Emerging role of long non-coding RNAs in normal and malignant hematopoiesis

Abstract

Long noncoding RNAs (lncRNAs) have recently been discovered and are increasingly recognized as vital components of modern molecular biology. Accumulating evidence shows that lncRNAs have emerged as important mediators in diverse biological processes such as cell differentiation, pluripotency, and tumorigenesis, while the function of lncRNAs in the field of normal and malignant hematopoiesis remains to be further elucidated. Here, we widely reviewed recent advances and summarize the characteristics and basic mechanisms of lncRNAs and keep abreast of developments of lncRNAs within the field of normal and malignant hematopoiesis. Based on gene regulatory networks at different levels of lncRNAs participation, lncRNAs have been shown to regulate gene expression from epigenetics, transcription and post transcription. The expression of lncRNAs is highly cell-specific and critical for the development and activation of hematopoiesis. Moreover, we also summarized the role of lncRNAs involved in hematological malignancies in recent years. LncRNAs have been found to play an emerging role in normal and malignant hematopoiesis, which may provide novel ideas for the diagnosis and therapeutic targets of hematological diseases in the foreseeable future.

Introduction

With the development of the genome-wide transcriptome studies, pervasive researches are currently focusing on non-protein-coding regulatory RNAs (ncRNAs), which were regarded as junk or noises of transcripts previously.^[1] The concept that non-coding RNAs do play crucial roles in regulating gene expression at the levels of transcription, RNA processing, and translation has been recognized for several years.^[2–4] According to the transcript size, ncRNAs are generally classified into two major groups: short ncRNAs (<200 nucleotides) or long ncRNAs (>200 nucleotides). MicroRNAs (miRNAs), a typical representative of short ncRNAs, have been best studied and known to induce mRNA degradation or block mRNA translation via the RNA interference pathway^[1,4] and recognized as powerful regulators of numerous genes and pathways in the pathogenesis of hematological diseases.^[5–8] In contrast, abundant long non-coding RNAs (lncRNAs) have recently been discovered and are increasingly recognized as vital components of modern molecular biology. Accumulating evidence shows that lncRNAs can modulate diverse biological processes such as cell proliferation, differentiation, pluripotency, apoptosis, and tumorigenesis.^[9–13] The exploration of the characteristics and mechanisms of them is at a relatively initial stage yet, and especially the function of lncRNAs in the field of hematopoiesis remains to be further elucidated. In this review, we will succinctly summarize the characteristics and mechanisms of lncRNAs and focus on the latest progress of lncRNAs in normal and malignant hematopoiesis.

Characteristics and Functions of Long Non-coding RNAs

Long non-coding RNAs are defined as a heterogeneous class of ncRNAs longer than 200 nucleotides which feature distinguishe them from small regulatory RNAs such as miRNAs, small nucleolar RNAs (snoRNAs), piwi-interacting RNAs (piRNAs), short interfering RNAs (siRNAs), and other short RNAs. LncRNAs could be localized to the nucleus or cytoplasm and are most abundant in the nucleus, which is different from mRNAs that are mostly transported to the cytoplasm.^[14,15] According to the NONCODE database (current version v5.0, http://www.noncode.org), which is an integrated knowledge database dedicated to non-coding RNAs and currently recruits the lncRNA information of 17 species, there are 172,216 and 131,697 lncRNA transcripts of human and mouse at present, respectively.

Due to the high heterogeneity of the sequence, structure and biological function of lncRNAs, there are various classification methods so far. Generally, in light of their proximity to protein-coding mRNAs, lncRNAs could be classified into the following categories^[16]: (1) the long intergenic ncRNA (lincRNA), which comes from the region between two genes; (2) intronic lncRNA, which originates from the intron region of secondary transcript (sometimes mRNA precursor sequence); (3) sense lncRNA, which overlaps with one or more exons of another protein-coding gene of the synonymous chain; (4) antisense lncRNA, which overlaps with one or more exons of another protein-coding gene in the opposite strand; and (5) bidirectional lncRNAs, whose transcription start site is very close to the protein gene encoding on the antisense strand, but the direction of transcription is the opposite. Based on the features and special functions of lncRNAs, it also includes lncRNA-activating (lncRNA-a), transcribed pseudogene lncRNAs, telomere-associated ncRNAs (TERRAs), transcribed ultraconserved regions (T-UCRs), enhancer RNAs (eRNAs), circular RNAs, etc.^[17–19]

