Regulation mechanism and pathogenic role of lncRNA plasmacytoma variant translocation 1 (PVT1) in human diseases

Abstract

Plasmacytoma variant translocation 1 (PVT1) is a long non-coding RNA (lncRNA) gene identified as a recurrent breakpoint of Burkitt’s lymphomas. Human PVT1 gene is located on region 8q24.21, a well-known cancer risk region, and encodes at least 26 linear ncRNA isoforms and 26 circular RNA isoforms, as well as 6 microRNAs. Several PVT1 functioning models have been reported recently such as competing endogenous RNA (ceRNA) activity and regulating protein stability of oncogenes, especially MYC oncogene. The promoter of PVT1 gene is a boundary element of tumor-suppressor DNA. CircPVT1 derived from PVT1 gene is also a critical non-coding oncogenic RNA. Although substantial advancements have been made in understanding the roles of PVT1 in cancer recently, the detailed mechanisms underlying its functions remain unclear. Herein, we summarize the recent progressions on the mechanisms underlying PVT1 regulated gene expression at different levels. We also discuss the interaction between lncRNA and protein, RNA and DNA, as well as the potential cancer therapy strategy by targeting these networks.

Introduction

Long non-coding RNAs (lncRNAs), the RNAs containing more than 200 nucleotides while lacking extended open reading frames, are involved in the regulation of cell survival, proliferation, metabolism, differentiation, as well as other functions.¹ With the development of genome-wide sequencing technology, hundreds of types of functional lncRNAs have been identified, and their biological functions have been elucidated. A variety of lncRNAs exist throughout the genome.² LncRNAs exhibit a significant temporal and spatial specificity during histological development and differentiation. During the differentiation process, different splicing manners and/or dynamic expression may happen. Numerous lncRNAs have been demonstrated to function in tumorigenesis and organ development,³ and many of them can regulate carcinogenesis through impacting the oncogenes and/or tumor suppressing genes.⁴

Accumulating evidence highlights that PVT1 is a critical gene expression regulator in differentiation, development, heart diseases and cancers. Previous studies have revealed that PVT1 plays critical roles in the generation, growth, and metastasis of human cancers, and it is frequently upregulated in various cancers including lung, pancreas, colorectal, breast, gastric, and cervical cancer.⁵ Therefore, PVT1 is a potential diagnostic and therapeutic biomarker for some cancers. Studies have identified specific regulatory functions and mechanisms of PVT1 in a series of crucial biological processes, including cell survival, differentiation, proliferation, and chromatin. Via crosstalk with other RNA species and/or through different chromatin-based mechanisms, PVT1 participates in remodeling of chromatin, and regulation of transcriptional and/or post-transcriptional events. PVT1 can function as scaffolds, decoys, guides, or enhancer RNA.⁶

As supported by increasing evidence, PVT1 may have competing endogenous RNA (ceRNA) activity.⁷ Moreover, PVT1 gene promoter may compete with protein coding gene promoter. Cho et al reported that the promoter of PVT1 gene can inhibit the MYC gene expression by competing with the MYC promoter.⁸ More and more studies have demonstrated that PVT1 can bind to DNAs, mRNAs, microRNAs (miRNAs), and/or proteins, thereby regulating a variety of cellular processes. This review summarizes the characteristics of PVT1, including their biological functions and the related mechanisms, which was the most comprehensive to date.

LncRNA PVT1

PVT1 is encoded by a gene that resides in a cancer-associated region: a long arm of mouse chromosome 15 (qD1) and human chromosome 8 (8q24). In 1992, for the first time, Huppi K et al⁵ found PVT1 transcripts accompanies chromosomal translocation and amplification in murine lymphocytic-B neoplasms. The PVT1 gene locus was determined as a cluster of T(8;22) and T(2;8) variant MYC-activating chromosomal translocation breakpoints, localized 400 kb downstream of MYC.⁵ Human PVT1 genomic locus is localized 54 kb downstream of proto-oncogene MYC⁶ (Fig. 1). These two genes have some interactions, including feedback regulation, and they synergistically drive tumorigenesis as the oncogenic function of MYC relies on the expression of PVT1.^9,10 The PVT1 locus contains at least 12 exons, which gives rise to multiple alternatively spliced non-protein coding transcripts, and encodes at least 52 ncRNA variants with oncogenic functions, including 26 circular and 26 linear RNA isoforms and 6 miRNAs: miR-1208, miR-1207-5p, miR-1207-3p, miR-1205, and miR-1204⁷ (Fig. 1). Recent studies have identified several functioning models of PVT1, such as protein stability regulation for important oncogenes especially MYC oncogene and competing endogenous RNA activity.

Figure 1.

Schematic view of human PVT1 gene locus and alternative splicing. PVT1 located in the region of 8q24.21 harboring MYC/PVT1 loci and PVT1-encoded five miRNAs and probable mode of biogenesis of circPVT1. The positive feedback and promoter-enhancer competition between PVT1 and MYC were shown. The rectangles represent the exons.

