Landscape of NcRNAs involved in drug resistance of breast cancer

Breast cancer (BC) leads to the most amounts of deaths among women. Chemo-, endocrine-, and targeted therapies are the mainstay drug treatments for BC in the clinic. However, drug resistance is a major obstacle for BC patients, and it leads to poor prognosis. Accumulating evidences suggested that noncoding RNAs (ncRNAs) are intricately linked to a wide range of pathological processes, including drug resistance. Till date, the correlation between drug resistance and ncRNAs is not completely understood in BC. Herein, we comprehensively summarized a dysregulated ncRNAs landscape that promotes or inhibits drug resistance in chemo-, endocrine-, and targeted BC therapies. Our review will pave way for the effective management of drug resistance by targeting oncogenic ncRNAs, which, in turn will promote drug sensitivity of BC in the future.


Introduction
Breast cancer (BC) is a significant global health challenge [1]. It is a heterogeneous disease, involving numerous categories. There are five main categories of BC, stratified by the expressions of estrogen receptor (ER), progesterone receptor (PR), human epidermal growth factor receptor 2 (HER2), and Ki-67. The corresponding categories are Luminal A (LA), Luminal B (LB), Human epidermal growth factor receptor 2 (HER2) + , Normal breast-like (NBl) and Basal subtype [Triple negative breast cancer (TNBC)] [2,3]. LA tumors typically show strong ER and PR levels and scarce HER2 and Ki-67 levels. LB cancers display strong ER and PR levels, strong or weak HER2 levels, and elevated Ki-67 levels. Given their distinct gene expressions, LA and LB tumors are generally more responsive to endocrine therapy, compared to chemotherapy [4]. In contrast, HER2 tumors have no ER and PR expressions, instead, they express HER2 and Ki-67. HER2 tumors are, therefore, better managed with targeted therapies, and adequately respond to neoadjuvant chemotherapy [4,5]. The NBl form expresses ER and PR, and does not express HER2 and Ki-67. Therefore, these also respond well to chemotherapy. Lastly, TNBC responds well to neoadjuvant chemotherapy, however, the distant recurrence rates are markedly higher than other cancer forms [4]. Despite massive developments in various treatment regimen, a large quantity of patients still experienced disease recurrence and reduced survival due to new or acquired resistance to treatments, which, in turn, enhances metastatic risk [6]. Unfortunately, once metastasis occurs, the five-year overall survival (OS) rate becomes less than 25% [7]. Numerous cancer drug resistance pathways involve modifications in drug efflux, DNA repair, escape from apoptosis, immune system evasion, improvised and differential metabolisms, drug target mutations, and epigenetic alterations [8].
Noncoding RNAs (NcRNAs) are known to regulate drug resistance in BC patients. Hence, it is critical to elucidate the correlation and underlying mechanism of the relationship governing ncRNAs and drug resistance in BC. Scientists reported that > 80% of the entire human genome undergoes transcription [9,10]. Interestingly, only < 2% of the transcription produces functional proteins, and the rest generates ncRNAs. NcRNAs are largely separated into two categories, depending on their size and function: (1) short ncRNAs: < 200-nucleotides long, include microRNAs (miRNAs), small interfering RNAs (siRNAs), small nucleolar RNAs (snoRNAs), and Piwi-interacting RNAs (piRNAs); and (2) long non-coding RNAs (lncRNAs): > 200-nucleotides long, transcribed via RNA polymerase II, and contains a 5' cap, transcription start site, and polyadenylation [11]. There is a peculiar class of lncRNAs called circular RNAs (circRNAs), and they are ubiquitously found within mammals [12]. LncRNAs serve essential roles in tumor pathogenesis via both transcriptional and post-transcriptional regulation [13,14]. In general, cytoplasmic lncRNAs modulate cell signaling, as well as transcript stability or protein translation, while nuclear lncRNAs regulate chromatin associations, as well as transcriptional and mRNA stability regulation [15]. MiRNAs belong to a category of small ncRNA that suppress protein-coding gene expression by targeting respective transcripts [16]. Several studies suggested that ncRNAs modulate gene expression at the epigenetic, transcriptional, post-transcriptional, translational and even sub-cellular localization levels [17]. Therefore, ncRNAs are known to regulate multiple facets of BC progression like cell proliferation, angiogenesis, epithelial-mesenchymal transition (EMT), cancer stem cells (CSCs), drug resistance, and metastasis [17].
In this report, we performed a review of the detailed mechanisms behind the ncRNAs-mediated regulation of chemo-, endocrine-, and targeted therapeutic resistance in BC. Moreover, our review identified possible therapeutic targets that may potentially diminish drug resistance or enhance BC treatment efficacy.