According to recent advances, the characteristics of lncRNAs can be summarized as follows: Firstly, no different than mRNA, most lncRNAs whose promoter can also bind transcription factors are also polyadenylated, spliced, and modified with 5′-cap and poly-A tail, and also transcribed by RNA polymerase II (RNAPII). They have dynamic expression and different splicing modes during differentiation.^[20,21] Secondly, lncRNAs are relatively conservative in function although they contain fewer longer exons and lower evolutionary sequence conservation compared with mRNAs.^[22,23] Thirdly, most lncRNAs are expressed at relatively lower levels but have more obvious temporal and spatial expression specificity compared with mRNAs in the process of tissue differentiation and development.^[24–26]

Up to now, the precise mechanism of lncRNA is not entirely clear. Nevertheless, based on gene regulatory networks at different levels of lncRNA participation, lncRNAs have been shown to regulate gene expression in three ways: epigenetics, transcription, and post-transcription^[27–29] [Figure 1]. First, lncRNAs can catalyze the synthesis of chromatin remodeling complexes into specific genomic loci. For example, the recruitment of polycomb complex to the HOXD gene cluster by lncRNA HOTAIR and Xist/RepA results in three methylations (me3K27) of histone H3 27th lysine in the X chromosome and induces heterochromatin formation, which finally inhibits gene expression in this region.^[30] Second, lncRNAs may participate in transcriptional regulation of target genes by regulating the transcription of neighboring protein-coding genes, interacting with transcription factors, or forming three-helix complexes with DNA. For instance, lncRNA pncRNA-D (promoter-associated ncRNA-D) can bind to the gene cyclinD1 and recruit RNA binding protein TLS (Translocated in LipoSarcoma) to regulate histone acetyltransferase activity of protein CBP and P300, and then inhibiting the transcription of cyclin D1.^[31] Third, lncRNAs may affect any step in post-transcriptional gene expression including regulating alternative splicing of mRNA precursor, being spliced into non-coding small RNA, regulating mRNA stability and abundance, or the role of competitive endogenous RNA (ceRNA).^[32–34]

Figure 1.

Schematic diagram of the basic regulatory mechanism of lncRNAs. The purple ones are lncRNAs. lncRNAs: Long non-coding RNAs.

Long Non-coding RNAs in Normal Hematopoiesis

Hematopoietic stem cells (HSCs) are characterized by the ability to execute a cascade of cell fates, including self-renewal, controlled expansion of progenitor cells, and timely differentiation into terminally mature blood cells.^[35] The process of differentiation of hematopoietic lineages is critically driven by the interaction of external stimuli and intracellular regulatory programs. Lineage-specific lncRNA molecules are also emerging as important regulators of gene expression during hematopoiesis [Table 1 and Figure 2].

Table 1.

Long non-coding RNAs involved in the normal hematopoiesis.

Figure 2.

Schematic diagram of lncRNA regulating normal hematopoietic differentiation. The purple ones are the name of lncRNAs. lncRNAs: Long non-coding RNAs; Th1: Type 1 helper T cells; Th2: Type 2 helper T cells; Th17: Type 17 helper T cells; Treg: Regulatory T cells; lincRNA-EPS: lincRNA erythroid prosurvival; Fas-AS1 (or Saf): Fas-antisense 1; HOTAIRM1: HOX antisense intergenic RNA myeloid 1; EGO: Eosinophil granule ontogeny; NeST (Tmevpg1 or IFNG-AS1): Nettoie Salmonella pas Theiler's; cleanup Salmonella not Theiler's; GATA3-AS1: GATA3-antisense 1; TH2-LCR: TH2-locus control region; Flicr: Foxp3 long intergenic non-coding RNA; Inc-EGFR: Lnc-epidermal growth factor receptor; lncRNA-CSR: LncRNA-class switch DNA recombination; CRNDE: Colorectal neoplasia differentially expressed.

