Roles of miRNA and lncRNA in triple-negative breast cancer

Roles of miRNA and lncRNA in triple-negative breast cancer miRNA和lncRNA在三阴性乳腺癌中的作用 first-author corresp ‡Corresponding Author ‡Corresponding Author †E-mail:bdd114@163.com †E-mail:bdd114@163.com bdd114@163.com College of Life Sciences and Medicine, Zhejiang Sci-Tech University, Hangzhou 310018, China College of Life Sciences and Medicine, Zhejiang Sci-Tech University, Hangzhou 310018, China Triple-negative breast cancer (TNBC) is currently the most malignant subtype of breast cancer without effective targeted therapies, which makes its pathogenesis an important target for research. A growing number of studies have shown that non-coding RNA (ncRNA), including microRNA (miRNA) and long non-coding RNA (lncRNA), plays a significant role in tumorigenesis. This review summarizes the roles of miRNA and lncRNA in the progression, diagnosis, and neoadjuvant chemotherapy of TNBC. Aberrantly expressed miRNA and lncRNA are listed according to their roles. Further, it describes the multiple mechanisms that lncRNA shows for regulating gene expression in the nucleus and cytoplasm, and more importantly, describes lncRNA-regulated TNBC progression through complete combining with miRNA at the post-transcriptional level. Focusing on miRNA and lncRNA associated with TNBC can provide new insights for early diagnosis and treatment—they can be targeted in the future as a novel anticancer target of TNBC. 三阴性乳腺癌(TNBC)作为乳腺癌中最恶性的亚型,具有异质性高、增殖能力高、转移性强等特点,且缺乏有效的靶向治疗,因而其发病机制成为研究的重点.越来越多的研究表明,小RNA (miRNA)和长链非编码RNA(lncRNA)在内的非编码RNA在肿瘤的发生和发展中起着重要的作用.本文总结归纳了近些年来与TNBC相关的miRNA和lncRNA,介绍了lncRNA调节基因表达的多种机制,概述了miRNA和lncRNA在TNBC进展、诊断以及新辅助化疗中的作用.本文探索miRNA和lncRNA与TNBC的关系,旨在为癌症的早期诊断和治疗提供新思路,使其成为治疗癌症的新靶点. Biomarker Long non-coding RNA (lncRNA) MicroRNA Regulation mechanism Triple-negative breast cancer (TNBC) 生物标志物 长链非编码RNA(lncRNA) 小RNA(miRNA) 调节机制 三阴性乳腺癌(TNBC) Introduction 1 The Human Genome Project has shown that coding genes only account for 1.5% of the human genome, the remainder being non-protein-coding sequences (Harrow et al., 2012 2012 ). Most of these DNA sequences are transcribed into non-protein-coding RNAs, which account for the majority of all RNA transcripts (Mattick, 2011 2011 ; St. Laurent et al., 2015 2015 ). There are multiple types of non-coding RNA (ncRNA), all of which can be roughly divided into long non-coding RNAs (lncRNAs) and short non-coding RNAs (sncRNAs) according to their length. The latter consist of small interfering RNAs (siRNAs), small nucleolar RNAs (snoRNAs), microRNAs (miRNAs), PIWI-interacting RNAs (piRNAs), etc. (Taft et al., 2010 2010 ; Boon et al., 2016 2016 ). Initially, ncRNA was viewed as “dark matter” or “transcriptional noise” (Evans et al., 2016 2016 ). However, with the development of RNA sequencing technology, the recognition and research of the role of ncRNA is becoming more prominent. It is thought to participate in different levels of gene expression, including chromatin architecture, epigenetic memory, transcription, RNA splicing, translation, and others (Mattick and Makunin, 2006 2006 ; Atkinson et al., 2012 2012 ; Chadwick and Scott, 2013 2013 ). Today, research increasingly suggests that miRNA and lncRNA are associated with different types of cancer, such as gastric cancer, colorectal cancer, cervical cancer, ovarian cancer, prostate cancer, bladder cancer, breast cancer (BC), and other types of cancer (Huarte, 2015 2015 ; Zhang R et al., 2016 2016 ; Delás and Hannon, 2017 2017 ). BC is one of the most prevalent malignancies affecting women worldwide. The latest data from the American Cancer Society show that there were estimated 42 260 deaths attributable to BC, and 271 270 new cases of BC in 2019, which comprise around 30 percent of all cancer diagnoses in women (Siegel et al., 2019 2019 ). According to individual features, BC is categorized into five tumor subtypes (Sørlie, 2004 2004 ). These are: estrogen receptor (ER)-positive (+) tumors; progesterone receptor (PR)-positive (+) tumors; and ER and PR-negative (−) tumors, which are composed of the “basal-like” subtype, the “normal-like” subtype, and the human epidermal growth factor receptor 2 (HER2)-enriched subtype (Amorim et al., 2016 2016 ; Verma et al., 2019 2019 ). Triple-negative breast cancer (TNBC) is categorized under the basal-like subtype, which is characterized by the lack of expression of both ER and PR, together with the absence of HER2 (Karagoz et al., 2015 2015 ). TNBC accounts for 15% of all BCs and is usually correlated with increased metastasis, which leads to high mortality as well as poor prognosis (Mayer et al., 2014 2014 ; Wang PS et al., 2018 2018 ). Furthermore, TNBC has a weak response to HER2 antagonists and hormone therapy (Collignon et al., 2016 2016 ). It has become a major remedial challenge and there are no effective targeted agents (Li HY et al., 2017 2017 ; Khaled and Bidet, 2019 2019 ). Thus, early detection biomarkers and feasible targeted therapy are especially important for TNBC patients. Role of lncRNA in TNBC 1 LncRNAs are non-coding transcripts that are usually longer than 200 nucleotides (Paraskevopoulou and Hatzigeorgiou, 2016 2016 ). LncRNAs can be classified according to the relative location to the protein-coding gene as follows: intergenic lncRNA, intronic lncRNA, sense lncRNA, antisense lncRNA, and bidirectional lncRNA (Smith and Mattick, 2017 2017 ). Functionally, lncRNAs are involved