Alternative splicing from one primary transcript to generate multiple protein isoforms represents a major proteomic diversity driver in human cells.¹¹ PVT1 is a lncRNA with multiple alternatively spliced transcripts polyadenylated at 3′ end and capped at 5′ end.^7,12 PVT1 isoforms exhibit significantly different expression manners across different human tissues: heart and adrenal gland have the highest expression levels, while white blood cells and lymph nodes have the lowest expression levels.⁷ PVT1 has been shown to play crucial roles in cancers as well as other diseases. Different PVT1 exons could be expressed differentially and might have different functions. Ilboudo A et al found that the expression manners of most PVT1 exons are consistent in prostate cancer (PCa). More specifically, PVT1 exon 9 was consistently overexpressed in the aggressive PCa cell lines compared to their non-tumorigenic mother cell lines. Among all the 12 PVT1 exons, PVT1 exon 9 was the only one exhibiting a very consistent expression, suggesting that the overexpression of PVT1 exon 9 is closely correlated with the aggressiveness in this PCa model.^13,14 Pal G et al utilized data from 1000 genomes to analyze the PVT1 locus and found there was a significant difference in chromosomal region spanning PVT1 exons 4A and 4B between African and non-African populations, and the gene expression of PVT1 exons 4A and 4B was dramatically enhanced in PCa tissues compared to benign prostatic hyperplasia and normal prostate tissues. These results suggest that PVT1 exons 4A and 4B might have clinical implications in PCa.¹⁵ A novel splicing variant transcript of PVT1 lacking exon 4 (PVT1^ΔE4) has also been reported in clear cell renal cell carcinoma (ccRcc), which has a higher endogenous expression level than full-length transcript but can similarly enhance cell invasion and proliferation as full-length transcript does. In addition, study showed that SRSF1 decreased the inclusion of full-length transcript exon 4 while enhanced the expression of PVT1^ΔE4 in ccRcc.¹⁶ Mfossa A et al investigated the expression patterns of possible circRNA variants for numerous genes including PVT1 in mouse utero and primary cortical neurons and found three (circ-0005724, circ-0005721 and circ-0000604) among five circular transcripts were significantly amplified. Two circular variants (circ-0005724 and circ-0000604) were more stable than the linear cognates in primary cortical neurons. Moreover, the circular and linear transcripts were highly enriched in brain and liver, respectively, and the expression of PVT1 transcripts elevated during the development of embryonic brain.¹⁷

The role of PVT1 in pretranscription regulation

PVT1 influences all the stages of gene life cycle—from chromatin remodeling and epigenetic regulation to transcriptional and posttranscriptional control to protein metabolism (Fig. 2).

Figure 2.

The mechanisms of PVT1 in pretranscription regulation. a Listed are a few examples of PVT1 gene rearrangements and fusion transcripts. b Listed are five PVT1-encoded miRNAs. c showed the mechanisms of PVT1 in epigenetic modification. d showed schematic representing the model of promoter-enhancer competition between PVT1 and MYC. PVT1 promoter regulates MYC expression in cis manner.

PVT1 can act as a fusion partner

With the development of sequencing technologies, a total of 98 different PVT1 fusion transcripts have been identified in both solid tumors and hematological malignancies, which arise from rearrangements of the 8q24 chromosomal region and induce abnormalities of this region.¹⁸ The roles of lncRNA gene fusions in joining two protein-coding genes have not been sufficiently investigated. PVT1 is a well-known fusion partner, and PVT1 fusion transcripts are powerful driver in cancers. Most PVT1 fusions are characterized by amplification of genomic locus (8q24.21).¹⁸ Analysis of Reactome pathways reveals that some PVT1 fusion partners converge in carcinogenic events, like NOTCH1 signaling, TP53 regulation, AP transcription factor family activity, and UB-specific processing proteases.¹⁹