LncRNAs in Erythropoiesis

Erythropoiesis is a developmental process that is critically controlled by multiple regulators to ensure the proper generation of mature red blood cells and the transportation of oxygen to tissues.^[36] Inspired by the “chromatin-state maps” approach pioneered by Guttman et al^[59] less than a decade ago, the Biomedical Research group of Cambridge identified the first erythroid-specific lncRNA lincRNA erythroid prosurvival (lincRNA-EPS), which could facilitate erythropoiesis by repressing the expression of Pycard, a proapoptotic gene, without altering erythroid differentiation.^[36,37] Subsequent studies also discovered multiple lncRNAs that are dynamically expressed during erythropoiesis and are targeted by key erythroid transcription factors such as GATA1, TAL1, or KLF1.^[60]AlncRNA-EC7 was one of the identified lncRNAs. Reduction of alncRNA-EC7 expression in erythroblasts induced BAND3 (a major anion exchange protein present on erythrocyte membranes^[61]) gene expression via chromatin interactions between the alncRNA-EC7 locus and the neighboring region of the BAND3 promoter leading to impaired erythrocyte maturation.^[36,38] Recently, a research group also released their findings that lncRNA Fas-antisense 1 (Fas-AS1 or Saf) was induced during differentiation through the activity of essential erythroid transcription factors GATA-1 and KLF1. They further discovered that Saf was also negatively regulated by NF-κB and that over-expression of Saf in erythroblasts derived from CD34⁺ hematopoietic stem/progenitor cells of healthy donors could reduce surface levels of Fas and consequently conferred protection against Fas-mediated cell death signals.^[39,40] Although current studies of lncRNAs in erythropoiesis are largely done in the murine models, these advances expand the repertoire of lncRNA functions and provide a novel genetic pathway that can be exploited with effective targets for the treatment of various anemia-related diseases in the future.^[36]

LncRNAs in Myeloid Hematopoiesis

Almost a decade ago, Zhang et al^[62] unveiled the first myeloid lineage-specific lncRNA HOTAIRM1 (HOX antisense intergenic RNA myeloid 1) which is transcribed between the human HOXA1 and HOXA2 genes. In-depth research revealed that HOTAIRM1 contributed to three-dimensional conformational changes of chromosomes which were required for the temporal collinear activation of HOXA genes.^[41] Functional studies showed that knockdown of HOTAIRM1 could quantitatively impaire all-trans retinoic acid (ATRA)-induced myeloid differentiation and selectively attenuated differentiation-related transcripts such as CD11b, CD18, HOXA1, and HOXA4.^[62] Subsequent studies showed that the master transcription factor PU.1 during myeloid differentiation could directly activate the expression of HOTAIRM1 through binding to the regulatory region of HOTAIRM1.^[41] A recent study revealed that the high expression of HOTAIRM1 could enhance ATRA-induced PML-RARA degradation by affecting autophagic flux.^[42] Conclusively, these advances indicate that HOTAIRM1 may be a novel potential therapeutic target for acute promyelocytic leukemia (APL).

The lncRNA EGO (eosinophil granule ontogeny) is a novel, nested, non-coding RNA, expressed during eosinophil development from CD34⁺ human HSCs and mature eosinophils. RNA silencing assays investigated that EGO regulated granule protein MBP (major basic protein) and EDN (eosinophil derived neurotoxin) transcript expression in developing CD34 hematopoietic progenitors.^[43]

