1
|
Chen M, Deng Y, Li Z, Ye Y, Zeng L, He Z, Peng G. SCPLPA: An miRNA-disease association prediction model based on spatial consistency projection and label propagation algorithm. J Cell Mol Med 2024; 28:e18345. [PMID: 38693850 PMCID: PMC11063733 DOI: 10.1111/jcmm.18345] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/31/2023] [Revised: 04/01/2024] [Accepted: 04/08/2024] [Indexed: 05/03/2024] Open
Abstract
Identifying the association between miRNA and diseases is helpful for disease prevention, diagnosis and treatment. It is of great significance to use computational methods to predict potential human miRNA disease associations. Considering the shortcomings of existing computational methods, such as low prediction accuracy and weak generalization, we propose a new method called SCPLPA to predict miRNA-disease associations. First, a heterogeneous disease similarity network was constructed using the disease semantic similarity network and the disease Gaussian interaction spectrum kernel similarity network, while a heterogeneous miRNA similarity network was constructed using the miRNA functional similarity network and the miRNA Gaussian interaction spectrum kernel similarity network. Then, the estimated miRNA-disease association scores were evaluated by integrating the outcomes obtained by implementing label propagation algorithms in the heterogeneous disease similarity network and the heterogeneous miRNA similarity network. Finally, the spatial consistency projection algorithm of the network was used to extract miRNA disease association features to predict unverified associations between miRNA and diseases. SCPLPA was compared with four classical methods (MDHGI, NSEMDA, RFMDA and SNMFMDA), and the results of multiple evaluation metrics showed that SCPLPA exhibited the most outstanding predictive performance. Case studies have shown that SCPLPA can effectively identify miRNAs associated with colon neoplasms and kidney neoplasms. In summary, our proposed SCPLPA algorithm is easy to implement and can effectively predict miRNA disease associations, making it a reliable auxiliary tool for biomedical research.
Collapse
Affiliation(s)
- Min Chen
- Hunan Institute of TechnologySchool of Computer Science and EngineeringHengyang 421002China
| | - Yingwei Deng
- Hunan Institute of TechnologySchool of Computer Science and EngineeringHengyang 421002China
| | - Zejun Li
- Hunan Institute of TechnologySchool of Computer Science and EngineeringHengyang 421002China
| | - Yifan Ye
- Hunan Institute of TechnologySchool of Computer Science and EngineeringHengyang 421002China
| | - Lijun Zeng
- Hunan Institute of TechnologySchool of Computer Science and EngineeringHengyang 421002China
| | - Ziyi He
- Hunan Institute of TechnologySchool of Computer Science and EngineeringHengyang 421002China
| | - Guofang Peng
- Hunan Institute of TechnologySchool of Computer Science and EngineeringHengyang 421002China
| |
Collapse
|
2
|
Veryaskina YA, Titov SE, Kovynev IB, Pospelova TI, Fyodorova SS, Shebunyaeva YY, Sumenkova DV, Zhimulev IF. MicroRNA Expression Profile in Bone Marrow and Lymph Nodes in B-Cell Lymphomas. Int J Mol Sci 2023; 24:15082. [PMID: 37894763 PMCID: PMC10606460 DOI: 10.3390/ijms242015082] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/22/2023] [Revised: 09/26/2023] [Accepted: 09/27/2023] [Indexed: 10/29/2023] Open
Abstract
Hodgkin's lymphomas (HL) and the majority of non-Hodgkin's lymphomas (NHL) derive from different stages of B-cell differentiation. MicroRNA (miRNA) expression profiles change during lymphopoiesis. Thus, miRNA expression analysis can be used as a reliable diagnostic tool to differentiate tumors. In addition, the identification of miRNA's role in lymphopoiesis impairment is an important fundamental task. The aim of this study was to analyze unique miRNA expression profiles in different types of B-cell lymphomas. We analyzed the expression levels of miRNA-18a, -20a, -96, -182, -183, -26b, -34a, -148b, -9, -150, -451a, -23b, -141, and -128 in lymph nodes (LNs) in the following cancer samples: HL (n = 41), diffuse large B-cell lymphoma (DLBCL) (n = 51), mantle cell lymphoma (MCL) (n = 15), follicular lymphoma (FL) (n = 12), and lymphadenopathy (LA) (n = 37), as well as bone marrow (BM) samples: HL (n = 11), DLBCL (n = 42), MCL (n = 14), FL (n = 16), and non-cancerous blood diseases (NCBD) (n = 43). The real-time RT-PCR method was used for analysis. An increase in BM expression levels of miRNA-26b, -150, and -141 in MCL (p < 0.01) and a decrease in BM levels of the miR-183-96-182 cluster and miRNA-451a in DLBCL (p < 0.01) were observed in comparison to NCBD. We also obtained data on increased LN levels of the miR-183-96-182 cluster in MCL (p < 0.01) and miRNA-18a, miRNA-96, and miRNA-9 in FL (p < 0.01), as well as decreased LN expression of miRNA-150 in DLBCL (p < 0.01), and miRNA-182, miRNA-150, and miRNA-128 in HL (p < 0.01). We showed that miRNA expression profile differs between BM and LNs depending on the type of B-cell lymphoma. This can be due to the effect of the tumor microenvironment.
Collapse
Affiliation(s)
- Yuliya A. Veryaskina
- Department of the Structure and Function of Chromosomes, Laboratory of Molecular Genetics, Institute of Molecular and Cellular Biology, SB RAS, 630090 Novosibirsk, Russia; (S.E.T.); (I.F.Z.)
- Laboratory of Gene Engineering, Institute of Cytology and Genetics, SB RAS, 630090 Novosibirsk, Russia
| | - Sergei E. Titov
- Department of the Structure and Function of Chromosomes, Laboratory of Molecular Genetics, Institute of Molecular and Cellular Biology, SB RAS, 630090 Novosibirsk, Russia; (S.E.T.); (I.F.Z.)
- AO Vector-Best, 630117 Novosibirsk, Russia
| | - Igor B. Kovynev
- Department of Therapy, Hematology and Transfusiology, Novosibirsk State Medical University, 630091 Novosibirsk, Russia; (I.B.K.); (T.I.P.); (S.S.F.); (Y.Y.S.); (D.V.S.)
| | - Tatiana I. Pospelova
- Department of Therapy, Hematology and Transfusiology, Novosibirsk State Medical University, 630091 Novosibirsk, Russia; (I.B.K.); (T.I.P.); (S.S.F.); (Y.Y.S.); (D.V.S.)
| | - Sofya S. Fyodorova
- Department of Therapy, Hematology and Transfusiology, Novosibirsk State Medical University, 630091 Novosibirsk, Russia; (I.B.K.); (T.I.P.); (S.S.F.); (Y.Y.S.); (D.V.S.)
| | - Yana Yu. Shebunyaeva
- Department of Therapy, Hematology and Transfusiology, Novosibirsk State Medical University, 630091 Novosibirsk, Russia; (I.B.K.); (T.I.P.); (S.S.F.); (Y.Y.S.); (D.V.S.)
| | - Dina V. Sumenkova
- Department of Therapy, Hematology and Transfusiology, Novosibirsk State Medical University, 630091 Novosibirsk, Russia; (I.B.K.); (T.I.P.); (S.S.F.); (Y.Y.S.); (D.V.S.)
| | - Igor F. Zhimulev
- Department of the Structure and Function of Chromosomes, Laboratory of Molecular Genetics, Institute of Molecular and Cellular Biology, SB RAS, 630090 Novosibirsk, Russia; (S.E.T.); (I.F.Z.)
| |
Collapse
|
3
|
Wang Z, Dai R, Ahmed SA. MicroRNA-183/96/182 cluster in immunity and autoimmunity. Front Immunol 2023; 14:1134634. [PMID: 36891312 PMCID: PMC9986322 DOI: 10.3389/fimmu.2023.1134634] [Citation(s) in RCA: 3] [Impact Index Per Article: 3.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/30/2022] [Accepted: 02/09/2023] [Indexed: 02/22/2023] Open
Abstract
MicroRNAs (miRNAs) are crucial post-transcriptional regulators of gene expression in ubiquitous biological processes, including immune-related pathways. This review focuses on the miR-183/96/182 cluster (miR-183C), which contains three miRNAs, miR-183, -96, and -182, having almost identical seed sequences with minor differences. The similarity among seed sequences allows these three miRNAs to act cooperatively. In addition, their minor differences permit them to target distinct genes and regulate unique pathways. The expression of miR-183C was initially identified in sensory organs. Subsequently, abnormal expression of miR-183C miRNAs in various cancers and autoimmune diseases has been reported, implying their potential role in human diseases. The regulatory effects of miR-183C miRNAs on the differentiation and function of both innate and adaptive immune cells have now been documented. In this review, we have discussed the complex role of miR-183C in the immune cells in both normal and autoimmune backgrounds. We highlighted the dysregulation of miR-183C miRNAs in several autoimmune diseases, including systemic lupus erythematosus (SLE), multiple sclerosis (MS), and ocular autoimmune disorders, and discussed the potential for utilizing miR-183C as biomarkers and therapeutic targets of specific autoimmune diseases.
Collapse
Affiliation(s)
- Zhuang Wang
- Department of Biomedical Sciences and Pathobiology, Virginia-Maryland College of Veterinary Medicine (VMCVM), Virginia Tech, Blacksburg, VA, United States
| | - Rujuan Dai
- Department of Biomedical Sciences and Pathobiology, Virginia-Maryland College of Veterinary Medicine (VMCVM), Virginia Tech, Blacksburg, VA, United States
| | - Sattar Ansar Ahmed
- Department of Biomedical Sciences and Pathobiology, Virginia-Maryland College of Veterinary Medicine (VMCVM), Virginia Tech, Blacksburg, VA, United States
| |
Collapse
|
4
|
Stage-Specific Non-Coding RNA Expression Patterns during In Vitro Human B Cell Differentiation into Antibody Secreting Plasma Cells. Noncoding RNA 2022; 8:ncrna8010015. [PMID: 35202088 PMCID: PMC8878715 DOI: 10.3390/ncrna8010015] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/13/2021] [Revised: 01/31/2022] [Accepted: 02/03/2022] [Indexed: 11/17/2022] Open
Abstract
The differentiation of B cells into antibody secreting plasma cells (PCs) is governed by a strict regulatory network that results in expression of specific transcriptomes along the activation continuum. In vitro models yielding significant numbers of PCs phenotypically identical to the in vivo state enable investigation of pathways, metabolomes, and non-coding (ncRNAs) not previously identified. The objective of our study was to characterize ncRNA expression during human B cell activation and differentiation. To achieve this, we used an in vitro system and performed RNA-seq on resting and activated B cells and PCs. Characterization of coding gene transcripts, including immunoglobulin (Ig), validated our system and also demonstrated that memory B cells preferentially differentiated into PCs. Importantly, we identified more than 980 ncRNA transcripts that are differentially expressed across the stages of activation and differentiation, some of which are known to target transcription, proliferation, cytoskeletal, autophagy and proteasome pathways. Interestingly, ncRNAs located within Ig loci may be targeting both Ig and non-Ig-related transcripts. ncRNAs associated with B cell malignancies were also identified. Taken together, this system provides a platform to study the role of specific ncRNAs in B cell differentiation and altered expression of those ncRNAs involved in B cell malignancies.