in gene expression, subcellular transport, protein degradation, and organelle biogenesis (Mattick et al., 2009 2009 ; Taft et al., 2010 2010 ). LncRNAs regulate gene expression in different ways, including through epigenetic regulation, transcriptional regulation, post-transcriptional regulation, and translational regulation (Sun et al., 2017 2017 ). Recent studies have found that aberrant expression of lncRNAs, including AFAP1-AS1 (actin filament-associated protein 1 antisense RNA 1), MALAT1 (metastasis associated lung adenocarcinoma transcript 1), NRON (non-coding repressor of the nuclear factor of activated T cells), and RMST (rhabdomyosarcoma 2-associated transcript), significantly regulates TNBC cell proliferation, migration, metastasis, and tumorigenicity (Yang et al., 2016b 2016b ; Zuo et al., 2017 2017 ; Wang L et al., 2018 2018 ; Niu et al., 2019 2019 ). In this section, we summarize the roles of lncRNA in TNBC progression from two distinct levels. LncRNA-regulated gene expression at the transcriptional level 2 Previous studies have demonstrated that lncRNAs have various working mechanisms, such as those that work through DNA, RNA, and proteins (Prensner and Chinnaiyan, 2011 2011 ). Recently, lncRNAs were reported to bind to defined DNA sequences to regulate gene expression at the transcriptional level (Wang PS et al., 2018 2018 ). Using a database from The Cancer Genome Atlas (TCGA), it was discovered that lncRNA MIR100HG was over-expressed in TNBC but not in other cancers. High expression of lncRNA MIR100HG in TNBC patients was associated with poor prognosis. Knockdown of MIR100HG expression significantly decreased TNBC cell proliferation and impaired tumor growth. Nuclear cytoplasmic separation and quantitative polymerase chain reaction (qPCR) experiments demonstrated that MIR100HG was located mainly in the nucleus. In addition, they found an obvious change in CDKN1B , a cell cycle-related gene, between the MIR100HG knockdown and control groups. CDKN1B , which encodes the p27 protein, regulates cell cycle progression and acts as a tumor suppressor (Yoon et al., 2012 2012 ; Zhao et al., 2015 2015 ). Furthermore, experiments show that MIR100HG binds to p27 gene locus to form RNA–DNA triplex structures, which subsequently regulate the expression of p27 (Wang SW et al., 2018 2018 ). Hence, lncRNA MIR100HG influences cell proliferation in TNBC at the transcriptional level. Luo et al. ( 2018 2018 ) found that lncRNA LINC01638 over-expression dramatically promotes breast cell proliferation in vitro and is associated with poor outcomes in TNBC patients. Furthermore, LINC01638 interacts with c-MYC to prevent its degradation; c-MYC transcriptionally enhances metadherin (MTDH) expression by activating the MTDH promoter. Given that MTDH contributes widely to therapeutic resistance, tumor growth and metastasis, Liang et al. ( 2015 2015 ) found that MTDH promotes breast tumorigenicity by regulating TWIST1, ultimately inducing epithelial–mesenchymal transition (EMT) in TNBC. In addition, c-MYC is reported to combine with other lncRNAs. For example, earlier research has shown that c-MYC transcriptionally promotes SNHG12 (snoRNA host gene 12) expression through direct interaction with its promoter region. What is more, the expression of SNHG12 is significantly increased in TNBC, which correlates with tumor size and lymph node metastasis. Enforced expression of SNHG12 promotes TNBC cell proliferation and migration (Wang et al., 2017 2017 ). LncRNA-regulated gene expression at the post-transcriptional level 2 Increasing evidence also shows that lncRNAs may regulate gene expression at the post-transcriptional level (Costa, 2005 2005 ). As important cytoplasmic regulators, miRNAs act as post-transcriptional regulators of their messenger RNA (mRNA) targets via mRNA degradation (Catalanotto et al., 2016 2016 ). Research increasingly suggests that, in TNBC, high expression of lncRNA can competitively combine with miRNA, acting as a sponge to suppress miRNA functions and promote cancer progression. For example, Wang LH et al. ( 2019 2019 ) observed that lncRNA HCP5 (human histocompatibility leukocyte antigen (HLA) complex P5) was up-regulated in TNBC cell lines and specimens. Using bioinformatic methods, they found that microRNA-219a-5p (miR-219a-5p) not only combines with 3' untranslated region (3' UTR) of BIRC3 (baculoviral inhibitor of apoptosis (IAP) repeat containing 3) mRNA to inhibit its expression, but also complementarily binds to HCP5 . Further, experiments demonstrated that HCP5 functions as a competing endogenous RNA (ceRNA) to impair miR-219a-5p-dependent BIRC3 down-regulation, suggesting that lncRNA HCP5 , associated with TNBC cell apoptosis and proliferation, plays an important role in carcinogenesis. Further, Li et al. ( 2020 2020 ) found that over-expression of lncRNA XIST (X-inactive specific transcript) interacts with miR-454, which inhibits cell proliferation and EMT, and induces apoptosis in TNBC. MALAT1 was found to likely serve as a ceRNA to sponge miR-129-5p in TNBC cells (Zuo et al., 2017 2017 ). Some studies have shown that there is no one-to-one match from lncRNA to miRNA. Zheng et al. ( 2019 2019 ) showed that MALAT1 regulates the expression of BLCAP (bladder cancer-associated protein) mRNA by binding to miR-339-5p in BC cells. LncRNA also regulates protein stabilization at the post-transcriptional level to promote TNBC progression. Shen et