Development and validation of a novel circular RNA as an independent prognostic factor in acute myeloid leukemia

Prognostic value of circular RNAs expression and their correlation with clinicopathological features in acute myeloid leukemia: a systematic review and meta-analysis

Acute myeloid leukemia (AML) prognosis is affected by unique factors to each individual and studies have indicated that dysregulated expression of circRNAs may serve as prognostic biomarkers for AML. Therefore, we conducted this study to assess the prognostic value of circRNAs expression and it's correlation with clinicopathological features. Comprehensive search was conducted in WOS, Scopus, PubMed, Google Scholar, ProQuest, and grey literature. The certainty of evidence was assessed using the modified GRADE approach for prognostic and clinicopathological meta-analysis. The hazard ratio (HR) was employed to assess the prognostic value of dysregulated expression of circRNAs in patient survival, while the risk ratio (RR) was utilized to analyze the correlation between circRNAs and clinicopathological features. Our results demonstrated that dysregulation of circRNAs expression was associated with poor prognosis related to overall survival (OS) indicator (HR:2.05; 95%CI: 1.75-2.40) and also related to non-OS indicators such as (EFS, LFS, RFS, and DFS) (HR:2.09, 95%CI: 1.47-2.97). Priori and post-hoc subgroup analysis was conducted to describe variables that potentially affected heterogeneity and effect size. We also evaluated the association between dysregulated expression of circRNAs and 19 clinicopathological parameters. Our results show that there is significant relationship between the dysregulated expression of circRNAs and the mentioned parameters: type M6 vs. other types (RR:1.51, 95% CI:1.12-2.03), FLT3-ITD mutation (RR:1.17, 95%CI: 1.00-1.36), and risk status (RR:1.35, 95% CI: 1.13-1.60). This systematic review and meta-analysis suggest that the investigation of circRNAs expression changes can serve as valuable biomarkers for the assessment of prognosis in AML patients.

Exosomal circ_0006896 promotes AML progression via interaction with HDAC1 and restriction of antitumor immunity

BACKGROUND

Drug resistance and immune escape continue to contribute to poor prognosis in AML. Increasing evidence suggests that exosomes play a crucial role in AML immune microenvironment.

METHODS

Sanger sequencing, RNase R and fluorescence in situ hybridization were performed to confirm the existence of circ_0006896. The role of circ_0006896 in the progression of AML was assessed by in vitro and in vivo functional experiments. Flow cytometry, RT-qPCR and adoptive T cell-transfer immunotherapy were conducted to assess the function of exosomal circ_0006896 in CD8+ T cell dysfunction. RNA pull-down assay, mass spectrometry, immunofluorescence, co-immunoprecipitation and western blot were performed to identify and confirm the circ_0006896 interacting proteins.

RESULTS

CircRNA expression patterns in exosomes differ significantly between AML and controls compared to lncRNAs or mRNAs. A new crucial exosomal circRNA, circ_0006896, is upregulated in both AML cells and exosomes and correlates with the prognosis and relapse of AML. In vitro and in vivo studies suggest that circ_0006896 significantly promotes AML cell proliferation, reduces chemotherapy sensitivity, and more importantly, impairs the efficacy of adoptive T cell-transfer immunotherapy. Mechanistically, circ_0006896 physically interacts with the catalytic domain of histone deacetylase HDAC1, decreasing histone H3 acetylation, and impairing the transcription of genes involved in arachidonic acid metabolism, ultimately inhibiting lipid peroxidation and ferroptosis in AML cells. Exosomal circ_0006896 disrupts CD8+ T cell function by interacting with HDAC1, impairing LEF1 transcription and subsequently decreasing the expression of cytotoxic molecules IFN-γ and Granzyme B.

CONCLUSIONS

We demonstrate a self-driven progression mediated by exosomal circRNAs and CD8+ T cells, highlighting the potential of targeting circRNAs in AML immunotherapy.

Immune infiltration-related genes regulate the progression of AML by invading the bone marrow microenvironment

In this study, we try to find the pathogenic role of immune-related genes in the bone marrow microenvironment of AML. Through WGCNA, seven modules were obtained, among which the turquoise module containing 1793 genes was highly correlated with the immune infiltration score. By unsupervised clustering, the turquoise module was divided into two clusters: the intersection of clinically significant genes in the TCGA and DEGs to obtain 178 genes for mutation analysis, followed by obtaining 17 genes with high mutation frequency. Subsequently, these 17 genes were subjected to LASSO regression analysis to construct a riskscore model of 8 hub genes. The TIMER database, ImmuCellAI portal website, and ssGSEA elucidate that the hub genes and risk scores are closely related to immune cell infiltration into the bone marrow microenvironment. In addition, we also validated the relative expression levels of hub genes using the TCGA database and GSE114868, and additional expression levels of hub genes in AML cell lines in vitro. Therefore, we constructed an immune infiltration-related gene model that identify 8 hub genes with good risk stratification and predictive prognosis for AML.

