1. Long Intergenic Noncoding RNAs (LincRNAs)
Several lincRNAs have been recently identified as key players in breast cancer pathogenesis and metastasis.
(A) Linc00337: Linc00337 is located on chromosome 1 and it has been implicated in breast, lung, gastric, colorectal, and esophageal squamous cell carcinoma progression via various mechanisms
[1][2][3][4][5]. Subcellular localization analysis revealed that it is mainly localized in the nucleus being implicated in epigenetic regulation of gene expression
[1][5]. In breast cancer, linc00337 levels are elevated compared to adjacent normal breast tissues
[1]. Moreover, linc00337 silencing decreases the viability and cancer cell proliferation, while Linc00337 overexpression has the opposite effect
[1]. Further in vitro and in vivo analysis revealed that Linc00337 not only enhances the malignant phenotype of breast cancer cells but also promotes chemoresistance to the chemotherapeutic drug paclitaxel
[6] through M2-like macrophages
[1], which are considered to interact with tumor cells and promote tumor development
[7][8][9]. Specifically, Linc00337 was found to upregulate the expression of M2 tumor-associated macrophage markers promoting cell migration and EMT as well as resistance to paclitaxel, a known chemotherapeutic agent used in breast cancer treatment.
(B) Linc00460: Linc00460 is located on the 13 chromosome and is 935 bp in length
[10]. It has recently been reported to be involved in the regulation of the malignant phenotype of multiple cancers including breast, lung, colorectal, prostate, colon, and ovarian cancer and it has been proposed as a potential novel diagnostic and therapeutic target
[11][12][13][14][15][16][17]. Moreover, Linc00460 has been found to serve as a ceRNA targeting a number of tumor suppressor miRNAs and finally leading to oncogenesis
[12]. Specifically in breast cancer, linc00460 was shown to serve as a ceRNA for Fibroblast Growth Factor 7 (FGF-7) mRNA by sponging miR-489-5p leading to upregulation of FGF7 expression and AKT activity and ultimately oncogenesis
[14]. Further to this, high levels of Linc00460 are correlated with shorter overall survival in breast cancer patients
[14] while its silencing prevented tumor growth in in vivo experiments and attenuated the malignant progression of breast cancer cells. Consistent with these finding, Linc00460 overexpression enhanced tumor growth and malignant progression
[14].
(C) Linc00518: Linc00518 is located on human chromosome 6p24.3 and shows relatively low expression in most normal human tissues
[18]. However, it is highly expressed in various types of cancer such as melanoma and breast cancer and it is thought to be involved in cancer progression
[18][19]. Specifically, regarding breast cancer, it was recently shown that overexpression of Linc00518 in MCF-7 breast cancer cells recruited DNMT on caudal type homeobox 2 (CDX2) gene promoter and its methylation decreased the CDX2 expression leading to activation of the Wnt signaling pathway with accompanying upregulation of β-catenin, c-Myc, CyclinD1, Slug, Snail, Twist, and downregulation of E-cadherin
[20], clearly showing promotion of EMT. Linc00518 silencing on the other hand further validated the overexpression findings as it resulted in decreased proliferation, migration, and invasion, enhanced apoptosis and inactivation of Wnt signaling pathway, indicating reduced tendency to EMT
[20]. Moreover, Linc00518 silencing enhanced the antitumor effect of the chemotherapeutic agent doxorubicin and promoted cancer cell apoptosis, suggesting that Linc00518 increases resistance to chemotherapy
[19].
These findings were verified in vivo in nude mice injected with MCF-7 cells that had been previously transfected with short hairpin RNA (shRNA-Linc00518). Tumors grown from these cells displayed reduced growth and metastasis rates, suggesting that Linc00518 by itself promotes tumorigenesis and metastasis. Finally, Linc00518 serves as molecular sponge of miR-199a and inhibits multidrug resistance-associated protein (MRP1) expression which increases the sensitivity of breast cancer cells to doxorubicin and paclitaxel
[19].