al. ( 2019 2019 ) demonstrated that the promoter of LINC00152 contains binding sites for the transcriptional factor yin yang 1 (YY1). High YY1 expression decreases LINC00152 transcriptional activity. Furthermore, up-regulated LINC00152 in TNBC does not influence PTEN (phosphatase and tensin homologue) mRNA expression but can repress PTEN stability via promotion of NEDD4-1 (neural precursor cell expressed, developmentally down-regulated-4-1)-mediated ubiquitination, which in TNBC, involves cancer proliferation and metastasis. Similarly, lncRNA ZEB1-AS1 (zinc finger E-box-binding homeobox 1 antisense 1) maintains ZEB1 mRNA stability by binding with ELAVL1 (embryonic lethal, abnormal vision like 1). However, ZEB1 can regulate the expression of ZEB1-AS1 by combining with its promoter. That feedback loop can facilitate TNBC progression (Luo et al., 2020 2020 ). In addition, research showed that lncRNA MALAT1 binds to the TDP-43 (transactive response (TAR) DNA-binding protein 43), which is a predominantly nuclear protein, to regulate alternative splicing, transcription, and RNA stability (Winton et al., 2008 2008 ). In summary, lncRNA significantly regulates gene expression both in the nucleus and in cytoplasm (Fig. 1 1 ). LncRNA: long non-coding RNA; mRNA: messenger RNA; miR: microRNA; MALAT1: metastasis associated lung adenocarcinoma transcript 1; HCP5: human histocompatibility leukocyte antigen (HLA) complex P5; BIRC3: baculoviral inhibitor of apoptosis (IAP) repeat containing 3; TDP-43: transactive response (TAR) DNA-binding protein 43 LncRNA in TNBC diagnosis 2 Cancer is the leading cause of death in the world. There is growing evidence that early diagnosis holds the key towards effective treatment outcome. Thus, multiple studies have concentrated on exploring biomarkers for cancer detection and progression. Plentiful lncRNAs are aberrantly expressed in TNBC patients, suggesting the high diagnostic value of lncRNAs at present. For example, Liu M et al. ( 2017 2017 ) found that lncRNAs ANRIL (antisense non-coding RNA in the inhibitor of cyclin-dependent kinase 4 (INK4) locus), HIF1A-AS2 (hypoxia inducible factor 1 α-antisense RNA 2), and UCA1 (urothelial cancer associated 1) were over-expressed in plasma of BC patient, and could potentially distinguish between TNBC and non-TNBC. They constructed a regression equation named TNBC SigLnc-3 based on these three lncRNAs, whose area under the curve (AUC) value was 0.934. It was superior to that of ANRIL , HIF1A-AS2 , and UCA1 alone. Compared with non-tumor tissues, Zhang KJ et al. ( 2016 2016 ) found that AFAP1-AS1 was clearly up-regulated in TNBC tissues. A series of cell experiments including methylthiazolyldiphenyl-tetrazolium bromide (MTT) assay showed that inhibiting the expression of AFAP1-AS1 could reduce cell migration and invasion in TNBC. Later, Zhang et al. ( 2018 2018 ) provided mechanistic evidence that the expression of c-MYC and Wnt/β-catenin pathways is viral to promote tumorigenesis. Therefore, high expression of AFAP1-AS1 might have the potential as a novel biomarker of BC (Ma et al., 2019 2019 ). Yang et al. ( 2019 2019 ) found that lncRNA POU3F3 (POU class 3 homeobox 3) was up-regulated more in tumor tissues than in adjacent healthy tissues of TNBC patients. LncRNA POU3F3 over-expression promoted cell proliferation and inhibited cell apoptosis, and it may have diagnostic and prognostic values. In contrast, lncRNAs NRON , RMST , and PTCSC3 (papillary thyroid carcinoma susceptibility candidate 3) expression was down-regulated in TNBC. Previous studies demonstrated that lncRNA NRON maintained human immunodeficiency virus-1 (HIV-1) latency by inducing Tat (transactivator of transcription) protein degradation (Li J et al., 2016 2016 ). Niu et al. ( 2019 2019 ) found that lncRNA NRON inhibited cancer cell proliferation by down-regulating lncRNA snaR (small nuclear factor 90 (NF90)-associated RNA). As an alternatively spliced lncRNA gene, RMST was down-regulated in TNBC and low expression of RMST was associated with worse prognosis (Yang et al., 2016a 2016a ). Wang N et al. ( 2019a 2019a ) demonstrated that lncRNA PTCSC3 inhibited TNBC cell proliferation by down-regulating lncRNA H19 . Previous studies have shown that H19 was aberrantly up-regulated in BC tissues and cells and it promoted the proliferation and invasion (Zhang KJ et al., 2016 2016 ; Li Z et al., 2017 2017 ). Further analysis found that the lncRNA H19 in 30 early-stage BC patients and 30 healthy controls revealed an AUC value of 0.81, with a sensitivity of 56.7% and specificity of 86.7% (Zhang KJ et al., 2016 2016 ). These studies indicate that lncRNA severs as a novel diagnostic biomarker. However, large-scale clinical trials are needed to demonstrate that lncRNA can serve as a diagnostic biomarker for TNBC. Here, we divided lncRNAs in TNBC into two categories: oncogenic lncRNA and tumor suppressor lncRNA. Also, changes in lncRNA expression and its mechanism in TNBC are summarized in Tables 1 1 and 2 2 . LncRNA: long non-coding RNA; TNBC: triple-negative breast cancer; lincRNA: long intergenic ncRNA; RoR: regulator of reprogramming; ARF6: adenosine diphosphate (ADP)-ribosylation factor 6; DUSP7: dual specificity phosphatase 7; LYPD1: leukocyte antigen-6 (Ly6)/PLAUR domain-containing protein 1; DNA-PKcs: DNA-dependent protein kinase catalytic subunit; EGFR: epidermal growth factor receptor; ANRIL: antisense non-coding RNA in the inhibitor