Screening of a Prognostic Gene Signature for Relapsed/Refractory Acute Myeloid Leukemia Based on Altered Circulating CircRNA Profiles

Background

Relapsed/refractory acute myeloid leukemia (R/R-AML) has dismal prognosis due to chemotherapy resistance. Circular RNAs (circRNAs) have shown emerging roles in chemotherapy resistance in various cancers including hematologic malignancies. However, the potential roles of circRNAs in AML progression and drug resistance remain largely undetermined.

Methods

In this study, circulating circRNAs expression profiles were analyzed among R/R-AML, de novo AML and healthy controls (HC) using a human circRNA Array. Bioinformatic analysis was carried out to explore the differentially expressed circRNAs (DE-circRNAs). GO, KEGG pathway analysis, along with circRNA-miRNA-mRNA network analysis, were conducted to identify the potential biological pathways involved in R/R-AML. Finally, the UALCAN database was used to assess the prognosis of different target DE-circRNAs-related mRNAs.

Results

Forty-eight DE-circRNAs were upregulated, whereas twenty-seven DE-circRNAs were downregulated in R/R-AML samples. Up-regulated DE-circRNAs in R/R-AML samples were mainly enrichment in the biological processes and pathways of cell migration, microRNAs in cancers, Rap1 and Ras signaling pathways. Six DE-circRNAs were randomly selected to further explore their relationships with R/R-AML. GO and KEGG pathway analyses of the six candidate DE-circRNAs-related target mRNAs were mainly involved in the regulation of signal transduction and Ras signaling pathway. By overlapping our RNA-sequencing results of differentially expressed genes (DEGs) in R/R-AML samples with the candidate DE-circRNAs-predicted target mRNAs, we identified sixty-eight overlapping targeted mRNAs. Using UALCAN database analysis, we identified that AML patients with six upregulated DE-circRNA-related genes (ECE1, PI4K2A, SLC9A6, CCND3, PPP1R16B, and TRIM32) and one downregulated gene DE-circRNA-related genes (ARHGAP10) might have a poor prognosis.

Conclusion

This study revealed the overall alterations of circRNAs in R/R-AML. DE-circRNAs and their related genes might be used as potential early, sensitive and stable biomarkers for AML diagnosis, R/R-AML monitoring, and even as novel treatment targets for R/R-AML.

Dysregulated Expression Patterns of Circular RNAs in Cancer: Uncovering Molecular Mechanisms and Biomarker Potential

Circular RNAs (circRNAs) are stable, enclosed, non-coding RNA molecules with dynamic regulatory propensity. Their biogenesis involves a back-splicing process, forming a highly stable and operational RNA molecule. Dysregulated circRNA expression can drive carcinogenic and tumorigenic transformation through the orchestration of epigenetic modifications via extensive RNA and protein-binding domains. These multi-ranged functional capabilities have unveiled extensive identification of previously unknown molecular and cellular patterns of cancer cells. Reliable circRNA expression patterns can aid in early disease detection and provide criteria for genome-specific personalized medicine. Studies described in this review have revealed the novelty of circRNAs and their biological ss as prognostic and diagnostic biomarkers.

Circular RNA as Diagnostic and Prognostic Biomarkers in Hematological Malignancies:Systematic Review

