-inducible factor 1 (HIF-1) [48,49]. HIF-1 stimulates drug efflux by the overexpression of MDR-1 and P-gp genes [12,50]. Based on the ‘reversed pH gradient’ concept in which extracellular environment of cancer cells have decreased pH, base anticancer drugs show weak distribution, enabling tumour cells to avoid apoptosis and resistance to the therapy [51,52]. Furthermore, secreting colony-stimulating factor-1 (CSF-1) by tumour-associated macrophages (TAMs) supports the proliferation and survival of cancer cells in glioblastoma multiform [53,54].

2.7. Cancer stem cells

Two models have been proposed for the cancer initiation: 1) the stochastic model proposes that each cancer cell dedifferentiates into a cancer stem cell (CSC), 2) the hierarchical model suggests that CSCs are the progenitors of differentiated subpopulation of tumour cells [9]. CSCs are resistance to most anticancer agents, including chemotherapy. Resistance to chemotherapy of CSCs is related to mechanisms are discussed above, such as ABC transporters, changes in DNA repair mechanisms, gaining EMT phenotype, TME obstacles, overactivation of pro-survival signals, overactivation of anti-apoptotic signals, and overinhibition of pro-apoptotic signals [55,56]. Drug inactivating enzymes also make the CSCs resistance to chemotherapeutic drugs. For example, platinum drugs are inactivated by the thiol glutathione [57] or TMZ, paclitaxel, epirubicin, and doxorubicin (DOX) by the aldehyde dehydrogenase (ALDH) [58–60]. Furthermore, since chemotherapeutic drugs target proliferative cells and CSCs are quiescent, they are resistance to chemotherapy [9].

3. LncRNAs and their roles in cancer

As mRNAs, lncRNAs are transcribed by pol II, spliced, 5` capped, and 3` polyadenylated [61]. They can be classified based on the genomic loci: 1) intergenic lncRNAs are located between two protein-coding genes, 2) intronic lncRNAs are located between two exons and within an intronic region, 3) antisense lncRNAs originate from transcription of complementary strands, 4) bidirectional lncRNAs stem from bidirectional transcription of protein-coding genes, and 5) enhancer RNAs (eRNAs) stem from enhancer regions [62]. Furthermore, lncRNAs are classified based on their mode of action: 1) signal lncRNAs express specifically in response to different stimuli [63], 2) guide lncRNAs direct enzymatically active or regulatory proteins to proper locations in the genome, 3) decoy lncRNAs act as molecular sink to limit the availability of regulatory factors and modulate gene expression, and 4) scaffold lncRNAs provide an transient assembly platform for regulatory factors and enzymatic complexes [61].

An increasing number of studies have demonstrated diverse roles of lncRNAs in cancer (Fig. 1). Since lncRNAs can act as oncogenes or tumour suppressor genes or both, dysfunction or aberrant expression of lncRNAs is closely associated with cancer cell proliferation, migration, invasion, apoptosis, immune escape, metabolic disorders, maintenance of stemness, and angiogenesis [64,65]. Table 1 summarizes the roles of various lncRNAs in several cancers. Furthermore, increasing studies suggested lncRNAs as potential biomarkers in cancer detection and diagnosis [66,67]. Expression of many lncRNAs is more tissue-specific than mRNAs [68], thus they can be used as reliable markers for tumour origin compared with mRNAs. Moreover, obtaining of lncRNAs is easy and less invasive due to presence of lncRNAs in body fluids such as plasma and urine [69]. For example, the lncRNA PCA3 detection in the urine has been reported as a diagnostic biomarker in prostate cancer and the lncRNA HULC detection in the plasma makes it as a diagnostic biomarker in hepatocellular carcinoma [70]. All of these features, introduce lncRNAs as superior diagnostic and therapeutic biomarkers. This vital information introduces promising targets for cancer therapy based on novel technologies including, siRNAs, ribozymes, antisense oligos, aptamers, nanobodies, CRISPR, ZNFs, TALENs, and RNA decoys [71].

