Long Non-Coding RNA Signatures in Lymphopoiesis and Lymphoid Malignancies
Abstract
:1. Introduction: A Glance into Long Non-Coding RNAs
2. LncRNAs in Normal Lymphopoiesis
2.1. LncRNAs in Normal B Lymphopoiesis
2.2. LncRNAs in Normal T Lymphopoiesis
2.3. LncRNAs in Normal NK Lymphopoiesis
3. Alterations in lncRNAs in LYMPHOID Malignancy
3.1. Alterations in lncRNAs in Acute Lymphocytic Leukemia (ALL)
3.1.1. Alterations in lncRNAs in B-ALL
3.1.2. Alterations in lncRNAs in T-ALL
3.2. Alterations in lncRNAs in Chronic Lymphocytic Leukemia (CLL)
4. Alterations in lncRNAs in Non-Hodgkin Lymphoma
4.1. Alterations in lncRNAs in B-Cell Lymphomas
4.2. Alterations in lncRNAs in T/NK-Cell Lymphomas
5. Future Prospectives and Clinical Applications of lncRNAs
6. Conclusions
Author Contributions
Funding
Institutional Review Board Statement
Informed Consent Statement
Data Availability Statement
Acknowledgments
Conflicts of Interest
Abbreviations
ALL | Acute lymphocytic leukemia |
BL | Burkitt’s lymphoma |
CASC15 | Cancer susceptibility candidate 15 |
CLL | Chronic lymphocytic leukemia |
DDX5 | DEAD-box RNA helicase |
DLBCL | Diffuse large B-cell lymphoma |
FLICR | Foxp3 long intergenic noncoding RNA |
Flatr | Foxp3-specific lncRNA anticipatory of Tregs |
FL | Follicular lymphoma |
GAS5 | Growth arrest-specific 5 |
HSC | Hematopoietic stem cells |
HOTAIR | Hox transcript antisense intergenic RNA |
HOTTIP | HOXA transcript at the distal tip |
HOXA-AS2 | HOXA cluster antisense RNA 2 |
IFNγ-AS1 | Interferon gamma antisense RNA 1 |
LncRNAs | Long non-coding RNAs |
LEF1-AS1 | Lymphoid enhancer-binding factor 1-antisense RNA 1 |
MALAT1 | Metastasis associated lung adenocarcinoma transcript 1 |
MEG3 | Maternally expressed gene 3 |
MYB-AS1 | MYB antisense RNA 1 |
MIAT | Myocardial infarction associated transcript |
MCL | Mantle-cell lymphoma |
mTOR | Mammalian target of rapamycin |
NcRNAs | Non-coding RNAs |
NK cell | Natural killer cell |
NEAT1 | Nuclear enriched abundant transcript 1 |
NHL | Non-Hodgkin lymphoma |
NKTCL | Natural killer/T-cell lymphoma |
PAIR | PAX5-activated intergenic repeat |
PANDA | P21-associated ncRNA DNA damage-activated |
PRC2 | Polycomb repressive complex 2 |
PI3K | Phosphatidylinositol 3-kinase |
PiRNAs | PIWI-interacting RNAs |
RNASeq | RNA-sequencing |
RT-PCR | Reverse transcription polymerase chain reaction |
SncRNAs | Small non-coding RNAs |
SiRNAs | Small interfering RNAs |
SMAD1-AS1 | SMAD1 antisense RNA 1 |
ShRNA | Short hairpin RNA |
XIST | X-inactive specific transcript |
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Alteration | Subtype | Target | Function | Ref. | |
---|---|---|---|---|---|
Oncogenic lncRNAs | |||||
TCL6 | Upregulated | ETV6-RUNX1 | Unknown | Low expression associated with poor disease-free survival | [71] |
LINC0098 | Upregulated | Pre B-ALL t(12:21) ETV6-RUNX1 and High hyperdiploid | miR-330-5p | miRNA sponge | [85] |
BALR-2 | Upregulated | B-ALL t (12;21), t (1;19) and MLL-rearrangement | JUN and BIM | Increases cell growth and prednisolone resistance, associated with poor survival | [74] |
RP11-137H2.4 | Upregulated | B-ALL | NRAS/BRAF/NF-κB MAPK pathways | Inhibits proliferation and migration | [80] |
ENST00000443469 | Upregulated | B-ALL MLL-rearrangement | LAMP5 | Promotes cell proliferation and inhibits apoptosis | [82] |
LINC00152 | Upregulated | B-ALL | Unknown | Associated with risk of early relapse | [81] |
BALR-6 | Upregulated | B-ALL MLL-rearrangement | SP1-mediated transcription of CREB1 | Promotes cell proliferation and inhibits apoptosis | [86] |
CRNDE | Upregulated | B-ALL | miR-345-5p | Promotes cell proliferation and inhibits apoptosis | [87] |