Lymphoid Differentiation-related lncRNAs

CD4⁺ T cells play central roles in mediating adaptive immunity against various pathogens. With T-cell receptor activation by specific cytokines, naive CD4⁺ T cells may differentiate into one of several lineages of T helper (Th) cells, including Th1, Th2, Th17, and inducible regulatory T cell (iTreg), as defined by their pattern of cytokine production and function.^[63] The diversity of CD4⁺ T-cell subsets enables the adaptive immune system to adapt to many challenges during the expression of genes encoding cytokines and transcription factors.^[64]NeST (Nettoie Salmonella pas Theiler's; cleanup Salmonella not Theiler's), formally known as Tmevpg1 or IFNG-AS1, is a long non-coding RNA specifically expressed in Th1 cells by a T-bet (a Th1-specific key transcription factor) dependent mechanism. NeST RNA was found to bind WDR5, a component of the histone H3 lysine 4 methyltransferase complex and to alter histone 3 methylation at the interferon-gamma locus, ultimately leading to the regulation of the expression of IFN-γ.^[44,45] Another Th1-specific lncRNA is linc-MAF-4 whose expression is negatively correlated with MAF, a Th2-associated transcription factor. Studies suggest that linc-MAF-4 could regulate MAF transcription by recruiting chromatin modifiers and that down-regulation of linc-MAF-4 could skew T-cell differentiation toward the Th2 phenotype.^[46]

Hu et al^[47,48] identified 1524 lincRNA clusters from early T-cell progenitors to terminally differentiated T-helper subsets, among which lincR-Ccr2-5′AS, regulated by GATA-3 (a zinc-finger transcription factor, highly expressed in Th2 cells and critical to Th2 differentiation by regulating Th2 gene expression), was considered to be an essential part of the regulation in Th2-specific gene expression and important for Th2 cell migration. In the same year, another research group also reported a GATA-3-associated lncRNA GATA3-AS1 which was specifically expressed in primary Th2 cells. Their results indicate that the expression of GATA3-AS1 and GATA3 might be co-regulated by the same regulatory elements and might have shared functions in Th2 cell responses.^[49] By whole-genome sequencing (RNA-seq), Spurlock et al^[50] identified a cluster of antisense lncRNAs TH2-LCR, which was transcribed from the RAD50 locus that is co-expressed with IL4, IL5, and IL13 genes under Th2 polarizing conditions. Their analyses demonstrated that TH2-LCR is significantly required for the expression of genes encoding Th2 cytokines.

The differentiation of Th17 cells requires the nuclear hormone receptor RORγt which focuses on the activity of a cytokine-regulated transcriptional network including genes encoding the signature Th17 cytokines (IL-17A, IL-17F, IL-22).^[65] Huang and colleagues identified the lncRNA Rmrp, RNA component of mitochondria RNA-processing endoribonuclease (RNase MRP), as a key DDX5 (DEAD-box protein 5, an RNA helicase possessing an important role in gene expression)-associated RNA, which could regulate the function of RORγt transcriptional complexes at a subset of critical genes implicated specifically in the Th17 effector program.^[51,52]

Regulatory T cells (Tregs) characterized by the transcription factor FoxP3 are a fundamental component in maintaining immune homeostasis by negatively regulating several immunocyte lineages, especially during autoimmune, tumor, and lymphoproliferative pathologies.^[66] A recent study identified a lncRNA Flicr whose expression profile and genomic localization displayed Treg specificity, partially overlapping Foxp3. Further assays revealed that Flicr dampens the Treg signature and may lower Treg stability, allowing stronger antiviral responses by destabilizing Foxp3.^[53] Another novel Treg-related lncRNA is lnc-EGFR (lnc-epidermal growth factor receptor), whose up-regulation positively correlates with the expression of EGFR/Foxp3. Mechanism research shows that lnc-EGFR is a potential enhancer of EGFR and its downstream AP-1/NF-AT1 axis, and could augment immunosuppression by promoting Treg cell differentiation which may offer a potential therapeutic target for certain carcinomas.^[54]

Wang et al^[55,56] revealed that the expression of CD244, a T-cell-inhibitory molecule in CD8⁺ T-cell immune responses during tuberculosis (TB) infection, correlated with high levels of a lncRNA lncRNA-CD244. Functional assays demonstrated that lncRNA-CD244 could mediate IFN-γ and TNF-α expression and improve the protective immunity of CD8⁺ T cells by interacting with EZH2 (enhancer of zeste homolog 2, a chromatin-modification enzyme).^[56]