The PVT1-MYC/MYC-PVT1 fusion was fully studied in cancers. PVT1 fusion genes were first described when PVT1 displaced intron 1 and exon 1 in colorectal adenocarcinoma, which resulted in rearrangement of DNA.²⁰ Later, two different PVT1-MYC fusions were identified, both of which involved PVT1 the 5′ end (with exon 1 or exon 1 and 3) fused to MYC (exons 2 and 3).²¹ PVT1-MYC fusion is present in 0.18% of Genomics Evidence Neoplasia Information Exchange (GENIE) cases in American Association for Cancer Research (AACR) projects with breast invasive ductal carcinoma, endometrial endometrioid adenocarcinoma, Burkitt lymphoma, diffuse large B-cell lymphoma, and colon adenocarcinoma, not otherwise specified having the greatest prevalence.²² In a multiple myeloma study, two highly expressed chimeric genes, PVT1-WWOX harboring der(16)t(16;22)ins(16;8) (q23;q24) and PVT1-NBEA harboring t(8;13) (q24;q13), were identified. The PVT1-WWOX in which PVT1 exon 1 was fused to WWOX exon 9 and PVT1-NBEA chimera in which PVT1 exon 1 was fused to NBEA exon 2 were correlated with the high expression of abnormal WWOX and NBEA, respectively. Both WWOX and NBEA are tumor suppressors in multiple myeloma.²³ In a study on acute myelogenous leukemia, the genomic junctions of PVT1-NSMCE2 were found to be located within intron 1 of PVT1 and in a region upstream of exon 1 of NSMCE2, and PVT1-NSMCE2 was also accompanied by amplification of 8q24. NSMCE2 rearrangement can induce chromosomal breakage and loss.²⁴ PVT1-NDRG1, a highly recurrent fusion gene in which PVT1 exon 1 is fused to the 3′ end of NDRG1, has been identified in medulloblastoma,²¹ breast cancer²⁵ and hepatocellular carcinoma.²⁶ However, the functions of PVT1-NDRG1 need to be further elucidated. EVI1 is a proto-oncogene associated with human myeloid leukemia. The aberrant expression of EVI1 in acute myeloid leukemia (AML) is correlated with the t (3;8) (q26;q24). Further study showed that the breakpoints in t (3;8) (q26;q24) are located at EV1/MDS1 on chromosome 3 and distal to PVT1 on chromosome 8, and this rearrangement can induce aberrant expression of EVI1, thus increasing tumorigenesis.²⁷ Notably, all of these fusion genes contain PVT1 exon 1. Using whole transcriptome analysis, Kim et al identified six different inter-chromosomal fusion genes (PVT1-PPAPDC1A, PVT1-ATE1, PVT1-APIP, PDHX-PVT1, and PVT1-PDHX) in human gastric cancer²⁸; two variants were identified for PVT1/PDHX, with PVT1 exon 1 being fused to PDHX exon 9 or 2, and two PVT1/APIP variants were identified with PVT1 exon 1 being fused to APIP exon 2 or 6. All the identified fusions involved PVT1 exon 1 except PDHX/PVT1, where PDHX exon 3 is fused to PVT1 exon 4. The PVT1 fusion partners APIP and ATE1 were found to be amplified, indicative of important role for PVT1 in DNA rearrangement.

These studies suggest that PVT1 exon 1 is frequently involved in DNA rearrangement, and PVT1 can thereby act as a fusion partner in cancers, impact regulation of oncogenes and tumor suppressors, and promote tumorigenesis.

PVT1 can encode miRNAs

Increasing evidence has shown that the miRNAs residing in PVT1 locus are the key driver for the oncogenic roles of PVT1. Reports have shown that miRNAs can act as tumor suppressors or oncogenes due to their frequent deregulation in cancers. Critically, miRNAs can be applied as cancer therapeutic targets or for cancer phenotype evaluation. As mentioned above, PVT1 encodes a series of non-coding RNAs, including a group of six annotated miRNAs: miR-1208, miR-1207-3p, miR-1207-5p, miR-1206, miR-1205, and miR-1204.^5,29

Residing in PVT1 exon (1b), mir-1204 is fused to the light chain of immunoglobulin in a subset of Burkitt's lymphoma and highly present in tumors with amplified PVT1-MYC fusion.⁵ The miR-1204 expression level is higher in PVT1-MYC fusion-positive than in -negative medulloblastomas, which has a correlation with malignant phenotypes.²¹ Studies showed that P53 can induce the expression of the PVT1 locus, thereby activating miR-1204 transcription. Reversely, ectopic expression of miR-1204 can enhance P53 level and induce cell death, indicative of a positive feedback loop between them.^30,31 Mir-1205, which is encoded on the PVT1 intron 3 locus, can increase growth of castration-resistant PCa by targeting Egl-9 family hypoxia inducible factor 3 (EGLN3)³² and fry-like (FRYL).³³

PVT1 has been demonstrated to have a positively correlated expression pattern with its encoded miRNAs. However, paradoxical conclusions were reported between mir-1207 pair and PVT1. Takahashi Y et al showed that different from other PVT1 encoded miRNAs, miR-1207-5p is the only miRNA inhibited by PVT1. MiR-1207-5p can decrease CASP9 and suppress apoptosis in colorectal cancer.³⁴ Cui M et al demonstrated that PVT1 could strengthen cancer stem cell-like properties in nasopharyngeal carcinoma (NPC) through activating PI3K/AKT signal pathway and inhibiting miR-1207.³⁵ Das DK et al found that miR-1207-3p, but not miR-1207-5p, is remarkably downregulated in PCa and promotes tumorigenesis by targeting fibronectin type III domain containing 1 (FNDC1).³⁶ Moreover, Yan C et al demonstrated that miR-1207-5p and PVT1 were consistently induced by estrogen and promote breast cancer tumorigenesis by targeting STAT6.³⁷ You L et al showed that gemcitabine increased the miR-1207 pair (miR-1207-3p and miR-1207-5p) and decreased PVT1 levels through upregulating microprocessor complex subunit DGCR8 and ribonuclease III Drosha and targeting RhoA (by miR-1207-3p) and SRC (by miR-1207-5p).³⁸ Alvarez ML et al showed that miR-1207-5p up-regulation induced by TGFβ1 and glucose is independent of PVT1. Similar with PVT1, miR-1207-5p upregulates FN1, PAI-1, and TGF-β1 independent of host gene in diabetic nephropathy.¹² The functions of miR-1206 and miR-1208 associated with PVT1 have not been reported yet. However, circPVT1 knockdown enhances radiosensitivity in NSCLC by sponging miR-1208.³⁹ The functions of PVT1-encoded miRNAs have not been elucidated sufficiently, and further studies are required and may provide novel insights into the PVT1 functions (Fig. 2B).