of cyclin-dependent kinase 4 (INK4) locus; UTR: untranslated region; EZH2: enhancer of zeste homolog 2; ABCG2: adenosine triphosphate (ATP)-binding cassette transporter G2; LINK-A: long intergenic non-coding RNA for kinase activation; EMT: epithelial–mesenchymal transition; MTDH: metadherin; SPOP: speckle-type POZ protein; HOXC6: homeobox C6; BRCA1: breast carcinoma susceptibility gene 1; PTEN: phosphatase and tensin homologue LncRNA Change Biological function Mechanism RoR Up Promotes invasion, metastasis, and tumor growth in TNBC (Eades et al., 2015 2015 ) As a competitive endogenous RNA sponge, regulates lincRNA RoR/miR-145/ARF6 pathway snaR Up Promotes proliferation, migration, and invasion in TNBC (MDA-MB-231) cells (Lee et al., 2016 2016 ) Unclear MIAT Up Promotes proliferation, migration, invasion, and EMT in MDA-MB-231 cells (Luan et al., 2017 2017 ) As a competitive RNA sponge, regulates the expression of DUSP7 by combining miR-155-5p HULC Up Promotes metastasis and malignancy of breast cancers (Wang N et al., 2019b 2019b ) As a competitive RNA sponge, regulates the expression of LYPD1 by combining miR-6754-5p LINP1 Up Enhances repair of DNA double-strand breaks; increases the sensitivity of tumor-cell response to radiotherapy (Zhang YY et al., 2016 2016 ) Serves as a scaffold linking Ku80 and DNA-PKcs, involved in EGFR signaling ANRIL Up Promotes TNBC cell proliferation and tumor growth; promotes carcinogenesis; inhibits apoptosis (Xu et al., 2017 2017 ) Acts as a molecular “sponge” for miR-199a sponging; miR-199a targets ANRIL at 3' UTR DANCR Up Promotes tumor growth, cell proliferation, and invasion in MDA-MB-231 cells; poor survival (Sha et al., 2017 2017 ) Associated with increased binding of EZH2 on the promoters of CD44 and ABCG2 LINK-A Up Promotes tumorigenesis in TNBC (Lin et al., 2016 2016 ) Active LINK-A-dependent signaling pathway MALAT1 Up Promotes cell proliferation, migration, and invasion in TNBC cells; poor survival (Zuo et al., 2017 2017 ) Target miR-129-5p LUCAT1 Up Accelerates cell proliferation, cell cycle progression, and metastasis; attenuates cell apoptosis (Mou and Wang, 2019 2019 ) Directly binds to miR-5702 HOTAIR Up Increases breast cancer cell invasion and migration; increases the rate of primary tumor growth (Gupta et al., 2010 2010 ) Reprograms chromatin state MIR100HG Up Facilitates cell proliferation in TNBC; controls the cell cycle (Wang SW et al., 2018 2018 ) Participates in the formation of RNA–DNA triplex structures through p27 locus SNHG12 Up Promotes TNBC cell proliferation and migration (Wang et al., 2017 2017 ) Regulates MMP13 expression AFAP1-AS1 Up Promotes cell proliferation, invasion, and tumor growth; inhibits cell apoptosis; poor prognosis (Zhang et al., 2018 2018 ) Activates Wnt/β-catenin pathway; increases the expression of c-MYC and EMT molecules NEAT1 Up Regulates apoptosis and cell cycle progression in TNBC cells (Shin et al., 2019 2019 ) Modulates chemoresistance and cancer stemness Linc01638 Up Promotes tumor proliferation and metastasis (Luo et al., 2018 2018 ) Activates MTDH-Twist1 signaling; prevents SPOP-mediated c-Myc degradation Linc00339 Up Promotes TNBC proliferation; inhibits cell cycle arrest; suppresses apoptosis (Wang XL et al., 2019 2019 ) Through miR-377-3p/HOXC6 signaling pathway Linc00152 Up Promotes tumor growth and cell invasion (Wu et al., 2018 2018 ) Inactivates the BRCA1/PTEN through DNA methyltransferases LncRNA: long non-coding RNA; TNBC: triple-negative breast cancer; snaR : small nuclear factor 90 (NF90)-associated RNA; HOTAIR : Hox transcript antisense RNA; sONE : antisense mRNA transcript of endothelial nitric-oxide synthase (eNOS); mTOR: mammalian target of rapamycin; PI3K: phosphoinosmde-3-kinase LncRNA Change Biological function Mechanism   GAS5 Down Suppresses TNBC cell proliferation and invasion (Li SQ et al., 2018 2018 ) Competitively binds miR-196a-5p   NRON Down Suppresses cancer cell proliferation in TNBC (Niu et al., 2019 2019 ) Down-regulates lncRNA snaR   NEF Down Suppresses migration and invasion of TNBC cells (Song et al., 2019 2019 ) Negatively regulates the expression of miR-155   RMST Down Suppresses cell proliferation, invasion, and migration; enhances cell apoptosis in TNBC (Wang L et al., 2018 2018 ) Regulates the cell cycle and induces the block of the G0/G1 phase   DRHC Down Suppresses the proliferation of TNBC cell lines; correlates with tumor size (Yu et al., 2019 2019 ) Reduces expression of lncRNA HOTAIR   PTCSC3 Down Suppresses TNBC cell proliferation (Wang H et al., 2019 2019 ) Reduces the expression of lncRNA H19   sONE Down Represses TNBC aggressiveness (Youness et al., 2019 2019 ) Induces the expression of miR-34a, miR-15a, miR-16, and let-7a   Aim Down Suppresses TNBC cell migration and invasion (Liu et al., 2017b 2017b ) Restrains Wnt/β-catenin/mTOR/PI3K signaling Role of miRNA in TNBC 1 miRNAs are small ncRNAs that are generally 18 to 22 nucleotides in length. The vast majority of all human miRNAs are encoded in introns, exons, intro–exon junctions, or their own genes. The process of miRNA biogenesis is composed of several stages. First, miRNA is transcribed as primary miRNA (pri-miRNA) via RNA polymerase II or III. Then it is cropped into a hairpin-shaped precursor miRNA (pre-miRNA), helped by Drosha and DGCR8. Next, pre-miRNA is exported to cytoplasm mediated by transporters and becomes mature miRNA (Shukla et al., 2011 2011 ; Anfossi