Long noncoding RNA and bone sarcoma

Introduction

Epigenetics encompasses the molecular changes that affect gene expression without direct alteration of the primary DNA sequence. Examples include DNA methylation, chromatin modification, nucleosome positioning, and dysregulation of noncoding RNAs (ncRNAs) [ ]. Historically, the majority of genetic studies have focused on protein-coding RNAs even though ncRNAs make up 98% of all human transcripts [ ]. These ncRNAs, which can be nonfunctional, can also serve as important epigenetic regulators [ ]. These ncRNAs are classified into three structural groups: small noncoding RNAs (sncRNAs), circular RNAs (circRNAs), and long noncoding RNAs (lncRNAs). The sncRNAs are less than 200 nucleotides, and include subtypes such as microRNAs (miRNAs), PIWI-associated RNAs (piRNAs), and transcription initiation RNAs (tiRNAs) [ , ]. Unlike the more common linear RNA variants, cirRNAs are loops of RNA generated by back-splicing, whereby the 3′ and 5′ ends of a linear RNA strand are covalently connected, and thus form an uninterrupted RNA “circle” [ ]. By definition, lncRNAs are greater than 200 nucleotides in length and will be the focus herein. Interestingly, although they are noncoding, some lncRNAs undergo the posttranscriptional modifications such as splicing, polyadenylation, and capping attributed to coding mRNA processing. lncRNAs are relatively common as they account for over 68% of all ncRNAs, and serve diverse modulatory functions through chromatin modification, transcription, mRNA stabilization, or direct action with other RNA species [ ]. With the development of whole-genome sequencing technology, lncRNAs have gained notoriety for their roles in cancer [ ]. Among the various malignancies they promote, sarcomas are clearly implicated [ ].

Bone sarcomas are rare malignancies originating from mesenchymal cells that often present within long bones of the extremity, pelvis, or vertebra. In 2019 there were approximately 3500 patients in the United States newly diagnosed with primary bone sarcomas, representing less than 0.2% of all new cancers [ ]. Total deaths were estimated at 1660 cases per year, which is 0.3% of cancer-related mortality [ ]. Although they are in fact infrequent, they cause considerable mortality and morbidity for inflicted patients as available treatments often fail to address poorly localized variants. Osteosarcoma is the most common bone sarcoma, followed by Ewing's sarcoma, chondrosarcoma, and chordoma [ ], all of which will be addressed in this chapter. And while the standard treatment protocol for osteosarcoma and Ewing's sarcoma is quite aggressive, consisting of perioperative chemotherapy or radiation and extensive surgical resection, outcomes have not significantly improved for decades. According to the Surveillance, Epidemiology, and End Results (SEER) database, the 5-year overall survival rate for patients with bone sarcoma is 66.2%, and for those with metastatic disease the 5-year overall survival rate drops to 10%–30% [ ]. In patients with chondrosarcoma or chordoma, even worse outcomes are common as they are especially resistant to available chemotherapy and radiotherapy. In response, there has been an expansion of genetic and molecular biology works focused on novel targets in bone sarcoma therapy. In this chapter, we summarize the expression and function of bone sarcoma–related lncRNAs and their clinical applications.

Biogenesis, classification, and function of lncRNA

As shown in Fig. 34.1 , lncRNAs are classified according to their proximity to genomic protein-coding regions: (1) sense, (2) antisense, (3) intronic, (4) intergenic, and (5) bidirectional [ , , ]. Sense and antisense lncRNAs overlap at least one exon of another transcript on a consecutive strand [ , , ]. Intronic lncRNAs are transcribed from an intron without exon overlapping. Intergenic lncRNAs are transcribed from the genomic interval between two coding genes from either strand [ , , ]. Bidirectional lncRNAs are transcribed along with the complementary strand of a neighboring coding transcript in close genomic proximity [ , ]. As an additional measure of categorization, lncRNAs are known to have five possible origins: (1) a protein-coding gene is damaged and transformed into lncRNA, (2) a chromosomal rearrangement where two nontranscribed regions are juxtaposed and give rise to a multi-exon lncRNA, (3) duplication of a noncoding gene by retrotransposition creates either a functional gene or nonfunctional retropseudogene without protein-coding capacity, (4) two local, tandem duplication events generate neighboring repeats within noncoding RNA, and (5) insertion of a transposable sequence produces a functional noncoding RNA ( Fig. 34.2 ) [ ].

Whatever their origin, lncRNA may show abnormal expression in cancerous tissues and promote a deadly phenotype via several mechanisms. Within the nucleus, lncRNAs regulate transcription by acting as enhancer RNA, recruiting chromatin modifying complexes, or by integrating with transcriptional factors [ , ]. Alternatively, they can directly modify the spatial conformation of chromosomes or pre-mRNA splicing ( Fig. 34.3 ) [ , ]. Within the cytoplasm, lncRNAs regulate mRNA stability, translation, or compete with miRNA-binding sites [ ]. With direct protein binding, they affect DNA methylation, histone methylation, acetylation, ubiquitination, and organelle formation [ , ]. Emerging research has made clear that lncRNAs have robust oncogenic or tumor-suppression roles, and through their large-scale regulatory processes stimulate tumorigenesis, proliferation, metastasis, and chemotherapeutic resistance in cancers such as bone sarcomas [ , , ].

Expression and function of lncRNAs in osteosarcoma

Despite wide surgical resection and aggressive perioperative chemotherapy, the 5-year overall survival rate has plateaued at 70% for past four decades. Highly anticipated cancer immunotherapy works, which have been efficacious in several other malignancies, have shown relatively poor results in osteosarcoma [ ]. Moreover, the tendency for osteosarcoma to undergo pulmonary metastasis, recur, and develop chemotherapeutic resistance remains significant obstacles to therapy [ ]. Given these barriers, there has been an emergence of proposed novel targets and therapeutics that precisely target the aberrancies of osteosarcoma, including works in lncRNAs. In an lncRNA microarray analysis, 25,733 lncRNAs were compared between nine human primary osteosarcoma tissues and their paired adjacent normal tissue samples, and researchers found 403 lncRNAs upregulated and 798 downregulated [ ]. Furthermore, a pathway analysis concluded the differential expression was a result of known signaling pathways, with 34 pathways upregulated and 32 pathways downregulated [ ]. These findings and others have prompted an emerging and recent body of research outlining the crucial roles of lncRNAs in osteosarcoma growth, proliferation, metastasis, chemotherapeutic resistance, and impact on patient outcomes.