NcRNAs regulate chemotherapeutic resistance in BC
Chemotherapy is a well-known and effective BC treatment that improves prognosis and OS of patients [18]. Chemotherapy includes anthracyclines and/or taxane administration, and in select patients, cyclophosphamide, methotrexate, and/or 5-flurouracil (5-FU) are used [19]. The mechanism underlying chemoresistance likely involves both genetic and epigenetic alterations like drug-driven mutations, drug metabolic enzyme abnormalities, cell-cycle-and apoptosis-related genes, DNA methylation, and histone modifications [20]. Moreover, most chemotherapeutic medications destroy DNA, and in response, cells elicit a DNA damage response (DDR), which may inadvertently induce drug resistance [21]. In addition, drug efflux is a commonly examined mechanism of cancer drug resistance, and enhanced drug efflux is commonly present in multidrug resistance (MDR) [22,23]. Up-regulations in the levels of ATP-binding cassette (ABC) superfamily members like P-gp (ABCB1), multidrug-resistance-associated protein 1 (MRP1/ABCC1), multidrug-resistance-associated protein 7 (MRP7/ABCC10), and BC resistance protein (BCRP/ABCG2) are frequently observed in drug resistance associated with various forms of cancers [24][25][26].

LncRNA BORG
LncRNA BORG levels are very susceptible to cytotoxic medications, and promotes a transcriptional response that mediates survival and chemoresistance of TNBC cells. Mechanically, the chemo-resistant BORG traits depend on the robust activation of the NF-κB axis via a new BORGbased feedback loop, and via its ability to interact with and activate RPA1 [36].

LncRNA NONHSAT101069
Overexpressing lncRNA NONHSAT101069 enhances epirubicin resistance and EMT processing of BC cells. In terms of underlying mechanism, NONHSAT101069 functions as a competing endogenous RNA (ceRNA) and sequesters miR-129-5p, which, in turn, promotes epirubicin resistance, metastasis, and EMT processing of BC cells via the Twist1 axis [37].

LncRNA FTH1P3
FTH1P3 upregulation accelerates cell proliferation, migration, cell cycle and migration via suppression of miR-224-5p in uveal melanoma cell lines [38]. FTH1P3 levels are enriched in PTX-resistant BC tissue specimen and cells.

LncMat2B
LncMat2B is ubiquitously expressed in the cisplatin-resistant MCF-7 cell line. Moreover, its incorporation into wild type MCF-7 cells reduces sensitivity to cisplatin exposure by diminishing DNA damage and reactive oxygen species (ROS) formation [48].
Linc00668 promotes BC cell resistance to DOX via interaction with SND1. This enables the expression of downstream SND1 targets [53].

LncTUG1
NLK is a negative modulator of the WNT network [82]. LncRNA TUG1 mediates its action through the regulation of the miR-197/NLK axis to enhance cisplatin sensitivity in TNBC patients [83].

LncRNA EGOT
Eosinophil granule ontogeny transcript (EGOT) is generated/released by ITPR1, a ligand-gated ion channel involved in the calcium secretion from the intracellular storage [84,85]. LncRNA EGOT augments autophagy, which, in turn, makes BC more susceptible to PTX cytotoxicity, owing to an elevation in ITPR1 levels [86].