Objectives: While various serum and tissue biomarkers have been explored for tumor diagnosis, the sensitivity and specificity have not yield optimal results. Circular RNAs (circRNAs) are more stable, conserved, and tissue-specific than linear RNA. Recent reports indicate that circRNAs could serve as potential biomarkers in the diagnosis or/and prognosis of tumors. In this study, we systematically examined the relationship between circRNA expression and diagnostic and prognostic outcomes in patients with hematological tumors. Methods: We searched several databases, including Google Scholar, MEDLINE, Scopus, PubMed, Embase, ScienceDirect, Ovid-Medline, Chinese National Knowledge Infrastructure, WanFang and SinoMed, with a cutoff date of June 12, 2024. The study protocol was PROSPERO (CRD42020188627). Result: A total of 73 studies were included in our review, comprising 39 diagnostic studies and 65 prognostic studies. Clinical parameters were assessed based on pooled adds ratios and 95% confidence intervals (CIs). Overall survival (OS) was evaluated using hazard ratios (HRs) and 95% CIs. The pooled area under the curve was 0.86, indicating the potential to identify hematological tumor patients, with sensitivity and specificity of 79% each. The diagnostic score for circRNAs related to hematological malignancies was 2.12. Notably, different hematological malignancies subgroups displayed varying prognoses. Specifically, lymphoid leukemia circRNA showed a negative impacct on prognosis (HR = 1.25, 95% CI: 1.10-1.43, P < 0.001). Conclusion: Our findings provide compelling evidence that circRNA may be serve as a promising alternative for the diagnosis and prognosis of hematological tumors.

CircZBTB46 Protects Acute Myeloid Leukemia Cells from Ferroptotic Cell Death by Upregulating SCD

Circular RNAs (circRNAs) have been shown to be closely linked to the tumorigenesis and treatment response of hematological malignancies. However, the biological functions and clinical implications of circRNAs in acute myeloid leukemia (AML) remain largely unknown. CircRNA microarray datasets were analyzed to screen differentially expressed circRNAs in AML patients. It was found that circZBTB46 was significantly upregulated in AML patients and AML cells. Moreover, the expression of circZBTB46 was associated with the stages of AML patients and showed high sensitivity and specificity for diagnosing AML. Silencing of circZBTB46 inhibited AML cell proliferation and induced cell cycle arrest. Importantly, the depletion of circZBTB46 notably increased ferroptosis and enhanced RSL3-induced ferroptosis in AML cells. Mechanistically, circZBTB46 upregulated the expression of stearoyl-CoA desaturase 1 (SCD) possibly by acting as a miRNA sponge. Finally, the circZBTB46 knockdown repressed the tumor growth of AML in vivo. In conclusion, circZBTB46 protects AML cells from ferroptosis and promotes the proliferation by upregulating SCD, thus suggesting that circZBTB46 may be a potential therapeutic target for AML.

Hsa_circ_0015278 Regulates FLT3-ITD AML Progression via Ferroptosis-Related Genes

AML with the FLT3-ITD mutation seriously threatens human health. The mechanism by which circRNAs regulate the pathogenesis of FLT3-ITD mutant-type AML through ferroptosis-related genes (FerRGs) remains unclear. Differentially expressed circRNAs and mRNAs were identified from multiple integrated data sources. The target miRNAs and mRNAs of the circRNAs were predicted using various databases. The PPI network, ceRNA regulatory network, GO, and KEGG enrichment analyses were performed. The "survival" and the "pROC" R packages were used for K-M and ROC analysis, respectively. GSEA, immune infiltration analysis, and clinical subgroup analysis were performed. Finally, circRNAs were validated by Sanger sequencing and qRT-PCR. In our study, 77 DECircs-1 and 690 DECircs-2 were identified. Subsequently, 11 co-up-regulated DECircs were obtained by intersecting DECircs-1 and DECircs-2. The target miRNAs of the circRNAs were screened by CircInteractome, circbank, and circAtlas. Utilizing TargetScan, ENCORI, and miRWalk, the target mRNAs of the miRNAs were uncovered. Ultimately, 73 FerRGs were obtained, and the ceRNA regulatory network was constructed. Furthermore, MAPK3 and CD44 were significantly associated with prognosis. qRT-PCR results confirmed that has_circ_0015278 was significantly overexpressed in FLT3-ITD mutant-type AML. In summary, we constructed the hsa_circ_0015278/miRNAs/FerRGs signaling axis, which provides new insight into the pathogenesis and therapeutic targets of AML with FLT3-ITD mutation.

CircPTK2 promotes cell viability, cell cycle process, and glycolysis and inhibits cell apoptosis in acute myeloid leukemia by regulating miR-582-3p/ALG3 axis

BACKGROUND

Circular RNA (circRNA) regulates the pathogenesis of acute myeloid leukemia (AML). However, the mechanism of circRNA protein tyrosine kinase 2 (circPTK2) in AML remains unclear.