Table 1. The roles of lncRNAs in cancer

LncRNA	Oncogene/TSG	Cancer	Effect	Mechanism	Ref
DANCR	Oncogene	Prostate	↑Invasion, metastasis	↓ TIMP 2/3 transcription	^[72]
MALAT1	Oncogene	Thyroid	↑Angiogenesis	↑FGF2 secretion	^[73]
LUCAT1	Oncogene	Breast	↑Stemness	As a miR-5582-3p sponge	^[74]
HOTTIP	Oncogene	Ovarian	↑Immune escape	↑PD-L1 transcription	^[75]
PVT1	Oncogene	Gastric	↑Angiogenesis	↑VEGFA transcription	^[76]
HOTAIR	Oncogene	Liver	↑Stemness	↓SETD2 transcription	^[77]
SLNCR1	Oncogene	Melanoma	↑Invasion	↑MMP9 transcription	^[78]
IGFBP4–1	Oncogene	Lung	↑Proliferation, metastasis	↑Aerobic glycolysis	^[79]
HULC	Oncogene	Liver	↑Angiogenesis	↑SPHK1 transcription	^[80]
GAS5	TSG	Cervical	↓Metastasis, ↑Apoptosis	NA	^[81]
AOC4P	TSG	HCC	↓Metastasis	↑Vimentin degradation, ↓EMT	^[82]
MEG3	TSG	Breast	↓Proliferation, invasion, angiogenesis	↓AKT pathway	^[83]
FENDRR	TSG	NSCLC	↓Stemness	↓MDR1 transcription	^[84]
LINC01133	TSG	Colorectal	↓Metastasis, EMT	Interacts with SRSF6	^[85]

TSG, tumour suppressor gene; TIMP 2/3, tissue inhibitors of matrix metalloproteinases 2/3; FGF2, fibroblast growth factor-2; PD-L1, programmed death-ligand 1; VEGFA, vascular endothelial growth factor A; MMP9, matrix metalloproteinase-9; SPHK1, sphingosine kinase 1; HCC, hepatocellular carcinoma; NSCLC, non-small-cell lung carcinoma.

Figure 1. Roles of lncRNAs in cancer

4. Autophagy in cancer

Although Christian de Duve firstly introduced the term ‘autophagy’ in 1963 [86], the significance of autophagy in health and disease was highlighted when Yoshinori Ohsumi was awarded the 2016 Nobel Prize in Physiology or Medicine for his work on identification and characterization of autophagy mechanisms [87]. Autophagy is a highly conserved process in response to environmental stresses such as starvation in which cells start to recycle and degrade macromolecules, including organelles, proteins, carbohydrates, and lipids as an energy supply and for synthesis of vital components [88]. In this process, cellular organelles and components are engulfed by autophagosomes, double-membrane vesicles, for delivery to the lysosome which provides proteases for degradation of autophagosomes contents [89]. The molecular mechanism of autophagy contains several conserved autophagy-related genes (ATGs). The formation of the autophagosome consists of three steps: initiation, nucleation, and elongation (Fig. 2). The initiation step begins with the activation of ULK1 (ATG1) complex (compromising ATG13, ATG101, FIP200, ULK1, and ULK2) which phosphorylates and activates class III PI3 K complex (compromising ATG14, UVRAG, VPS15, VPS34, AMBRA1, and Beclin-1) leads to generating phosphatidylinositol 3‐phosphate (PI3P) on the endoplasmic reticulum (ER) structure called the omegasome. PI3P recruits WIPI2 and DFCP1 to the omegasome for expanding and growth of the structure [90]. In the next step, ATG conjugation system is required for the elongation of the omegasome. WIPI2 directly binds to ATG16L1 which recruits the ATG12~ ATG5–ATG16L1 complex that enhances the ATG3-mediated conjugation of γ-aminobutyric acid receptor-associated proteins (GABARAPs) and microtubule-associated protein light chain 3 (LC3) proteins to membrane-resident phosphatidylethanolamine (PE) [91]. As a result, the omegasome expands and autophagic components are surrounded and enveloped in a double-membrane vesicle, autophagosome [92]. In the final step, autophagosome fusion with lysosome is mediated by the Rab GTPases (Rab7), SNAREs (soluble N-ethylmaleimide-sensitive factor activating protein receptors), ESCRT (endosomal sorting complex required for transport), and class C Vps proteins [93]. Following digestion of the autophagosome components, essential products such as amino acids and fatty acids export back into cytosol by lysosomal transporters or permeases, playing a crucial role in survival of starving cells [94,95].