LncRNA-ARA
LncRNA-ARA regulates cell adhesion-and cell cycle progression-linked axes. Jiang et al. reported that ARA deficiency reverses drug resistance, and suppresses cell proliferation, migration, while promoting apoptosis and G2/M arrest in ADR-resistant cells [87].

MiR-17 and MiR-20b
Nuclear receptor coactivator 3 (NCO3) is a nuclear receptor coactivator which accelerates BC tumor pathogenesis by increasing the ER and PR transcriptional activities [94]. Moreover, miR-17 and miR-20b deficiencies induce PTX resistance in BC by up-regulating NCOA3 levels [95]. In addition, JAB1 is ubiquitously found in BC, and it activates pro-survival cellular networks to confer tamoxifen resistance in ERα-positive BC [96]. MiR-17 also suppresses JAB1's oncogenic activity, which results in the suppression of tumor development while sensitizing TNBC cells to chemotherapeutic treatments [97].

MiR-20a
MiR-20a overexpression sensitizes BC cells to chemotherapeutic medications (PTX). Mechanically, miR-20a physically interacts with the 3' UTR of MAPK1, thereby down-regulating levels of P-gp and c-Myc by suppressing the MAPK/ERK network. In the meantime, c-Myc binds to the promoter of the miR-20a gene to induce transcription of the miR-20a gene [99].
In a study, miR-200c-141 cluster overexpression in an in vivo CSC-enriched claudin-low tumor model, reduced tumor development and stem cell functionality, thus resulting in the absence of EMT characteristics, along with an enhancement of chemotherapeutic (DOX and carboplatin) sensitivity [120].

MiR-27b-3p
CBLB is an upstream factor of the PI3K/Akt network. It regulates sensitivity of cetuximab in gastric cancer [124]. GRB2, another essential upstream factor in the MAPK/ Erk network is known to resist ovarian cancer therapy by cisplatin. This occurs through the activation of the MAPK/ Erk network [125]. Mechanically, miR-27b-3p reverses the PTX-mediated resistance by specifically reducing its target genes (CBLB and GRB2), and thus down-regulating the MAPK/Erk and PI3K/Akt networks [126].

MiR-451
β-catenin is central to the Wnt/β-catenin network. Upon activation of Wnt signaling, β-catenin is rescued from degradation, resulting in its accumulation in the cytoplasm, followed by its translocation to the nucleus, activation of target genes (c-Myc and cyclin D1), which ultimately enhances tumor pathogenesis [136][137][138]. MiR-451 accelerates apoptosis and cell-cycle arrest of PTX-resistant cells via direct binding of the YWHAZ/β-catenin network [139].

NcRNAs with endocrine therapy resistance in BC
Approximately 70% of all BC patients exhibit ubiquitous ER expression [141,142]. As such, it is a promising target for endocrine therapy. Two major ER isoforms (ERα and ERβ), encoded by 2 distinct genes (ESR1 and ESR2), regulate the nuclear and extranuclear ER axes [143,144]. At present, three forms of endocrine therapies are used in clinics: (a) aromatase inhibitors (AI), (b) selective ER modulators (SERMs) and (c) selective ER degraders (SERDs) that antagonize ER [145]. The first of these SERMs is tamoxifen, a drug used frequently till this day to treat ER-positive patients. However, patients soon become resistant to this drug, which limits its use [146,147]. AI blocks the enzyme aromatase, which regulates estrogen production. This prevents the development of hormone-receptor-positive BC cells. AI is primarily employed in postmenopausal women, and it performs better than tamoxifen in this demographic [148]. Fulvestrant is the preferred SERD for treating cancer patients. Both preclinical and clinical trials revealed that this is effective even in the tamoxifen-resistant (TR) models, and do not elicit agonistic activity in oestrogen-sensitive tissues like the endometrium [149,150]. Scientists uncovered several underlying mechanisms that produce endocrine resistance, namely, deregulation of the classical estrogen signaling, activation of growth factor receptor networks, changes in the cell cycle and apoptotic process, and epigenetic modification [151]. Herein, we detailed the ncRNAs-related pathways involved in endocrine therapy resistance and sensitivity, particularly, in terms of the dysregulated signaling pathways: (i) ER signaling pathway, (ii) autophagy signaling pathway, (iii) PI3K/Akt/mTOR signaling pathway, (iv) and other prosurvival signaling pathways ( Fig. 3 and Table 3).

