Evaluation of latent membrane protein 1 and microRNA-155 for the prognostic prediction of diffuse large B cell lymphoma

MicroRNA and Other Non-Coding RNAs in Epstein-Barr Virus-Associated Cancers

EBV is a direct causative agent in around 1.5% of all cancers. The oncogenic properties of EBV are related to its ability to activate processes needed for cellular proliferation, survival, migration, and immune evasion. The EBV latency program is required for the immortalization of infected B cells and involves the expression of non-coding RNAs (ncRNAs), including viral microRNAs. These ncRNAs have different functions that contribute to virus persistence in the asymptomatic host and to the development of EBV-associated cancers. In this review, we discuss the function and potential clinical utility of EBV microRNAs and other ncRNAs in EBV-associated malignancies. This review is not intended to be comprehensive, but rather to provide examples of the importance of ncRNAs.

Up-regulation of miR-155 potentiates CD34+ CML stem/progenitor cells to escape from the growth-inhibitory effects of TGF-ß1 and BMP signaling

microRNAs (miRNAs or miRs) play key roles in different stages of chronic myeloid leukemia (CML) pathogenesis. The present study aimed to demonstrate whether miR-155 enables CD34⁺ CML cells to escape from the growth-inhibitory effects of TGF-β1 and bone morphogenetic protein (BMP) signaling. Among differentially expressed miRNAs in CD34⁺ CML cells, miR-155 was highly up-regulated. QRT-PCR revealed an inverse correlation between miR-155 and two key members of the TGF-β pathway-TGF-βR2 and SMAD5. Results showed that SMAD5 is not only up-regulated through BMPs treatment, but recombinant TGF-β1 can also induce SMAD5 in CML cells. We also demonstrated that TGF-β1-mediated phosphorylation of SMAD1/5 was abolished by pre-treatment with the blocking TGF-βR2 antibody, suggesting a possible involvement of TGF-βR2. Additionally, overexpression of miR-155 significantly promoted the proliferation rate of CD34⁺ CML cells. Results showed that siRNA-mediated knockdown of SMAD5 had a promoting effect on CD34⁺ CML cell proliferation, suggesting that SMAD5 knock-down recapitulates the proliferative effects of miR-155. Importantly, TGF-β1 and BMP2/4 treatment had inhibitory effects on cell proliferation; however, miR-155 overexpression enabled CD34⁺ CML cells to evade the anti-proliferative effects of TGF-β1 and BMPs. Consistently, down-regulation of miR-155 augmented the promoting effects of TGF-β1 and BMP signaling on inducing apoptosis in CD34⁺ CML stem cells. Our findings demonstrated that targeting of SMAD5 and TGF-βR2 links miR-155 to TGF-β signaling in CML. Overexpression of miR-155 enables CD34⁺ CML cells to evade growth-inhibitory effects of the TGF-β1 and BMP signaling, providing new perspectives for miR-155 as a therapeutic target for CML.

Non-Coding RNAs in Diffuse Large B-Cell Lymphoma

Diffuse large B-cell lymphoma (DLBCL) is the most common type of non-Hodgkin lymphoma worldwide. The molecular mechanisms underlying DLBCL have not been fully elucidated, and approximately 40% of patients who undergo standard chemoimmunotherapy still present with primary refractory disease or relapse. Non-coding RNAs (ncRNAs), a group of biomolecules functioning at the RNA level, are increasingly recognized as vital components of molecular biology. With the development of RNA-sequencing (RNA-Seq) technology, accumulating evidence shows that ncRNAs are important mediators of diverse biological processes such as cell proliferation, differentiation, and apoptosis. They are also considered promising biomarkers and better candidates than proteins and genes for the early recognition of disease onset, as they are associated with relative stability, specificity, and reproducibility. In this review, we provide the first comprehensive description of the current knowledge regarding three groups of ncRNAs-microRNAs (miRNAs), circular RNAs (circRNAs), and long non-coding RNAs (lncRNAs)-focusing on their characteristics, molecular functions, as well as diagnostic and therapeutic potential in DLBCL. This review provides an exhaustive account for researchers to explore novel biomarkers for the diagnosis and prognosis of DLBCL and therapeutic targets.

Prediction of protein structural classes by different feature expressions based on 2-D wavelet denoising and fusion

BACKGROUND

Protein structural class predicting is a heavily researched subject in bioinformatics that plays a vital role in protein functional analysis, protein folding recognition, rational drug design and other related fields. However, when traditional feature expression methods are adopted, the features usually contain considerable redundant information, which leads to a very low recognition rate of protein structural classes.

RESULTS

We constructed a prediction model based on wavelet denoising using different feature expression methods. A new fusion idea, first fuse and then denoise, is proposed in this article. Two types of pseudo amino acid compositions are utilized to distill feature vectors. Then, a two-dimensional (2-D) wavelet denoising algorithm is used to remove the redundant information from two extracted feature vectors. The two feature vectors based on parallel 2-D wavelet denoising are fused, which is known as PWD-FU-PseAAC. The related source codes are available at https://github.com/Xiaoheng-Wang12/Wang-xiaoheng/tree/master.

CONCLUSIONS

Experimental verification of three low-similarity datasets suggests that the proposed model achieves notably good results as regarding the prediction of protein structural classes.

Prognostic and Clinicopathological Significance of MiR-155 in Hematologic Malignancies: A Systematic Review and Meta-analysis

Background: Aberrant miR-155 expression has been reported in various types of hematologic malignancies. However, the prognostic and clinicopathological value of miR-155 remains unclear. Here, we performed this systemic review and meta-analysis to comprehensively evaluate the prognostic and clinicopathological significance of miR-155 expression in hematologic malignancies.

Methods: We systematically searched the PubMed, EMBASE, ISI Web of Science, Cochrane library databases and OVID to identify eligible studies published from Jan 1, 2008 to Aug 1, 2018. The pooled hazard ratios (HRs) and odds ratios (ORs) with corresponding 95% confidence intervals (CIs) were used to detect the prognostic and clinicopathological role of miR-155 in hematologic malignancies.

Results: A total of 18 studies including 2316 patients were enrolled in the present meta-analysis, indicating significant association between elevated miR-155 expression and poor overall survival (OS) in 2114 patients (pooled HR = 1.72, 95%CI [1.50-1.97], p<0.001). Elevated miR-155 expression level was related to shorter event free survival (EFS, pooled HR = 1.55, 95%CI [0.94-2.57], P=0.002), disease free survival (DFS, pooled HR = 1.38, 95%CI [1.13-1.68], P=0.001), progress free survival (PFS, pooled HR = 1.58, 95%CI [1.06-2.35], p<0.001) and treatment free survival (TFS, pooled HR = 1.67, 95%CI [1.16-2.39], P=0.006). Additionally, overexpression of miR-155 was found to be significantly related to FLT3/ITD presence (OR=4.751, 95%CI [3.229-6.990], P<0.001), more WT1 mutation (OR=2.090, 95%CI [1.240-3.522], P=0.006) and less CEBPA mutation (OR=0.477, 95%CI [0.286-0.794], P=0.004) in 552 AML patients.

Conclusion: MiR-155 expression was found to be associated with several leukemia-related phenotype and poor prognosis in hematologic malignancies. Therefore, miR-155 overexpression might be a convinced unfavorable prognostic indicator that helps the clinical decision-making process.