Functional Relationships between Long Non-Coding RNAs and Estrogen Receptor Alpha: A New Frontier in Hormone-Responsive Breast Cancer Management
Abstract
:1. Introduction
2. Ligand-Induced and Constitutive Activity of ERα
3. lncRNAs and Cancer
4. Current Methods for the Functional Analysis of lncRNAs
Method | Reference |
---|---|
Determination of the intracellular lncRNA localization | |
Quantitative PCR (qPCR) | [34] |
RNA-fluorescent in situ hybridization (RNA-FISH) | [35] |
RNA-FISH combined with stochastic optical reconstruction microscopy (STORM) | [36] |
lncRNA labeling with aptamers linked to fluorescent tags | [37,38] |
lncRNA depletion or over-expression | |
Small interfering RNA (siRNA) silencing | [78,79] |
Short hairpin RNA (shRNA) silencing | [80] |
Antisense oligonucleotide (ASO) silencing | [79] |
CRISPR/Cas9 knock-out/knock-in | [81] |
The establishment of secondary and three-dimensional lncRNA structures | |
Shotgun secondary structure fragment analysis | [40] |
Solution-state nuclear magnetic resonance (NMR) spectroscopy | [43,44] |
Small-angle scattering (SAS) | [45] |
X-ray diffraction and cryo-electron microscopy | [39] |
Computational prediction | [41,42,46] |
The determination of lncRNA-protein interactions (LPIs) | |
Cross-linking immunoprecipitation (CLIP) | [49,50] |
Targets of RNA-binding proteins identified by editing (TRIBE) | [51] |
Digestion-optimized RNA immunoprecipitation cDNA library sequencing (DO-RIP-seq) | [52] |
RNA-affinity purification followed by mass spectrometry | [53,54,55,56] |
RNA-affinity purification followed by protein microarrays | [57] |
The isolation of target RNA molecules by biotinylated antisense probes | [54,58] |
The isolation of target RNA molecules by peptide nucleic acid oligomers | [55] |
HB-tag-based affinity RNA purification | [56] |
Chromatin isolation with RNA purification (ChIRP) | [59,60] |
RNA chromosome conformation capture (R3C) | [61] |
LPI computational prediction | [72] |
The biophysical characterization of quantitative and qualitative LPIs | |
Electrophoretic mobility shift assay (EMSA) | [62] |
Filter-binding assays | [82] |
Surface plasmon resonance | [63,64] |
The evaluation of the coding capacity of lncRNAs | |
Ribosome profiling | [83] |
Mass spectrometry | [84] |
Global translation initiation sequencing (GTI-seq) | [73] |
5. LncRNA Mechanisms in Breast Cancer
5.1. Estrogen-Inducible lncRNAs
5.1.1. lncRNA H19
5.1.2. HOX Transcript Antisense RNA (HOTAIR)
5.1.3. lncRNA ERINA
5.1.4. Myocardial Infarction-Associated Transcript (MIAT)
5.1.5. Long Intergenic Non-Protein Coding RNA 472 (LINC00472) and Long Intergenic Non-Protein Coding RNA 1016 (LINC01016)
5.1.6. lncRNA DSCAM-AS1 Regulation by Unliganded ERα
5.2. lncRNAs Able to Regulate ERα Expression
5.3. Enhancer RNAs (eRNAs)
LncRNAs | Expression in BC | Regulation | Cellular Functions | References |
---|---|---|---|---|
lncRNA H19 | Up-regulation | Estrogen-dependent | Proliferation, tumorigenesis, migration, invasion, and EMT | [90,92,93] |
HOTAIR (HOX transcript antisense RNA | Up-regulation | Estrogen-dependent | Proliferation, invasion, migration, survival, epigenetic regulation, and chemotherapy resistance | [94,97] |
LncRNA ERINA | Up-regulation | Estrogen-dependent | Proliferation, survival, and chemotherapy resistance | [101] |