LncRNA HOTAIR
HOTAIR is markedly elevated in tumors of TR BC patients, relative to their primary tumors prior to treatment. Direct association between HOTAIR and ER results in high levels of nuclear ER, even under estrogen-depleted conditions. This enables ER genomic targeting and induces transcription of the ER-target genes. Hence, HOTAIR augments the ER axis, and elicits tamoxifen resistance in BC [153].

BCAR4
BCAR4 accelerates BC progression. Godinho et al. reported that BCAR4 levels in BC are strongly correlated with aggressiveness and tamoxifen resistance via regulation of the HER2 axis [154].

LncRNA H19
Autophagy is a potential mechanism for tamoxifen resistance. Beclin1 (a key mediator of autophagy) overexpression makes cells unresponsive to estrogen-based signaling, which leads to tamoxifen resistance in BCs [155]. H19 overexpression augments autophagy and induces tamoxifen resistance in ER-positive BC cells by diminishing methylation in the Beclin 1 promotor region using the H19/SAHH/DNMT3B network [156]. In addition, H19 deficiency makes endocrine therapy resistant (ETR) cells susceptible to tamoxifen and fulvestrant, in an H19-dependent manner. H19 also modulates ERα levels in ETR cells, and protects against fulvestrant-based apoptosis [157].

DILA1
DILA1 binds to Cyclin D1, and is ubiquitously expressed in tamoxifen-resistant BC. Mechanistically, DILA1 prevents Cyclin D1 phosphorylation at Thr286 via direct association with Thr286, which blocks its degradation, thus enhancing Cyclin D1 levels in BC [163].

LINC ERINA
High lincRNA ERINA levels are strongly associated with worse ER-positive BC patient outcome and responsiveness to CDK inhibitors in BC cell lines. Mechanistically, ERINA is induced by estrogen, and promotes cell cycle progression by regulating the TF E2F1 [164].
Silencing miR-125b in letrozole-resistant cells prevents the constitutive activation of the AKT/mTOR axis, and overcomes letrozole resistance, by sensitizing cells to the AI treatment [168].

MiR-21
Aberrant expression of miR-21 involved in chemoresistance of tumor [174]. Silencing of miR-21 confers the sensitivity to tamoxifen and fulvestrant by enhancing autophagic cell death through inhibition of the PI3K/AKT/ mTOR by targeting PTEN [175].

MiR-125a-3p
CDK3 is a potential target of miR-125a-3p in ER-positive BC [187]. MiR-125a-3p can function as a novel tumor suppressor in ER-positive BC by targeting CDK3, which may be a potential therapeutic approach for tamoxifen resistant BC therapy [188].

MiR-26a/b
Hu-antigen R (HuR) is an RNA-interacting protein (RBP) which binds to the AU-rich regions in the 3'UTR of transcripts to enhance their stability [189]. Reduced miR-26a/b and enhanced HuR levels post-transcriptionally augments ERBB2 expression, which, in turn, mediates the acquired tamoxifen resistance in ER-positive BC cells [190].

MiR-190
MiR-190 suppresses the Wnt/β-catenin axis to enhance antiestrogen responsiveness by regulating SRY-related high mobility group box 9 (SOX9). In addition, recent evidences suggest a mechanism involving ZEB1-miR-190-SOX9 that mediates resistance to endocrine therapy in BC. ZEB1 interacts with the miR-190 promoter region to competitively inhibit ERα interaction, which enhances resistance to endocrine therapy [191].