Collapse
|
5
|
Liang C, Li Y, Wang LN, Zhang XL, Luo JS, Peng CJ, Tang WY, Huang LB, Tang YL, Luo XQ. Up-regulated miR-155 is associated with poor prognosis in childhood acute lymphoblastic leukemia and promotes cell proliferation targeting ZNF238. ACTA ACUST UNITED AC 2021; 26:16-25. [PMID: 33357126 DOI: 10.1080/16078454.2020.1860187] [Citation(s) in RCA: 8] [Impact Index Per Article: 2.7] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/02/2023]
Abstract
OBJECTIVES Acute lymphoblastic leukemia (ALL) is one of the most common malignancies in children. Our aim was to identify a novel miRNA that can predict prognosis of childhood ALL patients and explore its potential mechanism. METHODS The miRNA expression profiles of childhood ALL were analyzed using GEO database and HiSeq instruments. The expression of miR-155 was examined by RT-PCR in 42 ALL patients. To investigate the role of miR-155 in ALL, four ALL cell lines (CEM-C1, Jurkat, MOLT-3 and MOLT-4) were transfected with miR-155 mimics, miR-155 inhibitors or corresponding controls. Dual-luciferase reporter system was applied to confirm the miR-155 target ZNF238. Moreover, proliferation and apoptosis were evaluated by MTT and flow cytometry. RESULTS Dataset GSE56489 and GSE23024 demonstrated that miR-155 was up-regulated and ZNF238 was down-regulated at diagnosis status of ALL. High miR-155 expression was associated with poor outcome. Overexpressed miR-155 promoted ALL cell proliferation and inhibited apoptosis. Dual-luciferase reporter result showed that miR-155 directly regulated ZNF238. Silencing ZNF238 promoted cell proliferation in ALL cells. DISCUSSION Our research indicating that miR-155 might possess potential value as a biomarker for predicting the prognosis of individuals. However, the role of ZNF238 in childhood ALL remain unknown. In the present study, we found the possible role of ZNF238 as a new tumor suppressor in ALL, which might be necessary for the antiproliferative functions of normal cells to counteract ALL formation. CONCLUSION Our results propose that miR-155 is in association with poor prognosis of childhood ALL. Furthermore, miR-155 could promote cell proliferation targeting ZNF238.
Collapse
Affiliation(s)
- Cong Liang
- Department of Pediatrics, The First Affiliated Hospital, Sun Yat-sen University, Guangzhou, People's Republic of China
| | - Yu Li
- Department of Pediatrics, The First Affiliated Hospital, Sun Yat-sen University, Guangzhou, People's Republic of China
| | - Li-Na Wang
- Department of Pediatrics, The First Affiliated Hospital, Sun Yat-sen University, Guangzhou, People's Republic of China
| | - Xiao-Li Zhang
- Department of Pediatrics, The First Affiliated Hospital, Sun Yat-sen University, Guangzhou, People's Republic of China
| | - Jie-Si Luo
- Department of Pediatrics, The First Affiliated Hospital, Sun Yat-sen University, Guangzhou, People's Republic of China
| | - Chun-Jin Peng
- Department of Pediatrics, The First Affiliated Hospital, Sun Yat-sen University, Guangzhou, People's Republic of China
| | - Wen-Yan Tang
- Department of Pediatrics, The First Affiliated Hospital, Sun Yat-sen University, Guangzhou, People's Republic of China
| | - Li-Bin Huang
- Department of Pediatrics, The First Affiliated Hospital, Sun Yat-sen University, Guangzhou, People's Republic of China
| | - Yan-Lai Tang
- Department of Pediatrics, The First Affiliated Hospital, Sun Yat-sen University, Guangzhou, People's Republic of China
| | - Xue-Qun Luo
- Department of Pediatrics, The First Affiliated Hospital, Sun Yat-sen University, Guangzhou, People's Republic of China
| |
Collapse
|
6
|
Chen LY, Han BQ, Zhang XM, Yu XB, Yao DD, Yu LQ. MicroRNA-383-5p predicts favorable prognosis and inhibits the progression of diffuse large B-cell lymphoma. Oncol Lett 2021; 22:515. [PMID: 33986875 DOI: 10.3892/ol.2021.12776] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.7] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/11/2020] [Accepted: 02/10/2021] [Indexed: 01/03/2023] Open
Abstract
The roles of microRNA (miRNA/miR)-383-5p have been reported in several malignancies, including breast cancer, gastric cancer, ovarian cancer and lung adenocarcinoma. However, its function in diffuse large B-cell lymphoma (DLBCL) remains unclear. Thus, the present study aimed to investigate the role of miR-383-5p in DLCBL. Reverse transcription-quantitative PCR analysis was performed to detect miR-383-5p expression in 80 paired tissue samples from patients with DLBCL and control subjects, as well as related cancer cell lines. Kaplan-Meier survival analysis was performed, and the prognostic value of miR-383-5p was determined via Cox regression analysis. Furthermore, the association between miR-383-5p expression and the clinicopathological characteristics of patients with DLBCL was investigated. The Cell Counting Kit-8, crystal violet staining and Transwell assays were performed to assess the effects of miR-383-5p on cell proliferation and invasion, respectively. The results demonstrated that miR-383-5p expression was upregulated in human DLBCL tissues and cell lines. In addition, miR-383-5p expression was closely associated with clinical stage and extranodal invasion in patients with DLBCL. Notably, high miR-383-5p expression was able to predict a favorable clinical prognosis in patients with DLBCL. Furthermore, overexpression of miR-383-5p significantly inhibited the proliferation and invasion of DLBCL cells, the effects of which were reversed following miR-383-5p knockdown. Taken together, the results of the present study suggest that miR-383-5p may predict favorable prognosis, and thus may be used as a prognostic biomarker for patients with DLBCL. In addition, miR-383-5p appears to play critical roles in inhibiting the proliferation and invasion of DLBCL cells, and thus may be used as a potential therapeutic target in patients with DLBCL.
Collapse
Affiliation(s)
- Li-Yan Chen
- Department of Hematology, The Second Affiliated Hospital of Harbin Medical University, Harbin, Heilongjiang 150001, P.R. China
| | - Bi-Qing Han
- Department of Hematology, The Second Affiliated Hospital of Harbin Medical University, Harbin, Heilongjiang 150001, P.R. China
| | - Xiao-Min Zhang
- Department of Hematology, The Second Affiliated Hospital of Harbin Medical University, Harbin, Heilongjiang 150001, P.R. China
| | - Xing-Bao Yu
- Department of Hematology, The Second Affiliated Hospital of Harbin Medical University, Harbin, Heilongjiang 150001, P.R. China
| | - Dan-Dan Yao
- Department of Hematology, The Second Affiliated Hospital of Harbin Medical University, Harbin, Heilongjiang 150001, P.R. China
| | - Li-Qian Yu
- Department of Hematology, The Second Affiliated Hospital of Harbin Medical University, Harbin, Heilongjiang 150001, P.R. China
| |
Collapse
|
7
|
Alterations in The Plasma Expression of mir-15b, mir-195 and the Tumor-Suppressor Gene DLEU7 in Patients with B-Cell Chronic Lymphocytic Leukemia. Rep Biochem Mol Biol 2021; 10:20-29. [PMID: 34277865 DOI: 10.52547/rbmb.10.1.20] [Citation(s) in RCA: 3] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/07/2020] [Accepted: 10/29/2020] [Indexed: 01/07/2023]
Abstract
Background Chronic lymphocytic leukemia (CLL) is one of the most prevalent forms of leukemia in adults. Inactivation of the DLEU7 gene is frequently observed in patients with CLL. Furthermore, microRNAs (miRNAs) have been observed to have a critical role in the pathogenesis of several cancers, including leukemia. Considering the tumor-suppressive role of DLEU7, as well as the tumor suppressor or oncogenic role of microRNAs (miRNAs), the aim of the present study was to evaluate the potential miRNAs targeting the DLEU7 gene in B-cells and explore expression changes these genes in the plasma of B-CLL patients. Methods The miRNAs interacting with the DLEU7 gene were predicted and selected using bioinformatics tools. A total of 80 plasma samples were collected from 40 patients with B-cells and 40 healthy individuals, then subjected to RNA extraction and cDNA synthesis. The expression profiles of the predicted miRNAs and the DLEU7 gene in the plasma of B-CLL patients and healthy individuals were determined by RT-qPCR analysis. Results The bioinformatics prediction indicated that miR-15b and miR-195 target the DLEU7 gene. The expression levels of miR-15b and miR-195 were significantly higher in the plasma of patients with B-CLL compared to the healthy individuals (91.6, p= 0.001) (169, p= 0.001). However, the expression level of the DLEU7 gene was found to be significantly lower in the patient group compared to healthy controls (0.304, p= 0.001). Conclusion Both miR-15b and miR-195, have the potential to function as novel and non-invasive biomarkers in the diagnosis and prognosis of patients with B-CLL.
Collapse
|
8
|
Abnormal Expression of BTLA and CTLA-4 Immune Checkpoint Molecules in Chronic Lymphocytic Leukemia Patients. J Immunol Res 2020; 2020:6545921. [PMID: 32775467 PMCID: PMC7407019 DOI: 10.1155/2020/6545921] [Citation(s) in RCA: 18] [Impact Index Per Article: 4.5] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/28/2019] [Revised: 02/07/2020] [Accepted: 02/11/2020] [Indexed: 02/06/2023] Open
Abstract
Chronic lymphocytic leukemia (CLL) is characterized by the peripheral accumulation of neoplastic B cells and is frequently complicated by the systemic immunosuppression associated with an impairment in B and T lymphocyte activation. We hypothesized that the expression of immune checkpoint suppressors B and T lymphocyte attenuator (BTLA) and cytotoxic T lymphocyte antigen (CTLA-4) is disturbed in both lymphocyte subpopulations in CLL. The expression of CTLA-4 and BTLA mRNA was determined by real-time PCR, while CTLA-4 protein expression (surface or intracellular) was estimated in BTLA+ lymphocytes by flow cytometry. In CLL patients, we observed a higher gene transcript level of BTLA and CTLA-4 than in healthy individuals in both freshly isolated and PMA stimulated B and T cells. Remarkably, lower amounts of both inhibitory proteins were found in peripheral blood (PB) CLL B cells, whereas normal BTLA and elevated CTLA-4 were found in T cells. Consistently, there was a prevalence of CTLA-4+ cells within circulating BTLA+ T cells cells of patients confronting PB healthy cells. After in vitro stimulation, the only change found in CLL patients was a decrease in BTLA expression in B and T lymphocytes. In contrast, healthy lymphocytes responded more vigorously as regards the BTLA and CTLA expression with substantially higher frequency of CD69+ cells under the stimulating condition compared to corresponding cells from the CLL group. Our results indicate that CLL development is associated with the affected expression of BTLA and CTLA-4 checkpoint receptors in PB and its impaired expression might be associated with lowering of the threshold for B cell activation and proliferation, while upregulated CTLA-4 expression in CLL peripheral BTLA+ T cells may contribute to suppressed T cell effector functions. This hypothesis needs to be validated in future studies, which would allow us to explain how the increased or decreased expression of these molecules affects the cell function.