Figure 2. Molecular schematic of autophagy process

4.1. The roles of autophagy in cancer

Autophagy plays dual roles in cancer biology and its regulation contributes to the oncogenes or tumour suppressor proteins expression, whereas the activation of oncogenes leads to the suppression of autophagy and enhancement of tumour formation, and negative regulation of tumour suppressor factors induces autophagy and suppresses cancer initiation [96].

4.1.1. Autophagy and tumour promotion

Several studies demonstrated that autophagy promotes growth and survival of cancer cells [97,98]. Stressful conditions, such as nutrient deprivation and hypoxia, in the TME especially in the central part of solid tumours, activates autophagy to survive under these stresses by providing substrates for the production of adenosine triphosphate (ATP) [96,99]. Under hypoxic conditions, hypoxia-inducible factor-1 alpha (HIF-1α) induces autophagy activation and cancer progression [100]. Therefore, autophagy promotes tumour cell survival via enhancing tolerance to stress and supplying nutrients to encounter the metabolic demands of tumours. The deletion of core autophagy proteins also supports tumour promotion roles of autophagy. It has been reported that autophagy suppression by deletion of Beclin-1 induces cell death [101,102]. Wei et al. reported that deletion of FIP200 and subsequent suppression of autophagy in mouse model of breast cancer suppresses tumour initiation and progression [103]. Moreover, it has been found that ATG5 overexpressed in prostate [104] and gastric [105] cancers, while ATG7 overexpressed in bladder cancer [106].

Several studies showed links between autophagy, metastasis, and CSCs. Cufí et al. reported that autophagy inhibition reduces the migratory and invasive capabilities in breast CSCs, leading to decreased expression of the mesenchymal marker (vimentin) and an increase of the epithelial marker (CD24) [107]. In another study, Galavotti et al. found that the upregulation of DRAM1 and SQSTM1, as autophagy regulators, are correlated with the expression of mesenchymal markers in glioblastoma CSCs [108].

4.1.2. Autophagy and tumour suppression

As mentioned above, autophagy plays a dual role in tumorigenesis. It has been shown that almost 50% of breast, prostate, and ovarian cancers carry one allele of Beclin-1 [109–111]. Beclin-1, a key component of in the nucleation of autophagosome and a tumour suppressor, haploinsufficiency suppresses autophagy and leads to cancer progression [112]. Other studies also reported downregulation of Beclin-1 in different cancers, including HCC [113], osteosarcoma [114], and glioblastoma [115]. Mutation of another autophagic factor, UVRAG, inhibits autophagy and causes gastric and colon cancers [116,117]. Moreover, autophagy prevents tumorigenesis through the decreasing of reactive oxygen species (ROS) and oxidative stress [96,118].

Apart from the prometastatic potential of autophagy, it can also prevent the metastatic capability of tumour cells. It has been shown that autophagy adversely correlates with metastasis and EMT in pancreatic, breast, glioblastoma, and gastric CSCs [119]. Catalano et al. revealed that downregulation of Beclin-1, ATG5 or ATG7 in glioblastoma cells increases migration and invasion of tumour cells and upregulates EMT regulators, suggesting that autophagy reduces EMT and metastasis in glioblastoma cells [120].

4.2. Autophagy in chemoresistance

Similar to the paradoxical role of autophagy in tumorigenesis and tumour inhibition, autophagy can induce resistance or sensitivity to anticancer drugs. Thus, we delineate autophagy roles in the chemoresistance of cancer therapy.

4.2.1. Inhibition of autophagy overcomes resistance

Several studies have verified that tumour resistance to chemotherapy can be enhanced via upregulation of autophagy, thus inhibition of autophagy augments resistance to the therapeutic agents. Furthermore, elevated levels of autophagy has been reported in patients with poor prognosis. Thus, developing pharmacological components for inhibiting autophagy has attracted increasing attention. The Food and Drug Administration (FDA) approved chloroquine (CQ) and hydroxychloroquine (HSQ) as autophagy inhibitors which are combined with anticancer therapies in (pre)clinical trials. CQ and HSQ are antimalarial drugs that are concentrated in acidic lysosomes, raise the pH, inhibit lysosomal activity, and subsequently inhibit autophagy [121].

