LINC00649 underexpression is an adverse prognostic marker in acute myeloid leukemia

Relationship between long non-coding RNAs and Hippo signaling pathway in gastrointestinal cancers; molecular mechanisms and clinical significance

Long non-coding RNAs (lncRNAs) play a significant biological role in the regulation of various cellular processes such as cell proliferation, differentiation, apoptosis and migration. In various malignancies, lncRNAs interplay with some main cancer-associated signaling pathways, including the Hippo signaling pathway to regulate the various cellular processes. It has been revealed that the cross-talking between lncRNAs and Hippo signaling pathway involves in gastrointestinal (GI) cancers development and progression. Considering the clinical significance of these lncRNAs, they have also been introduced as potential biomarkers in diagnostic, prognostic and therapeutic strategies in GI cancers. Herein, we review the mechanisms of lncRNA-mediated regulation of Hippo signaling pathway and focus on the corresponding molecular mechanisms and clinical significance of these non-coding RNAs in GI cancers.

Computational analysis of heat shock proteins and ferroptosis-associated lncRNAs to predict prognosis in acute myeloid leukemia patients

Owing to their functional diversity in many cancers, long noncoding RNAs (lncRNAs) are receiving special attention. LncRNAs not only function as oncogenes or tumor suppressors by participating in various signaling pathways but also serve as predictive markers for various types of cancer, including acute myeloid leukemia (AML). Considering this, we investigated lncRNAs that may act as a mediator between two processes, i.e., heat shock proteins and ferroptosis, which appear to be closely related in tumorigenesis. Using a comprehensive bioinformatics approach, we identified four lncRNAs (AL138716.1, AC000120.1, AC004947.1, and LINC01547) with prognostic value in AML patients. Of interest, two of them (AC000120.1 and LINC01547) have already been reported to be AML-related, and AC004947.1 is considered to have oncogenic potential. In particular, the signature obtained showed a lower survival probability with high-risk patients, and vice versa. To our knowledge, this is the first predictive model of lncRNA that may correlate with the processes of heat shock proteins and ferroptosis in AML. Nevertheless, validation using patient samples is warranted.

A retrospective assessment of real-world experience with venetoclax and azacitidine therapy in elderly acute myeloid leukemia

This study aimed to examine the effect of venetoclax coupled with azacytidine in treating older adults with relapsed and refractory (R/R) acute myeloid leukemia (AML). The clinical data of 10 senior patients with AML over 65 years old who were treated with venetoclax and azacytidine, including six patients with R/R AML, were retrospectively evaluated. This study comprised seven males and three females with a median age of 71 years. Five patients had at least one relapse, and one patient did not achieve remission after four cycles of azacytidine monotherapy, considering it resistant. AML with myelodysplasia-related changes was found in four cases. One of the 10 patients died early after 1-13 cycles of venetoclax plus azacytidine treatment due to a protracted period of neutropenia and severe lung infection induced by medications. Six of the remaining nine patients, including six R/R patients, achieved a complete remission (CR) or a CR with incomplete hematologic recovery (CRi). After two cycles of therapy, one patient did not react. Neutropenia lasted an average of 10.5 (6-15) days in all patients, with the most severe cases occurring in the second and third weeks of therapy. Three patients who tested positive for the TP53 gene mutation had the following outcomes: One relapsed patient has been in progression-free remission (PFS) for the past 24 months, whereas another has been in full remission but relapsed 2 months later. Another patient experienced complete remission in myelology for 4 months, but the variable allele fraction (VAF) value steadily rose, suggesting that the illness was on the verge of progressing. IDH2 gene alterations were found in three of four patients who obtained maintained CR for more than 18 months following recurrence. Venetoclax in combination with azacytidine is a successful and well-tolerated therapy for R/R AML in the elderly. Venetoclax and azacytidine may help patients with TP53 mutations and reduce VAF. The IDH2 mutation might be a good predictor of veneclax sensitivity. A notable adverse response in the treatment phase of the regimen is severe infection induced by neutropenia.