(D) Linc00641: LINC00641 is a novel lncRNA located on chromosome 14, locus 14q11.2
[21]. Recent studies have demonstrated that Linc00641 can serve as a ceRNA via sponging specific miRNAs thus inhibiting the malignant progression of many cancer types including breast, glioma, bladder, lung, and cervical cancer
[22][23][24][25][26]. In breast cancer, Linc00641 was shown to interact and inhibit miR-194-5p, whose expression is higher in breast cancer tissues compared to normal and is thought to promote breast cancer growth and metastasis by modulating the Wnt/β-catenin signaling cascade acting as oncogene
[27]. The use of bioinformatic databases such as TANRIC and GEPIA also revealed that Linc00461 levels are diminished in human breast cancer tissues compared to normal-adjacent tissues
[24] and are negatively correlated to tumor size, lymph node metastasis, and clinical stages showing that Linc00641 functions as tumor suppressor in breast cancer. In fact, in vitro overexpression of Linc00641 showed inhibition of breast cancer proliferation by preventing transition to the G1/S phase of the cell cycle, inhibition of migration and invasion in many cancer types, and induction of apoptosis. Moreover, in vivo studies revealed that Linc00641 overexpression notably reduces the tumor growth and the metastasis of breast cancer cells
[24].
(E) Linc00894: Linc00894 is a lncRNA derived from X chromosome and it was found to be upregulated in breast cancer tissues compared to adjacent normal ones as well as in the AU565 aggressive breast cancer cell line compared to the less aggressive MCF-7 cells
[28]. Additionally, Linc00894 silencing resulted in reduced proliferation of breast cancer cells, and reduced invasion capacity while its overexpression had the exact opposite results enhancing the metastatic properties of breast cancer cells. These results were also validated in vivo using the xenograft model in mice
[28]. Specifically, elimination of Linc00894 reduced the volume and the weight of breast tumors and also impaired lung metastasis compared to control tumors
[28]. In addition, breast cancer patients with high Linc00894 expression had shorter overall survival compared to those with low expression indicating that Linc00894 promotes cancer progression
[28]. Again, Linc00894, similarly to Linc02163 and Linc01977 functions at the post-transcriptional level as a ceRNA. In fact, miR-429 was shown via bioinformatic analysis to be regulated by Linc00894. In brief, Linc00894 was found to competitively bind to miR-429 and regulate the expression of transcriptional factor zinc finger E-box binding homeobox 1 (ZEB1) which leads to breast cancer progression
[28].
(F) Linc00922: Linc00922 is located on chromosome 16 and was recently implicated in cancer initiation and progression of breast, ovarian, lung, and liver cancer
[29][30][31][32][33]. Wang et al., in 2021 investigated in detail the role of Linc00922 in breast cancer progression
[30]. Using the microarray dataset GSE26910 and the GEO database they revealed that Linc00922 expression is elevated in breast cancer tissues compared to its adjacent counterparts. Furthermore, they observed that ectopic expression of Linc00922 activated the Wnt signaling pathway that is known to be activated in breast cancer and is correlated with poor prognosis in breast cancer patients promoting EMT, cell proliferation, migration, and invasion, as well as tumor growth and metastasis in vivo
[34]. Fluorescent in situ hybridization (FISH) analysis revealed that Linc00922 is mainly localized in the nucleus of MCF-7 breast cancer cells where it acts as an oncogene recruiting three different DNMTS; DNMT1, DNMT3A, and DNMT3B in the promoter region of NKD inhibitor of Wnt signaling pathway 2 (NKD2), thus epigenetically regulating NKD2 expression. This is indeed critical, as NKD2 is often methylated and poorly expressed in breast cancer while it also antagonizes the Wnt signaling pathway, suppressing tumor growth and metastasis
[35][36][37].
(G) Linc01087: LINC01087 is another newly discovered lncRNA which is located on 2q21.1 chromosome and has been shown to play a crucial role in glioma and breast cancer
[38][39]. Contrary to all previously-discussed lincRNAs, RNA-sequencing data from breast cancer patients revealed that Linc01087 is significantly downregulated in patients with triple negative breast cancer (TNBC), who have worse prognosis and high risk of recurrence and metastasis, compared to samples from cancer-free women while it is upregulated in patients with luminal breast cancer, who usually have better prognosis
[40][41]. In addition, Kaplan–Meier plotter analysis showed that TNBC patients with low Linc011087 levels displayed positive lymph node status but patients with luminal breast cancer and high Linc01087 expression had extended relapse free survival (RFS)
[42]. Thus, it is obvious that the low levels of Linc01087 are associated with disease progression of BC patients while high levels seem to have a protective effect.