A study investigated the effect of autophagy inhibition on DOX-treated triple-negative breast cancer cells. They found that combination of DOX and an inhibitor of autophagy, 3-methyladenine (3-MA), sensitized cancer cells to DOX by switching cell death type from apoptosis to necroptosis [122]. The autophagy inhibitory activity of 3-MA is related to its ability in the prevention of autophagosome formation via inhibiting class III PI3 K [123]. Similarly, CQ reversed resistance to DOX in DOX-resistance breast cancer cells [124]. Furthermore, CQ considerably enhances tumour sensitivity to 5-FU both in vitro and in vivo [125,126]. Pantoprazole, a proton pump inhibitor (PPI), also inhibits autophagy by accumulation in acidic endosomes and rising their pH [127]. Qian et al. showed that pantoprazole sensitized cancer cells to seven clinically-used chemotherapy by inhibition of autophagy [128]. In addition to pharmaceutical components, genetically silencing of autophagy also have been proposed to increase tumour cells’ sensitivity to chemotherapy. For example, An et al. found that miR-23b-3p sensitized chemoresistance gastric cancer cells to chemotherapeutic agents such as 5-FU, vincristine, and cisplatin by targeting ATG12 and high-mobility group box 2 (HMGB2), suggesting inhibition of autophagy enhances tumour sensitivity to chemotherapy [129]. Anna et al. investigated the effects of autophagy inhibition via chloroquine treatment or CRISPR/Cas9 ATG5 knockout on ovarian CSCs. They revealed that autophagy inhibition reduces resistance to carboplatin [130].

4.2.2. Promotion of autophagy overcomes resistance

In contrast to a pro-survival role and ability in inhibition of apoptosis, autophagy also has a pro-death role in which excessive or uncontrolled autophagy can induce apoptosis or autophagic cell death (type II programmed cell death) [123]. Based on this concept, several studies have been designed to investigate the therapeutic potential of autophagy in different cancers.

Lee et al. investigated the effect of suberoylanilide hydroxamic acid (SAHA), a histone deacetylase (HDAC) inhibitor, on tamoxifen-resistant MCF-7 (TAMR/MCF-7) cells. They found that SAHA significantly increased autophagic cell death in TAMR/MCF-7 cells and suppressed tumour growth [131]. NVP-BEZ235, a dual inhibitor of phosphatidylinositol 3-kinase (PI3 K)/mammalian target of rapamycin (mTOR), suppressed cisplatin-resistant urothelial cancer cell proliferation by autophagy flux [132]. Similarly, Westhoff et al. reported that NVP-BEZ235 enhanced DOX–induced apoptosis and sensitized neuroblastoma cells to DOX [133]. It has been shown that RAD001, an autophagy activator, synergistically sensitized papillary thyroid cancer (PTC) cells to DOX via inducing autophagy [134].

5. LncRNAs, chemoresistance, and autophagy

As mentioned above, the expression of lncRNAs is extensively altered in cancers and participate in tumorigenesis by playing an oncogenic or tumour-suppressive role. Notably, increasing evidence has demonstrated that lncRNAs also play essential roles in resistance to cancer drugs, in particular chemotherapy agents. For example, Huang et al. surveyed the contribution of lncRNAs in resistance to docetaxel in breast cancer cell lines by sequencing of the whole genome. Their analyses revealed that 50 and 22 lncRNAs consistently upregulated and downregulated, respectively, in both docetaxel-resistant cell lines. Further analyses showed that four upregulated lncRNAs located near or within the ABCB1 locus, suggesting a regulatory relationship between the four lncRNAs and the ABCB1 gene. They also reported the lncRNA EPB41L4A-AS2 as a potential biomarker for sensitivity to docetaxel [135]. Table 2 summarizes some dysregulated lncRNAs are involved in chemoresistance. In this section, we review and discuss how lncRNAs mediate chemoresistance in the tumour by modulating autophagy.