Collapse
|
9
|
Zhang Y, Chen M, Cheng X, Wei H. MSFSP: A Novel miRNA-Disease Association Prediction Model by Federating Multiple-Similarities Fusion and Space Projection. Front Genet 2020; 11:389. [PMID: 32425980 PMCID: PMC7204399 DOI: 10.3389/fgene.2020.00389] [Citation(s) in RCA: 12] [Impact Index Per Article: 3.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/28/2020] [Accepted: 03/27/2020] [Indexed: 12/11/2022] Open
Abstract
Growing evidences have indicated that microRNAs (miRNAs) play a significant role relating to many important bioprocesses; their mutations and disorders will cause the occurrence of various complex diseases. The prediction of miRNAs associated with underlying diseases via computational approaches is beneficial to identify biomarkers and discover specific medicine, which can greatly reduce the cost of diagnosis, cure, prognosis, and prevention of human diseases. However, how to further achieve a more reliable prediction of potential miRNA-disease associations with effective integration of different biological data is a challenge for researchers. In this study, we proposed a computational model by using a federated method of combined multiple-similarities fusion and space projection (MSFSP). MSFSP firstly fused the integrated disease similarity (composed of disease semantic similarity, disease functional similarity, and disease Hamming similarity) with the integrated miRNA similarity (composed of miRNA functional similarity, miRNA sequence similarity, and miRNA Hamming similarity). Secondly, it constructed the weighted network of miRNA-disease associations from the experimentally verified Boolean network of miRNA-disease associations by using similarity networks. Finally, it calculated the prediction results by weighting miRNA space projection scores and the disease space projection scores. Leave-one-out cross-validation demonstrated that MSFSP has the distinguished predictive accuracy with area under the receiver operating characteristics curve (AUC) of 0.9613 better than that of five other existing models. In case studies, the predictive ability of MSFSP was further confirmed as 96 and 98% of the top 50 predictions for prostatic neoplasms and lung neoplasms were successfully validated by experimental evidences and supporting experimental evidences were also found for 100% of the top 50 predictions for isolated diseases.
Collapse
Affiliation(s)
- Yi Zhang
- School of Information Science and Engineering, Guilin University of Technology, Guilin, China
| | - Min Chen
- School of Computer Science and Technology, Hunan Institute of Technology, Hengyang, China
| | - Xiaohui Cheng
- School of Information Science and Engineering, Guilin University of Technology, Guilin, China
| | - Hanyan Wei
- School of Pharmacy, Guilin Medical University, Guilin, China
| |
Collapse
|
10
|
Prediction of Disease-related microRNAs through Integrating Attributes of microRNA Nodes and Multiple Kinds of Connecting Edges. Molecules 2019; 24:molecules24173099. [PMID: 31455026 PMCID: PMC6749327 DOI: 10.3390/molecules24173099] [Citation(s) in RCA: 8] [Impact Index Per Article: 1.6] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/13/2019] [Revised: 08/09/2019] [Accepted: 08/14/2019] [Indexed: 11/17/2022] Open
Abstract
Identifying disease-associated microRNAs (disease miRNAs) contributes to the understanding of disease pathogenesis. Most previous computational biology studies focused on multiple kinds of connecting edges of miRNAs and diseases, including miRNA-miRNA similarities, disease-disease similarities, and miRNA-disease associations. Few methods exploited the node attribute information related to miRNA family and cluster. The previous methods do not completely consider the sparsity of node attributes. Additionally, it is challenging to deeply integrate the node attributes of miRNAs and the similarities and associations related to miRNAs and diseases. In the present study, we propose a novel method, known as MDAPred, based on nonnegative matrix factorization to predict candidate disease miRNAs. MDAPred integrates the node attributes of miRNAs and the related similarities and associations of miRNAs and diseases. Since a miRNA is typically subordinate to a family or a cluster, the node attributes of miRNAs are sparse. Similarly, the data for miRNA and disease similarities are sparse. Projecting the miRNA and disease similarities and miRNA node attributes into a common low-dimensional space contributes to estimating miRNA-disease associations. Simultaneously, the possibility that a miRNA is associated with a disease depends on the miRNA's neighbour information. Therefore, MDAPred deeply integrates projections of multiple kinds of connecting edges, projections of miRNAs node attributes, and neighbour information of miRNAs. The cross-validation results showed that MDAPred achieved superior performance compared to other state-of-the-art methods for predicting disease-miRNA associations. MDAPred can also retrieve more actual miRNA-disease associations at the top of prediction results, which is very important for biologists. Additionally, case studies of breast, lung, and pancreatic cancers further confirmed the ability of MDAPred to discover potential miRNA-disease associations.
Collapse
|
11
|
Sharifi H, Shafiee A, Molavi G, Razi E, Mousavi N, Sarvizadeh M, Taghizadeh M. Leukemia-derived exosomes: Bringing oncogenic signals to blood cells. J Cell Biochem 2019; 120:16307-16315. [PMID: 31127656 DOI: 10.1002/jcb.29018] [Citation(s) in RCA: 8] [Impact Index Per Article: 1.6] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/24/2019] [Revised: 04/11/2019] [Accepted: 04/18/2019] [Indexed: 12/26/2022]
Abstract
Leukemia is a cancer, which is derived from leukocytes and precursors of leukocytes in the bone marrow. A large number of pivotal biological processes are linked to leukemia pathogenesis. More insights into these mechanisms can provide a better developing pharmacological platform for patients with leukemia. Among the different players in leukemia pathogenesis, exosomes have appeared as a new biological vehicle, which can transfer oncogenic signals to blood cells. Exosomes are nano-carriers, which enable transferring numerous cargos such as DNA fragments, RNAs, messenger RNAs, microRNAs, long noncoding RNA, and proteins. Targeting the contents of exosomes leads to the alteration of host cell behavior. Increasing evidence has indicated that leukemia-derived exosomes could be utilized as prognostic, diagnostic, and therapeutic biomarkers for individuals suffering from leukemia. In this regard, the importance of exosomes in terms of initiation and progression of leukemia was underlined in this study.
Collapse
Affiliation(s)
- Hossein Sharifi
- The Advocate Center for Clinical Research, Ayatollah Yasrebi Hospital, Kashan, Iran
| | - Alimohammad Shafiee
- Division of General Internal Medicine, Toronto General Hospital, Toronto, Canada
| | - Ghader Molavi
- Drug Applied Research Center, Tabriz University of Medical Sciences, Tabriz, Iran.,Department of Molecular Medicine, Faculty of Advanced Medical Sciences, Tabriz University of Medical Sciences, Tabriz, Iran
| | - Ebrahim Razi
- The Advocate Center for Clinical Research, Ayatollah Yasrebi Hospital, Kashan, Iran
| | - Nousin Mousavi
- Department of Surgery, Faculty of Medicine, Kashan University of Medical Sciences, Kashan, Iran
| | - Mostafa Sarvizadeh
- The Advocate Center for Clinical Research, Ayatollah Yasrebi Hospital, Kashan, Iran
| | - Mohsen Taghizadeh
- Research Center for Biochemistry and Nutrition in Metabolic Diseases, Kashan University of Medical Sciences, Kashan, Iran
| |
Collapse
|
12
|
Lim HJ, Abdellaoui N, Kim KH. Effect of miR-155 as a molecular adjuvant of DNA vaccine against VHSV in olive flounder (Paralichthys olivaceus). FISH & SHELLFISH IMMUNOLOGY 2019; 88:225-230. [PMID: 30822519 DOI: 10.1016/j.fsi.2019.02.056] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.4] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 12/11/2018] [Revised: 02/01/2019] [Accepted: 02/25/2019] [Indexed: 06/09/2023]
Abstract
Rhabdoviral G protein-based DNA vaccines have been recognized as a useful way to protect cultured fish from rhabdoviral diseases. In Korea, viral hemorrhagic septicemia virus (VHSV) genotype IVa has been the primary culprit of high mortalities of cultured olive flounder (Paralichthys olivaceus). In this study, we inserted a miR-155-expressing cassette into the VHSV's G protein-based DNA vaccine, and analyzed the effects of miR-155 on the antiviral activity and on the vaccine efficacy in olive flounder. Olive flounder fingerlings were intramuscularly (i.m.) immunized with 10 μg/fish (1st experiment) or 1 μg/fish (2nd experiment) of DNA vaccine plasmids. However, there were no significant differences in mortalities and serum neutralization titers between fish immunized with 1 μg and 10 μg plasmids/fish, suggesting that i.m. injection with 1 μg plasmids/fish would be enough to induce effective adaptive immune responses in olive flounder fingerlings. In survival rates, as fish immunized with just G protein expressing plasmids showed no or too low mortalities, the adjuvant effect of miR-155 was not discernible. Also, in the serum neutralization activities, although G gene or G gene plus miR-155 expressing DNA vaccines induced significantly higher activities than control vaccines (PBS and vacant vector), no significant differences were found between G gene alone and G gene plus miR-155 expressing DNA vaccines. In the serum virucidal activity, fish immunized with G gene plus miR-155 expressing DNA vaccine showed significantly higher activity against hirame rhabdovirus (HIRRV) at 3 days post-immunization (d.p.i.) compared to other groups, suggesting that miR-155 produced from the vector can enhance innate immune responses in olive flounder. The significantly enhanced serum virucidal activities against VHSV especially at 28 d.p.i. in the groups immunized with G gene alone and G gene plus miR-155 expressing DNA vaccines reflect the increased antibodies against G protein, which could activate the classical complement pathway and subsequent viral inactivation. As the available information on the DNA vaccines in olive flounder is not sufficient, more diverse researches on the protective efficacy of DNA vaccines are needed to make more practical use of DNA vaccines in olive flounder farms.
Collapse
Affiliation(s)
- Hyun Ju Lim
- Department of Aquatic Life Medicine, Pukyong National University, Busan, 48513, South Korea
| | - Najib Abdellaoui
- Department of Microbiology, Pukyong National University, Busan, 48513, South Korea
| | - Ki Hong Kim
- Department of Aquatic Life Medicine, Pukyong National University, Busan, 48513, South Korea.
| |
Collapse
|
13
|
The E3 ubiquitin ligase Itch is required for B-cell development. Sci Rep 2019; 9:421. [PMID: 30674954 PMCID: PMC6344599 DOI: 10.1038/s41598-018-36844-9] [Citation(s) in RCA: 13] [Impact Index Per Article: 2.6] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/23/2017] [Accepted: 02/12/2018] [Indexed: 11/20/2022] Open
Abstract
The E3 ubiquitin ligase Itch interacts with Foxo1 and targets it for ubiquitination and degradation during follicular helper T-cell differentiation, whereas the transcription factor Foxo1 plays a critical role in B-cell development. Thus, we proposed that Itch mediates B-cell differentiation. Unexpectedly, we found that Itch deficiency downregulated Foxo1 expression in B cells. Itch cKO (conditional knock out in B cells) mice had fewer pro-B cells in the bone marrow, more small resting IgM−IgD−B cells in the periphery, and lower B-cell numbers in the lymph nodes through decreased Foxo1-mediated IL-7Rα, RAG, and CD62L expression, respectively. Importantly, Itch deficiency reduced Foxo1 mRNA expression by up-regulating JunB-mediated miR-182. Finally, Foxo1 negatively regulated JunB expression by up-regulating Itch. Thus, we have identified a novel regulatory axis between Itch and Foxo1 in B cells, suggesting that Itch is essential for B-cell development.