et al., 2018 2018 ). Mature miRNA suppresses gene expression by guiding associated proteins to target sites in the 3' UTR of mRNAs (Gebert and MacRae, 2019 2019 ). miRNAs could regulate various biological processes, such as proliferation, stress responses, cell adhesion, motility, inflammation, cell survival, senescence, and apoptosis, all of which are fundamental to tumorigenesis (Hata and Kashima, 2016 2016 ). Increasing evidence suggests that the abnormal expression of miRNAs might be of clinical utility, especially in TNBC devoid of both predictive markers and potential therapeutic targets (Piasecka et al., 2018 2018 ). To date, more than 3000 miRNAs associated with the occurrence and progress of tumors have been identified (miRbase database). Like lncRNAs, miRNAs can be divided into two categories: oncogenic miRNAs and suppressor miRNAs. Changes in miRNA expression and its role in TNBC are summarized in Tables 3 3 and 4 4 . miRNA: microRNA; TNBC: triple-negative breast cancer; PTEN: phosphatase and tensin homologue; AKT: protein kinase B; ERK: extracellular signal-regulated kinase; MAPK: mitogen activated protein kinase; BTG2: B-cell translocation gene 2; UTR: untranslated region; EI24: etoposide-induced 2.4 miRNA Change Biological function Mechanism  miR-21 Up Promotes proliferation and invasion in TNBC cells (Fang et al., 2017 2017 ) Through targeting PTEN to regulate its expression  miR-25-3p Up Promotes TNBC cell proliferation in vitro and tumor growth in vivo (Chen H et al., 2018 2018 ) Activates the AKT and ERK-MAPK signaling pathways by inhibiting expression of BTG2  miR-93 Up Promotes proliferation, invasion, and metastasis (Hu et al., 2015 2015 ) Unclear  miR-455-3p Up Enhances the abilities of cell proliferation, invasion, and migration in TNBC cell lines (Li ZS et al., 2017 2017 ) Targets tumor suppressor EI24 by binding to its 3' UTR miRNA: microRNA; TNBC: triple-negative breast cancer; TGIF2: transforming growth factor-β (TGFB)-induced factor homeobox 2; CREB5: cyclic adenosine monophosphate (cAMP)-responsive element-binding protein 5; AKT3: v-akt murine thymoma viral oncogene homolog 3, protein kinase B γ; Erk: extracellular signal-regulated kinase; Ets‑1: E26 transformation-specific sequence-1; MCL-1: myeloid cell leukemia 1; FOSL1 : FOS-like antigen-1; UTR: untranslated region; ZO-1: tight junction protein; STAT5B: signal transducer and activator of transcription 5B gene; Hsp90: heat shock protein 90; Bcl-2: B-cell lymphoma 2; EMT: epithelial–mesenchymal transition; EPHA2: ephrin type-A receptor 2; ZEB1/2: zinc finger E-box-binding homeobox 1/2; CDH1: E-cadherin gene; XIAP: X-linked inhibitor of apoptosis protein; BIRC5: baculoviral IAP repeat-containing protein 5; LASP: Lim and SH3 domain protein; CORO1C: actin-binding protein coronin 1C; CDC25B: cell division cycle 25 phosphatases; TRAIL: tumor necrosis factor-related apoptosis inducing ligand; HAX-1: hematopoietic cell-specific protein-associated protein X 1; BOK: BCL2-related ovarian killer; MCT1: monocarboxylate transporter 1; RQCD1: required for cell differentiation 1 homolog; EGFR: epidermal growth factor receptor; PI3K: phosphoinositide 3-kinase; Runx1: Runt-related transcription factor 1; ACVR1: activin A receptor type 1; TNKS2: tankyrases 2; eEF2K: eukaryotic elongation factor 2 kinase; Daam1: disheveled-associated activator of morphogenesis-1; CCND1: cyclin D1; SIX1: Sine oculis homeobox 1; Cdc42: cell division control protein 42 homolog; VEGFA: vascular endothelial growth factor A miRNA Change Biologic function Mechanism miR-29c Down Inhibits proliferation and colony formation (Bhardwaj et al., 2017 2017 ) Through direct binding and regulation of TGIF2, CREB5, and AKT3 miR-30a-5p Down Suppresses the proliferation, migration, and invasion; modulates cell adhesion (Li WT et al., 2016 2016 ) Interrupts Erk/Ets‑1 network by decreasing the expression of β3 integrin in TNBC miR-34a Down inhibits proliferation and invasion; promotes sensitivity to dasatinib (Adams et al., 2016 2016 ) Targets the proto-oncogene c-SRC miR-101 Down Inhibits growth; induces apoptosis in vitro; suppresses tumorigenesis in vivo; increases paclitaxel sensitivity (Liu et al., 2015 2015 ) Through targeting MCL-1 to regulate its expression miR-130a Down Suppresses migration and invasion in TNBC cells (Chen XW et al., 2018 2018 ) Directly targets FOSL1 mRNA at its 3' UTR and increases ZO-1 miR-134 Down Reduces cellular proliferation and enhances apoptosis induced by cisplatin (O'Brien et al., 2015 2015 ) Reduces STAT5B, Hsp90, and Bcl-2 levels miR-200a/b/c Down Inhibits migration and proliferation in TNBC cells (Tsouko et al., 2015 2015 ); inhibits EMT (Rhodes et al., 2015 2015 ); induces cell apoptosis (Ren et al., 2014 2014 ) Regulates the oncogene EPHA2 by target its 3' UTR; regulates expression of genes associated with EMT including ZEB1/2, TWIST, and CDH1; targets XIAP and activates caspase‑3 miR-203 Down Inhibits cell proliferation and migration (Wang et al., 2012 2012 ) Targets the 3' UTR of BIRC5 and LASP miR-206 Down Decreases proliferation, migration, and invasion (Wang et al., 2014 2014 ) Induces G1-S cell cycle arrest and represses CORO1C mRNA and protein levels miR-211 Down Suppresses cell growth, cell cycle, migration, and invasion (Song and Zhao, 2015 2015 ) Targets the 3' UTR sequence of CDC25B miR-223 Down Increases the sensitivity of TRAIL-induced apoptosis in TNBC stem cells (Sun et al., 