Table 2. LncRNAs and their function in chemoresistance

LncRNA	Effect	Cancer	Drug	Mechanism	Ref
UCA1	↑Resistance	Bladder	Cisplatin	↑Wnt6 transcription	^[136]
CASC2	↓Resistance	Glioma	TMZ	Targeting miR‐181a, ↑PTEN transcription	^[137]
MALAT1	↑Resistance	Lung	Cisplatin	↑MRP1, MDR1 transcription	^[138]
FENDRR	↓Resistance	Osteosarcoma	Doxorubicin	↓ABCB1, ABCC1 transcription	^[139]
NEAT1	↑Resistance	Ovarian	Paclitaxel	Targeting miR-194, ↑ZEB1 transcription	^[140]
HOTAIR	↑Resistance	Gastric	Cisplatin	Targeting miR-126, ↑ PI3 K/AKT/MRP1 pathway activity	^[141]
MEG3	↓Resistance	Bladder	Cisplatin	↑Apoptosis	^[142]
PCAT6	↑Resistance	Colorectal	5-FU	Targeting miR-204, ↑HMGA2/PI3 K signalling activity	^[143]
GHET1	↑Resistance	Bladder	Gemcitabine	↑ABCC1 transcription	^[144]
KCNQ1OT1	↑Resistance	Tongue	Cisplatin	Targeting miR-211-5p	^[145]
TUG1	↑Resistance	Colorectal	5-FU	As a miR-197-3p sponge	^[146]

5.1. BLACAT1

LncRNA bladder cancer-associated transcript 1 (BLACAT1), located on 1q32.1 chromosome and with a length of 2616 bp, is overexpressed in many cancers which promotes tumour cells proliferation, migration, and invasion [147,148]. Several studies demonstrated that lncRNA BLACAT1 is involved in resistance to chemotherapy. It has been shown that BLACAT1 is upregulated in the oxaliplatin resistance of gastric cancer cells and tissue, whereas BLACAT1 knockdown suppresses tumour growth via decreasing drug resistance-related genes, including ABCB1 [149]. Huang et al. revealed that lncRNA BLACAT1 promotes chemoresistance through modulating autophagy. They indicated that the expression of BLACAT1, ATG7, MRP1, LC3-II/LC3-I, and Beclin-1 was meaningfully upregulated in cisplatin-resistant NSCLC cells compared with in cisplatin-sensitive cells. They also identified miR-17 as a target of lncRNA BLACAT1 and showed that BLACAT1 activates autophagy by inhibiting miR-17. BLACAT1/miR-17/ATG7 pathway contributes in resistance to cisplatin, which provide promising target for NSCLC treatment [150].

5.2. MALAT1

Metastasis-associated lung adenocarcinoma transcript 1 (MALAT1), located on 11q13 chromosome and with a length of 8.5 kb, contributes to cancer cell proliferation, migration, invasion, and angiogenesis [151]. Cai et al. found the significant upregulation of MALAT1 in TMZ‐resistant glioblastoma cells and MALAT1 promotes the chemoresistance by suppressing miR-101, whereas MALAT1 knockdown alleviates resistance of glioblastoma cells to TMZ through promoting apoptosis and inhibiting cell proliferation [152]. It has been shown that MALAT1 is overexpressed in chemoresistance gastric cancer and involved in chemoresistance by regulating autophagy [153,154]. YiRen et al. found that MALAT1 improves autophagy-associated chemoresistance in gastric cancer cells. They revealed that MALAT1 knockdown effectively inhibited autophagy and sensitized gastric cancer cells to cisplatin. Mechanistically, MALAT1 sequestrate miR-23b-3p which reduces inhibitory effect of miR-23b-3p on ATG12 [153]. In another study, Xi et al. indicated that lncRNA MALAT1 potentiates resistance to cisplatin by improving autophagy in cisplatin-resistance gastric cancer cells. They identified miR-30b as a direct target of MALAT1, whereas overexpression of miR-30b significantly reduced chemoresistance by inhibiting ATG5 [154].