Collapse
|
14
|
Zhang Y, Chen M, Cheng X, Chen Z. LSGSP: a novel miRNA–disease association prediction model using a Laplacian score of the graphs and space projection federated method. RSC Adv 2019; 9:29747-29759. [PMID: 35531537 PMCID: PMC9071959 DOI: 10.1039/c9ra05554a] [Citation(s) in RCA: 3] [Impact Index Per Article: 0.6] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/18/2019] [Accepted: 09/09/2019] [Indexed: 12/31/2022] Open
Abstract
Lots of research findings have indicated that miRNAs (microRNAs) are involved in many important biological processes; their mutations and disorders are closely related to diseases, therefore, determining the associations between human diseases and miRNAs is key to understand pathogenic mechanisms. Existing biological experimental methods for identifying miRNA–disease associations are usually expensive and time consuming. Therefore, the development of efficient and reliable computational methods for identifying disease-related miRNAs has become an important topic in the field of biological research in recent years. In this study, we developed a novel miRNA–disease association prediction model using a Laplacian score of the graphs and space projection federated method (LSGSP). This integrates experimentally validated miRNA–disease associations, disease semantic similarity scores, miRNA functional scores, and miRNA family information to build a new disease similarity network and miRNA similarity network, and then obtains the global similarities of these networks through calculating the Laplacian score of the graphs, based on which the miRNA–disease weighted network can be constructed through combination with the miRNA–disease Boolean network. Finally, the miRNA–disease score was obtained via projecting the miRNA space and disease space onto the miRNA–disease weighted network. Compared with several other state-of-the-art methods, using leave-one-out cross validation (LOOCV) to evaluate the accuracy of LSGSP with respect to a benchmark dataset, prediction dataset and compare dataset, LSGSP showed excellent predictive performance with high AUC values of 0.9221, 0.9745 and 0.9194, respectively. In addition, for prostate neoplasms and lung neoplasms, the consistencies between the top 50 predicted miRNAs (obtained from LSGSP) and the results (confirmed from the updated HMDD, miR2Disease, and dbDEMC databases) reached 96% and 100%, respectively. Similarly, for isolated diseases (diseases not associated with any miRNAs), the consistencies between the top 50 predicted miRNAs (obtained from LSGSP) and the results (confirmed from the above-mentioned three databases) reached 98% and 100%, respectively. These results further indicate that LSGSP can effectively predict potential associations between miRNAs and diseases. Lots of research findings have indicated that the mutations and disorders of miRNAs (microRNAs) are closely related to diseases. Therefore, determining the associations between human diseases and miRNAs is key to understand the pathogenic mechanisms.![]()
Collapse
Affiliation(s)
- Yi Zhang
- School of Information Science and Engineering
- Guilin University of Technology
- 541004 Guilin
- China
| | - Min Chen
- School of Computer Science and Technology
- Hunan Institute of Technology
- 421002 Hengyang
- China
| | - Xiaohui Cheng
- School of Information Science and Engineering
- Guilin University of Technology
- 541004 Guilin
- China
| | - Zheng Chen
- School of Computer Science and Technology
- Hunan Institute of Technology
- 421002 Hengyang
- China
| |
Collapse
|
15
|
Gao C, Zhou C, Zhuang J, Liu L, Wei J, Liu C, Li H, Sun C. Identification of key candidate genes and miRNA‑mRNA target pairs in chronic lymphocytic leukemia by integrated bioinformatics analysis. Mol Med Rep 2018; 19:362-374. [PMID: 30431072 PMCID: PMC6297738 DOI: 10.3892/mmr.2018.9636] [Citation(s) in RCA: 6] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/15/2018] [Accepted: 10/08/2018] [Indexed: 12/12/2022] Open
Abstract
Chronic lymphocytic leukemia (CLL) is a malignant clonal proliferative disorder of B cells. Inhibition of cell apoptosis and cell cycle arrest are the main pathological causes of this disease, but its molecular mechanism requires further investigation. The purpose of the present study was to identify biomarkers for the early diagnosis and treatment of CLL, and to explore the molecular mechanisms of CLL progression. A total of 488 differentially expressed genes (DEGs) and 32 differentially expressed microRNAs (miRNAs; DEMs) for CLL were identified by analyzing the gene chips GSE22529, GSE39411 and GSE62137. Functional and pathway enrichment analyses of DEGs demonstrated that DEGs were mainly involved in transcriptional dysregulation and multiple signaling pathways, such as the nuclear factor‑κB and mitogen‑activated protein kinase signaling pathways. In addition, Cytoscape software was used to visualize the protein‑protein interactions of these DEGs in order to identify hub genes, which could be used as biomarkers for the early diagnosis and treatment of CLL. Cytoscape software was also used to analyze the association between the predicted target mRNAs of DEMs and DEGs and increase knowledge about the miRNA‑mRNA regulatory network associated with the progression of CLL. Taken together, the present study provided a bioinformatics basis for advancing our understanding of the pathogenesis of CLL by identifying differentially expressed hub genes, miRNA‑mRNA target pairs and molecular pathways. In addition, hub genes may be used as novel biomarkers for the diagnosis of CLL and to guide the selection of CLL drug combinations.
Collapse
Affiliation(s)
- Chundi Gao
- College of First Clinical Medicine, Shandong University of Traditional Chinese Medicine, Jinan, Shandong 250014, P.R. China
| | - Chao Zhou
- Cancer Center, Weifang Traditional Chinese Hospital, Weifang, Shandong 261000, P.R. China
| | - Jing Zhuang
- Cancer Center, Weifang Traditional Chinese Hospital, Weifang, Shandong 261000, P.R. China
| | - Lijuan Liu
- Cancer Center, Weifang Traditional Chinese Hospital, Weifang, Shandong 261000, P.R. China
| | - Junyu Wei
- Cancer Center, Weifang Traditional Chinese Hospital, Weifang, Shandong 261000, P.R. China
| | - Cun Liu
- College of Traditional Chinese Medicine, Shandong University of Traditional Chinese Medicine, Jinan, Shandong 250014, P.R. China
| | - Huayao Li
- College of First Clinical Medicine, Shandong University of Traditional Chinese Medicine, Jinan, Shandong 250014, P.R. China
| | - Changgang Sun
- Cancer Center, Weifang Traditional Chinese Hospital, Weifang, Shandong 261000, P.R. China
| |
Collapse
|
16
|
Global Similarity Method Based on a Two-tier Random Walk for the Prediction of microRNA-Disease Association. Sci Rep 2018; 8:6481. [PMID: 29691434 PMCID: PMC5915491 DOI: 10.1038/s41598-018-24532-7] [Citation(s) in RCA: 26] [Impact Index Per Article: 4.3] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/31/2018] [Accepted: 04/03/2018] [Indexed: 12/15/2022] Open
Abstract
microRNAs (miRNAs) mutation and maladjustment are related to the occurrence and development of human diseases. Studies on disease-associated miRNA have contributed to disease diagnosis and treatment. To address the problems, such as low prediction accuracy and failure to predict the relationship between new miRNAs and diseases and so on, we design a Laplacian score of graphs to calculate the global similarity of networks and propose a Global Similarity method based on a Two-tier Random Walk for the prediction of miRNA-disease association (GSTRW) to reveal the correlation between miRNAs and diseases. This method is a global approach that can simultaneously predict the correlation between all diseases and miRNAs in the absence of negative samples. Experimental results reveal that this method is better than existing approaches in terms of overall prediction accuracy and ability to predict orphan diseases and novel miRNAs. A case study on GSTRW for breast cancer and conlon cancer is also conducted, and the majority of miRNA-disease association can be verified by our experiment. This study indicates that this method is feasible and effective.
Collapse
|
17
|
Chen M, Peng Y, Li A, Li Z, Deng Y, Liu W, Liao B, Dai C. A novel information diffusion method based on network consistency for identifying disease related microRNAs. RSC Adv 2018; 8:36675-36690. [PMID: 35558942 PMCID: PMC9088870 DOI: 10.1039/c8ra07519k] [Citation(s) in RCA: 12] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/09/2018] [Accepted: 10/17/2018] [Indexed: 12/27/2022] Open
Abstract
The abnormal expression of miRNAs is directly related to the development of human diseases. Predicting the potential candidate miRNAs associated with diseases can contribute to the detection, diagnosis, treatment and prevention of human complex diseases. The effective inference of the calculation method of the relationship between miRNAs and diseases is an effective supplement to biological experiments. It is of great help in the prevention, treatment and prognosis of complex diseases. This paper proposes a novel information diffusion method based on network consistency (IDNC) for identifying disease related microRNAs. The model first synthesizes the miRNA family information and the miRNA function similarity to reconstruct the miRNA network, and reconstruct the disease network by using the known disease and miRNA-related information and the semantic score between diseases. Then the global similarity of the two networks is obtained by using the Laplacian score of graphs. The global similarity score is a measure of the similarity between diseases and miRNAs. The disease–miRNA relation network was reconstructed by integrating the global similarity relation. The network consistency diffusion seed is then obtained by combining the global similarity network with the reconstructed disease–miRNA association network. Thereafter, the stable diffusion spectrum is generated as the prediction score by using the restarted random walk algorithm. The AUC value obtained by performing the LOOCV in the gold benchmark dataset is 0.8814. The AUC value obtained by performing the LOOCV in the predictive dataset is 0.9512. Compared with other frontier methods, our method has higher accuracy, which is further illustrated by case studies of breast neoplasms and colon neoplasms to prove that IDNC is valuable. The abnormal expression of miRNAs is directly related to the development of human diseases.![]()
Collapse
Affiliation(s)
- Min Chen
- College of Computer Science and Technology
- Hunan Institute of Technology
- 421002 Hengyang
- China
- College of Information Science and Engineering
| | - Yan Peng
- College of International Communication
- Hunan Institute of Technology
- 421002 Hengyang
- China
| | - Ang Li
- College of Computer Science and Technology
- Hunan Institute of Technology
- 421002 Hengyang
- China
| | - Zejun Li
- College of Computer Science and Technology
- Hunan Institute of Technology
- 421002 Hengyang
- China
- College of Information Science and Engineering
| | - Yingwei Deng
- College of Computer Science and Technology
- Hunan Institute of Technology
- 421002 Hengyang
- China
| | - Wenhua Liu
- College of Computer Science and Technology
- Hunan Institute of Technology
- 421002 Hengyang
- China
| | - Bo Liao
- College of Information Science and Engineering
- Hunan University
- Changsha 410082
- China
| | - Chengqiu Dai
- College of Computer Science and Technology
- Hunan Institute of Technology
- 421002 Hengyang
- China
| |
Collapse
|
18
|
Karaca E, Aykut A, Ertürk B, Durmaz B, Güler A, Büke B, Yeniel AÖ, Ergenoğlu AM, Özkınay F, Özeren M, Kazandı M, Akercan F, Sağol S, Gündüz C, Çoğulu Ö. MicroRNA Expression Profile in the Prenatal Amniotic Fluid Samples of Pregnant Women with Down Syndrome. Balkan Med J 2017; 35:163-166. [PMID: 29219113 PMCID: PMC5863254 DOI: 10.4274/balkanmedj.2017.0511] [Citation(s) in RCA: 18] [Impact Index Per Article: 2.6] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/01/2022] Open
Abstract
Background: Down syndrome, which is the most common human chromosomal anomaly that can affect people of any race and age, can be diagnosed prenatally in most cases. Prenatal diagnosis via culture method is time-consuming; thus, genetic analysis has thus been introduced and is continually being developed for rapid prenatal diagnosis. For this reason, the effective use of microRNA profiling for the rapid analysis of prenatal amniotic fluid samples for the diagnosis of Down syndrome was investigated. Aims: To evaluate the expression levels of 14 microRNAs encoded by chromosome 21 in amniotic fluid samples and their utility for prenatal diagnosis of Down syndrome. Study Design: Case-control study. Methods: We performed invasive prenatal testing for 56 pregnant women; 23 carried fetuses with Down syndrome, and 33 carried fetuses with a normal karyotype. Advanced maternal age and increased risk for Down syndrome in the screening tests were indications for invasive prenatal testing. The age of gestation in the study and control groups ranged between 17 and 18 weeks. The expression levels of microRNA were measured by real-time polymerase chain reaction. Results: The expression levels of microRNA-125b-2, microRNA-155, and microRNA-3156 were significantly higher in the study group than in the control group. Conclusion: The presence of significantly dysregulated microRNAs may be associated with either the phenotype or the result of abnormal development. Further large-scale comparative studies conducted in a variety of conditions may bring novel insights in the field of abnormal prenatal conditions.