MIAT (myocardial infarction-associated transcript) | Up-regulation | Estrogen-dependent | Proliferation, migration, invasion, chemotherapy resistance, and EMT | [102] |
LINC00472 | Up-regulation | Estrogen-dependent | Proliferation, survival, migration, and invasion | [110,111] |
LINC01016 | Up-regulation | Estrogen-dependent | Proliferation and survival | [114] |
LncRNA DSCAM-AS1 | Up-regulation | Estrogen-independent | Tumorigenic processes, DNA replication, chromosome, segregation, survival, and EMT | [113,116] |
TMPO-AS1 (TMPO antisense RNA1) | Up-regulation | Regulation of ERα expression | Proliferation and cell growth | [118] |
MIR2052HG | Up-regulation | Regulation of ERα expression | Proliferation and cell growth | [120,121] |
6. Prognostic and Clinical Significance of lncRNAs in Hormone-Responsive BC Treatments
7. Conclusions
Author Contributions
Funding
Institutional Review Board Statement
Informed Consent Statement
Data Availability Statement
Conflicts of Interest
Abbreviations
AI | Aromatase Inhibitor |
AKT | Ak strain Transforming gene |
ANRIL | Antisense Non-coding RNA in the INK4 Locus |
ASOs | Antisense Oligonucleotides |
BC | Breast Cancer |
BrCSCs | Breast Cancer Stem-like Cells |
c-MET | Mesenchymal Epithelial Transition cellular oncogene |
CBP | cAMP-regulated-enhancer (CRE)-binding protein (CREB)-Binding Protein |
CDK2 | Cyclin-dependent Kinase 2 |
CDK4-6 | Cyclin-dependent Kinase 4-6 |
ceRNA | Competing endogenous RNA |
ChIP-Seq | Chromatin Immunoprecipitation Sequencing |
ChIRP | Chromatin Isolation by RNA Purification |
CLIP | Cross-Linking Immunoprecipitation |
CRISPR/Cas9 | Clustered Regularly Interspaced Short Palindromic Repeats-CRISPR associated protein 9 |
DES | Diethylstilbestrol |
DO-RIP-seq | Digestion-Optimized RNA Immunoprecipitation cDNA library sequencing |
DSCAM-AS1 | Down Syndrome Cell Adhesion Molecule antisense1 |
DUSP7 | Dual Specificity Phosphatase 7 |
E2F1 | E2F transcription factor 1 |
EED | Embryonic Ectoderm Development |
EFEMP1 | EGF-containing fibulin-like extracellular matrix protein 1 |
EGR1 | Early Growth Response 1 |
EMSA | Electrophoretic mobility shift assay |
EMT | Epithelial-mesenchymal transition |
EREs | Estrogen Response Element |
ERINA | Estrogen inducible lncRNA |
ERK | Extracellular signal-Regulated Kinase |
eRNAs | Enhancer RNAs |
ERα | Estrogen Receptor α |
ERα+ | Estrogen Receptor α positive |
ESR1 | Estrogen Receptor 1 |
ET | Endocrine Therapy |
ETR | Endocrine Therapy Resistance |
EZH2 | Enhancer of Zeste Homolog 2 |
FOXO3 | Forkhead Box O3 |
GRO-Seq | Global Run-On sequencing |
GTI-seq | Global Translation Initiation sequencing |
H3K27Ac | Histone 3 lysine 27 acetylation |
H3K4 | Histone H3 lysine K4 |
HB | Histidine-Biotin |
HBD | Hormone Binding Domain |
HDAC | Histone Deacetylase |
HER2 | Human Epidermal growth factor Receptor 2 |
HGF | Hepatocyte Growth Factor |
hnRNPL | Heterogeneous nuclear Ribonucleoprotein L |
HOTAIR | HOX Transcript Antisense RNA |
ICI | Fulvestrant, ICI 182,780 |
KDM2A | Lysine demethylase 2A |
linc-ROR | Long Intergenic Non-Protein Coding RNA, Regulator Of Reprogramming |
LINC00472 | Long Intergenic Non-Protein Coding RNA 472 |
LINC01016 | Long Intergenic Non-Protein Coding RNA 1016 |
LMTK3 | Lemur Tyrosine Kinase 3 |