Hsa_circ_0001485 promoted osteogenic differentiation by targeting BMPR2 to activate the TGFβ-BMP pathway

Background

Circular RNAs (circRNAs) are a new type of stable noncoding RNA and have been proven to play a crucial role in osteoporosis. This study explored the role and mechanism of hsa_circ_0001485 in osteogenic differentiation.

Methods

Kyoto Encyclopedia of Genes and Genomes (KEGG) analysis and Gene Ontology (GO) enrichment analysis were performed according to the previous sequencing data in human bone marrow mesenchymal stem cells (BMSC) before and after the induction of osteogenic differentiation on the differentially expressed circRNAs, to screen out signaling pathways associated with osteogenic differentiation. The hFOB 1.19 cells were used to verify the function and mechanism of specific circRNAs in osteogenic differentiation. Additionally, small interfering fragments and overexpression plasmids were used to determine the role of specific circRNAs during osteogenic differentiation. Furthermore, pull-down experiments and mass spectrometry were performed to determine the proteins that bind to specific circRNAs.

Results

The KEGG and GO enrichment analyses showed that the TGFβ-BMP signaling pathway was related to the osteogenic differentiation process, and four circRNAs were associated with the pathway. The quantitative polymerase chain reaction analysis revealed that hsa_circ_0001485 expression was increased during the osteogenic differentiation process of BMSCs. Knockdown of hsa_circ_0001485 suppressed the activity of the alkaline phosphatase enzyme and the expression of RUNX2, osteopontin, and osteocalcin in the osteogenic hFOB 1.19 cells, whereas overexpression of hsa_circ_0001485 promoted their expression. Additionally, we found that hsa_circ_0001485 and BMPR2 targeted binding to activate the TGFβ-BMP signaling pathway and promoted osteogenic differentiation through mass spectrometry analysis.

Conclusion

This study demonstrates that hsa_circ_0001485 is highly expressed in the osteogenic hFOB 1.19 cells, which activate the TGFβ-BMP pathway through targeted binding of BMPR2, and plays a positive role in regulating osteogenic differentiation.

Establishment of tumor protein p53 mutation-based prognostic signatures for acute myeloid leukemia

PURPOSE

The tumor protein p53 gene (TP53) mutations are associated with poor prognosis of patients with acute myeloid leukemia (AML). This study aimed to establish TP53 mutation-based prognostic risk signatures.

PATIENTS AND METHODS

The transcriptomes and clinical characteristics of AML patients were acquired from The Cancer Genome Atlas database, including 11 TP53-mutant samples and 114 TP53-wildtype samples. Differentially expressed mRNAs and long non-coding RNAs (lncRNA) in TP53-mutant samples were identified. Weighted gene correlation network analysis was performed to generate survival-associated co-expression modules. LASSO regression analysis was conducted to build mRNA- and lncRNA-based prognostic risk signatures. Kaplan-Meier curve analysis and multivariate regression analysis were carried out to assess the prognostic values of the risk signatures. Receiver operating characteristic (ROC) analysis was performed to evaluate the accuracy of the signatures.

RESULTS

Based on the co-expression modules, a 5-mRNA risk signature and a 13-lncRNA risk signature were constructed to predict the overall survival for AML patients. Kaplan-Meier curves revealed that the high-risk patients had significantly shorter overall survival than the low-risk patients. ROC analysis yielded 1-, 3-, and 5-year AUCs of 0.681, 0.783, and 0.827 for mRNA signature and 0.85, 0.835, and 0.908 for lncRNA signature. Multivariate regression analysis revealed that both mRNA (HR = 1.45, P< 0.001) and lncRNA (HR = 1.19, P< 0.001) risk scores were independent prognostic factors for AML patients.

CONCLUSION

We provided a potential patients stratification tool for AML prognosis prediction and management, which established by effective TP53 mutation-related gene signatures.

LncRNA LINC00649 aggravates the progression of cervical cancer through sponging miR-216a-3p

AIM

Increasing studies have revealed the participation of lncRNAs in the occurrence and development of cervical cancer. This study explored the influence of lncRNA LINC00649 in cervical cancer.