2016 2016 ) Targets anti-apoptotic protein HAX-1 miR-296-5p Down Suppresses cell growth, migration, and invasion; impairs paclitaxel-induced apoptosis (Onyeagucha et al., 2016 2016 ) Decreases the expression of BOK miR-342-3p Down Decreases cell proliferation, viability, and migration (Romero-Cordoba et al., 2016 2016 ) Promotes lactate efflux changes by repressing MCT1 expression in the tumor cells miR-361-5p Down Inhibits migration and invasion in TNBC cells (Han JJ et al., 2018 2018 ) Targets RQCD1 to inhibit the EGFR/PI3K/Akt signaling pathway miR-378 Down Suppresses migration and invasion in TNBC cells; alleviates the aggressive phenotype of TNBC cells (Browne et al., 2016 2016 ) Targets the 3' UTR of Runx1 and inhibits its expression miR-384 Down Inhibits the proliferation and migration of MDA-MB-231 cells in vitro and in vivo (Wang YX et al., 2018 2018 ) Negatively regulates the Wnt/β-catenin signaling pathway by targeting ACVR1 miR-490-3p Down Inhibits cell growth and invasion in TNBC cells; impairs tumorigenesis of TNBC cells in nude mice (Jia et al., 2016 2016 ) Regulates the expression of TNKS2 by binding to its 3' UTR; blocks β-catenin signaling miR-603 Down Inhibits cell proliferation, survival, invasion, and tumorigenesis (Bayraktar et al., 2017 2017 ) Targets the 3' UTR region of eEF2K miR-613 Down Inhibits cell migration and invasion of TNBC cells (Xiong et al., 2018 2018 ) Targets the Daam1/Rho A signaling pathway miR-1296 Down Suppresses cell proliferation of TNBC cell lines (Phan et al., 2016 2016 ) Regulates the expression of CCND1 by binding to its 3' UTR miR-4306 Down Suppresses cell proliferation, migration, and invasion; inhibits tumor growth, lung metastasis, angiogenesis, and lymph node metastasis (Zhao et al., 2019 2019 ) Targets SIX1/Cdc42/VEGFA to inactivate related signaling pathways miRNA involved in TNBC progression 2 3.1.1 EMT In recent years, EMT, believed to be a major mechanism by which cancer cells become migratory and invasive, has received increasing attention (Tse and Kalluri, 2007 2007 ). Research shows that miRNAs are involved in the process of EMT. Previous study identified miR-125b as down-regulated in TNBC cells, which is associated with poor prognosis and chemoresistance (Mathe et al., 2015 2015 ). Functional in vitro studies have shown down-regulated expression of miR-125b in TNBC tissues as well as decreased cell migration and invasion. Hong et al. ( 2016 2016 ) found that mitogen-activated protein (MAP) kinase kinase 7 (MAP2K7) was a novel target of miR-125b and that its knockdown could inhibit EMT of TNBC cell (Hs578T). Data from TCGA show that miR-20a is up-regulated in human BC, especially in the triple-negative subtype. Liu et al. ( 2017a 2017a ) demonstrated that miR-20a could promote tumor initiation and growth, showing the oncogenic function of miRNA during breast tumorigenesis. E-cadherin (CDH1) promotes the formation of adherens junctions and the establishment of the polarized cell monolayer, the loss of which is a fundamental event in EMT (Reshetnikova et al., 2007 2007 ; Piasecka et al., 2018 2018 ). The connection between miR-20a and EMT was reported by De et al. ( 2017 2017 ), who found that in TNBC cells (MDA-MB-231) hsa-miR-20a could control downstream crucial markers such as CDH1, N-cadherin, and fibronectin, by regulating the expression of Twist-1 mRNA. Furthermore, reporter assays established that miR-20a could abrogate transforming growth factor-β (TGF-β) by silencing the expression of TGF-β receptor 2 (TGFBR2), resulting in the inhibition of MET (De et al., 2017 2017 ). miRNA-145 was reported to regulate tumor cell invasion in TNBC via targeting of adenosine diphosphate (ADP)-ribosylation factor 6 (ARF6). As a known regulator of cell invasion, ARF6 can change CDH1 localization and affect cell–cell adhesion (Eades and Zhou, 2014 2014 ). Alongside some other miRNAs, such as miR-655, it has been approved for suppressing EMT by targeting Prrx1 (paired-related homeobox 1) in TNBC (Lv et al., 2016 2016 ). 3.1.2 Migration, invasion, and metastasis A series of studies have indicated that miRNAs are associated with cell migration, invasion, and metastasis in TNBC. For example, miR-21, functioning as an oncogene, was elevated in BC patients compared with healthy controls. Liu et al. ( 2019 2019 ) found that miR-21 and lncRNA AWPPH (associated with poor prognosis of hepatocellular carcinoma) could up-regulate each other in TNBC cells. It was demonstrated that the over-expression of lncRNA AWPPH and miR-21 promotes cancer cell proliferation (Liu et al., 2019 2019 ), and further, that miR-21 combined with the 3' UTR of LZTFL1 (leucine zipper transcription factor-like 1) and the miR-21/LZTFL1 axis promotes cell proliferation and metastasis (Wang H et al., 2019 2019 ). Fang et al. ( 2017 2017 ) showed that inhibition of miR-21 expression could decrease the proliferation, viability, and invasiveness of the TNBC cell line (MDA-MB-468) and enhance apoptosis (Fang et al., 2017 2017 ). These results indicate that miR-21 may be a novel promising biomarker for TNBC diagnosis and prognosis. In addition, it was found that over-expression of miR-20a-5p could promote the migration and invasion of TNBC cells in vitro by significantly targeting RUNX3 as well as p21 (Bai et al., 2018 2018 ). This suggests that miR-20a-5p has potential clinical applications. Suppressor miRNAs play important roles in TNBC as well. miR-199a-5p