Collapse
Affiliation(s)
- Emin Karaca
- Department of Medical Genetics, Ege University School of Medicine, İzmir, Turkey
| | - Ayça Aykut
- Department of Medical Genetics, Ege University School of Medicine, İzmir, Turkey
| | - Biray Ertürk
- Department of Medical Genetics, Ege University School of Medicine, İzmir, Turkey
| | - Burak Durmaz
- Department of Medical Genetics, Ege University School of Medicine, İzmir, Turkey
| | - Ahmet Güler
- Clinic of Obstetrics and Gynecology, İzmir Ege Maternity and Women's Diseases Training Research Hospital, İzmir, Turkey
| | - Barış Büke
- Department of Obstetrics and Gynecology, Ege University School of Medicine, İzmir, Turkey
| | - Ahmet Özgür Yeniel
- Department of Obstetrics and Gynecology, Ege University School of Medicine, İzmir, Turkey
| | - Ahmet Mete Ergenoğlu
- Department of Obstetrics and Gynecology, Ege University School of Medicine, İzmir, Turkey
| | - Ferda Özkınay
- Department of Medical Genetics, Ege University School of Medicine, İzmir, Turkey
| | - Mehmet Özeren
- Clinic of Obstetrics and Gynecology, İzmir Ege Maternity and Women's Diseases Training Research Hospital, İzmir, Turkey
| | - Mert Kazandı
- Department of Obstetrics and Gynecology, Ege University School of Medicine, İzmir, Turkey
| | - Fuat Akercan
- Department of Obstetrics and Gynecology, Ege University School of Medicine, İzmir, Turkey
| | - Sermet Sağol
- Department of Obstetrics and Gynecology, Ege University School of Medicine, İzmir, Turkey
| | - Cumhur Gündüz
- Department of Medical Biology, Ege University School of Medicine, İzmir, Turkey
| | - Özgür Çoğulu
- Department of Medical Genetics, Ege University School of Medicine, İzmir, Turkey
| |
Collapse
|
19
|
Li J, Qin Y, Zhang H. Identification of key miRNA-gene pairs in chronic lymphocytic leukemia through integrated analysis of mRNA and miRNA microarray. Oncol Lett 2017; 15:361-367. [PMID: 29285196 PMCID: PMC5738675 DOI: 10.3892/ol.2017.7287] [Citation(s) in RCA: 7] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/21/2017] [Accepted: 10/17/2017] [Indexed: 12/17/2022] Open
Abstract
The aim of the present study was to explore the miRNA-Gene regulatory mechanism in chronic lymphocytic leukemia (CLL), and identify new targets for the therapy of CLL. The miRNA expression dataset GSE62137 and mRNA expression dataset GSE22529 were downloaded from National Center of Biotechnology Information Gene Expression Omnibus database. In CLL samples compared with normal B cell samples, differentially expressed miRNAs (DEMs) were identified via the GEO2R instrument of GEO and differentially expressed genes (DEGs) were obtained via the limma package of R. Functional enrichment analysis of the DEGs was performed via the Database for Annotation, Visualization and Integrated Discovery. The targets of the DEMs were identified based on the miRNAWalk platform. The overlaps between the DEGs and the targets of the DEMs were selected, and the miRNA-Gene regulatory network was constructed based on the overlaps and the corresponding DEMs. A total of 63 DEMs and 504 DEGs were identified in CLL samples compared with normal B cell samples. Eleven enriched functional clusters of the DEGs were obtained. 405 miRNA-Gene regulatory pairs were identified. The miRNA-Gene regulatory pairs contained 351 target genes of the DEMs, including 9 overlaps with the DEGs. A miRNA-Gene regulatory network was constructed. Bioinformatics methods could help us develop a better understanding of the molecular mechanism of CLL. MiRNAs may play a critical role in regulating the process of CLL. They may affect CLL by regulating the processes of immunoreactivity and protein degradation. Genes such as Neurogenic Locus Notch Homolog Protein 2, PR/SET domain 4 and A-kinase anchoring protein 12 may be their regulating targets in CLL.
Collapse
Affiliation(s)
- Jie Li
- Department of Transfusion Medicine, The Fifth Central Hospital of Tianjin, Tianjin 300450, P.R. China
| | - Yi Qin
- Institute of Medical Laboratory, Tianjin Medical University, Tianjin 300072, P.R. China
| | - Haiyan Zhang
- Department of Medical Record Management, The Fifth Central Hospital of Tianjin, Tianjin 300450, P.R. China
| |
Collapse
|
20
|
Li JQ, Rong ZH, Chen X, Yan GY, You ZH. MCMDA: Matrix completion for MiRNA-disease association prediction. Oncotarget 2017; 8:21187-21199. [PMID: 28177900 PMCID: PMC5400576 DOI: 10.18632/oncotarget.15061] [Citation(s) in RCA: 144] [Impact Index Per Article: 20.6] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/17/2016] [Accepted: 01/09/2017] [Indexed: 12/31/2022] Open
Abstract
Nowadays, researchers have realized that microRNAs (miRNAs) are playing a significant role in many important biological processes and they are closely connected with various complex human diseases. However, since there are too many possible miRNA-disease associations to analyze, it remains difficult to predict the potential miRNAs related to human diseases without a systematic and effective method. In this study, we developed a Matrix Completion for MiRNA-Disease Association prediction model (MCMDA) based on the known miRNA-disease associations in HMDD database. MCMDA model utilized the matrix completion algorithm to update the adjacency matrix of known miRNA-disease associations and furthermore predict the potential associations. To evaluate the performance of MCMDA, we performed leave-one-out cross validation (LOOCV) and 5-fold cross validation to compare MCMDA with three previous classical computational models (RLSMDA, HDMP, and WBSMDA). As a result, MCMDA achieved AUCs of 0.8749 in global LOOCV, 0.7718 in local LOOCV and average AUC of 0.8767+/−0.0011 in 5-fold cross validation. Moreover, the prediction results associated with colon neoplasms, kidney neoplasms, lymphoma and prostate neoplasms were verified. As a consequence, 84%, 86%, 78% and 90% of the top 50 potential miRNAs for these four diseases were respectively confirmed by recent experimental discoveries. Therefore, MCMDA model is superior to the previous models in that it improves the prediction performance although it only depends on the known miRNA-disease associations.
Collapse
Affiliation(s)
- Jian-Qiang Li
- College of Computer Science and Software Engineering, Shenzhen University, Shenzhen, 518060, China
| | - Zhi-Hao Rong
- School of Software, Beihang University, Beijing, 100191, China
| | - Xing Chen
- School of Information and Control Engineering, China University of Mining and Technology, Xuzhou, 221116, China
| | - Gui-Ying Yan
- Academy of Mathematics and Systems Science, Chinese Academy of Sciences, Beijing, 100190, China
| | - Zhu-Hong You
- Xinjiang Technical Institute of Physics and Chemistry, Chinese Academy of Science, ürümqi, 830011, China
| |
Collapse
|
21
|
Ding T, Xu J, Sun M, Zhu S, Gao J. Predicting microRNA biological functions based on genes discriminant analysis. Comput Biol Chem 2017; 71:230-235. [PMID: 29033260 DOI: 10.1016/j.compbiolchem.2017.09.008] [Citation(s) in RCA: 3] [Impact Index Per Article: 0.4] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/07/2017] [Accepted: 09/25/2017] [Indexed: 01/09/2023]
Abstract
Although thousands of microRNAs (miRNAs) have been identified in recent experimental efforts, it remains a challenge to explore their specific biological functions through molecular biological experiments. Since those members from same family share same or similar biological functions, classifying new miRNAs into their corresponding families will be helpful for their further functional analysis. In this study, we initially built a vector space by characterizing the features from miRNA sequences and structures according to their miRBase family organizations. Then we further assigned miRNAs into its specific miRNA families by developing a novel genes discriminant analysis (GDA) approach in this study. As can be seen from the results of new families from GDA, in each of these new families, there was a high degree of similarity among all members of nucleotide sequences. At the same time, we employed 10-fold cross-validation machine learning to achieve the accuracy rates of 68.68%, 80.74%, and 83.65% respectively for the original miRNA families with no less than two, three, and four members. The encouraging results suggested that the proposed GDA could not only provide a support in identifying new miRNAs' families, but also contributing to predicting their biological functions.
Collapse
Affiliation(s)
- Tao Ding
- School of Science, Jiangnan University, Wuxi, China; School of Mathematics and Statistics, Newcastle University, Newcastle upon Tyne, UK.
| | - Junhua Xu
- School of Science, Jiangnan University, Wuxi, China.
| | - Mengmeng Sun
- School of Science, Jiangnan University, Wuxi, China.
| | - Shanshan Zhu
- School of Science, Jiangnan University, Wuxi, China.
| | - Jie Gao
- School of Science, Jiangnan University, Wuxi, China.
| |
Collapse
|
22
|
Malpeli G, Barbi S, Zupo S, Tosadori G, Scardoni G, Bertolaso A, Sartoris S, Ugel S, Vicentini C, Fassan M, Adamo A, Krampera M, Scupoli MT, Croce CM, Scarpa A. Identification of microRNAs implicated in the late differentiation stages of normal B cells suggests a central role for miRNA targets ZEB1 and TP53. Oncotarget 2017; 8:11809-11826. [PMID: 28107180 PMCID: PMC5355306 DOI: 10.18632/oncotarget.14683] [Citation(s) in RCA: 10] [Impact Index Per Article: 1.4] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/17/2016] [Accepted: 12/12/2016] [Indexed: 12/11/2022] Open
Abstract
In the late B cell differentiation stages, miRNAs expression modifications promoting or inhibiting key pathways are only partially defined. We isolated 29 CD19+ human B cell samples at different stages of differentiation: B cells from peripheral blood; naïve, germinal center (GC) and subepithelial (SE) B cells from tonsils. SE cells were further split in activated and resting B cell. The miRNA expression profile of these B cells was assessed by microarray analysis and selected miRNAs were validated by quantitative RT-PCR and in situ hybridization on normal tonsils. The comparison of all samples showed changes in 107 miRNAs in total. Among 48 miRNAs differentially expressed in naïve, GC and SE cells, we identified 8 miRNAs: mir-323, mir-138, mir-9*, mir-211, mir-149, mir-373, mir-135a and mir-184, strictly specific to follicular cells that had never been implicated before in late stages of B cell development. Moreover, we unveiled 34 miRNAs able to discriminate between CD5− activated B cells and resting B cells. The miRNAs profile of CD5− resting B cells showed a higher similarity to naïve CD5+ than CD5− activated B cells. Finally, network analysis on shortest paths connecting gene targets suggested ZEB1 and TP53 as key miRNA targets during the follicular differentiation pathway. These data confirm and extend our knowledge on the miRNAs-related regulatory pathways involved in the late B cell maturation.