METHODS

Expression of LINC00649 and miR-216a-3p in cervical cancer was detected by reverse transcription quantitative real-time polymerase chain reaction (RT-qPCR). The Kaplan-Meier curve and Cox regression analyses were conducted to evaluate the clinical value of LINC00649 in cervical cancer. The roles of LINC00649 in cervical cancer cells were detected by transfecting siRNA through cellular function assays.

RESULTS

LINC00649 expression was increased in cervical cancer tissues, especially in squamous histology, positive lymph node metastasis, and high-FIGO stage tissues. The higher expression of LINC00649 predicted a shorter survival rate for patients. LINC00649 could bind directly with miR-216a-3p. Silence of LINC00649 could enhance the expression of miR-216a-3p and suppress the cervical cancer cell proliferation abilities, migration capacities, and invasion power. Whereas, transfection of miR-216a-3p inhibitor partially reverses the above cellular activities changes in cervical cancer cells.

CONCLUSIONS

The LINC00649 expression may act as a prognostic predictor and may aggravate cervical cancer progression by targeting miR-216a-3p, providing potential therapeutic targets for patients with cervical cancer.

Deciphering the Non-Coding RNA Landscape of Pediatric Acute Myeloid Leukemia

Pediatric acute myeloid leukemia (pedAML) is a heterogeneous blood cancer that affects children. Although survival rates have significantly improved over the past few decades, 20-30% of children will succumb due to treatment-related toxicity or relapse. The molecular characterization of the leukemic stem cell, shown to be responsible for relapse, is needed to improve treatment options and survival. Recently, it has become clear that non-coding RNAs, including long non-coding RNAs (lncRNAs) and microRNAs (miRNAs), play a role in the development of human diseases, including pediatric cancer. Nevertheless, non-coding RNA expression data in pedAML are scarce. Here, we explored lncRNA (n = 30,168) and miRNA (n = 627) expression in pedAML subpopulations (leukemic stem cells (LSCs) and leukemic blasts (L-blasts)) and their normal counterparts (hematopoietic stem cells and control myeloblasts). The potential regulatory activity of differentially expressed lncRNAs in LSCs (unique or shared with the L-blast comparison) on miRNAs was assessed. Moreover, pre-ranked gene set enrichment analyses of (anti-) correlated protein-coding genes were performed to predict the functional relevance of the differentially upregulated lncRNAs in LSCs (unique or shared with the L-blast comparison). In conclusion, this study provides a catalog of non-coding RNAs with a potential role in the pathogenesis of pedAML, paving the way for further translational research studies.

LncRNA LINC00649 recruits TAF15 and enhances MAPK6 expression to promote the development of lung squamous cell carcinoma via activating MAPK signaling pathway

Lung squamous cell carcinoma (LUSC) represents one of the commonest types of lung cancer featured with high morbidity and poor prognosis. Many types of research have documented that long noncoding RNAs (lncRNAs) exert crucial functions in the development of cancers, and LUSC is included. In our study, we aimed at unveiling the mechanism underlying long intergenic nonprotein coding RNA 0649 (LINC00649) in LUSC cells. As a result, LINC00649 was discovered to be with high expression in LUSC cells. Moreover, it was confirmed through functional assays that the knockdown of LINC00649 hindered the occurrence and progression of LUSC. Results of mechanism assays validated that E2F transcription factor 7 (E2F7) was a transcription activator of LINC00649 and induced its up-regulation in LUSC cells. Furthermore, LINC00649 recruited TAF15, which is TATA-box binding protein associated factor 15 to stabilize mitogen-activated protein kinase 6 (MAPK6) expression and activate the transcription of MAPK6, thereby enhancing MAPK6 expression to activate the MAPK signaling pathway. Eventually, results of rescue assays suggested that overexpression of MAPK6 offset the influence of LINC00649 silencing on LUSC progression. In summary, our research determined the E2F7/LINC00649/TAF15/MAPK6/MAPK signaling pathway in regulating LUSC development, which made LINC00649 a potential biomarker for LUSC treatment.