B cells develop from the common lymphoid progenitor cells in the bone marrow and the initial antigen-independent phase is characterized by immunoglobulin gene rearrangements.^[67] As the central drivers of immune humoral response, B cells development and function are influenced by a series of gene regulation.^[68] Using RNA-seq and de novo transcript assembly, researchers have identified several lncRNAs involved in the development, activation, proliferation, and differentiation of B cells, such as lncRNA-CSR and CRNDE.^[57,58,69]

Long Non-coding RNAs in Malignant Hematopoiesis

In addition to the normal hematopoietic process regulated by a variety of lncRNAs, abnormal interference of lncRNA regulation also inevitably leads to hematopoietic dysfunction, mainly in the occurrence of leukemia, lymphoma, and myeloma. At present, several lncRNAs related to hematological malignancies have been identified and summarized in the following sections [Table 2 and Figure 3].

Table 2.

Long non-coding RNAs involved in the malignant hematopoiesis.

Figure 3.

The relationship between lncRNA and its targets on the hematological diseases. The inner red part of the circle is the name of hematologic disease. The middle blue part of the circle is the name of lncRNAs. The outer yellow part of the circle is the target of hematologic disease regulated by lncRNAs. lncRNAs: Long non-coding RNAs; APL: Acute promyelocytic leukemia; AML: Acute myeloid leukemia; CML: Chronic myeloid leukemia; B-ALL: B-cell acute lymphocytic leukemia; CLL: Chronic leukemia; DLBCL: Diffuse large B-cell lymphoma; NHL: Non-Hodgkin lymphoma; HL: Hodgkin lymphoma; MM: Multiple myeloma; MDS: Myelodysplastic syndromes; AA: Aplastic anemia; NEAT1: Nuclear paraspeckle assembly transcript 1; RUNXOR: RUNX1 overlapping RNA; PLIN2: Perilipin 2; lncRNA-BGL3: LncRNA-BetaGlobinLocus 3; HOTAIR: Hox transcript antisense RNA; HULC: Highly up-regulated in liver cancer; UCA1: Urothelial carcinoma-associated 1; LUNAR1: LeUkemia-induced non-coding activator RNA; BALR-2: B-ALL-associated long RNA-2; CRNDE: Colorectal neoplasia differentially expressed; MIAT: Myocardial infarction-associated transcript; MINCR: MYC-induced lncRNA; PANDA: P21-associated ncRNA DNA damage activated; MEG3: Maternally expressed gene 3; MALAT1: Metastasis-associated lung adenocarcinoma transcript 1; RUNX1: Runt-related transcription factor 1; IGF1R: Insulin-like growth factor-1 receptor; HDAC: Histone deacetylase; CEBPA: CCAAT/enhancer-binding protein-α; GSK-3: Glycogen synthase kinase-3; PTEN: Gene of phosphate and tension homology deleted on chromosome 10; EZH2: Enhancer of zeste homolog 2; MAPK/ERK: Mitogen-activated protein kinase/extracellular regulated protein kinases; BMP4: Bone morphogenetic protein 4; LTBP3: Latent-transforming growth factor beta-binding protein 3; FGF1: Fibroblast growth factor 1.

AML-related lncRNAs

The expression of nuclear paraspeckle assembly transcript 1 (NEAT1), a novel lncRNA localized specifically to nuclear paraspeckles, has a vital regulatory role in many human malignancies^[70,99] and was indicated to be repressed by PML-RARα in de novo APL samples. Furthermore, significant NEAT1 up-regulation was observed during (ATRA)-induced NB4-cell differentiation.^[71]

Another group performed transcriptome-wide lncRNA expression profiling of acute myeloid leukemia (AML) and identified that lncRNAs up-regulated in AML are associated with a lower degree of DNA methylation and a higher ratio of being bound by transcription factors such as SP1, STAT4, ATF-2, and ELK-1 compared with those down-regulated in AML. Moreover, they found that a novel lncRNA LOC285758 is associated with the poor prognosis in patients with AML and regulates the proliferation of AML cell lines by enhancing the expression of HDAC2 (histone deacetylase 2), a potential therapeutic target in AML blasts.^[74,75]