Collapse
Affiliation(s)
- Giorgio Malpeli
- Department of Surgical Sciences, Dentistry, Gynecology and Pediatrics, Section of Surgery, University of Verona, Verona, Italy.,Department of Diagnostics and Public Health, Section of Pathological Anatomy, University of Verona, Verona, Italy
| | - Stefano Barbi
- Department of Diagnostics and Public Health, Section of Pathological Anatomy, University of Verona, Verona, Italy
| | - Simonetta Zupo
- Laboratory of Molecular Diagnostics, IRCCS-AOU San Martino-IST, Istituto Nazionale per la Ricerca sul Cancro, Genoa, Italy
| | - Gabriele Tosadori
- Center for BioMedical Computing (CBMC), University of Verona, Verona, Italy
| | - Giovanni Scardoni
- Center for BioMedical Computing (CBMC), University of Verona, Verona, Italy
| | - Anna Bertolaso
- Department of Diagnostics and Public Health, Section of Pathological Anatomy, University of Verona, Verona, Italy
| | - Silvia Sartoris
- Department of Medicine, Section of Immunology, University of Verona, Verona, Italy
| | - Stefano Ugel
- Department of Medicine, Section of Immunology, University of Verona, Verona, Italy
| | - Caterina Vicentini
- Department of Diagnostics and Public Health, Section of Pathological Anatomy, University of Verona, Verona, Italy.,Applied Research on Cancer-Network (ARC-NET), University of Verona, Verona, Italy
| | - Matteo Fassan
- Department of Medicine, Surgical Pathology and Cytopathology Unit, University of Padua, Padua, Italy
| | - Annalisa Adamo
- Department of Medicine, Section of Hematology, Stem Cell Research Laboratory, University of Verona, Italy
| | - Mauro Krampera
- Department of Medicine, Section of Hematology, Stem Cell Research Laboratory, University of Verona, Italy
| | | | - Carlo Maria Croce
- Department of Molecular Virology, Immunology and Medical Genetics, Comprehensive Cancer Center, The Ohio State University, Columbus, OH, USA
| | - Aldo Scarpa
- Department of Diagnostics and Public Health, Section of Pathological Anatomy, University of Verona, Verona, Italy.,Applied Research on Cancer-Network (ARC-NET), University of Verona, Verona, Italy
| |
Collapse
|
23
|
Szurián K, Csala I, Piurkó V, Deák L, Matolcsy A, Reiniger L. Quantitative miR analysis in chronic lymphocytic leukaemia/small lymphocytic lymphoma – proliferation centres are characterized by high miR-92a and miR-155 and low miR-150 expression. Leuk Res 2017; 58:39-42. [DOI: 10.1016/j.leukres.2017.04.002] [Citation(s) in RCA: 11] [Impact Index Per Article: 1.6] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/02/2017] [Revised: 03/30/2017] [Accepted: 04/03/2017] [Indexed: 02/06/2023]
|
24
|
Mirzaei H, Fathullahzadeh S, Khanmohammadi R, Darijani M, Momeni F, Masoudifar A, Goodarzi M, Mardanshah O, Stenvang J, Jaafari MR, Mirzaei HR. State of the art in microRNA as diagnostic and therapeutic biomarkers in chronic lymphocytic leukemia. J Cell Physiol 2017; 233:888-900. [PMID: 28084621 DOI: 10.1002/jcp.25799] [Citation(s) in RCA: 70] [Impact Index Per Article: 10.0] [Reference Citation Analysis] [Abstract] [Key Words] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/12/2017] [Accepted: 01/12/2017] [Indexed: 12/11/2022]
Abstract
Early diagnostic is one of the most important steps in cancer therapy which helps to design and choose a better therapeutic approach. The finding of biomarkers in various levels including genomics, transcriptomics, and proteomics levels could provide better treatment for various cancers such as chronic lymphocytic leukemia (CLL). The CLL is the one of main lymphoid malignancies which is specified by aggregation of mature B lymphocytes. Among different biomarkers (e.g., CD38, chromosomes abnormalities, ZAP-70, TP53, and microRNA [miRNA]), miRNAs have appeared as new diagnostic and therapeutic biomarkers in patients with the CLL disease. Multiple lines of evidence indicated that deregulation of miRNAs could be associated with pathological events which are present in the CLL. These molecules have an effect on a variety of targets such as Bcl2, c-fos, c-Myc, TP53, TCL1, and STAT3 which play critical roles in the CLL pathogenesis. It has been shown that expression of miRNAs could lead to the activation of B cells and B cell antigen receptor (BCR). Moreover, exosomes containing miRNAs are one of the other molecules which could contribute to BCR stimulation and progression of CLL cells. Hence, miRNAs and exosomes released from CLL cells could be used as potential diagnostic and therapeutic biomarkers for CLL. This critical review focuses on a very important aspect of CLL based on biomarker discovery covers the pros and cons of using miRNAs as important diagnostics and therapeutics biomarkers for this deadly disease.
Collapse
Affiliation(s)
- Hamed Mirzaei
- Department of Medical Biotechnology, School of Medicine, Mashhad University of Medical Sciences, Mashhad, Iran
| | - Sima Fathullahzadeh
- Medical Biotechnology Research Center, Ashkezar Branch, Islamic Azad University, Ashkezar, Yazd, Iran
| | - Razieh Khanmohammadi
- Department of pediatric dentistry, School of dentistry, Tehran University of Medical Sciences, Tehran, Iran
| | - Mansoreh Darijani
- Department of Oral and Maxillofacial Radiology, School of Dentistry, Kerman University of Medical Sciences, Kerman, Iran
| | - Fatemeh Momeni
- Applied Physiology Research Center, Isfahan Cardiovascular Research Institute, Isfahan University of Medical Sciences, Isfahan, Iran
| | - Aria Masoudifar
- Department of Molecular Biotechnology, Cell Science Research Center, Royan Institute for Biotechnology, ACECR, Isfahan, Iran
| | - Mohammad Goodarzi
- Faculty of Bioscience Engineering, Department of Biosystems, Katholieke Universiteit Leuven - KULeuven, Heverlee, Belgium
| | - Omid Mardanshah
- Department of Parasitology and Mycology, School of Medicine, Isfahan University of Medical Sciences, Isfahan, Iran
| | - Jan Stenvang
- Faculty of Health and Medical Sciences, Section for Molecular Disease Biology, Department of Veterinary Disease Biology, University of Copenhagen, Copenhagen, Denmark
| | - Mahmoud Reza Jaafari
- Nanotechnology Research Center, Mashhad University of Medical Sciences, Mashhad, Iran
| | - Hamid Reza Mirzaei
- Department of Immunology, School of Medicine, Tehran University of Medical Sciences, Tehran, Iran
| |
Collapse
|
25
|
MicroRNA expression patterns and target prediction in multiple myeloma development and malignancy. Genes Genomics 2017; 39:533-540. [PMID: 28458781 PMCID: PMC5387019 DOI: 10.1007/s13258-017-0518-7] [Citation(s) in RCA: 22] [Impact Index Per Article: 3.1] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/09/2016] [Accepted: 01/24/2017] [Indexed: 12/27/2022]
Abstract
Epigenetic changes have emerged as key causes in the development and progression of multiple myeloma (MM). In this study, global microRNA (miRNA) expression profiling were performed for 27 MM (19 specimens and 8 cell lines) and 3 normal controls by microarray. miRNA-targets were identified by integrating the miRNA expression profiles with mRNA expression profiles of the matched samples (unpublished data). Two miRNAs were selected for verification by RT-qPCR (miR-150-5p and miR-4430). A total of 1791 and 8 miRNAs were over-expressed and under-expressed, respectively in MM compared to the controls (fold change ≥2.0; p < 0.05). The miRNA-mRNA integrative analysis revealed inverse correlation between 5 putative target genes (RAD54L, CCNA2, CYSLTR2, RASGRF2 and HKDC1) and 15 miRNAs (p < 0.05). Most of the differentially expressed miRNAs are involved in survival, proliferation, migration, invasion and drug resistance in MM. Some have never been described in association with MM (miR-33a, miR-9 and miR-211). Interestingly, our results revealed 2 miRNAs, which are closely related to B cell differentiation (miR-150 and miR-125b). For the first time, we suggest that miR-150 might be potential negative regulator for two critical cell cycle control genes, RAD54L and CCNA2, whereas miR-125b potentially target RAS and CysLT signaling proteins, namely RASGRF2 and CYSLTR2, respectively. This study has enhanced our understanding on the pathobiology of MM and opens up new avenues for future research in myelomagenesis.
Collapse
|
26
|
Bedewy AML, Elmaghraby SM, Shehata AA, Kandil NS. Prognostic Value of miRNA-155 Expression in B-Cell Non-Hodgkin Lymphoma. Turk J Haematol 2017; 34:207-212. [PMID: 28148469 PMCID: PMC5544039 DOI: 10.4274/tjh.2016.0286] [Citation(s) in RCA: 13] [Impact Index Per Article: 1.9] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/08/2023] Open
Abstract
Objective: MicroRNA-155 (miRNA-155) resides within the B-cell integration cluster gene on chromosome 21. It can act either as an oncogene or as a tumor-suppressor gene, depending on the cell background in which miRNA-155 is performing its specific target gene controlling function. Therefore, the aim of this study was to investigate miRNA-155 expression in patients with B-cell non-Hodgkin lymphoma (NHL) and its relation to disease prognosis in diffuse large B-cell lymphoma (DLBCL) patients. Materials and Methods: Reverse transcription-polymerase chain reaction assay was performed to evaluate the expression levels of miRNA-155 in 84 patients with newly diagnosed B-cell NHL and 15 normal controls. Results: Compared with normal controls, miRNA-155 expression was significantly upregulated in patients. Moreover, higher levels of miRNA-155 were associated with the presence of B symptoms, involvement of extranodal sites, and high Eastern Cooperative Oncology Group (ECOG) score. Higher levels of miRNA-155 in DLBCL were associated with non-germinal B-cell-like type, the presence of B symptoms, involvement of extranodal sites, and higher International Prognostic Index (IPI) and ECOG scores. Only the high IPI score and high miRNA-155 expression indicated a higher risk of lower event-free survival using multivariate Cox regression analysis. Our data demonstrated that the expression of miRNA-155 was upregulated in newly diagnosed B-cell NHL patients. miRNA-155 is expressed at a lower level in GCB-subtype DLBCL. Low IPI score and miRNA-155 expression were predictors of longer event-free survival. Conclusion: Despite contradicting literature reports, the current findings suggest the potential value of miRNA-155 as a biomarker of prognosis and monitoring in B-cell NHL, and especially that of the DLBCL type.
Collapse
Affiliation(s)
- Ahmed M L Bedewy
- Alexandria University Faculty of Medicine, Medical Research Institute, Alexandria Governorate, Egypt
| | | | | | | |
Collapse
|
27
|
King JK, Ung NM, Paing MH, Contreras JR, Alberti MO, Fernando TR, Zhang K, Pellegrini M, Rao DS. Regulation of Marginal Zone B-Cell Differentiation by MicroRNA-146a. Front Immunol 2017; 7:670. [PMID: 28138326 PMCID: PMC5237642 DOI: 10.3389/fimmu.2016.00670] [Citation(s) in RCA: 15] [Impact Index Per Article: 2.1] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/17/2016] [Accepted: 12/19/2016] [Indexed: 11/13/2022] Open
Abstract
B-cell development in the bone marrow is followed by specification into functional subsets in the spleen, including marginal zone (MZ) B-cells. MZ B-cells are classically characterized by T-independent antigenic responses and require the elaboration of distinct gene expression programs for development. Given their role in gene regulation, it is not surprising that microRNAs are important factors in B-cell development. Recent work demonstrated that deficiency of the NFκB feedback regulator, miR-146a, led to a range of hematopoietic phenotypes, but B-cell phenotypes have not been extensively characterized. Here, we found that miR-146a-deficient mice demonstrate a reduction in MZ B-cells, likely from a developmental block. Utilizing high-throughput sequencing and comparative analysis of developmental stage-specific transcriptomes, we determined that MZ cell differentiation was impaired due to decreases in Notch2 signaling. Our studies reveal miR-146a-dependent B-cell phenotypes and highlight the complex role of miR-146a in the hematopoietic system.