MiR-214
Overexpression of UCP2 conferred drug resistance to chemotherapy and a higher survival through downregulation of ROS [192,193]. MiR-214 increases the sensitivity of BC cells to tamoxifen and fulvestrant through inhibition of autophagy by targeting UCP2 [194].

MiR-1254
Cell cycle and apoptosis regulator 1 (CCAR1) is an apoptosis mediator or transcriptional coactivator for nuclear receptors or P53. As such, it has multiple roles in regulating cancer cell progression [195,196]. CCAR1 5' UTR is a natural miRancer of the endogenous miR-1254, and it makes TR BC cells susceptible to tamoxifen [197].

MiR-375
Metadherin (MTDH) has been involved in BC metastasis. MTDH overexpression could induce EMT and modulate invasion as well as metastasis in BC [201]. Re-expression of miRNA-375 reverses both tamoxifen resistance and accompanying EMT-like properties by targeting MTDH in BC [199].

NcRNAs with targeted therapy resistance in BC
Erb-2/Her-2 is up-regulated in 20-30% of human invasive BCs, and is correlated with a worse patient outcome [202,203]. In terms of monoclonal antibodies, small molecular inhibitors are used to specifically bind a target molecule. At the present time, trastuzumab, lapatinib, and pertuzumab are commonly employed for HER-2-positive BCs treatment [204]. Trastuzumab is a humanized monoclonal antibody that interacts with the HER2 receptor to suppress HER2 dimer formation, thus interrupting downstream networks, which, in turn, inhibits cell proliferation and apoptosis [148]. Lapatinib is a HER2 kinase inhibitor, which improves prognosis of HER2-amplified BC [205]. Multiple mechanisms produce resistance to targeted therapies. These include, ErbB2 levels, enhanced pro-survival signaling via alternation in tyrosine kinases receptors or intracellular signaling, which markedly enhances cell proliferation [206,207]. Herein, we detailed the ncRNAsmediated mechanism governing targeted therapy resistance and BC sensitivity ( Fig. 4 and Table 4).

LncSNHG14
Polyadenylate-binding proteins (PABPs) are special proteins that associate in a sequence-specific fashion with single-stranded poly (A) by RNA recognition motif (RPM). PABPC1 regulates mRNA translation and degradation [208,209], and facilitates the stability of the 5' cap of transcripts. Mechanically, SNHG14 induces BC trastuzumab resistance by modulating PABPC1 levels via H3K27 acetylation [210].

LncRNA AFAP1-AS1
AFAP1-AS1 is ubiquitously expressed in trastuzumab-resistant cells, relative to sensitive cells. Enhanced AFAP1-AS1 expression is associated with worse response and reduced survival of BC patients. Exosome-mediated AFAP1-AS1 induces trastuzumab resistance via interaction with AUF1 and activation of ERBB2 translation [214].

MiR-16
FUBP1 is a TF and RBP that modulates both transcription and translation of multiple genes [224]. CCNJ is not well characterized in mammals, and it may modulate BC [225]. MiR-16 serves as a tumor suppressor to mediate trastuzumab and lapatinib anti-proliferative effects, and CCNJ and FUBP1 are newly confirmed targets of miR-16 [226].

Targeting oncogenic-NcRNAs to conquer drug resistance
In terms of the aforementioned ncRNAs-mediated drug resistance, multiple ncRNAs also possess great therapeutic target potential in future drug developments. Therefore, several researchers targeted oncogenic ncRNAs to address cancer drug resistance. Herein, we detailed the ncRNAs that are highly expressed in cancer cells, where they serve an oncogenic function to induce BC resistance to anti-cancer therapies (Fig. 5). With advancements in nanotechnology, multiple clinical trials either examined or are examining RNA-guided precision machines [227][228][229]. Among the annotated ncRNAs, miRNAs are most commonly examined. Additionally, lncRNAs and circRNAs were also identified as novel targets [230][231][232]. Doublestranded RNA-mediated interference (RNAi) and singlestranded antisense oligonucleotides (ASOs) are two main strategies that target lncRNAs. Till now, three approaches were proposed for targeting ncRNAs: ASOs, locked nucleic acids (LNAs), and morpholinos [233]. Fortunately, a clinical trial (NCT02950207) was launched to testify whether miR-100 silencing impacts patients' response rate to hormonal treatment in BC (https:// clini caltr ials. gov). Moreover, the researchers also examined miR-10b, and revealed that miR-10b LNAs enhances BC sensitivity to doxorubicin in mouse models, with no further damage to normal tissue. This suggests that reduced toxicity is strongly related to the delivery of this LNA nanoparticle [234].