Accumulating evidence has shown that the insulin-like growth factor type I receptor (IGF1R) is one of the most important regulators in the progression and therapeutic resistance of AML.^[100] A novel intragenic lncRNA IRAIN was discovered to directly interact with the IGF1R promoter and enhancer chromatin DNA sequences. Moreover, IRAIN was down-regulated both in leukemia cell lines and high-risk patients with AML.^[73]

Distinctive lncRNA profiles were found associated with common recurrent mutations in AML, such as FLT3-ITD (internal tandem duplications in the FLT3 gene) or NPM1, CEBPA, IDH2, and RUNX1 genes.^[101] Utilizing a novel R3C (RNA-guided chromatin conformation capture) method,^[102] Wang et al^[72] described a RUNX1-intragenic lncRNA RUNXOR (RUNX1 overlapping RNA), which is transcribed by an upstream promoter and overlaps with RUNX1 (one of the most frequently mutated genes in AML^[103]). RUNXOR was up-regulated in both AML samples and Ara-C-treated cell lines. The in-depth study showed that RUNXOR directly interacted with the RUNX1 promoter and enhancer chromatin DNA sequences through its 3′-terminal fragment.

Another lncRNA CCDC26, which is thought to transcriptionally regulate a set of genes and associated with pediatric AML,^[104,105] was also proved to controls growth of myeloid leukemia cells through regulation the expression of KIT,^[76] a receptor tyrosine kinase that have been considered to up-regulated in leukemia stem cells from patients with AML who relapsed after chemotherapy.^[106]

CML-related lncRNAs

A comprehensive analysis of lncRNAs in human chronic myeloid leukemia (CML) cells was performed and a novel lncRNA lncRNA-BGL3 was observed to serve as a key regulator of Bcr-Abl-mediated cellular transformation. Functional assays suggested that lncRNA-BGL3 was highly induced in response to the disruption of Bcr-Abl expression or by inhibiting Bcr-Abl kinase activity in cell lines and patients with CML. Notably, lncRNA-BGL3 may function as a ceRNA that binds a subset of microRNAs to cross-regulate PTEN (phosphatase and tensin homolog, a critical tumor suppressor gene) expression.^[78,79]

Hughes et al^[77] identified more than 900 lncRNAs which are regulated by CEBPA (CCAAT/enhancer-binding protein-α), a critical regulator of myeloid differentiation, and many of them are induced during myeloid differentiation of AML cell lines including lncRNA PLIN2. Another group recently further investigated the potential roles of CEBPA-related lncRNA PLIN2 during CML. Results indicated that both CEBPA and PLIN2 were up-regulated in the process of CML and there was a positive correlation between CEBPA and PLIN2 in patients with CML. Moreover, they found that CEBPA-mediated up-regulation of PLIN2 expression promotes the development of CML via GSK3 and Wnt/β-catenin signaling.^[107]

Recent studies have also reported some newly discovered lncRNAs that are associated with CML. For instance, lncRNA HOTAIR may play a crucial role in the development of multidrug resistance (MDR) to imatinib in CML via a PI3K/Akt-dependent mechanism.^[80] Another lncRNA HULC was also revealed to be positively correlated with imatinib (IM)-induced apoptosis of CML cells and lead to the reduction of c-Myc expression and inhibition of PI3K/Akt pathway activity.^[81]lncRNA UCA1 was identified as another important modulator of multidrug resistance protein-1 (MDR1) which is considered as the main reason for IM resistance in CML cells.^[82]

T-lymphocytic leukemia-related lncRNAs

LUNAR1 (LeUkemia-induced non-coding activator RNA) is a pivotal lncRNA involved in T-cell leukemia (T-ALL), an aggressive hematological neoplasm derived from malignant T-lymphocyte progenitors with aberrant NOTCH1 signaling.^[108] Evidence indicated that LUNAR1 is highly correlated with its coding neighbor gene IGF1R, which has been previously suggested to play a role in T-ALL.^[83,84] Trimarchi et al^[84] have revealed that the expression of LUNAR1 was up-regulated in primary T-ALL samples especially in ones with a Notch mutation, while down-regulated upon Notch inhibition.

