Identification and characterization of functional long noncoding RNAs in cancer

Abstract

Long noncoding RNAs (lncRNAs) have emerged as key regulators in a variety of cellular processes that influence disease states. In particular, many lncRNAs are genetically or epigenetically deregulated in cancer. However, whether lncRNA alterations are passengers acquired during cancer progression or can act as tumorigenic drivers is a topic of ongoing investigation. In this review, we examine the current methodologies underlying the identification of cancer-associated lncRNAs and highlight important considerations for evaluating their biological significance as cancer drivers.

Keywords: GEMMs; cancer; function; identification; lncRNA.

FIGURE 1

Identification and functional characterization of MALAT1. MALAT1 was identified as upregulated in metastatic (M) LUAD (lung adenocarcinoma) compared to nonmetastatic (NM) tissue. Functional characterization of MALAT1 has utilized various loss‐of‐function (LOF) and gain‐of‐function (GOF) models including polyadenylation cassette insertion (Malat1^STOP, ¹³⁴ ), promoter deletion (Malat1^Δ3, ¹³⁵ ), and locus deletion (Malat1^Δ7, ¹³³ ) genetically engineered mouse models (GEMMs), as well as transcript degradation with RNAi and ASO, and transgenic overexpression. Crossing Malat1^Δ3 or Malat1^STOP GEMMs to the MMTV‐PyMT BC (breast cancer) mouse model has resulted in either oncogenic (red box, ⁸² ) or tumor suppressor (green box, ¹³⁷ ) models for Malat1 function, due to observed decreases and increases in lung metastases, respectively.

FIGURE 2

Identification and functional characterization of NEAT1. NEAT1 was initially identified as being upregulated in prostate cancer (PCa) compared to normal (N) tissue, suggesting a potential oncogenic function (top, red box). Later, it was also identified as a p53 target with p53 binding to a conserved p53 Response Element (p53RE) in the NEAT1 promoter, as well as a paraspeckle component induced by cellular stress, suggesting a potential tumor suppressor function (top, green box). Functional characterization of NEAT1 has utilized various loss‐of‐function (LOF) and gain‐of‐function (GOF) models including a polyadenylation cassette insertion genetically engineered mouse model (GEMM), ¹⁴³ transcript degradation with RNAi or ASO, and exogenous overexpression. The Neat1^STOP GEMM has been shown to either decrease ⁹⁷ or increase ⁹⁹ tumor growth following chemical induction of SCC (squamous cell carcinoma) or when crossed to a PDAC (pancreatic ductal adenocarcinoma) GEMM, respectively, suggesting either oncogenic (bottom, red box) or tumor suppressor (bottom, green box) models for Neat1 function in cancer

FIGURE 3

Identification and functional characterization of PVT1. PVT1 was identified in murine lymphomas following the observation of translocations, viral insertions, and amplifications involving the Pvt1 locus. Functional characterization of PVT1 has utilized various loss‐of‐function (LOF) and gain‐of‐function (GOF) models including amplification genetically engineered mouse models (GEMMs) (Myc/Pvt1^AMP, Myc^AMP, ¹⁴⁵ ), locus deletion (PVT1^Δ), tumor‐specific mutagenesis of the Pvt1‐associated p53 Response Element (p53RE) (Δp53RE, ¹⁰³ ), transcript degradation with RNAi and ASO, and CRISPR‐mediated epigenetic activation and inhibition (CRISPRa/i). The increased tumor growth observed in a Myc/Pvt1 co‐amplification GEMM (Myc/Pvt1^AMP) compared to Myc amplification alone (Myc^AMP) when crossed to the MMTV‐Neu BC (breast cancer) GEMM suggests an oncogenic function for Pvt1 (red box, ¹⁴⁵ ). However, the increased tumor growth in Pvt1‐associated p53RE mutagenized lung tumors following Cre‐mediated tumor initiation in a Kras‐driven lung adenocarcinoma (LUAD) GEMM suggests a tumor suppressor function (green box, ¹⁰³ )

FIGURE 4

Identification and functional characterization of THOR THOR was identified as a testis‐specific ultra‐conserved lncRNA aberrantly expressed in cancer tissues. ¹⁶⁵ Hosono and colleagues generated several in vitro and in vivo loss‐of‐function (LOF) and gain‐of‐function (GOF) models to functionally characterize THOR. LOF models included transcript degradation with RNAi and ASO, and THOR partial locus deletion (THOR−/−) in both human cells injected in severe combined immunodeficiency disease (SCID) mice and in a genetically engineered zebrafish model (THOR−/−) embryonically injected with NRAS to induce melanoma. GOF models included THOR overexpression (OE) in vitro and OE of human THOR (hTHOR) in p53‐deficient zebrafish (p53−/−) embryonically injected with NRAS to induce melanoma. Overexpression of THOR plays an oncogenic role (red box) in cancer by binding to IGF2BP1 and increasing the stability of its mRNA targets to promote cancer progression