Integrated analysis of differentially expressed genes and a ceRNA network to identify hub lncRNAs and potential drugs for multiple sclerosis

OBJECTIVE

Multiple sclerosis (MS) is an autoimmune neuroinflammatory disease of the nervous system. However, the precise molecular mechanisms underlying MS have yet to be fully elucidated. In this study, our aim was to provide novel insight into the pathogenesis of MS and provide a resource for identifying new biomarkers and therapeutics for MS.

METHODS

In this study, we analyzed the gene expression profiles (GSE21942) and miRNA expression profiles (GSE61741) of MS patient samples that were downloaded from the GEO database and identified differentially expressed mRNAs and miRNAs (DEmRNAs, DEmiRNAs). Next, we constructed a protein-protein interaction (PPI) network and a MS-specific ceRNA network (MCEN) by integrating expression profiles, interaction pairs of mRNA-miRNAs and lncRNA-miRNAs. Then, according to the modular structure of the PPI network, we identified hub DEmRNAs and generated a ceRNA subnetwork so that we could analyze the key lncRNAs that were associated with MS.

RESULTS

We first identified 4 modules by constructing a PPI network using DEmRNAs. Functional enrichment analysis showed these modules were enriched in immune-related pathways. Then, we constructed the MCEN and the hub gene-associated ceRNA subnetwork using a comprehensive computational approach. We identified three key lncRNAs (LINC00649, TP73-AS1 and MALAT1) and further identified key lncRNA-mediated ceRNAs within the subnetwork. Finally, by analyzing LINC00649-miR-1275-CD20, we identified 6 drugs that may represent novel drugs for MS.

CONCLUSION

Collectively, our results provide novel insight for the discovery of biomarkers and therapeutics for MS and provide a suitable foundation from which to design future investigations of the pathogenic mechanisms associated with MS.

Long noncoding RNA LINC00649 functions as a microRNA‑432‑5p sponge to facilitate tumourigenesis in colorectal cancer by upregulating HDGF

Long intergenic nonprotein coding RNA 649 (LINC00649) is a functional regulator in acute myeloid leukaemia. However, the contribution of LINC00649 in colorectal cancer (CRC) has yet to be confirmed. Accordingly, the present investigation was devoted to exploring the detailed functions of LINC00649 and reveal the mechanisms underlying the LINC00649-induced promotion of CRC progression. LINC00649 expression in CRC was investigated by reverse transcription-quantitative PCR. Knockdown of LINC00649 was achieved using small interfering RNAs or short hairpin RNA, followed by functional experiments. The binding between LINC00649 and microRNA (miR)-432-5p was predicted by a bioinformatics tool, and corroborated by luciferase reporter assay and RNA immunoprecipitation. In the present study, LINC00649 was expressed at a high level in CRC. The aberrant expression of LINC00649 exhibited an inverse association with CRC patient prognosis. Functionally, the downregulation of LINC00649 exerted anticarcinogenic activities in CRC by decreasing cell proliferation, migration, and invasion and inducing cell apoptosis. Furthermore, the growth of CRC cells in vivo was attenuated after LINC00649 deficiency. Mechanistically, LINC00649 functioned as a competitive endogenous RNA by competitively binding to miR-432-5p in CRC cells, inducing an increase in hepatoma-derived growth factor (HDGF). Ultimately, functional rescue experiments highlighted that the exogenous introduction of miR-432-5p inhibitor or HDGF overexpression plasmid partially abated the inhibitory effects of LINC00649 silencing. In conclusion, LINC00649 promoted the aggressiveness of CRC cells by adjusting the miR-432-5p/HDGF axis. Thus, the LINC00649/miR-432-5p/HDGF pathway may be a promising target for CRC therapy.