(H) Linc01119: Linc01119 is located on chromosome 2, locus 2p21 and has been implicated in the initiation and progression of colorectal and breast cancer
[43][44]. A recent study specifically showed that inhibition of Linc01119 using specific inhibitor led to significant reduction in the cell growth of Hs578T, MDA-MB-468, and CAL51 TNBC cell lines in vitro as well as reduction of tumor growth in vivo
[43]. Moreover, Linc01119 was found to stimulate the expression of the suppressor of cytokine signaling 5 (SOCS5) which inhibits the Janus activated kinase (JAK1/2) and the phosphorylation of signal transducer and activator of transcription (STAT1/3) pathway, thus promoting breast cancer cell growth in vitro and tumorigenesis in vivo
[43][44][45][46]. Additionally, Kaplan–Meier plot analysis revealed an association between high Linc01119 and SOCS5 expression levels and shorter RFS in breast cancer patients
[43].
(I) Linc01977: Linc01977 is also a newly described lncRNA located on chromosome 17, locus 17q25.3, has a length of 1799bp and was recently proposed as a prognostic marker for lung and breast cancer
[47][48]. Moreover, Linc01977 silencing in MDA-MB-231 and MCF-7 breast cancer cells impaired breast cancer cell growth and motility and also rendered cells more sensitive to the chemotherapeutic drug doxorubicin (DOX)
[48]. Notably, and in accordance with these findings, bioinformatic analysis using The Cancer Genome Atlas (TCGA) and GSE155478 datasets revealed that Linc01977 expression is elevated in breast cancer cell lines with DOX resistance while breast cancer patients with remarkably high levels of Linc01977 have significantly lower overall survival compared to those with lower Linc01977 levels
[48]. Similar to Linc02163, Linc01977 is also mainly localized in the cytoplasm and functions as a ceRNA by sponging, or specifically binding, miR-212-3p and by increasing the levels of its target gene Golgi membrane protein 1 (GOLM1) that encodes a Golgi associated protein and promotes an oncogenic phenotype in many cancer types
[49][50].
(J) Linc02163: Among other lincRNAs found to be deregulated in cancer, Linc02163 was recently shown to play a role in colorectal and breast cancer
[51][52]. Linc02163 is located on chromosome 5q21.2 and it was found to be upregulated in breast cancer tissues compared to adjacent normal tissues with the findings being verified in four different breast cancer cell lines (SKBR3, MDA-MB-231, MCF-7, and BT-474) as compared to human immortalized breast epithelial cell line MCF-10A
[52]. Moreover, Linc02163 silencing resulted in reduced cell proliferation, migration, and invasion of breast cancer cells and increased apoptosis
[52]. Interestingly, nuclear/cytoplasmic fractionation revealed that Linc02163 is mostly localized in the cytoplasm where it is suggested to have a post-transcriptional role functioning as a ceRNA for miRNAs and consequently decreasing the regulatory impact of these miRNAs on their target mRNAs
[53][54]. For instance, in vivo studies using a xenograft mouse model showed that it can serve as a ceRNA for the miR-511-3p upregulating high-mobility group A2 (HMGA2) gene
[52], which is a specific target of miR-511-3p. Furthermore, survival analysis using the Kaplan–Meier plotter revealed that patients with high Linc02163 levels exhibited shorter overall survival, larger tumor size, and greater metastatic potential, indicating that Linc02163 expression is correlated with poor prognosis for breast cancer patients
[52].
(K) Linc02615: Last but not least, Linc02615 was very recently discovered but little is known regarding its expression and function. It is located on chromosome 4, locus 4q28.2 and has a length of 742 bases. Similarly to Linc01087 and contrary to all previously described lincRNAs, its expression is lower in breast cancer tissues compared to healthy ones and it is therefore postulated to function as a tumor suppressor
[55], based on data extracted from the CoLncRNA database using a bioinformatic approach
[55].
2. Small Nucleolar RNAs (snoRNAs)
The vast majority of snoRNAs are hosted inside the intron sequences of protein-coding and non-protein-coding genes, termed small nucleolar RNA host genes (SNHGs). During splicing, introns are removed and exons are connected together to form the mature mRNA. After splicing though, introns are not lost or degraded but are further processed into snoRNAs and function in the nucleolus
[56] (see
Figure 1 below).
Figure 1. Schematic representation of the process by which snoRNAs are generated. SnoRNAs (depicted as yellow, pink, or brown boxes) are usually hosted within the intron sequences of genes known as small nucleolar RNA host genes (SNHGs). Following splicing, exons are connected together to generate the mature mRNA, and the introns are further processed into snoRNAs that are now fully functional in the nucleolus.
To date, there are 22 members of the SNHG family (SNHG1 to SNHG22) many of which have been shown to be deregulated in cancer, being critically involved in processes such as cancer cell proliferation, tumor progression, metastasis, and chemoresistance
[56].