METHODS

Quantitative real-time polymerase chain reaction (qRT-PCR) assay was adopted for circPTK2, miR-582-3p and alpha-1,3-mannosyltransferase (ALG3) mRNA levels. 3-(4, 5-Dimethyl-2-thiazolyl)-2, 5-diphenyl-2-H-tetrazolium bromide (MTT) assay, and 5'-ethynyl-2'-deoxyuridine (EdU) assay were conducted for cell proliferation. Flow cytometry analysis was employed for cell apoptosis and cell cycle process. The glycolysis level was estimated by specific commercial kits. Western blot assay was utilized for protein levels. Dual-luciferase reporter assay and RNA immunoprecipitation (RIP) assay were performed to verify the interaction between miR-582-3p and circPTK2 or ALG3.

RESULTS

CircPTK2 level was enhanced in AML peripheral blood samples and cells. CircPTK2 knockdown restrained AML cell proliferation and glycolysis and promoted cell apoptosis and cell cycle arrest. Mechanically, circPTK2 functioned as the sponge for miR-582-3p to positively ALG3 expression in AML cells. Moreover, miR-582-3p inhibition ameliorated the impacts of circPTK2 knockdown on AML cell processes. MiR-582-3p overexpression regulated cell phenotypes by targeting ALG3.

CONCLUSION

CircPTK2 contributed to AML cell malignant behaviors by modulation of miR-582-3p/ALG3 axis, which might provide a potential target for AML therapy.

Functions and clinical significance of circular RNAs in acute myeloid leukemia

Circular RNAs (circRNAs) are a class of covalently closed single-stranded RNA molecules. Four types of circRNAs have been reported in animal cells, and they have typical characteristics in their biogenesis, nuclear export and degradation. Advances in our understanding of the molecular functions of circRNAs in sponging microRNAs, modulating transcription, regulating RNA-binding proteins, as well as encoding proteins have been made very recently. Dysregulated circRNAs are associated with human diseases such as acute myeloid leukemia (AML). In this review, we focus on the recently described mechanisms, role and clinical significance of circRNAs in AML. Although great progress of circRNAs in AML has been achieved, substantial efforts are still required to explore whether circRNAs exert their biological function by other mechanisms such as regulation of gene transcription or serving as translation template in AML. It is also urgent that researchers study the machineries regulating circRNAs fate, the downstream effectors of circRNAs modulatory networks, and the clinical application of circRNAs in AML.

The Down-Regulation of Circ_0059707 in Acute Myeloid Leukemia Promotes Cell Growth and Inhibits Apoptosis by Regulating miR-1287-5p

Acute myeloid leukemia (AML) is the most common type of hematological malignancy. Recently, an increasing number of reports have shown that many circular RNAs can act as effective targets for AML. However, the roles of circ_0059707 in AML remain largely unclear. In this study, we found that the expression levels of circ_0059707 were significantly decreased in AML patients with respect to normal controls (p < 0.001). Low expression levels of circ_0059707 were also associated with a poor prognosis. Furthermore, circ_0059707 overexpression inhibited cell growth and promoted apoptosis in leukemia cells, compared with control cells. Circ_0059707- and empty plasmid-transfected cells were injected subcutaneously into BALB/c nude mice. We found that the tumor volume was significantly lower in mice in the circ_0059707 group than in control mice (p < 0.01). Nuclear pyknosis, nuclear fragmentation, nuclear dissolution, and cell necrosis were observed in the circ_0059707 group by HE staining. CircInteractome analysis showed that 25 microRNAs (miRNAs), including miR-1287-5p, ©-miR-1825, a©hsa-miR-326, may be potential targets for circ_0059707. The expression of these miRNAs was analyzed in both the GEO GSE51908 and the GSE142700 databases. miR-1287-5p expression was lower in AML patients compared with controls in both the GSE51908 and the GSE142700 datasets. Moreover, we demonstrated that miR-1287-5p expression was down-regulated in AML patients and up-regulated in circ_0059707-overexpressing cells. Collectively, our research demonstrated that the down-regulation of circ_0059707 was highly evident in de novo AML patients. Our analysis also demonstrated that circ_0059707 inhibited cell growth and promoted apoptosis by up-regulating miR-1287-5p.

Circular RNAs Activity in the Leukemic Bone Marrow Microenvironment

Acute myeloid leukemia (AML) is a hematological malignancy originating from defective hematopoietic stem cells in the bone marrow. In spite of the recent approval of several molecular targeted therapies for AML treatment, disease recurrence remains an issue. Interestingly, increasing evidence has pointed out the relevance of bone marrow (BM) niche remodeling during leukemia onset and progression. Complex crosstalk between AML cells and microenvironment components shapes the leukemic BM niche, consequently affecting therapy responsiveness. Notably, circular RNAs are a new class of RNAs found to be relevant in AML progression and chemoresistance. In this review, we provided an overview of AML-driven niche remodeling. In particular, we analyzed the role of circRNAs and their possible contribution to cell-cell communication within the leukemic BM microenvironment. Understanding these mechanisms will help develop a more effective treatment for AML.