Collapse
Affiliation(s)
- Jennifer K King
- Division of Rheumatology and STAR Program, Department of Medicine, University of California Los Angeles, Los Angeles, CA, USA; Cellular and Molecular Pathology Ph.D.Program, Department of Pathology and Laboratory Medicine, University of California, Los Angeles, CA, USA
| | - Nolan M Ung
- Department of Pathology and Laboratory Medicine, University of California Los Angeles , Los Angeles, CA , USA
| | - May H Paing
- Department of Pathology and Laboratory Medicine, University of California Los Angeles , Los Angeles, CA , USA
| | - Jorge R Contreras
- Cellular and Molecular Pathology Ph.D.Program, Department of Pathology and Laboratory Medicine, University of California, Los Angeles, CA, USA; Department of Pathology and Laboratory Medicine, University of California Los Angeles, Los Angeles, CA, USA
| | - Michael O Alberti
- Department of Pathology and Laboratory Medicine, University of California Los Angeles , Los Angeles, CA , USA
| | - Thilini R Fernando
- Department of Pathology and Laboratory Medicine, University of California Los Angeles , Los Angeles, CA , USA
| | - Kelvin Zhang
- Department of Biological Chemistry, University of California Los Angeles, Los Angeles, CA, USA; Howard Hughes Medical Institute, University of California Los Angeles, Los Angeles, CA, USA
| | - Matteo Pellegrini
- Jonsson Comprehensive Cancer Center, University of California Los Angeles, Los Angeles, CA, USA; Molecular Cell and Developmental Biology, University of California Los Angeles, Los Angeles, CA, USA; Eli and Edythe Broad Center of Regenerative Medicine and Stem Cell Research, University of California Los Angeles, Los Angeles, CA, USA
| | - Dinesh S Rao
- Department of Pathology and Laboratory Medicine, University of California Los Angeles, Los Angeles, CA, USA; Jonsson Comprehensive Cancer Center, University of California Los Angeles, Los Angeles, CA, USA; Eli and Edythe Broad Center of Regenerative Medicine and Stem Cell Research, University of California Los Angeles, Los Angeles, CA, USA
| |
Collapse
|
28
|
Circulating microRNA-192 as a diagnostic biomarker in human chronic lymphocytic leukemia. Cancer Gene Ther 2016; 23:327-332. [DOI: 10.1038/cgt.2016.34] [Citation(s) in RCA: 90] [Impact Index Per Article: 11.3] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/29/2016] [Revised: 05/25/2016] [Accepted: 06/02/2016] [Indexed: 02/06/2023]
|
29
|
Husakova M. MicroRNAs in the key events of systemic lupus erythematosus pathogenesis. Biomed Pap Med Fac Univ Palacky Olomouc Czech Repub 2016; 160:327-42. [DOI: 10.5507/bp.2016.004] [Citation(s) in RCA: 34] [Impact Index Per Article: 4.3] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/25/2015] [Accepted: 01/22/2016] [Indexed: 12/17/2022] Open
|
30
|
Abstract
Potential ionising radiation exposure scenarios are varied, but all bring risks beyond the simple issues of short-term survival. Whether accidentally exposed to a single, whole-body dose in an act of terrorism or purposefully exposed to fractionated doses as part of a therapeutic regimen, radiation exposure carries the consequence of elevated cancer risk. The long-term impact of both intentional and unintentional exposure could potentially be mitigated by treatments specifically developed to limit the mutations and precancerous replication that ensue in the wake of irradiation The development of such agents would undoubtedly require a substantial degree of in vitro testing, but in order to accurately recapitulate the complex process of radiation-induced carcinogenesis, well-understood animal models are necessary. Inbred strains of the laboratory mouse, Mus musculus, present the most logical choice due to the high number of molecular and physiological similarities they share with humans. Their small size, high rate of breeding and fully sequenced genome further increase its value for use in cancer research. This chapter will review relevant m. musculus inbred and F1 hybrid animals of radiation-induced myeloid leukemia, thymic lymphoma, breast and lung cancers. Method of cancer induction and associated molecular pathologies will also be described for each model.
Collapse
|
31
|
du Plessis WJ, Kleynhans L, du Plessis N, Stanley K, Malherbe ST, Maasdorp E, Ronacher K, Chegou NN, Walzl G, Loxton AG. The Functional Response of B Cells to Antigenic Stimulation: A Preliminary Report of Latent Tuberculosis. PLoS One 2016; 11:e0152710. [PMID: 27050308 PMCID: PMC4822853 DOI: 10.1371/journal.pone.0152710] [Citation(s) in RCA: 20] [Impact Index Per Article: 2.5] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/17/2016] [Accepted: 03/17/2016] [Indexed: 01/11/2023] Open
Abstract
Mycobacterium tuberculosis (M.tb) remains a successful pathogen, causing tuberculosis disease numbers to constantly increase. Although great progress has been made in delineating the disease, the host-pathogen interaction is incompletely described. B cells have shown to function as both effectors and regulators of immunity via non-humoral methods in both innate and adaptive immune settings. Here we assessed specific B cell functional interaction following stimulation with a broad range of antigens within the LTBI milieu. Our results indicate that B cells readily produce pro- and anti-inflammatory cytokines (including IL-1β, IL-10, IL-17, IL-21 and TNF-α) in response to stimulation. TLR4 and TLR9 based stimulations achieved the greatest secreted cytokine-production response and BCG stimulation displayed a clear preference for inducing IL-1β production. We also show that the cytokines produced by B cells are implicated strongly in cell-mediated communication and that plasma (memory) B cells (CD19+CD27+CD138+) is the subset with the greatest contribution to cytokine production. Collectively our data provides insight into B cell responses, where they are implicated in and quantifies responses from specific B cell phenotypes. These findings warrant further functional B cell research with a focus on specific B cell phenotypes under conditions of active TB disease to further our knowledge about the contribution of various cell subsets which could have implications for future vaccine development or refined B cell orientated treatment in the health setting.
Collapse
Affiliation(s)
- Willem J. du Plessis
- SA MRC Centre for TB Research, DST/NRF Centre of Excellence for Biomedical Tuberculosis Research, Division of Molecular Biology and Human Genetics, Faculty of Medicine and Health Sciences, Stellenbosch University, Cape Town, South Africa
| | - Léanie Kleynhans
- SA MRC Centre for TB Research, DST/NRF Centre of Excellence for Biomedical Tuberculosis Research, Division of Molecular Biology and Human Genetics, Faculty of Medicine and Health Sciences, Stellenbosch University, Cape Town, South Africa
| | - Nelita du Plessis
- SA MRC Centre for TB Research, DST/NRF Centre of Excellence for Biomedical Tuberculosis Research, Division of Molecular Biology and Human Genetics, Faculty of Medicine and Health Sciences, Stellenbosch University, Cape Town, South Africa
| | - Kim Stanley
- SA MRC Centre for TB Research, DST/NRF Centre of Excellence for Biomedical Tuberculosis Research, Division of Molecular Biology and Human Genetics, Faculty of Medicine and Health Sciences, Stellenbosch University, Cape Town, South Africa
| | - Stephanus T. Malherbe
- SA MRC Centre for TB Research, DST/NRF Centre of Excellence for Biomedical Tuberculosis Research, Division of Molecular Biology and Human Genetics, Faculty of Medicine and Health Sciences, Stellenbosch University, Cape Town, South Africa
| | - Elizna Maasdorp
- SA MRC Centre for TB Research, DST/NRF Centre of Excellence for Biomedical Tuberculosis Research, Division of Molecular Biology and Human Genetics, Faculty of Medicine and Health Sciences, Stellenbosch University, Cape Town, South Africa
| | - Katharina Ronacher
- SA MRC Centre for TB Research, DST/NRF Centre of Excellence for Biomedical Tuberculosis Research, Division of Molecular Biology and Human Genetics, Faculty of Medicine and Health Sciences, Stellenbosch University, Cape Town, South Africa
| | - Novel N. Chegou
- SA MRC Centre for TB Research, DST/NRF Centre of Excellence for Biomedical Tuberculosis Research, Division of Molecular Biology and Human Genetics, Faculty of Medicine and Health Sciences, Stellenbosch University, Cape Town, South Africa
| | - Gerhard Walzl
- SA MRC Centre for TB Research, DST/NRF Centre of Excellence for Biomedical Tuberculosis Research, Division of Molecular Biology and Human Genetics, Faculty of Medicine and Health Sciences, Stellenbosch University, Cape Town, South Africa
| | - Andre G. Loxton
- SA MRC Centre for TB Research, DST/NRF Centre of Excellence for Biomedical Tuberculosis Research, Division of Molecular Biology and Human Genetics, Faculty of Medicine and Health Sciences, Stellenbosch University, Cape Town, South Africa
- * E-mail:
| |
Collapse
|
32
|
|
33
|
Robaina MC, Faccion RS, Mazzoccoli L, Rezende LMM, Queiroga E, Bacchi CE, Thomas-Tikhonenko A, Klumb CE. miR-17-92 cluster components analysis in Burkitt lymphoma: overexpression of miR-17 is associated with poor prognosis. Ann Hematol 2016; 95:881-91. [PMID: 27044389 DOI: 10.1007/s00277-016-2653-7] [Citation(s) in RCA: 28] [Impact Index Per Article: 3.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/15/2016] [Accepted: 03/22/2016] [Indexed: 12/22/2022]
Abstract
Burkitt lymphoma (BL) is an aggressive B cell lymphoma characterized by the reciprocal translocation of the c-Myc gene with immunoglobulin genes. Recently, MYC has been shown to maintain the neoplastic state via the miR-17-92 microRNA cluster that suppresses chromatin regulatory genes and the apoptosis regulator Bim. However, the expression and prognostic impact of miR-17-92 members in pediatric BL (pBL) are unknown. Therefore, we investigated miR-17, miR-19a, miR-19b, miR-20, and miR-92a expression and prognostic impact in a series of 41 pBL samples. In addition, Bim protein expression was evaluated and compared to miR-17, miR-19a, miR-19b, miR-20, and miR-92a levels and patient outcomes. The expression of miR-17-92 members was evaluated by qPCR and Bim protein by immunohistochemistry. Log-rank test was employed to assess prognostic impact. We found that upregulated expression of miR-17 and miR-20a correlates with lack of pro-apoptotic Bim expression. Patients bearing tumors with upregulated miR-17 displayed decreased overall survival (OS), and multivariate analysis revealed that miR-17 was a significant predictor of shortened OS. Using hairpin inhibitors, we showed that inhibition of miR-17 resulted in enhanced Bim expression in a BL cell line overexpressing the miR-17-92 cluster. Our results describe for the first time miR-17, miR-19a, miR-19b, miR-20a, and miR-92a expression profiles in pBL. The prognostic impact of miR-17 should be validated in a larger series, and may provide new therapeutic avenues in the era of anti-miRNA therapy research. Additional functional studies are further required to understand the specific role of miR-17-92 cluster members in BL.