3. Small Nucleolar RNAs in Breast Cancer
For instance, in breast cancer, the observed enhancement in protein synthesis is thought to be due to elevated rRNA expression for which elevated snoRNA biogenesis is required
[57]. Thus, several snoRNAs have been identified to be implicated in breast cancer pathogenesis and have prognostic value in breast cancer.
SNHG1 was found to be significantly upregulated in human breast cancer tissues and cell lines
[58] and shown to promote breast cancer cell proliferation and metastasis both in vitro and in vivo
[58]. Regarding the molecular mechanism of action, SNHG1 was shown to act as a sponge for miR-193a-5p finally activating the expression of homeobox A1 (
HOXA1) oncogene
[58] but it was also shown to act through regulation of miR-382 and miR-448 expression
[59][60]. Moreover, SNHG1 was upregulated under hypoxic conditions in breast cancer cells MDA-MB-231 in a hypoxia-inducible factor-1 (HIF-1) dependent manner and was found to be co-expressed with miR-199a-3p regulating its target gene transcription factor A mitochondrial (TFAM), ultimately leading to breast cancer cell metastasis
[61]. Finally, SNHG1 was found to act as sponge for miR-18b-5p regulating the expression of telomerase reverse transcriptase (TERT). Interestingly, in vivo experiments combining SNHG1 knockdown and TERT inhibition dramatically inhibited breast tumor growth
[62].
Similarly, SNHG3 expression was dramatically elevated in breast cancer cells and tissues, while overexpression of SNHG3 in MCF-7 band MDA-MB-231 cells induced breast cancer cell proliferation, EMT, migration, and invasion, through regulating miR-186-5p and ZEB1 expression
[63]. Further, SNHG3 silencing led to breast cancer cell growth inhibition both in vitro and in vivo
[58] and it was found to act as sponge for miR-154-3p regulating Notch signaling. Lastly, secretion of SNHG3 from breast cancer associated fibroblasts promotes breast cancer cell proliferation via its action as a sponge for miR-330-5p
[64] which inhibits pyruvate kinase M1/M2 (PKM) and miR-384 which inhibits hepatoma derived growth factor (HDGF) and also induces breast cancer cell migration, and invasion
[65].
SNHG5 acts as a sponge for miR-154-5p, which normally suppresses proliferating cell nuclear antigen (PCNA), and therefore promotes cell cycle progression in breast cancer cells and inhibits apoptosis at the same time
[66]. SNHG6 promotes breast cancer cell proliferation, migration, and invasion by acting as a sponge for miR-26a-5p, which inhibits vasodilator-stimulated phosphoprotein (VASP)
[67]. SNHG7 has also been connected to breast cancer pathogenesis and metastasis through a number of studies showing that breast cancer cells and tissues express elevated SNHG7 levels that are correlated to tumor stage, distant metastasis, lymph node metastasis, and reduced overall survival
[68][69][70]. Specifically, SNHG7 binds to c-Myc oncogene and enhances its expression
[71] while it also acts as a sponge for miR-34a
[70] as silencing studies showed that it affects the expression of miR-34a and the Notch-1 pathway that it regulates
[70]. Furthermore, it acts as a sponge for miR-186
[69] and miR-381
[68], which are also implicated in breast cancer pathogenesis while it was also shown to bind to miR-15a
[72].
In accordance with the above, SNHG14 and SNHG15 were also shown to promote cancer cell proliferation, migration, and invasion
[73][74][75][76]. Specifically, SNHG14 expression was found elevated in breast cancer cells and tissues and its silencing attenuated cancer cell proliferation, migration, and invasion while at the same time enhancing apoptosis. Notably, overexpression yielded the exact opposite effects
[62]. Regarding the molecular mechanism of action, SNHG14 was shown to directly interact as sponge with miR-543 and regulated Krüppel-like factor 7 (KLF7). Furthermore, SNHG14 acts by epigenetically regulating the acetylation of histones including histone H3K27 but it can also act as a sponge for miR-193a-3p
[75]. Regarding SNHG15, it is also highly expressed in breast cancer tissues and cell lines and is positively associated with larger tumor size, lymph node metastasis, and decreased survival, while it also acts as a sponge for miR-411-5p
[74] and miR-211-3p
[76].
Finally, breast cancer cell proliferation, migration, and invasion are also promoted through the action of SNHG16
[77][78], SNHG17
[79], and SNHG20
[80] via sponging miR20a, miR-124-3p, and miR-495, respectively.