PVT1 can act as an epigenetic modulator

A hallmark function of PVT1 is its ability to interact with histone-modifying complexes, mediating epigenetic regulation (Fig. 3). Studies showed that PVT1 can act at chromatin level as signal, guide, or scaffold to modulate gene expression. Enhancer of zeste homolog 2 (EZH2) is an enzymatic subunit and histone methyltransferase of polycomb repressive complex 2 (PRC2), which is an epigenetic multiprotein complex and plays critical roles in the progression of cancers and other diseases. Histone methyltransferase enhancer of EZH2 is responsible to catalyze mono-, di-, and tri-methylate lysine 27 of histone H3 (H3K27me1/2/3) and induces silencing of the involved genes.⁴⁰

Figure 3.

The mechanisms of PVT1 in epigenetic modification. PVT1 can act as scaffold binds to chromatin and epigenetic modifier, guide the epigenetic modifier to gene promotor. PVT1 can facilitate enhancer and promoter element interactions, critical for gene activation. Listed are a few examples of PVT1 regulation from epigenetic regulation and chromatin remodeling to transcriptional control.

Epigenetic modification complex PRC2 was found to communicate with PVT1. PVT1 combines with EZH2 and recruits EZH2 to anti-tumor gene promoter regions, then enhances histone H3K27 trimethylation and decreases gene transcription levels.⁴¹ PVT1 increases proliferation of gastric cancer cells through silencing p15^INK4a and p16^INK4b by the occupancy of EZH2, which is recruited by PVT1.⁴¹ Similarly, PVT1 binds EZH2, and down-regulates P57 expression, and changes the biology of ovarian cancer cells.⁴² PVT1 can regulate histone methylation of angiopoietin-like 4 (ANGPTL4), thereby promoting cholangiocarcinoma (CCA) oncogenesis and development by binding to PRC2.⁴³ Similar mechanism targeting protein ANGPTL4 was also reported in preeclampsia patients.⁴⁴ Similarly, PVT1 can also downregulate large tumor suppressor kinase 2 (LATS2) in non-small cell lung cancer (NSCLC) through methylation of the LATS2 promoter and recruitment of EZH2.⁴⁵

PVT1 suppresses cell apoptosis and enhances cell proliferation by stabilizing expression of murine double minute 2 (MDM2), suppressing expression of P53 and recruiting EZH2 in hepatocellular carcinoma (HCC).⁴⁶ PVT1 regulates proliferation of thyroid cancer cells by modulating thyroid-stimulating hormone receptor (TSHR) and recruiting EZH2.⁴⁷ PVT1 can also recruit EZH2 to the mir-200b promoter and inhibit its expression via increasing the trimethylation level of its histone H3K27. The cell proliferation and migration promoting effects of PVT1 in cervical cancer relies on the silencing of miR-200b.⁴⁸ PVT1 can also regulate miR-195 through promoting the methylation of H3K27me3 in the promoter region via recruiting EZH2.⁴⁹ A study on diabetic nephropathy (DN) patients revealed that substantial C-phosphate-G (CpG) island sites are localized at the promoter region of forkhead box A1 (FOXA1), where PVT1 recruits EZH2 to accumulate H3K27me3, thereby suppressing the level of FOXA1. Reversely, the silencing of PVT1 attenuated the damage and suppressed apoptosis of podocytes in DN through increasing FOXA1.⁵⁰ Apart from regulating the methylation of H3K27, Wang et al⁵¹ found that PVT1 can act as a scaffold for KAT2A, a chromatin modification factor, induce acetylation of H3K9, recruiting TIF1β to activate the transcription of NF90, thereby activating the KAT2A acetyltransferase, stabilizing HIF-1α, and enhancing malignant phenotype in NPC. Notably, different from inhibiting target genes, PVT1 can also bind to EZH2 and inhibit its recruitment to MYC promoter, thereby enhancing the expression of MYC by altering the status of H3K37me3 in hepatitis B virus-positive liver cancer.⁵²

DNA methylation as an epigenetic mechanism is also involved in the function of PVT1. PVT1 can recruit DNA methyltransferase 1 (DNMT1) to the mir-18b-5p promoter through EZH2 and suppress miR-18b-5p transcription via DNA methylation. Moreover, PVT1 can regulate proliferation of gallbladder cancer (GBC) cells via HIF-1α.⁵³ PVT1 also induces expression of miR-146a in prostate cancer by promoting DNA methylation of CpG island in its promoter. The functions of PVT1 in prostate cancer tumorigenesis relies on miR-146a, and overexpression of miR-146a can eliminate the effects of PVT1 knockdown.⁵⁴ In addition, it is worth mentioning that PVT1 itself is regulated by DNA methylation.^55,56