5.3. XIST

The X inactivate-specific transcript (XIST), transcribed from the inactive X chromosome, is dysregulated in glioma, HCC, colorectal cancer, gastric cancer, breast cancer, ovarian cancer, cervical cancer, nasopharyngeal carcinoma, and pancreatic cancer [155]. It was proved that the dysfunctional expression of lncRNA XIST is associated with tumour stage, distant metastasis, lymph node metastasis, and overall survival [156]. Zhu et al. reported that lncRNA XIST increases resistance to doxorubicin by regulating the miR-124/SGK1 axis in colorectal cancer, whereas XIST knockdown inhibits chemoresistance [157]. Xiao et al. also indicated that lncRNA XIST greatly upregulated in 5-FU resistance colorectal cancer cells which XIST knockdown reversed resistance to 5-FU [158]. Moreover, lncRNA XIST is able to regulate chemoresistance through modulating autophagy. It has been demonstrated that lncRNA XIST is overexpressed in NSCLC tumours and cisplatin-resistant cells. Knockdown of lncRNA XIST significantly alleviated chemoresistance in cisplatin-resistant A549 cells. Mechanistically, lncRNA XIST targets miR-17 to attenuate ATG7 expression. Thus, lncRNA XIST knockdown attenuates resistance to cisplatin via autophagy suppression [159].

5.4. SNHGs

Small nucleolar RNA host genes (SNHGs) have acknowledged roles in various cancers. For example, SNHG1 is involved in proliferation and invasion of glioma cells [160] or SNHG12 promotes gastric cancer progression and associated with poor prognosis of patients by targeting miR-16 [161]. Recent studies indicated that lncRNA SNHGs are able to influence the response of cancer cells to chemotherapy agents. Wang et al. reported that knockdown of SNHG12 attenuates the resistance of NSCLC cells to cisplatin, paclitaxel, and gefitinib by inducing apoptosis [162]. Another study demonstrated that SNHG6 increases resistance to 5-FU in colorectal cancer cells, whereas knockdown of SNHG6 inhibits tumour growth in animal model and improves 5-FU therapy. It has been shown that SNHG6 promotes resistance to 5-FU by promoting autophagy. Mechanistically, SNHG6 promotes ULK1-induced autophagy by sponging miR‑26a‑5p [163]. Another member of the SNHGs family that enhances resistance through activating autophagy is SNHG14. Zhang et al. found that SNHG14 overexpression enhances resistance of pancreatic cancer cells to gemcitabine by stimulating autophagy. They revealed that SNHG14 acts as a sponge for miR-101 which could inhibit autophagy [164].

5.5. HULC

Highly upregulated in liver cancer (HULC), located on 6p24.3 chromosome with a length of approximately 500 bp, dysregulated in different cancers and contributes in tumour cell proliferation, survival, growth, invasion, and angiogenesis [165]. It has been reported that lncRNA HULC overexpressed in gastric cancer patients compared with healthy ones and knockdown of HULC enhances sensitivity of gastric cancer cells to chemotherapeutic agents [166]. Xiong et al. found that lncRNA HULC can activate autophagy via stabilizing silent information regulator 1 (Sirt1) protein in HCC. Furthermore, they demonstrated that HULC downregulates the expression of miR-6825-5p, miR6845-5p, and miR6886-3p, leading to a higher expression of ubiquitin-specific peptidase 22 (USP22) and Sirt1. Moreover, silencing HULC using siRNAs sensitized HCC cells to oxaliplatin, 5-FU, and pirarubicin. They suggested that HULC/USP22/Sirt1/protective autophagy axis may be a potential target in developing strategy for sensitizing HCC to chemotherapy [167].

5.6. CASC2

Cancer susceptibility candidate 2 (CASC2), located on 10q26 chromosome, is a tumour suppressor lncRNA which aberrantly expressed in human cancers, including gastric, colorectal, glioma, lung, and bladder cancers [168]. Several studies have been proved the role of CASC2 in resistance to chemotherapy drugs. For example, it has been demonstrated that overexpression of CASC2 enhances cisplatin sensitivity in gastric cancer, whereas CASC2 knockdown increased chemoresistance [169]. Similarly, upregulation of CASC2 in cisplatin-resistance HCC and oesophageal squamous cell carcinoma cells enhances cisplatin sensitivity by targeting miR-222 and miR-181a, respectively [170,171]. Jiang et al. found that CASC2 is downregulated in glioma. They showed that lncRNA CASC2 upregulation enhances sensitivity of glioma cells to TMZ by inhibiting autophagy. Mechanistically, CASC2 negatively regulates miR-193a-5p and its target gene, mTOR, which is an autophagy inhibitor [172].