LNA | Locked nucleic acid-modified oligonucleotides |
lncRNA H19 | Long non-coding RNA H19 |
lncRNA ROR | Long non-coding RNA Regulator Of Reprogramming |
lncRNAs | Long non-coding RNAs |
LPI | LncRNA-Protein iInteraction |
LSD1 | Lysine-Specific Demethylase 1 |
MAFG-AS1 | MAF BZIP Transcription Factor G -AS1 |
MAPK | Mitogen-activated protein kinase |
MEK | Mitogen-activated protein kinase kinase |
MIAT | Myocardial Infarction-Associated Transcript |
miR-155-5p | microRNA-155-5p |
miR-339-5p | microRNA-339-5p |
MIR2052HG | MIR2052 Host Gene |
MLL1 | Mixed Lineage Leukemiaprotein-1 |
MLL3 | Mixed Lineage Leukemiaprotein-3 |
MLLs | Mixed Lineage Leukemias |
mRNA | messenger RNA |
mTOR | Mammalian Target Of Rapamycin |
ncRNAs | Non-coding RNAs |
NGS | Next-generation sequencing |
NMR | Nuclear Magnetic Resonance |
ORF | Open Reading Frame |
PI3K | Phosphatidylinositol-3 Kinase |
PKC | Protein Kinase C |
PR | Progesterone Receptor |
PRC2 | Polycomb Repressive Complex 2 |
PTM | Post-Translational Modification |
qPCR | Quantitative PCR |
R3C | RNA chromosome conformation capture |
RB1 | Retinoblastoma protein 1 |
RNA Pol II | RNA Polymerase II |
RNA-FISH | RNA-Fluorescent In Situ Hybridization |
RNA-Seq | RNA Sequencing |
RSK1 | Ribosomal S6 Kinase 1 |
SAS | Small-angle Scattering |
SERDs | Selective Estrogen Receptor Down-regulators |
SERMs | Selective Estrogen Receptor Modulators |
shRNAs | Short hairpin RNAs |
siRNAs | Small interfering RNAs |
sncRNAs | Small non-coding RNAs |
STORM | Stochastic Optical Reconstruction mMicroscopy |
SUZ12 | Suppressor of Zeste 12 homolog |
TDG | Thymine DNA glycosylase |
TM4SF1 | Transmembrane-4 L-six family member-1 |
TMPO | Thymopoietin |
TMPO-AS1 | TMPO antisense RNA1 |
TRIBE | Targets of RNA-binding proteins Identified By Editing |
UCA1 | Urothelial Carcinoma-Associated protein1 |
XIST | X-Inactive Specific Transcript |
ZEB1 | Zinc Finger E-Box Binding Homeobox 1 |
ZEB2 | Zinc Finger E-Box Binding Homeobox 2 |
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Melone, V.; Salvati, A.; Brusco, N.; Alexandrova, E.; D’Agostino, Y.; Palumbo, D.; Palo, L.; Terenzi, I.; Nassa, G.; Rizzo, F.; Giurato, G.; Weisz, A.; Tarallo, R. Functional Relationships between Long Non-Coding RNAs and Estrogen Receptor Alpha: A New Frontier in Hormone-Responsive Breast Cancer Management. Int. J. Mol. Sci. 2023, 24, 1145. https://doi.org/10.3390/ijms24021145
Melone V, Salvati A, Brusco N, Alexandrova E, D’Agostino Y, Palumbo D, Palo L, Terenzi I, Nassa G, Rizzo F, Giurato G, Weisz A, Tarallo R. Functional Relationships between Long Non-Coding RNAs and Estrogen Receptor Alpha: A New Frontier in Hormone-Responsive Breast Cancer Management. International Journal of Molecular Sciences. 2023; 24(2):1145. https://doi.org/10.3390/ijms24021145
Chicago/Turabian StyleMelone, Viola, Annamaria Salvati, Noemi Brusco, Elena Alexandrova, Ylenia D’Agostino, Domenico Palumbo, Luigi Palo, Ilaria Terenzi, Giovanni Nassa, Francesca Rizzo, Giorgio Giurato, Alessandro Weisz, and Roberta Tarallo. 2023. "Functional Relationships between Long Non-Coding RNAs and Estrogen Receptor Alpha: A New Frontier in Hormone-Responsive Breast Cancer Management" International Journal of Molecular Sciences 24, no. 2: 1145. https://doi.org/10.3390/ijms24021145