The role of PVT1 in transcription regulation

The transcription stages include initiation, elongation, and termination. Transcription initiates from binding of RNA polymerase II (RNA Pol II) to a gene’s promoter region supported by general transcription factors (TFs), and other TFs accelerate transcription by binding to enhancer region. When the polymerase meets the terminator, the transcription is terminated. PVT1 can affect gene expression through direct binding to TFs and impacting binding of polymerase to promotor. Liu SJ et al conducted a CRISPR interference (CRISPRi)-based genome-scale identification with an sgRNA library along the PVT1 locus in ENCODE (ENCyclopedia of DNA Elements Project) cancer cell lines. The sgRNAs outside of 1 kb window around the TSSs had no effect on the transcription of major PVT1 isoform, suggesting the observed pro-growth phenotype is mediated by transcriptional interference.⁵⁷ Pyfrom SC et al performed a novel computational method PLAIDOH to calculate the transcript cis-regulatory predictive scores of cancer-specific lncRNAs and found that PVT1 has a dramatical high enhancer cis-regulatory score,⁵⁸ which was validated to suppress MYC in cis via promoter competing for common intragenic enhancer elements.⁸ These results suggest that PVT1 promoter has a PVT1 gene independent tumor suppressing function. The regulation of MYC in cis by PVT1 locus might be attributed to the MYC gene body that functions independently of the transcribed RNA, or DNA within PVT1 promoter or sequence-specific functions of mature PVT1 transcript. Guo L et al found a strong enrichment of RNA Pol II at the place where the MYC promoter interacts with the BET inhibitor (BETi) resistance-specific PVT1 enhancer in leukemia cells, raising the possibility that combination therapy may block the loading of RNA Pol II at this place. CDK7 inhibitor can block loading of RNA Pol II at PVT1 enhancer, thereby inhibiting MYC transcription, thereby exerting a synergistic effect on BETi-resistant leukemia.⁵⁹ Moreover, our previous work demonstrated that PVT1 can bind to the HIF-1α promoter and induce the transcription, thereby driving progression of pancreatic cancer (PC), indicating that PVT1 can regulate unlinked gene expression through with enhancers and/or promoters.⁶⁰ However, the mechanisms underlying the functions of PVT1 in elongation and termination processes require further research.

The role of PVT1 in posttranscription regulation

Following transcription, a variety of RNA-binding proteins (RBPs) regulate the pre-mRNAs, including capping, polyadenylating, splicing, editing, and transferring them from nucleus to cytoplasm. The mRNA stability is very important for translation. PVT1 plays critical roles in mRNA splicing, stability, and translation, and it can also indirectly regulate mRNA expression by competing endogenous RNA or acting as a miRNA sponge (Fig. 4).

Figure 4.

The mechanisms of PVT1 in posttranscription regulation. e listed PVT1 can interact with proteins and/or mRNAs to form RNP complexes, or act as scaffold for two or more proteins, thus stabilizing and protecting mRNAs from degradation, which regulate posttranscriptional gene regulation. f listed PVT1 acting as miRNA sponges attenuates the miRNA′ effect on downregulating mRNA expression (Table 1). g listed CircPVT1 acting as molecular sponges for miRNAs (Table 2).

PVT1 can enhance the mRNA and protein stability

Modulation of mRNA degradation is a control step in gene expression for regulation of protein synthesis, and the combination between PVT1 and MYC has been well studied. As a tumorigenesis driver, MYC regulates a large number of genes involved in multiple oncogenic processes. PVT1 promotes MYC stability via protecting it against proteasome-dependent degradation and decreasing its phosphorylation at threonine 58 (Thr58).^9,20 Not only in cancers, in skeletal muscle cells, during muscle atrophy, PVT1 also interacts with MYC, and the up-regulated PVT1 blocks the phosphorylation and degradation of MYC.⁶¹ Notably, m⁶A modification of PVT1 transcripts enhances its interaction with MYC and stabilizes the MYC protein in epidermal progenitor cells.⁶² Besides PVT1-MYC pair, the positive feedback loop between PVT1 and other TFs has also been reported in a variety of tumors. PVT1 can block protein degeneration and ubiquitination via direct binding to proteins. For example, PVT1 directly binds to FOXM1 and stabilizes FOXM1, thereby enhancing gastric cancer cell proliferation and invasion.⁶³ PVT1 binds to the VHL region of HIF-1α⁶⁰ and HIF-2α⁶⁴ proteins and enhances their stability by blocking ubiquitination-dependent degradation in PC and ccRcc, respectively. In turn, these TFs can also bind to the enhancer of PVT1 to transactivate its expression.^60,63,64 Wang F et al found that PVT1 can bind to NOP2 and enhance the stability of NOP2; moreover, PVT1 functions depending on the presence of NOP2 in hepatocellular carcinoma.⁶⁵

PVT1 can act as miRNA sponges

Competing endogenous RNAs (ceRNAs), also called miRNA decoys or miRNA sponges, have been identified as drivers in many diseases, especially cancers. The ceRNAs encompass different RNAs (lncRNAs, circRNAs, or pseudogenes) competing with each other to attract miRNAs. PVT1 can act as a miRNA sponge to suppress miRNAs binding to their mRNA targets, thereby promoting the stability of the target mRNAs, and regulating protein expression. Table 1 and Table S1 list the related diseases and miRNAs sponged by PVT1.