5.7. KCNQ1OT1

The KCNQ1 opposite strand/antisense transcript 1 (KCNQ1OT1), located on 11p15.5 chromosome, participates in tumorigenesis and chemoresistance of different cancers. For example, Ren et al. demonstrated that lncRNA KCNQ1OT1is highly expressed in lung adenocarcinoma and correlates with big tumour size, lymphatic metastasis, poor differentiation, and TNM stages. They reported that knockdown of KCNQ1OT1 attenuates resistance of lung adenocarcinoma to paclitaxel [173]. Another study also proved that knockdown of KCNQ1OT1 enhances sensitivity of osteosarcoma cells to cisplatin [174]. Li et al. found that KCNQ1OT1 enhances resistance of colon cancer to oxaliplatin by targeting autophagy. Their further analyses indicated that KCNQ1OT1 acts as a sponge for miR-34a, leading to the upregulation of ATG4B and promoting protective autophagy. Thus, chemoresistance of colon cancer cells is regulated by KCNQ1OT1/miR-34a/Atg4B axis which suggests a novel target for developing colon cancer therapeutics [175].

5.8. GAS5

Growth arrest-specific 5 (GAS5) located on 1q25 chromosome, is a tumour suppressor lncRNA that downregulates in many cancers and its level of expression regulates proliferation, apoptosis, EMT, and metastasis of several cancers [176]. Duo to tumour-suppressive role, GAS5 inhibits tumour progression and chemoresistance. For example, GAS5 overexpression in epithelial ovarian cancer effectively enhances the sensitivity of cells to cisplatin and increases apoptosis [177]. Overexpression of GAS5 decreases tumour growth in mice, while GAS5 knockdown significantly increased cell resistance to gemcitabine and 5-FU in pancreatic cancer cells [178]. Zhang et al. also reported that GAS5 could affect chemoresistance by regulating autophagy. They found that expression of GAS5 in NSCLC tissues is substantially higher than adjacent ones. Moreover, they reported that knockdown of GAS5 increases cisplatin IC50 of lung cancer cell lines, while overexpression of GAS5 decreases cisplatin IC50 of cisplatin resistance cells. They also indicated that knockdown of GAS5 in lung cancer cells and its overexpression in cisplatin resistance cells decreases and increases autophagy, respectively. Thus, GAS5 increases cisplatin sensitivity via inhibiting autophagy [179].

5.9. H19

H19, located on 11p15.5 chromosome, is an oncogene lncRNA that contributes to various human cancers, including gastric, thyroid, breast, and HCC [180]. LncRNA H19 is involved in proliferation, invasion, migration, and metastasis of cancer cells [181,182]. It has been shown that lncRNA H19 modulates the resistance of breast cancer to tamoxifen [183,184]. Gao et al. found that knockdown of H19 enhances the sensitivity of breast cancer cells to tamoxifen by inhibiting EMT and Wnt pathway [183], while Wang et al. indicated that H19 promotes resistance to tamoxifen in breast cancer through increasing autophagy [184]. Overexpression of H19 promotes tamoxifen resistance and autophagy by downregulating methylation of Beclin-1 promoter [184]. Another study reported that H19 enhances the resistance of colorectal cancer to 5-FU through acting as a sponge for miR-194–5p and promoting Sirt1-mediated autophagy [185].

5.10. HOTAIR

Aberrant expression of HOX transcript antisense intergenic RNA (HOTAIR), located on 12q13.13 chromosome with a length of 2158 bp, has been reported in various human cancers [186,187]. LncRNA HOTAIR plays important roles in tumour proliferation, progression, angiogenesis, poor prognosis, and drug resistance [187]. It has been shown that HOTAIR overexpression induces chemoresistance in ovarian cancer. It is suggested that lncRNA HOTAIR enhances DDR and NF-κB pathway [188]. Xiao et al. also found that knockdown of HOTAIR inhibits cell proliferation and reverses chemoresistance by targeting miR-203a-3p and Wnt/β-catenin pathway in colorectal cancer [189]. Sun at al. conducted a study to reveal the effect of HOTAIR on autophagy and chemoresistance. They resulted that HOTAIR modulates resistance to cisplatin by affecting the expression of Beclin-1, MDR, and P-gp in endometrial cancer cell line [190].