was under-expressed in plasma of TNBC patients when compared with healthy controls; and cell proliferation could be reduced by transfecting miR-199a-5p mimic into breast cells (Shin et al., 2014 2014 ). Chen et al. ( 2016 2016 ) found the tumor-suppressive role of miR-199a-5p in TNBC via multiple experiments. Over-expression of miR-199a-5p inhibited cell proliferation, invasion, and migration ability, which attributed to EMT, by altering EMT-related gene expression, such as CDH1 and ZEB1 (Chen et al., 2016 2016 ). miR-200b, one member of the miR-200 family, was significantly down-regulated in TNBC cells and tissues compared with other types of BC. Yang et al. ( 2017 2017 ) demonstrated that miR-200b suppressed TNBC metastasis by targeting ARHGAP18 (Rho GTPase-activating protein 18) and enhancing Rho A activation. miRNA in TNBC diagnosis 2 In recent years, the number of cancer patients has increased rapidly. Thus, early detection or screening methods are very important to enable tumor diagnosis. Multiple studies are focused on exploring biomarkers for BC detection and progression. Many miRNAs are aberrantly expressed in TNBC patients and tissues; for example, miR-20a, miR-25, miR-21, and miR-96 are up-expressed in BC patients (Fang et al., 2017 2017 ; Chen H et al., 2018 2018 ; Razaviyan et al., 2018 2018 ; Kolesnikov et al., 2019 2019 ), while other miRNAs are down-expressed in BC cells, such as miR-205 and miR-29c (Zhang et al., 2015 2015 ; Bhardwaj et al., 2017 2017 ). Razaviyan et al. ( 2018 2018 ) found that miR-96 was up-expressed in MDA-MB-231 cell and TNBC clinical samples at the best cut-off point of 0.18. miR-96-5p has a receiver operating characteristic (ROC) AUC of 0.83, a sensitivity of 80%, and a specificity of 75% (Razaviyan et al., 2018 2018 ). Previous research has shown that miR-96 can reduce BC cell migration and invasion by decreasing the Palladin protein. Thus, it indicates a tumor-suppressive role of miR-96 and a potential anti-metastatic drug (Gilam et al., 2016 2016 ). Zhang et al. ( 2015 2015 ) found that miR-205 was under-expressed in 58 cases of BC patient sera compared with 93 controls with an AUC, sensitivity, and specificity of 0.87, 86.2%, and 82.8%, respectively. Their study determined that miR-205 has high clinical diagnostic value in the detection of BC. In addition, miR-20a was regarded as a biomarker for TNBC compared with luminal subtypes of BC; its AUC value was 0.949 via ROC analysis. The high expression of miR-20a in TNBC cells supports the characteristic of TNBC as the most aggressive subtype of BC (Kolesnikov et al., 2019 2019 ). Roles of miRNA and lncRNA in neoadjuvant chemotherapy 1 As a subtype of BC, TNBC has different characteristics than other subtypes of BC, such as a younger age incidence and being lymph node negative. It also has a high recurrence rate and invades easily (Lehmann et al., 2011 2011 ; Zhao et al., 2017 2017 ). However, due to the lack of estrogen, progesterone, or HER2 receptors, neither endocrine therapy nor conventional targeted therapy is the most effective treatment. At present, the primary treatments for TNBC patients include chemotherapy, surgery, and radiotherapy. Studies have shown that preoperative neoadjuvant chemotherapy in TNBC patients has a more prominent pathological complete response (PCR) rate compared with other subtypes of BC (Liedtke et al., 2008 2008 ; Gülben et al., 2014 2014 ; Biswas et al., 2017 2017 ). Chemotherapy is an important treatment option for cancer, yet it also has drawbacks, such as drug resistance. It is because of drug resistance that tumor cells lose sensitivity to chemotherapy—one of main causes of chemotherapy failure. Recent studies have found that miRNA and lncRNA not only play important roles in the initiation and progression of human tumors but also are involved in drug resistance in malignant tumors (Deng et al., 2016 2016 ; Fu et al., 2019 2019 ). LncRNA UCA1 , located on the human chromosome 19p13.12-positive strand, is the most abundant subtype in various malignant tumors, such as bladder cancer and BC (Wang et al., 2006 2006 ; Huang et al., 2014 2014 ). Liu et al. ( 2016 2016 ) showed that knockdown of lncRNA UCA1 can increase the tamoxifen sensitivity of MCF-7 and T47D cells through inhibition of the Wnt/β-catenin pathway. Moreover, Wu and Luo ( 2016 2016 ) found that lncRNA UCA1 increases tamoxifen resistance in BC cells by inhibiting the mammalian target of rapamycin (mTOR) signaling pathway. Furthermore, miR-18a significantly modulates tamoxifen resistance by regulating cell cycle proteins. Li XN et al. ( 2016 2016 ) found that the miR-18a inhibitor reduced the sensitivity of MCF-7 cells to tamoxifen, while miR-18a mimics sensitized BT474 cells to tamoxifen. Researchers have found that, acting as a molecular sponge for miR-222, over-expression of lncRNA GAS5 (growth arrest-specific transcript 5) enhanced cell sensitivity to tamoxifen in MCF-7R cells, which suppresses phosphatase and tensin homologs (Gu et al., 2018 2018 ). Expression levels of lncRNA H19 have shown an obvious increase in most BC patients and have been reported to increase BC chemotherapeutic resistance. Han JG et al. ( 2018 2018 ) investigated the expression level of lncRNA H19 in paclitaxel-resistant and paclitaxel-sensitive cell lines. They found that the level of lncRNA H19 expression was higher in paclitaxel-resistant cells. Moreover, knockdown of H19 suppressed