Table 1.

Related diseases and miRNAs sponged by PVT1.

Related diseases	miRNAs	Target genes or signaling pathways	Function	References
Acute kidney injury (AKI)	miR-20a-5p	NLRP3	Modulate NLRP3-mediated pyroptosis	66
Atrial fibrillation	miR-145-5p	IL-16	Boost the extracellular matrix remodeling of atrial fibroblasts	67
Bladder cancer	miR-194-5p	BCLAF1	Increase malignant phenotypes	68
Cardiac hypertrophy	miR-196b	OSMR	Knockdown attenuates the myocardial hypertrophy	69
Cardiotoxicity	miR-187-3p	AGO1	Aggravate doxorubicin-induced cardiomyocyte apoptosis	70
Cervical cancer	miR-140-5p	SMAD3	Promote the proliferation and metastasis	71
Clear cell renal cell carcinoma (ccRcc)	miR-328-3p	FAM193B	Promote the proliferation of ccRCC cells	72
Diabetic cataract (DC)	miR-214-3p	MMP2, regulated by SP1	Modulate the proliferation and apoptosis of lens epithelial cells	73
Diabetic nephropathy (DN)	miR-23b-3p	WT1	Knockdown alleviates high glucose-induced proliferation and fibrosis in human mesangial cells	74
Diabetic osteoarthritis (DOA)	miR-146a	TGF-β/SMAD4 pathway	Promote cartilage degradation	75
Esophageal squamous cell carcinoma (ESCC)	miR-203	LASP1	Promote ESCC progression	76
Gallbladder cancer (GBC)	miR-143	HK2	Knockdown inhibits cell proliferation, migration, and invasion	77
Gastric cancer	miR-186	HIF-1α	promoted the GC cell proliferation and invasion	78
Glioma	miR-128-3p	GREM1 and BMP Signaling Pathway	Promote tumorigenesis and progression	79
Ischemic stroke	miR-24-3p	STAT3, regulated by SOX2	Depleting improves ischemic stroke	80
Myocardial ischemia/reperfusion (I/R) injury	miR-186	Beclin-1	Knockdown protects cardiomyocytes apoptosis and autophagy	81
Neuropathic pain	miR-186-5p	CXCL13/CXCR5	Depletion alleviates neuropathic pain, astrocytic activation and reduced the expression of neuroinflammatory factors and proteins	82
Non-small cell lung cancer (NSCLC)	miR-200a and miR-200b	MMP9	Promote the invasive ability of NSCLC cells	83
Osteoarthritis (OA)	miR-27b-3p	TRAF3	Inhibit IL-1β-induced injury in chondrocytes	84
Osteosarcoma (OS)	miR-497	HK2	Contribute to OS cell glucose metabolism, cell proliferation, and motility	85
Papillary thyroid carcinoma (PTC)	miR-30a	IGF1R	Enhance the viability and invasion	86
PM2.5-exposed lung cancer	miR-199a-5p	Caveolin 1	Affect the role of lentinan in PM2.5-exposed lung cancer cells	87
Pulpitis	miR-455-5p	SOCS3 and PLXNC1	Involve in the pathogenesis of pulpitis	88
Retinoblastoma (RB)	miR-488-3p	NOTCH2	Silencing inhibits cell proliferation, migration, invasion, and cell cycle progression and induces cell apoptosis	89
Rheumatoid arthritis (RA)	miR-543	SCUBE2	Regulate apoptosis of fibroblast-like synoviocytes	90
RSV-infected asthma	miR-203a	E2F3	Involve in the mechanism of α-asarone in treating RSV-induced asthma	91
Temporomandibular joint osteoarthritis (TMJ OA)	miR-211-3p	TNF-α	Induce chondrocyte apoptosis	92

First, the researchers analyzed their concerned disease-related lncRNAs by microarray analysis or in the public databases TCGA or GEO and determined the research target PVT1. Then, the structure and function of PVT1 were analyzed, and the expression pattern of PVT1 in cells as well as the correlation between PVT1 levels and clinical prognosis was investigated. The results showed that PVT1 was closely related to the concerned disease (often upregulated in cancers or other diseases). PVT1 was identified as an oncogenic lncRNA that could act as a prognostic or prognostic biomarker in cancers. Furthermore, gain- and loss-of-function assays revealed that PVT1 could enhance proliferation, migration, and invasion of cancer cells, inhibit apoptosis, promote tumor growth and angiogenesis of tumor tissues in mice, and impair sensitivity to antineoplastic drugs in vitro and in vivo, suggesting that PVT1 affects the progression of cancer. Finally, subcellular localization was conducted for subsequent analysis from the perspective of ceRNA.