Conclusions
BC is the most common cancer among women, and the major contributor to cancer-related deaths in women [235]. Technological enhancements in early diagnosis and therapy have markedly reduced BC-related mortality, while improving patient outcome to a certain extent [236]. However, close to 35% of BC patients experience recurrence and metastasis. Moreover, they also experience resistance to chemo-, endocrine-, and radiotherapies [237,238].
The often encountered drug resistance within BC patients severely restricts therapeutic efficacy, and negatively impacts BC patient prognosis [239]. Emerging evidences revealed that ncRNAs can function as diagnostic indicators for multiple diseases, estimator of drug response, and as targets of new drug development [240]. Herein, we summarized the dysregulated ncRNAs governing drug resistance in BC, thereby providing a comprehensive ncRNAs landscape for drug resistance in BC. Some ncRNAs regulate drug resistance and sensitivity via a complex regulatory network. For instance, lncRNA H19 modulate endocrine resistance by regulating autophagy and ERα in BC. Meanwhile, different ncRNAs also influence drug efficacy by targeting the same target molecule. For instance, PTEN modulates drug resistance by simultaneously regulating lncPTENP1, miR-132, miR-212, lncHCP5, miR-519a, GAS5, and miR-129-5p levels in BC. Several studies demonstrated a concrete mechanism of ncRNAs modulating drug resistance, however, some reports only suggested a role of few ncRNAs in regulating drug resistance. This review highlights the direction of future anti-cancer drug development, particularly, approaches that weaken drug resistance by inhibiting drug resistance-related oncogenic ncRNAs. Other studies demonstrated that ncRNAs possess great potential in treating tumor. For example, small molecules were recently shown to abrogate HOTAIR activity by interrupting the HOTAIR/EZH2 scaffold association. This offers a novel approach of inhibition with enhanced applicability in humans. EZH2 inhibitor compounds like DZNep was previously suggested as potential medications targeting solid tumors in clinics [241]. Dysregulated ncRNAs are widely present in tumor drug resistance. A clinical trial must also be launched to enhance drug sensitivity by targeting ncR-NAs, as mentioned above. Hence, given the significance of ncRNAs in drug resistance, additional investigations are warranted to identify potential therapeutic targets and approaches that enhance drug sensitivity in BC.
In conclusion, we recommend an extensive investigation, involving clinical trials, to examine the mechanisms behind drug resistance, and subsequently, develop ncR-NAs-based therapies to fight BC. Additionally, miRNA, circRNA and TRFs, and other ncRNAs were not reported to modulate drug resistance. However, additional investigations are needed to confirm their association, if any, with drug resistance. Data availability Not applicable.

Declarations
Conflict of interest The authors declare that they have no conflict of interest.
Ethical approval Not applicable.

Consent for publication Not applicable.
Open Access This article is licensed under a Creative Commons Attribution 4.0 International License, which permits use, sharing, adaptation, distribution and reproduction in any medium or format, as long as you give appropriate credit to the original author(s) and the source, provide a link to the Creative Commons licence, and indicate if changes were made. The images or other third party material in this article are included in the article's Creative Commons licence, unless indicated otherwise in a credit line to the material. If material is not included in the article's Creative Commons licence and your intended use is not permitted by statutory regulation or exceeds the permitted use, you will need to obtain permission directly from the copyright holder. To view a copy of this licence, visit http:// creat iveco mmons. org/ licen ses/ by/4. 0/.