5.11. Other lncRNAs

In addition to mentioned lncRNAs, there are other ones mediate chemoresistance by modulating autophagy. For example, lncRNA AC023115.3 suppresses resistance to cisplatin in glioblastoma cells by inhibiting autophagy. Mechanistically, AC023115.3 reduces the inhibitory effect of miR-26a on glycogen synthase kinase 3 (GSK3) [191]. GSK3 induces degradation of Mcl-1, a Bcl-2 family member, leading to a decrease in autophagy [191]. Cai et al. conducted a microarray analysis to compare differential lncRNA expression in doxorubicin-resistant gallbladder cancer cells and their parental cells. They found that gallbladder cancer drug resistance-associated lncRNA1 (GBCDRlnc1) regulates chemoresistance by activating autophagy, whereas GBCDRlnc1 knockdown sensitized gallbladder cancer cells to doxorubicin via inhibiting autophagy [192]. It has been shown that the expression of linc00515 and ATG14 is considerably higher in melphalan-resistant myeloma cells. Linc00515 knockdown inhibits chemoresistance and autophagy in myeloma cells. Mechanistically, linc00515 targets miR-140-5p, which attenuates inhibitory effect of miR-140-5p on ATG14 [193]. Wang et al. reported that lncRNA CTA significantly downregulated in osteosarcoma tissues and its low expression markedly associated with tumour size, the advanced clinical stage, and poor prognosis. They found that overexpression of CTA sensitized osteosarcoma cells to doxorubicin via inhibiting autophagy. LncRNA CTA directly targets miR-210 [194].

6. Conclusions and perspectives

LncRNAs, as a large and heterogeneous subclass of ncRNAs, play indispensable role in different aspects of tumorigenesis and are considered as novel biomarkers in cancer diagnosis and prognosis. Regarding to pivotal roles of lncRNAs in chemoresistance and modulation of autophagy, antisense oligonucleotides (ASOs), small interfering RNAs (siRNAs), and gene-editing tools including CRISPR/Cas9 to target lncRNAs should be used inside tumour cells and reverse resistance to chemotherapy agents.

Although most of the studies have discussed on the lncRNAs typically function as sponges for autophagy-related miRNAs, they also have more complex functions in the regulation of autophagy, including transcriptional regulation, histone remodelling, and protein–protein interactions. Certainly, more studies to address these functions and interactions will open new doors for finding new targets and new strategies for overcoming chemoresistance in cancer therapy. On the other hand, classifying the roles of lncRNAs based on different types of autophagy, such as mitophagy, will help to investigate their functions more specifically. Furthermore, it should also be noticed that lncRNAs exert their functions directly or indirectly through binding to single or multiple molecules. Therefore, comprehensive study and deep insight into the molecular targets of lncRNAs in autophagy is crucial for reversing chemoresistance. Moreover, there are some challenges in modulating autophagy in drug resistance which can be considered in future investigations, including creating balance between tumorigenesis and tumour suppressive roles of autophagy, selectively targeting autophagic machinery, and defining the role of cellular context in upregulation or downregulation of autophagy. However, to promote therapeutic interventions in cancer by targeting the functional relationship between lncRNAs and autophagy, further studies on pre-clinical and clinical trials are urgently required.

Disclosure of potential conflicts of interest

The authors declare that there is no conflict of interest.

Additional information

Funding

This work was supported by the [Zhejiang Provincial Science and Technology Projects] under Grant [Nos. LGF18H160041 to LJQ, LGD19H160001 to JKT]; [National Natural Science Foundation of China] under Grant [Nos. 81772537 to JKT; 81374014 to JKT; 81502482 to JGZ]; and [Zhejiang Provincial Research Projects of Medical and Healthy Industries] under Grant [Nos. 2017KY193 and 2017KY210 to JGZ].