After the target lncRNA-PVT1 was identified, the miRNA docking site of PVT1 was predicted with RegRNA, miRDB, miRWalk, miRBase, miRPathDB, miRanda, TargetScan, or starBase bioinformatics data resources.^93,94 Then, the sequence and function of target miRNA were analyzed, and the expression pattern of miRNA in cells as well as the correlation between PVT1 levels and clinical prognosis was investigated. To confirm the ceRNA relationship between PVT1 and the targeted miRNA, PVT1 was silenced/overexpressed in vitro and in vivo, followed by analysis using luciferase assay and RNA immunoprecipitation (RIP) assay. Furthermore, the biological functions of miRNA were also analyzed using gain- and loss-of-function assays. Functional experiments showed that miRNA could inhibit cell proliferation, migration, and invasion, while promote cell apoptosis. In addition, functional rescue experiments further demonstrated that there was an antagonistic effect between PVT1 and the target miRNA.

After PVT1 and miRNA were identified, the final mRNA needs to be determined. The above bioinformatics data resources were used to predict the target genes of miRNA. TCGA and GEO data or RT-PCR, Western blot and/or immunohistochemical assay were used again to analyze the expression level of target mRNA, and the clinical prognosis, binding relationship, and the correlation between PVT1 and miRNA were analyzed. The target mRNA was proved to function in carcinogenesis. After finding the target mRNA of miRNA, the lncRNA-miRNA-mRNA were correlated, and it was accurately demonstrated that this ceRNA network did affect the occurrence and development of cancers or other diseases. Thus, a relatively complete ceRNA regulatory network was basically formed. This ceRNA network involving PVT1 and miRNA in cancers characterizes the signaling pathways mediating tumorigenesis, tumor metastasis and chemoresistance in a variety of cancers.⁹⁵ More importantly, though identified as an oncogenic lncRNA at the very beginning, PVT1 was demonstrated to play critical roles in non-cancer diseases, such as diabetes and its complications, osteoarthritis, and myocardial infarction, among others (Table 1 and Table S1).

The role of PVT1 in relation with circPVT1

CircPVT1, located on chromosome 8q24, is generated by circularization from exon 2 of the PVT1 gene, the same genetic locus encoding for PVT1 (Fig. 1). However, current reports showed that PVT1 and circPVT1 are independently transcripted by different promoters. PVT1 primarily localizes in the nucleus, while circPVT1 generally localizes in the cytoplasm, indicative of different post-transcriptional regulation for circPVT1 and PVT1.⁹⁶ Both circRNAs and circPVT1 have significant importance in pathological processes like cancer. Circular RNA profile allows circPVT1 to act as a prognostic marker and proliferative factor in many cancers. Studies focusing on circPVT1 showed that circPVT1 can enhance proliferation migration, and invasion of cancer cells, as well as drug resistance.⁹⁷ CircPVT1 was also identified as a senescence-associated circRNA (SAC-RNA). Several proliferative proteins such as IGF2BP1, KRAS and HMGA2, encoded by let-7 target mRNAs, can prevent senescence, and the levels of these proteins can be decreased by circPVT1 silencing.⁹⁸

The interaction between circPVT1 and PVT1 has been highlighted in a few studied malignancies. Current reports indicated their cooperation with an undifferentiated and/or more aggressive cell phenotype, thereby promoting cancer progression. Martina Ghetti et al found that upregulation of circPVT1 and PVT1 through genomic rearrangements or amplification and/or promoted transcription can enhance proliferation of malignant cells in acute lymphoblastic leukemia (circular PVT1), Burkitt lymphoma, acute promyelocytic leukemia, acute myeloid leukemia, and multiple myeloma (linear PVT1).⁷

Numerous studies showed that circRNAs function as miRNA sponges or ceRNAs. The role of circPVT1 in oncogenesis has also been correlated with their function as ceRNA. CircPVT1 and miRNAs could act as sponges for RNA-binding proteins through binding to tumor suppressors. Table 2 and Table S2 list the related diseases and miRNAs sponged by circPVT1.

Table 2.

Related diseases and miRNAs sponged by circPVT1.