Deregulation of CircANXA2, Circ0075001, and CircFBXW7 Gene Expressions and Their Predictive Value in Egyptian Acute Myeloid Leukemia Patients

Background

Aim of the Work

Methods

Results

Conclusion

Circ_0092291 attenuates angiotensin II-induced cell damages in human aortic vascular smooth muscle cells via mediating the miR-626/COL4A1 signal axis

Abdominal aortic aneurysm (AAA) is a potentially fatal vascular disease, and the dysregulated circular RNAs (circRNAs) play key roles in AAA progression. Circ_0092291 was downregulated in AAA patients, but its function in AAA remains unclear. This research was performed for the functional analysis of circ_0092291 and its mechanism exploration with mircoRNA-626 (miR-626) and collagen type IV alpha1 chain (COL4A1) in AAA. Human aortic vascular smooth muscle cells (T/G HA-VSMC) were treated with angiotensin II (Ang II). Levels of circ_0092291, miR-626, and COL4A1 were determined using reverse transcription-quantitative polymerase chain reaction (RT-qPCR). Inflammatory cytokines were examined by enzyme-linked immunosorbent assay (ELISA). Cell apoptosis was measured using caspase3 activity assay and flow cytometry. Angiopoiesis was assessed via tube formation assay. The protein analysis was conducted by western blot. Dual-luciferase reporter assay, RNA immunoprecipitation (RIP), and RNA pull-down assays were used to validate the molecular binding. Circ_0092291 downregulation was found in AAA samples and Ang II-treated cells. Inflammatory response and cell apoptosis were reduced while angiopoiesis and ECM level were facilitated after overexpression of circ_0092291 in Ang II-treated T/G HA-VSMC cells. MiR-626 was a miRNA target for circ_0092291, and miR-626 inhibition protected T/G HA-VSMC from Ang II-induced cell injury. Moreover, the regulation of circ_0092291 was achieved by serving as a miR-626 sponge in Ang II-treated cells. COL4A1 was affirmed as a target for miR-626 and circ_0092291 resulted in the level change of COL4A1 by sponging miR-626. Additionally, miR-626 downregulation inhibited the cell damages caused by Ang II through increasing the level of COL4A1 and the function of circ_0092291 was attributed to the upregulation of COL4A1. The evidence indicated that circ_0092291 could suppress the Ang II-induced cell dysfunction by targeting the miR-626/COL4A1 signaling axis. Circ_0092291 might improve the diagnosis and treatment of AAA.Key Points.Biological mechanism, Apoptosis, Molecular target.

Circular RNA circSMARCA5 is a prognostic biomarker in patients with malignant tumor: a meta-analysis

Background

Malignant tumor is one of the most serious diseases endangering human health. Circular RNAs play an important role in the tumorigenesis and progression of various malignant tumors. Although various studies have investigated the biological function of circular RNA circSMARCA5 in malignant tumors, the prognostic value of circSMARCA5 in malignant tumor patients has not been systematically analyzed.

Methods

Relevant studies were obtained from the PubMed and Web of Science database. The quality of the enrolled studies was evaluated using the Newcastle-Ottawa Scale quality assessment system. Survival features and clinicopathological features were assessed using pooled hazard ratios and odds ratios with 95% confidence intervals, respectively.

Results

Overall, 7 relevant publications were enrolled in the meta-analysis. CircSMARCA5 expression was significantly correlated with better OS (HR = 0.51, 95%CI 0.41–0.65) or DFS/RFS/PFS (HR = 0.56, 95%CI 0.43–0.73) in malignant tumors. In the pooled analyses of clinicopathological characteristics, malignant tumors with higher circSMARCA5 were better differentiated (OR = 0.41, 95%CI 0.19–0.88). CircSMARCA5 expression was correlated with less advanced TNM stage (OR = 0.33, 95%CI 0.19–0.55). Moreover, malignant tumors with higher circSMARCA5 expression have less advanced lymph node metastasis (OR = 0.26, 95%CI 0.08–0.79).

Conclusion

These results indicated that circSMARCA5 was a promising biomarker in malignant tumors, which may potentially facilitate clinical decisions in the future.

Supplementary Information

The online version contains supplementary material available at 10.1186/s12885-021-08316-3.