B-lymphocytic leukemia-related lncRNAs

Unbiased microarray profiling was performed on human B-ALL samples and indicated that the expression of a subset of lncRNAs, termed BALRs (B-ALL associated long RNAs), corresponds with specific cytogenetic abnormalities in B-ALL. A functional assay suggested that knockdown of BALR-2 (a lncRNA among BALRs) led to apoptosis of B-ALL cell lines alone and up-regulated BALR-2 was correlated with poor patient response to prednisone and worse overall survival.^[85]

By employing methyl-CpG-binding domain protein-enriched genome-wide sequencing (MBD-Seq), Subhash et al^[86] identified 5800 hypermethylated and 12,570 hypomethylated chronic lymphocytic leukemia (CLL)-specific differentially methylated genes (cllDMGs), among which hypermethylated CRNDE and hypomethylated AC012065.7 were two novel lncRNAs validated in CLL samples. Notably, survival analysis revealed that hypermethylation of CRNDE and hypomethylation of AC012065.7 were correlated with poor outcome in patients with CLL. In addition, lncRNA MIAT is another lncRNA whose expression level was considered to be positively correlated with the aggressive CLL forms carrying either 17p-deletion, 11q-deletion, or trisomy 12 over indolent form carrying 13p-deletion.^[87]

Lymphoma and multiple myeloma-related lncRNAs

Viré et al^[88] firstly reported a lncRNA corresponding to an antisense transcript of Fas (FAS-AS1) which could effectively regulate Fas-mediated apoptosis in non-Hodgkin lymphoma (NHL). Results suggested that the FAS-AS1 expression was repressed because of its promotor being hyper-methylated by EZH2 (enhancer of zeste homologue 2), a histone-lysine N-methyltransferase enzyme that participates in histone methylation and leads to transcriptional repression, which is often mutated or over-expressed in lymphomas.^[88] Functional assays indicated that treatment with Bruton's tyrosine kinase (BTK) inhibitor or EZH2 knockdown significantly could decrease the levels of EZH2 and then enhancing Fas-mediated apoptosis, which may provide a novel therapeutic target in lymphomas.^[89]

Burkitt lymphoma is an aggressive hematological neoplasm with a poor prognosis and the deregulation of the oncogenic transcription factor MYC is considered to be the major driving force in lymphoma development.^[109] Doose et al^[90] identified 13 lncRNAs differentially expressed in IG-MYC-positive Burkitt lymphoma, among which a lncRNA named MYC-induced lncRNA (MINCR) showing a strong correlation with MYC expression in MYC-positive lymphomas. MINCR knockdown was associated with a reduction in MYC binding to the promoters of selected cell cycle genes. These findings suggested novel therapeutic opportunities for the fight against not only malignant lymphoma but possibly, all cancers that rely on MYC expression.

The long non-coding RNA PANDA (P21-associated ncRNA DNA damage activated), which is induced in a p53-dependent manner and interacts with the transcription factor NF-YA to limit expression of pro-apoptotic genes,^[91] was recently reported to be down-regulated in patients with diffuse large B-cell lymphoma (DLBCL) and functioned as a tumor suppressor gene through silencing MAPK/ERK signaling pathway.^[92]

A differential expression profiling between Hodgkin lymphoma (HL) and normal germinal center (GC)-B cells was performed and selected two lncRNAs (LINC00116 and LINC00461) which was over-expression in HL, DLBCL and lymphoblastoid cell lines, and another lncRNA (FLJ42351) which has a remarkable Reed-Sernberg (RS) cell-specific expression in HL and part of Burkitt lymphoma cell lines.^[93]