Gestational Age Dependence of the Maternal Circulating Long Non-Coding RNA Transcriptome During Normal Pregnancy Highlights Antisense and Pseudogene Transcripts

In the post-genomic era, our understanding of the molecular regulators of physiologic and pathologic processes in pregnancy is expanding at the whole-genome level. Longitudinal changes in the known protein-coding transcriptome during normal pregnancy, which we recently reported (Gomez-Lopez et al., 2019), have improved our definition of the major operant networks, yet pregnancy-related functions of the non-coding RNA transcriptome remain poorly understood. A key finding of the ENCODE (Encyclopedia of DNA Elements) Consortium, the successor of the Human Genome Project, was that the human genome contains approximately 60,000 genes, the majority of which do not encode proteins. The total transcriptional output of non-protein-coding RNA genes, collectively referred to as the non-coding transcriptome, is comprised mainly of long non-coding RNA (lncRNA) transcripts (Derrien et al., 2012). Although the ncRNA transcriptome eclipses its protein-coding counterpart in abundance, it has until recently lacked a comprehensive, unbiased, genome-scale characterization over the timecourse of normal human pregnancy. Here, we annotated, characterized, and selectively validated the longitudinal changes in the non-coding transcriptome of maternal whole blood during normal pregnancy to term. We identified nine long non-coding RNAs (lncRNAs), including long intergenic non-coding RNAs (lincRNAs) as well as lncRNAs antisense to or otherwise in the immediate vicinity of protein-coding genes, that were differentially expressed with advancing gestation in normal pregnancy: AL355711, BC039551 (expressed mainly in the placenta), JHDM1D-AS1, A2M-AS1, MANEA-AS1, NR_034004, LINC00649, LINC00861, and LINC01094. By cross-referencing our dataset against major public pseudogene catalogs, we also identified six transcribed pseudogenes that were differentially expressed over time during normal pregnancy in maternal blood: UBBP4, FOXO3B, two Makorin (MKRN) pseudogenes (MKRN9P and LOC441455), PSME2P2, and YBX3P1. We also identified three non-coding RNAs belonging to other classes that were modulated during gestation: the microRNA MIR4439, the small nucleolar RNA (snoRNA) SNORD41, and the small Cajal-body specific ncRNA SCARNA2. The expression profiles of most hits were broadly suggestive of functions in pregnancy. These time-dependent changes of the non-coding transcriptome during normal pregnancy, which may confer specific regulatory impacts on their protein-coding gene targets, will facilitate a deeper molecular understanding of pregnancy and lncRNA-mediated molecular pathways at the maternal-fetal interface and of how these pathways impact maternal and fetal health.

Long non-coding RNA LINC00649 regulates YES-associated protein 1 (YAP1)/Hippo pathway to accelerate gastric cancer (GC) progression via sequestering miR-16-5p

Although long non-coding RNA (LncRNA) LINC00649 is reported to be closely associated with acute myeloid leukemia (AML), prostate cancer and colorectal cancer, its role in regulating other types of cancer, such as gastric cancer (GC), has not been studied. This study analyzed the expression status of LINC00649 in GC tissues and cells by performing Real-Time qPCR analysis, and we found that LINC00649 tended to be enriched in cancerous tissues and cells but not in their normal counterparts, which were supported by the data from TCGA dataset. Next, by performing the gain- and loss-of-function experiments, we expectedly found that LINC00649 acted as an oncogene to accelerate GC cell proliferation, migration and epithelial-mesenchymal transition (EMT) in vitro and promote its tumorigenesis in vivo. Moreover, the online miRDB software predicted that miR-16-5p bound to both LINC00649 and 3' untranslated region (3'UTR) of YAP1 mRNA, which were validated by the following dual-luciferase reporter gene system assay and RNA pull-down assay. Finally, we proved that LINC00649 exerted its tumor-promoting effects in GC by regulating the miR-16-5p/YES-associated protein 1 (YAP1)/Hippo pathway. Mechanistically, knock-down of LINC00649 suppressed YAP1 expressions by releasing miR-16-5p, resulting in the recovery of the Hippo pathway, which suppressed the expression levels of the downstream oncogenes, including EGFR, SOX2 and OCT4, leading to the inhibition of the malignant phenotypes in GC cells. In conclusion, this study, for the first time, evidenced that LINC00649 promoted GC progression by targeting the miR-16-5p/YAP1/Hippo signaling pathway, which provided potential diagnostic and therapeutic indicators for GC treatment for clinical utilization.