ZEB1-AS1 | Upregulated | B-ALL | IL11/STAT3 pathway | Increases cell proliferation | [88] |
Tumor suppressive lncRNAs | |||||
IUR | Downregulated | B-ALL Ph+ | STAT5 and CD71 | Increases cell growth and survival | [75] |
LINC00221 | Downregulated | B-ALL | miR 152-3P and ATP2A2 | Promotes apoptosis and inhibits tumor proliferation | [76] |
CASC15 | Upregulated | B-ALL ETV6-RUNX1 | SOX4 | Promotes apoptosis and inhibits tumor proliferation | [74,78] |
lnc-NKX2-3-1 | Upregulated | B-ALL ETV6-RUNX1 | Unknown | Unknown | [72] |
lnc-TIMM21-5 | Upregulated | B-ALL ETV6-RUNX1 | Unknown | Unknown | [72] |
lnc-ASTN1-1 | Upregulated | B-ALL ETV6-RUNX1 | Unknown | Unknown | [72] |
lnc-RTN4R-1 | Upregulated | B-ALL ETV6-RUNX1 | Unknown | Unknown | [72] |
Alteration | Target | Function | Ref. | |
---|---|---|---|---|
SNHG1 | Upregulated | miR 124-3P | Promotes cell proliferation and migration | [107] |
PVT1 | Upregulated | miR-486-5p, NOP2 and Myc | Increases cell viability, deregulates cell cycle, and inhibits apoptosis | [97] |
ARIEL | Upregulated | ARID5B | Increases cell growth and survival | [93] |
LUNAR1 | Upregulated | IGF1R | Increases cell growth | [99,108] |
NALT | Upregulated | Notch signaling | Induces cell proliferation | [100] |
NEAT1 | Upregulated | miR-146b-5p | Promotes cell proliferation and growth | [101] |
AWPPH | Upregulated | ROCK2 | Promotes cell proliferation and inhibits apoptosis | [104] |
T-ALL-R-LncR1 | Upregulated | Par-4/THAP1 protein complex | Inhibits apoptosis | [105] |
H19 | Upregulated | SOX2, OCT4 and NANOG | Maintains stemness, promotes cell proliferation, and inhibits apoptosis | [102,109] |
LINC00853 | Downregulated | CCR9 expression | Inhibits cell proliferation and migration | [110] |
EBLN3P | Upregulated | miR-655-3p | Increases proliferation, invasion, and migration | [106] |
PPM1A-AS | Upregulated | Notch, PI3K-AKT, and JAK-STAT signaling | Regulates cell proliferation and apoptosis | [111] |
LINC00478 | Upregulated | mir-125b | Increases cell growth and invasiveness | [112] |
Alteration | Target | Function | Ref. | |
---|---|---|---|---|
Lnc-IRF2-3 | Upregulated | Unknown | Promotes cell proliferation and inhibits apoptosis | [113] |
Lnc-ZNF667-AS1 | Upregulated | Unknown | Poor prognosis and survival | [113] |
treRNA | Upregulated | ZAP70 | Poor prognosis and survival | [114] |
MIAT | Upregulated | OCT4 | Inhibits apoptosis and increases aggressiveness | [115] |
GAS5 | Downregulated | miR-222 | Promotes tumorigenesis and metastasis | [116] |
LincRNA-P21 | Downregulated | p53 | Inhibits apoptosis | [117] |
BM742401 | Downregulated | Cas9 and 8 | Promotes cell proliferation and inhibits apoptosis | [118] |
DLEU2 | Downregulated | miR-15a and miR-16-1 | A tumor suppressor | [37] |
LEF1-AS1 | Upregulated | LEF1 | Inhibits apoptosis | [119] |
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Baghdadi, H.; Heidari, R.; Zavvar, M.; Ahmadi, N.; Shakouri Khomartash, M.; Vahidi, M.; Mohammadimehr, M.; Bashash, D.; Ghorbani, M. Long Non-Coding RNA Signatures in Lymphopoiesis and Lymphoid Malignancies. Non-Coding RNA 2023, 9, 44. https://doi.org/10.3390/ncrna9040044
Baghdadi H, Heidari R, Zavvar M, Ahmadi N, Shakouri Khomartash M, Vahidi M, Mohammadimehr M, Bashash D, Ghorbani M. Long Non-Coding RNA Signatures in Lymphopoiesis and Lymphoid Malignancies. Non-Coding RNA. 2023; 9(4):44. https://doi.org/10.3390/ncrna9040044
Chicago/Turabian StyleBaghdadi, Hamed, Reza Heidari, Mahdi Zavvar, Nazanin Ahmadi, Mehdi Shakouri Khomartash, Mahmoud Vahidi, Mojgan Mohammadimehr, Davood Bashash, and Mahdi Ghorbani. 2023. "Long Non-Coding RNA Signatures in Lymphopoiesis and Lymphoid Malignancies" Non-Coding RNA 9, no. 4: 44. https://doi.org/10.3390/ncrna9040044