Multiple myeloma (MM) is another large class of hematological malignancy characterized by the impaired osteogenic differentiation of mesenchymal stromal cells (MSCs). Zhuang et al^[110] revealed that lncRNA maternally expressed gene 3 (MEG3, a tumor suppressor) played an essential role in osteogenic differentiation in bone marrow MSCs, partly by activating transcription of BMP4, a member of the transforming growth factor (TGF) family and participate in embryonic development, hematopoietic development, and mesenchymal development.^[94,110] Functional assays indicated that MEG3 knockdown significantly reduced the expression of key osteogenic markers, including Runt-related transcription factor 2, osterix, and osteocalcin.^[110]

Furthermore, another research group also reported an MM-related lncRNA MALAT1 (metastasis-associated lung adenocarcinoma transcript 1), which have been widely considered to play a role in the development of numerous cancers,^[111,112] could initiate the activation of the key transcription factor Sp1 on Latent TGF-binding proteins (LTBP3, an important regulator for efficient secretion, folding, and activation of TGF-s and regulates the bioavailability of TGF- especially in the bone^[113]) promoter in MSCs from MM.^[95]

Myelodysplastic syndromes and aplastic anemia-related lncRNAs

Myelodysplastic syndromes (MDSs) are a group of myeloid clonal diseases with a high risk of transformation to AML.^[114] Up to now, the molecular pathogenesis of MDS remains to be explored. Liu et al^[96] have developed a network-based lncRNA co-module function annotation method, which integrated correlations between lncRNA, protein-coding genes and non-coding miRNAs, and generated lncRNA expression profiles from the HSCs from patients with MDS and healthy donors. Linc-RPIA was identified to potentially bind miR-429, which act as tumor-suppressor, and may be involved in the regulation of tumor-related genes, including FOXO1 and TP53.^[96] A recent study revealed HOXB-AS3, a lncRNA located at the human HOXB cluster, maybe a potential risk factor in myeloid neoplasm especially MDS.^[97] They demonstrated that high expression of HOXB-AS3 could promote myeloid cell proliferation which was consistent with previous researches.^[101,115] Furthermore, clinical correlation analysis also showed that HOXB-AS3 was an adverse prognostic marker in patients with low IPSS index, compared with higher risk ones.^[97]

Aplastic anemia (AA) is a group of hematopoietic failure syndrome caused by multiple factors.^[116] At present, the underlying molecular mechanisms of AA are largely unknown. In a research of bone marrow mesenchymal stem cells (BMSCs) differentiation from AA patients, Jiang et al^[98] found fibroblast growth factor 1 (FGF1) could regulate the expression of lncRNA TDRG1 through promoting acetylation in the TDRG1 promoter, thus enhancing the proliferation of BMSCs. This finding is a novel insight into the treatment of aplastic anemia patients. However, more research is needed to deepen the explanation of the relationship between lncRNA and AA.

Conclusion and Future Perspectives

To date, there is a large body of evidence to suggest that long non-coding RNAs are becoming fundamental regulators in diverse biological processes including cell proliferation, differentiation, pluripotency, apoptosis, and tumorigenesis and are increasingly recognized as vital components of modern molecular biology. With the publication of various studies in succession, the role of lncRNAs in hematopoiesis shows up prominently. Here we widely reviewed recent advances and summarize the characteristics and basic mechanisms of lncRNAs and keep abreast of developments of lncRNAs within the field of normal and malignant hematopoiesis. Based on gene regulatory networks at different levels of lncRNAs participation, lncRNAs have been shown to regulate gene expression from epigenetics, transcription, and post-transcription. The expression of lncRNAs is highly cell-specific and critical for the development and activation of hematopoiesis. Moreover, we also summarized the role of lncRNAs involved in hematological malignancies in recent years. With the advent of the post-genome era, there must be many additional hematopoiesis-related lncRNAs to be discovered and the underlying precise mechanisms also need to be further excavated. We believe that lncRNAs may provide novel ideas for the diagnosis and therapeutic targets of hematological diseases in the foreseeable future.

Funding

This study was supported by a grant from the Beijing Natural Science Foundation (No. 7162175).

Conflicts of interest

None.