the Akt (protein kinase B) signaling pathway, which is associated with paclitaxel-resistance, to trigger apoptosis. Thus, they theorized that H19 might restore drug resistance in paclitaxel-resistant TNBC by regulating the Akt signaling pathway. In recent years, researchers have found that knockdown of lncRNA HOTAIR (Hox transcript antisense RNA) could reduce drug‑resistance via phosphoinosmde-3-kinase (PI3K)/Akt/mTOR signaling pathways (Li ZX et al., 2019 2019 ). With increasing attention paid to drug resistance, more lncRNAs are being reported to play vital roles in drug resistance in various cancers. In addition to the above lncRNAs, Chen et al. ( 2017 2017 ) identified difficult lncRNAs associated with drug resistance in cancer, including PVT1 (plasmacytoma variant translocation 1), ANRIL , MRUL (multidrug resistance (MDR)-related and upregulated lncRNA), and CCAL (colorectal cancer-associated lncRNA). At present, studies on cancer drug resistance related to lncRNAs and miRNAs are still in their infancy, and the role of ncRNA in chemotherapy resistance demands further investigation. Clinical significance of miRNA and lncRNA in BC 1 BC is the third highest incident cancer worldwide and the second most common cause of death from cancer in women. The burden of BC is an important challenge for women’s health throughout the world (Ferlay et al., 2010 2010 ; Hiatt and Brody, 2018 2018 ). Li N et al. ( 2019 2019 ) described and studied the impact of geographical location, the social development index (SDI), age, and gender in BC events, death, and disability-adjusted life years (DALYs). Disease reduction has been observed in higher SDI regions and the gap between lower and higher SDI regions may become wider. Action is needed to address the BC burden to reduce disease in low SDI regions. miRNAs and lncRNAs have great potential as effective biomarkers because of their high stability and efficient detection in body fluids (Kunej et al., 2014 2014 ; Matamala et al., 2015 2015 ). Numerous recent studies have shown that the expression levels of lncRNAs and miRNAs were associated with clinicopathological features. For example, Chen et al. ( 2012 2012 ) found that high miR-155 expression showed significant correlation with higher tumor grade, advanced tumor stage, and lymph node metastasis, but no relation with age, tumor size, tumor histology, the status of ER, or PR and HER2 expression. Wang and Zhang ( 2012 2012 ) found that the relative expression of miR-21 had no connection with gender, age, ER, PR, and KI-67 status. Using TCGA, researchers found that over-expressed miRNA-18a, miRNA-205, and miRNA-744 in breast tumor samples were all connected with better overall survival in ER/PR-positive and lymph node-negative diseases (Kim et al., 2017 2017 ). High MALAT1 expression in BC tissue was significantly correlated with lymph metastasis, tumor size, and adverse 5-year disease-free survival (Miao et al., 2016 2016 ; Li J et al., 2018 2018 ). Tian et al. ( 2018 2018 ) identified 48 lncRNAs correlated with clinicopathological features (including tumor size, lymph node metastasis, histological grade, tumor-node-metastasis (TNM) stage, and ER, PR, and HER-2 statuses of BC), and 32 lncRNAs involved in the survival of BC. They found that the increased levels of MALAT1 and TUSC7 (tumor suppressor candidate 7) expression were respectively connected with positive PR and positive HER-2 statuses. Moreover, high expression of CCAT2 (colon cancer-associated transcript 2), MALAT1, or NEAT1 (nuclear paraspeckle assembly transcript 1) had shorter overall survival (Tian et al., 2018 2018 ). Certainly, the relationship between miRNAs or lncRNAs and clinical characteristics should be explored through further research with large sample sizes. The utilization of miRNAs and lncRNAs as biomarkers of BC has the potential to change present therapies. Conclusions and prospect 1 In this study, we discussed the role of miRNA and lncRNA in TNBC progression and summarized lncRNAs and miRNAs which are abnormally expressed in TNBC. Previous studies have demonstrated that many miRNAs and some lncRNAs are involved in the occurrence and developmental progress of breast malignant tumors. This informs our reflections on the significance of the combination of lncRNAs and miRNAs in treating various cancers, including TNBC. It is well known that most miRNAs are able to function by binding to the 3' UTR of the mRNA to regulate target gene expression. However, new research has shown that miRNAs can also influence gene expression by attaching to the open reading frame (ORF) region of target genes. This raises important questions as to whether miRNAs and other ncRNAs regulate gene expression through other binding sites. As for cancer drug resistance, owing to the complexity of mechanisms caused by various factors, the research is still preliminary. 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This article does not contain any studies with human or animal subjects performed by any of the authors. 10.1631/jzus.B1900709 Project supported by the Zhejiang Provincial Natural Science Foundation of China (No. LY18C050006) and the Key Research and Development Project of Zhejiang Province (No. 2020C02039) 2019-12-19 2020-05-28 2022-01-05 Copyright © Zhejiang University and Springer-Verlag GmbH Germany, part of Springer Nature 2020 2020 Journal of Zhejiang University-SCIENCE B (Biomedicine and Biotechnology) 09 21