Related diseases	miRNAs	Target genes or signaling pathways	Function	References
Adenomyosis (ADS)	miR-145	TALIN1	Promote eutopic endometrial cell proliferation and invasion	99
Breast cancer (BCa)	MiR-29a-3p	AGR2-HIF-1α Pathway	Promote the progression of breast cancer	100
Clear cell renal cell carcinoma (ccRcc)	miR-145-5p	TBX15	Promote ccRCC growth and metastasis	101
Colorectal cancer (CRC)	let-7	NRAS	Drive cancer cells towards oncogenicity	102
Epithelial ovarian cancer (EOC)	miR-149	NR	Enhance cell proliferation but inhibits apoptosis	103
Esophageal carcinoma (EC)	miR-4663	PAXs and PPARs	Promote cell invasive ability	104
Gastric cancer (GC)	miR-124-3p	ZEB1	Contribute to paclitaxel resistance of gastric cancer cells	105
Hepatocellular carcinoma (HCC)	miR-3666	SIRT7	Promote HCC cell growth	106
Lung adenocarcinoma (LADC)	miR-429	FOXK1	Interference inhibits the progression of lung ADC and enhances its sensitivity to DDP	107
Lung squamous cell carcinoma (LUSC)	miR-30d and miR-30e	CCNF, regulated by HuR	Promote the proliferation of LUSC cells	108
Myocardial infarction (MI)	miR-125b,miR-200a	p53/Traf6, Sirt7, Keap 1/Nrf 2, and PDCD4	Apoptotic signaling	109
Neck squamous cell carcinoma (HNSCC)	miR-497-5p	P53/YAP/TEAD	Increase the malignant phenotype	110
Non-small cell lung cancer (NSCLC)	miR-125b	E2F2	Promote NSCLC cell growth and invasion	111
Oral squamous cell carcinoma (OSCC)	miR-125b	STAT3	Regulate cell proliferation	112
Osteosarcoma (OS)	miR-137	TRIAP1	Boosted doxorubicin (DXR) resistance	113
Senescence	let-7	IGF2BP1, KRAS and HMGA2	Silencing promotes cell senescence and reverses the proliferative phenotype	98
Steroid-induced osteonecrosis of the femoral head (SIONFH)	miR-21-5p	SMAD7/TGFβ signaling pathway	Attenuate the apoptosis and cell viability inhibition	114
T cell acute lymphoblastic leukemia (T-ALL)	miR-30e	DLL4-NOTCH signaling	Knockdown inhibits the cell proliferation and increase the cell apoptosis	115

The role of SNPs at PVT1

The role of single nucleotide polymorphisms (SNP) at PVT1 associated with diseases was also explored. A pooling-based genome-wide SNP association study identified PVT1 as a candidate gene for end-stage renal disease (ESRD) in type 2 diabetes and found rs2720709 at PVT1 might contribute to ESRD susceptibility in diabetes.¹¹⁶ Similarly, SNP was also found to be associated with diabetic nephropathy.¹¹⁷ Zhou S et al¹¹⁸ found that the combined SNP actions in mir-146a rs2910164 and PVT1 rs13281615 impacted the function of lung in chronic obstructive pulmonary disease (COPD) smokers. An analysis of breast cancer susceptibility loci potential targets by capture Hi-C identified more than 70 variants correlated with risk of breast cancer, including the risk loci targeting PVT1.¹¹⁹ An intronic variant in PVT1 rs10505506 was associated with chest radiotherapy-induced breast cancer risk after Hodgkin lymphoma (HL) in female.¹²⁰ In addition, the risk allele (G) of SNP rs13281615 was observed to function in breast cancer via affecting the expression of PVT1.¹²¹ Moreover, the GG genotype of rs378854 was identified as a new risk variant for prostate cancer by increasing the expression of PVT1, but not MYC.¹²² SNP array data obtained from 52 ovarian tumors showed that PVT1, but not MYC, was significantly upregulated when compared with normal ovary, as well as tumors lacking copy number alterations.¹²³ A genome-wide association study (GWAS) showed that PVT1 rs2114358∗A was associated with event-free phenotype during an at least two-year GA treatment.¹²⁴ A GWAS on kidney transplants in 532 African American (AA) deceased donors (DDs) found that several SNPs in PVT1 affected renal allograft survival following transplantation independently or via interaction with apolipoprotein L1 gene (APOL1).¹²⁵ Moreover, the SNP-SNP interactions in region of CASC11-MYC-PVT1 have a more significant influence than individual effects of SNP on risk of prostate cancer in AA men.¹²⁶ These studies consistently point to an important role of PVT1 in diseases.

Conclusions and perspectives

PVT1 has been demonstrated as the most potent long noncoding RNA with oncogenic functions. Recent studies have been performed on all aspects of PVT1, including its potential oncogenic roles, molecular alteration, biogenesis, as well as its bioactivities including regulating protein interactions, modulating miRNA expression, forming fusion genes, targeting regulatory genes, interacting with MYC and its circular transcripts—circPVT1, functioning as a ceRNA, among others. In this review, we summarized recent progress in PVT1 functions and metabolism. We speculate that the modes of action of PVT1 may also be applied to many other lncRNAs such as HOTAIR, H19, NEAT, MALAT1, HOTTIP, among others; thus, our summary of PVT1 may provide hints for studies of other lncRNAs.

Another research hotspot is the therapeutic potential of lncRNAs. A comprehensive inquiry on 9972 cancer cases of 21 types has demonstrated that PVT1 may act as a potential human cancer biomarker correlated with cancer prognosis and progression.¹²⁷ Besides its critical roles in diagnostic and prognostic process, PVT1 also has potential therapeutic roles. PVT1 can act either as a biomarker to make the existing cancer therapeutics more effective or as a potential target for designing novel therapeutic candidates. However, there will be a long way to go to be able to fully exploit PVT1 for cancer therapy and prognostication, which will be the next focus and research direction.

Conflict of interests

The authors declare that they have no conflict of interests.

Appendix A. Supplementary data

The following are the Supplementary data to this article: