Myeloid leukemia vulnerabilities at CTCF-enriched long noncoding RNA loci

Abstract The noncoding genome presents a largely untapped source of biological insights, including thousands of long noncoding RNA (lncRNA) loci. While some produce bona fide lncRNAs, others exert transcript-independent cis-regulatory effects, and a lack of predictive features renders mechanistic dissection challenging. Here, we describe MYNRL15, a CTCF-enriched lncRNA locus and pan-myeloid leukemia dependency initially identified by expression-guided CRISPR interference screens. We show that accessibility and integrity of the MYNRL15 locus is required for myeloid leukemia maintenance; its perturbation selectively impairs acute myeloid leukemia (AML) cells compared to hematopoietic stem and progenitor cells in vitro, and depletes AML xenografts in vivo. While the MYNRL15 transcript and neighboring protein-coding genes appear dispensable, dense CRISPR tiling of the locus revealed two crucial candidate cis-regulatory DNA elements which drive the perturbation phenotype. Disruption of these elements triggers the formation of a tumor-suppressive, long-range chromatin interaction. By integrating transcriptome profiling with a CRISPR-Cas9 knockout screen of genes from the gained interaction region, we pinpointed two downregulated, potent cancer dependency genes as effectors of MYNRL15 disruption: WDR61 and IMP3. Finally, guided by distinctive features of the MYNRL15 locus, we find that elevated CTCF density characterizes a set of lncRNA loci enriched in leukemia vulnerabilities (22.6-24.2% essentiality rate). A catalog of CTCF-enriched lncRNA loci (C-LNCs) in 18 cell types representing different cancer entities and tissues is provided with this study, towards refining the search for noncoding oncogenic vulnerabilities in leukemia and other malignancies.

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Myeloid leukemia vulnerabilities at CTCF-enriched long noncoding RNA loci

10.21203/rs.3.rs-727909/v1 ◽

2021 ◽

Author(s):

Michelle Ng ◽

Lonneke Verboon ◽

Hasan Issa ◽

Raj Bhayadia ◽

Oriol Alejo-Valle ◽

...

Keyword(s):

Long Noncoding Rna ◽

Myeloid Leukemia ◽

Noncoding Rna ◽

K562 Cells ◽

Cell Types ◽

Clinical Aspects ◽

Hematopoietic Stem ◽

Regulatory Effects

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A novel hypoxic long noncoding RNA KB-1980E6.3 maintains breast cancer stem cell stemness via interacting with IGF2BP1 to facilitate c-Myc mRNA stability

Oncogene ◽

10.1038/s41388-020-01638-9 ◽

2021 ◽

Author(s):

Pengpeng Zhu ◽

Fang He ◽

Yixuan Hou ◽

Gang Tu ◽

Qiao Li ◽

...

Keyword(s):

Breast Cancer ◽

Long Noncoding Rna ◽

Noncoding Rna ◽

Underlying Mechanism ◽

Rapid Expansion ◽

Breast Cancer Patients ◽

Coding Region ◽

Signaling Axis

AbstractThe hostile hypoxic microenvironment takes primary responsibility for the rapid expansion of breast cancer tumors. However, the underlying mechanism is not fully understood. Here, using RNA sequencing (RNA-seq) analysis, we identified a hypoxia-induced long noncoding RNA (lncRNA) KB-1980E6.3, which is aberrantly upregulated in clinical breast cancer tissues and closely correlated with poor prognosis of breast cancer patients. The enhanced lncRNA KB-1980E6.3 facilitates breast cancer stem cells (BCSCs) self-renewal and tumorigenesis under hypoxic microenvironment both in vitro and in vivo. Mechanistically, lncRNA KB-1980E6.3 recruited insulin-like growth factor 2 mRNA-binding protein 1 (IGF2BP1) to form a lncRNA KB-1980E6.3/IGF2BP1/c-Myc signaling axis that retained the stability of c-Myc mRNA through increasing binding of IGF2BP1 with m6A-modified c-Myc coding region instability determinant (CRD) mRNA. In conclusion, we confirm that lncRNA KB-1980E6.3 maintains the stemness of BCSCs through lncRNA KB-1980E6.3/IGF2BP1/c-Myc axis and suggest that disrupting this axis might provide a new therapeutic target for refractory hypoxic tumors.

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Cardiac pathologies in mouse loss of imprinting models are due to misexpression of H19 long noncoding RNA

eLife ◽

10.7554/elife.67250 ◽

2021 ◽

Vol 10 ◽

Author(s):

Ki-Sun Park ◽

Beenish Rahat ◽

Hyung Chul Lee ◽

Zu-Xi Yu ◽

Jacob Noeker ◽

...

Keyword(s):

Endothelial Cells ◽

Ventricular Function ◽

Mouse Models ◽

Long Noncoding Rna ◽

Noncoding Rna ◽

Relative Importance ◽

Maternal Loss ◽

Loss Of Imprinting

Maternal loss of imprinting (LOI) at the H19/IGF2 locus results in biallelic IGF2 and reduced H19 expression and is associated with Beckwith-Wiedemann syndrome (BWS). We use mouse models for LOI to understand the relative importance of Igf2 and H19 mis-expression in BWS phenotypes. Here we focus on cardiovascular phenotypes and show that neonatal cardiomegaly is exclusively dependent on increased Igf2. Circulating IGF2 binds cardiomyocyte receptors to hyperactivate mTOR signaling, resulting in cellular hyperplasia and hypertrophy. These Igf2-dependent phenotypes are transient: cardiac size returns to normal once Igf2 expression is suppressed postnatally. However, reduced H19 expression is sufficient to cause progressive heart pathologies including fibrosis and reduced ventricular function. In the heart, H19 expression is primarily in endothelial cells (ECs) and regulates EC differentiation both, in vivo and in vitro. Finally, we establish novel mouse models to show that cardiac phenotypes depend on H19 lncRNA interactions with Mirlet7 microRNAs.

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LncRNA-SMILR modulates RhoA/ROCK signaling by targeting miR-141 to regulate vascular remodeling in pulmonary arterial hypertension

AJP Heart and Circulatory Physiology ◽

10.1152/ajpheart.00717.2019 ◽

2020 ◽

Vol 319 (2) ◽

pp. H377-H391 ◽

Cited By ~ 1

Author(s):

Si Lei ◽

Fei Peng ◽

Mei-Lei Li ◽

Wen-Bing Duan ◽

Cai-Qin Peng ◽

...

Keyword(s):

Smooth Muscle ◽

Pulmonary Arterial Hypertension ◽

Arterial Hypertension ◽

Long Noncoding Rna ◽

Vascular Remodeling ◽

Noncoding Rna ◽

In Vivo Models ◽

Pulmonary Arterial

Smooth muscle-enriched long noncoding RNA (SMILR), as a long noncoding RNA (lncRNA), was increased in pulmonary arterial hypertension (PAH) patients and in vitro and in vivo models. SMILR activated RhoA/ROCK signaling by targeting miR-141 to disinhibit its downstream target RhoA. SMILR knockdown or miR-141 overexpression inhibited hypoxia-induced cell proliferation and migration via repressing RhoA/ROCK signaling in pulmonary arterial smooth muscle cells (PASMCs), which was confirmed in vivo experiments that knockdown of SMILR inhibited vascular remodeling and alleviated PAH in rats. SMILR may be a promising and novel therapeutic target for the treatment and drug development of PAH.

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The Role of STAT5 in HOXA9-Associated Leukemia

Blood ◽

10.1182/blood.v128.22.3919.3919 ◽

2016 ◽

Vol 128 (22) ◽

pp. 3919-3919

Author(s):

Peilin Ma ◽

Yuqing Sun ◽

Jingya Wang ◽

Weihua Song ◽

Tao Xu ◽

...

Keyword(s):

Binding Sites ◽

Myeloid Leukemia ◽

Tandem Duplication ◽

Conflicts Of Interest ◽

Hematopoietic Stem ◽

Constitutive Activation ◽

Oncogenic Mutation

Abstract Homeobox A9 (HOXA9) is a homeodomain-containing transcription factor that is essential for hematopoietic stem cell expansion and differentiation. Deregulation of HOXA9 is commonly observed in human acute myeloid leukemia (AML). About half of AML patients overexpress HOXA9 as a result of MLL rearrangements, NUP98 translocations, NPM1 mutations or CDX2/CDX4 overexpression. Despite its central importance in leukemia, the mechanism of transcriptional regulation by HOXA9 and its downstream effectors are poorly understood. HOXA9 physically interacts with MEIS1, a cofactor that greatly accelerates leukemia development in transplanted animals. Our group recently identified a number of transcription factors as HOXA9 potential collaborators by genomic profiling of HOXA9 binding sites and mass spectroscopy. One of these putative collaborators is signal transducer and activator of transcription 5 (STAT5), which coimmunoprecipitates with HOXA9. Furthermore STAT motifs extensively overlap with HOXA9 binding sites. STAT5 is important for survival, proliferation and differentiation of hematopoietic cells and constitutive activation of STAT5 has also been observed in human leukemias bearing oncogenic mutation of Jak2, Bcr-Abl, c-Kit and Flt3. FLT3 internal tandem duplication (FLT3-ITD) is observed in 25% of patients with MLL-partial tandem duplication (MLL-PTD) and is associated with HOXA9 upregulation and unfavorable prognosis. Therefore, we hypothesized that the interaction of HOXA9 and STAT5 may play a role in HOXA9-associated leukemogenesis. Treatment of human cell lines bearing MLL-AF9 and FLT3-ITD with specific FLT3 and STAT5 inhibitors showed that suppression of the constitutive activation of STAT5 significantly inhibits the hyper-proliferation of these cells. We then overexpressed FLT3-ITD or active mutation of STAT5 (STAT5 1*6) in mouse hematopoietic stem cells /progenitor cells (HSC/PCs) transduced with MLL-AF9 or HOXA9 and found that constitutively active STAT5 enhances cell proliferation in vitro. We next transduced HOXA9 into HSC/Pcs from wild type (WT) or FLT3-ITD transgenic mice and transplanted these cells into sublethally irradiated WT mice. All of these recipients developed myeloid leukemia, with recipients transplanted with FLT3-ITD (n=4) developing leukemia significantly earlier than WT controls (n=5, p<0.05), suggesting that FLT3-ITD mediated STAT5 activation enhanced HOXA9-induced leukemogenesis in vivo. To further assess the role of STAT5 in HOXA9-mediated transformation, we performed ChIP-Seq assay with HOXA9-transformed cells and identified nearly half of STAT5 binding sites (228 out of 596) colocalized with HOXA9. Most of these cobound sites are located in distal intergenic (61.0%) and intron (35.1%) regions. Five cobound regions (Il2rα, Fgf1, Pdlim5, Pim1, Fabp5) were selected and confirmed by ChIP-qPCR. To further characterize the interaction between HOXA9 and STAT5, GST pull-down assays were performed that showed that the c-terminal of HOXA9 is critical for interaction with STAT5. Overall, the findings suggest that STAT5 promotes HOXA9-induced transformation by functionally interacting with HOXA9 at HOXA9-regulated enhancers. Disclosures No relevant conflicts of interest to declare.

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Lentivirus-Mediated RNA Interference Targeting the Long Noncoding RNA HOTAIR Inhibits Proliferation and Invasion of Endometrial Carcinoma Cells In Vitro and In Vivo

International Journal of Gynecological Cancer ◽

10.1097/igc.0000000000000121 ◽

2014 ◽

Vol 24 (4) ◽

pp. 635-642 ◽

Cited By ~ 41

Author(s):

Jiaming Huang ◽

Peiqi Ke ◽

Luyan Guo ◽

Wei Wang ◽

Hao Tan ◽

...

Keyword(s):

Cell Cycle ◽

Cell Proliferation ◽

Endometrial Cancer ◽

Endometrial Carcinoma ◽

Cancer Cells ◽

Long Noncoding Rna ◽

Noncoding Rna ◽

Proliferation And Invasion

ObjectiveThe overexpression of long noncoding RNA HOTAIR is associated with various aggressive solid carcinomas. However, its relationship with endometrial carcinoma has not been reported. The present study aimed to investigate the expression of the long noncoding RNA HOTAIR in endometrial carcinoma, its relationship with the carcinoma’s clinicopathologic features, and the biological function of HOTAIR in regulating endometrial cancer cell proliferation and invasion in vitro and in vivo.MethodsThe expression of HOTAIR was detected in different tissues and cell lines by real-time PCR. Lentivirus-mediated HOTAIR-specific shRNAvectors were transfected into endometrial cancer HEC-1A cells. Cell proliferation and colony formation were examined by CCK-8 assays and colony formation assays, respectively. Invasion and migration were examined by Transwell assays. Flow cytometry assay was used to examine the cell cycle. In addition, xenograft model assays were performed to analyze the growth of endometrial cancer cells in vivo.ResultsOur data showed that HOTAIR expression was higher in endometrial cancer cells and tissues than in normal endometrial tissues. HOTAIR expression was closely related to the tumor stage (P= 0.045), myometrial invasion (P= 0.014), and lymph node metastasis (P= 0.033). The down-regulation of HOTAIR resulted in a significant inhibition of cell proliferation, migration, and invasion and in cell cycle arrest at the G0/G1 phase. Furthermore, HOTAIR depletion significantly suppressed the endometrial cancer tumorigenesis in vivo.ConclusionsThis study is the first to suggest that HOTAIR plays an important role in the carcinogenesis of endometrial cancer. Targeting HOTAIR may be a novel therapeutic strategy for endometrial cancer.

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The Long Noncoding RNA HOTAIR Promotes Colorectal Cancer Progression by Sponging miR-197

Oncology Research Featuring Preclinical and Clinical Cancer Therapeutics ◽

10.3727/096504017x15105708598531 ◽

2018 ◽

Vol 26 (3) ◽

pp. 473-481 ◽

Cited By ~ 18

Author(s):

Xinyang Lu ◽

Zhiqiang Liu ◽

Xiaofei Ning ◽

Lunhua Huang ◽

Biao Jiang

Keyword(s):

Colorectal Cancer ◽

Cancer Progression ◽

Long Noncoding Rna ◽

Noncoding Rna ◽

Migration And Invasion ◽

Downstream Target ◽

Potential Applications ◽

Colorectal Cancer Progression

The long noncoding RNA HOX transcript antisense RNA (HOTAIR) has been found to be overexpressed in many human malignancies and involved in tumor progression and metastasis. Although the downstream target through which HOTAIR modulates tumor metastasis is not well known, evidence suggests that microRNA-197 (miR-197) might be involved in this event. In the present study, the significance of HOTAIR and miR-197 in the progression of colorectal cancer was detected in vitro and in vivo. We found that HOTAIR expression was significantly increased in colorectal cancer cells and tissues. In contrast, the expression of miR-197 was obviously decreased. We further demonstrated that HOTAIR knockdown promoted apoptosis and inhibited cell proliferation, migration, and invasion in vitro and in vivo. Moreover, HOTAIR modulated the progression of colorectal cancer by competitively binding miR-197. Taken together, our study has identified a novel pathway through which HOTAIR exerts its oncogenic role and provided a molecular basis for potential applications of HOTAIR in the prognosis and treatment of colorectal cancer.

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Long noncoding RNA WEE2-AS1 plays an oncogenic role in glioblastoma by functioning as a molecular sponge for microRNA-520f-3p

Oncology Research Featuring Preclinical and Clinical Cancer Therapeutics ◽

10.3727/096504020x15982623243955 ◽

2020 ◽

Author(s):

Hengzhou Lin ◽

Dahui Zuo ◽

Jiabin He ◽

Tao Ji ◽

Jianzhong Wang ◽

...

Keyword(s):

Long Noncoding Rna ◽

Noncoding Rna ◽

Molecular Mechanisms ◽

Cell Counting ◽

Migration And Invasion ◽

Tumor Diameter ◽

Polymerase Chain ◽

Specificity Protein

The long noncoding RNA WEE2 antisense RNA 1 (WEE2-AS1) plays anoncogenic role in hepatocellular carcinoma and triple negative breast cancerprogression. In this study, we investigated the expression and roles of WEE2-AS1 inglioblastoma (GBM). Furthermore, the molecular mechanisms behind the oncogenicactions of WEE2-AS1 in GBM cells were explored in detail. WEE2-AS1 expressionwas detected using quantitative real-time polymerase chain reaction. The roles ofWEE2-AS1 in GBM cells were evaluated by the Cell Counting Kit-8 assay, flowcytometric analysis, and Transwell cell migration and invasion assays, and tumorxenograft experiments. WEE2-AS1 expression was evidently enhanced in GBM tissuesand cell lines compared with their normal counterparts. An increased level of WEE2-AS1 was correlated with the average tumor diameter, Karnofsky Performance Scalescore, and shorter overall survival among GBM patients. Functionally, depleted WEE2-AS1 attenuated GBM cell proliferation, migration, and invasion in vitro, promoted cellapoptosis, and impaired tumor growth in vivo. Mechanistically, WEE2-AS1 functionedas a molecular sponge for microRNA-520f-3p (miR-520f-3p) and consequentlyincreased specificity protein 1 (SP1) expression in GBM cells. A series of recoveryexperiments revealed that the inhibition of miR-520f-3p and upregulation of SP1 couldpartially abrogate the influences of WEE2-AS1 downregulation on GBM cells. Inconclusion, WEE2-AS1 can adsorb miR-520f-3p to increase endogenous SP1expression, thereby facilitating the malignancy of GBM. Therefore, targeting theWEE2-AS1-miR-520f-3p-SP1 pathway might be a promising therapy for themanagement of GBM in the future.

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Long noncoding RNA SNHG1 promotes TERT expression by sponging miR-18b-5p in breast cancer

10.21203/rs.3.rs-218768/v2 ◽

2021 ◽

Author(s):

yujuan Kang ◽

Lin Wan ◽

Qin Wang ◽

Yanling Yin ◽

Jiena Liu ◽

...

Keyword(s):

Breast Cancer ◽

Long Noncoding Rna ◽

Noncoding Rna ◽

Malignant Tumors ◽

Positive Role ◽

Nucleolar Rna ◽

Human Malignant Tumors ◽

Tert Expression

Abstract Background: Long noncoding RNA (lncRNA) small nucleolar RNA host gene 1 (SNHG1) plays a positive role in the progression of human malignant tumors. However, the molecular mechanism of SNHG1 remains elusive in breast cancer. Results: LncRNA SNHG1 was upregulated and had a positive relationship with poor prognosis according to bioinformatics analysis. Silencing SNHG1 inhibited tumorigenesis in breast cancer both in vitro and in vivo. Mechanistically, SNHG1 functioned as a ceRNA to promote TERT expression by sponging miR-18b-5p. Moreover, miR-18b-5p acted as a tumor repressor in breast cancer. Finally, E2F1, a transcription factor, enhanced SNHG1 transcription.Conclusions: Our results provide a comprehensive understanding of the oncogenic mechanism of lncRNA SNHG1 in breast cancer. Importantly, we identified a novel E2F1–SNHG1–miR-18b-5p–TERT axis, which may be a potential therapeutic target for breast cancer.

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