Collapse
Affiliation(s)
- Marcela Cristina Robaina
- Programa de Pesquisa em Hemato-Oncologia Molecular, Instituto Nacional de Câncer, Rio de Janeiro, Brazil.,Division of Cancer Pathobiology, Children's Hospital of Philadelphia, Philadelphia, PA, USA
| | - Roberta Soares Faccion
- Programa de Pesquisa em Hemato-Oncologia Molecular, Instituto Nacional de Câncer, Rio de Janeiro, Brazil
| | - Luciano Mazzoccoli
- Programa de Pesquisa em Hemato-Oncologia Molecular, Instituto Nacional de Câncer, Rio de Janeiro, Brazil
| | | | | | | | - Andrei Thomas-Tikhonenko
- Division of Cancer Pathobiology, Children's Hospital of Philadelphia, Philadelphia, PA, USA.,Department of Pathology and Laboratory Medicine, Perelman School of Medicine at the University of Pennsylvania, Philadelphia, PA, USA
| | - Claudete Esteves Klumb
- Programa de Pesquisa em Hemato-Oncologia Molecular, Instituto Nacional de Câncer, Rio de Janeiro, Brazil. .,Laboratório de Hemato-Oncologia Celular e Molecular, Praça da Cruz Vermelha, 23, 6th floor, Rio de Janeiro, RJ, CEP: 20230-130, Brazil.
| |
Collapse
|
34
|
Samadi AK, Bilsland A, Georgakilas AG, Amedei A, Amin A, Bishayee A, Azmi AS, Lokeshwar BL, Grue B, Panis C, Boosani CS, Poudyal D, Stafforini DM, Bhakta D, Niccolai E, Guha G, Vasantha Rupasinghe HP, Fujii H, Honoki K, Mehta K, Aquilano K, Lowe L, Hofseth LJ, Ricciardiello L, Ciriolo MR, Singh N, Whelan RL, Chaturvedi R, Ashraf SS, Shantha Kumara HMC, Nowsheen S, Mohammed SI, Keith WN, Helferich WG, Yang X. A multi-targeted approach to suppress tumor-promoting inflammation. Semin Cancer Biol 2015; 35 Suppl:S151-S184. [PMID: 25951989 PMCID: PMC4635070 DOI: 10.1016/j.semcancer.2015.03.006] [Citation(s) in RCA: 85] [Impact Index Per Article: 9.4] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/15/2014] [Revised: 03/13/2015] [Accepted: 03/16/2015] [Indexed: 12/15/2022]
Abstract
Cancers harbor significant genetic heterogeneity and patterns of relapse following many therapies are due to evolved resistance to treatment. While efforts have been made to combine targeted therapies, significant levels of toxicity have stymied efforts to effectively treat cancer with multi-drug combinations using currently approved therapeutics. We discuss the relationship between tumor-promoting inflammation and cancer as part of a larger effort to develop a broad-spectrum therapeutic approach aimed at a wide range of targets to address this heterogeneity. Specifically, macrophage migration inhibitory factor, cyclooxygenase-2, transcription factor nuclear factor-κB, tumor necrosis factor alpha, inducible nitric oxide synthase, protein kinase B, and CXC chemokines are reviewed as important antiinflammatory targets while curcumin, resveratrol, epigallocatechin gallate, genistein, lycopene, and anthocyanins are reviewed as low-cost, low toxicity means by which these targets might all be reached simultaneously. Future translational work will need to assess the resulting synergies of rationally designed antiinflammatory mixtures (employing low-toxicity constituents), and then combine this with similar approaches targeting the most important pathways across the range of cancer hallmark phenotypes.
Collapse
Affiliation(s)
| | - Alan Bilsland
- Institute of Cancer Sciences, University of Glasgow, Glasgow, Scotland, UK
| | - Alexandros G Georgakilas
- Physics Department, School of Applied Mathematics and Physical Sciences, National Technical University of Athens, Athens, Greece
| | - Amedeo Amedei
- Department of Experimental and Clinical Medicine, University of Florence, Florence, Italy
| | - Amr Amin
- Department of Biology, College of Science, United Arab Emirates University, Al Ain, United Arab Emirates; Faculty of Science, Cairo University, Cairo, Egypt
| | - Anupam Bishayee
- Department of Pharmaceutical Sciences, College of Pharmacy, Larkin Health Sciences Institute, Miami, FL, United States
| | - Asfar S Azmi
- Department of Pathology, Wayne State Univeristy, Karmanos Cancer Center, Detroit, MI, USA
| | - Bal L Lokeshwar
- Department of Urology, University of Miami, Miller School of Medicine, Miami, FL, United States; Miami Veterans Administration Medical Center, Miami, FL, United States
| | - Brendan Grue
- Department of Environmental Science, Dalhousie University, Halifax, Nova Scotia, Canada; Department of Microbiology and Immunology, Dalhousie University, Halifax, Nova Scotia, Canada
| | - Carolina Panis
- Laboratory of Inflammatory Mediators, State University of West Paraná, UNIOESTE, Paraná, Brazil
| | - Chandra S Boosani
- Department of BioMedical Sciences, School of Medicine, Creighton University, Omaha, NE, United States
| | - Deepak Poudyal
- Department of Drug Discovery and Biomedical Sciences, South Carolina College of Pharmacy, University of South Carolina, Columbia, SC, United States
| | - Diana M Stafforini
- Huntsman Cancer Institute and Department of Internal Medicine, University of Utah, Salt Lake City, UT, United States
| | - Dipita Bhakta
- School of Chemical and Biotechnology, SASTRA University, Thanjavur, Tamil Nadu, India
| | | | - Gunjan Guha
- School of Chemical and Biotechnology, SASTRA University, Thanjavur, Tamil Nadu, India
| | - H P Vasantha Rupasinghe
- Department of Environmental Sciences, Faculty of Agriculture and Department of Pathology, Faculty of Medicine, Dalhousie University, Halifax, Nova Scotia, Canada
| | - Hiromasa Fujii
- Department of Orthopedic Surgery, Nara Medical University, Kashihara, Nara, Japan
| | - Kanya Honoki
- Department of Orthopedic Surgery, Nara Medical University, Kashihara, Nara, Japan
| | - Kapil Mehta
- Department of Experimental Therapeutics, University of Texas MD Anderson Cancer Center, Houston, TX, United States
| | - Katia Aquilano
- Department of Biology, University of Rome "Tor Vergata", Rome, Italy
| | - Leroy Lowe
- Getting to Know Cancer, Truro, Nova Scotia, Canada.
| | - Lorne J Hofseth
- Department of Drug Discovery and Biomedical Sciences, South Carolina College of Pharmacy, University of South Carolina, Columbia, SC, United States
| | - Luigi Ricciardiello
- Department of Medical and Surgical Sciences, University of Bologna, Bologna, Italy
| | | | - Neetu Singh
- Advanced Molecular Science Research Centre (Centre for Advanced Research), King George's Medical University, Lucknow, Uttar Pradesh, India
| | - Richard L Whelan
- Department of Surgery, St. Luke's Roosevelt Hospital, New York, NY, United States
| | - Rupesh Chaturvedi
- School of Biotechnology, Jawaharlal Nehru University, New Delhi, India
| | - S Salman Ashraf
- Department of Chemistry, College of Science, United Arab Emirates University, Al Ain, United Arab Emirates
| | - H M C Shantha Kumara
- Department of Surgery, St. Luke's Roosevelt Hospital, New York, NY, United States
| | - Somaira Nowsheen
- Medical Scientist Training Program, Mayo Graduate School, Mayo Medical School, Mayo Clinic, Rochester, MN, United States
| | - Sulma I Mohammed
- Department of Comparative Pathobiology, Purdue University Center for Cancer Research, West Lafayette, IN, United States
| | - W Nicol Keith
- Institute of Cancer Sciences, University of Glasgow, Glasgow, Scotland, UK
| | | | - Xujuan Yang
- University of Illinois at Urbana Champaign, Champaign, IL, United States
| |
Collapse
|
35
|
Abstract
Recent years have witnessed the discovery of several classes of noncoding RNAs (ncRNAs), which are indispensable for the regulation of cellular processes. Many of these RNAs are regulatory in nature with functions in gene expression regulation such as piwi-interacting RNAs, small interfering RNAs and micro RNAs. Long noncoding RNAs (lncRNAs) comprise the most recently characterized class. LncRNAs are involved in transcriptional regulation, chromatin remodeling, imprinting, splicing, and translation, among other critical functions in the cell. Recent studies have elucidated the importance of lncRNAs in hematopoietic development. Dysregulation of lncRNA expression is a feature of various diseases and cancers, and is also seen in hematopoietic malignancies. This article focuses on lncRNAs that have been implicated in the pathogenesis of hematopoietic malignancies.
Collapse
Affiliation(s)
- Norma I Rodríguez-Malavé
- Cellular and Molecular Pathology Program, Department of Pathology and Laboratory Medicine, University of California Los Angeles, Department of Pathology and Laboratory Medicine, Jonsson Comprehensive Cancer Center and Broad Stem Cell Research Center, University of California Los Angeles Cellular and Molecular Pathology Program, Department of Pathology and Laboratory Medicine, University of California Los Angeles, Department of Pathology and Laboratory Medicine, Jonsson Comprehensive Cancer Center and Broad Stem Cell Research Center, University of California Los Angeles
| | - Dinesh S Rao
- Cellular and Molecular Pathology Program, Department of Pathology and Laboratory Medicine, University of California Los Angeles, Department of Pathology and Laboratory Medicine, Jonsson Comprehensive Cancer Center and Broad Stem Cell Research Center, University of California Los Angeles Cellular and Molecular Pathology Program, Department of Pathology and Laboratory Medicine, University of California Los Angeles, Department of Pathology and Laboratory Medicine, Jonsson Comprehensive Cancer Center and Broad Stem Cell Research Center, University of California Los Angeles Cellular and Molecular Pathology Program, Department of Pathology and Laboratory Medicine, University of California Los Angeles, Department of Pathology and Laboratory Medicine, Jonsson Comprehensive Cancer Center and Broad Stem Cell Research Center, University of California Los Angeles
| |
Collapse
|
36
|
du Plessis WJ, Walzl G, Loxton AG. B cells as multi-functional players during Mycobacterium tuberculosis infection and disease. Tuberculosis (Edinb) 2015; 97:118-25. [PMID: 26611659 DOI: 10.1016/j.tube.2015.10.007] [Citation(s) in RCA: 14] [Impact Index Per Article: 1.6] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/18/2015] [Revised: 09/28/2015] [Accepted: 10/15/2015] [Indexed: 12/21/2022]
Abstract
Immunity to tuberculosis is still understood to be driven and maintained by T-cell derived immune responses. With a steady influx of data, it is becoming clear that B cells, the mediators of humoral immunity, have the capacity to function in roles not previously appreciated within the traditional B cell dogma. In this review we aim to discuss B cells, from its generation through to its functioning as effectors in both the innate and adaptive immune response, within the tuberculosis domain.
Collapse
Affiliation(s)
- Willem J du Plessis
- SA MRC Centre for TB Research, DST/NRF Centre of Excellence for Biomedical Tuberculosis Research, Division of Molecular Biology and Human Genetics, Faculty of Medicine and Health Sciences, Stellenbosch University, PO Box 241, Cape Town 8000, South Africa
| | - Gerhard Walzl
- SA MRC Centre for TB Research, DST/NRF Centre of Excellence for Biomedical Tuberculosis Research, Division of Molecular Biology and Human Genetics, Faculty of Medicine and Health Sciences, Stellenbosch University, PO Box 241, Cape Town 8000, South Africa
| | - André G Loxton
- SA MRC Centre for TB Research, DST/NRF Centre of Excellence for Biomedical Tuberculosis Research, Division of Molecular Biology and Human Genetics, Faculty of Medicine and Health Sciences, Stellenbosch University, PO Box 241, Cape Town 8000, South Africa.
| |
Collapse
|
37
|
Abstract
Systemic lupus erythematosus is a prototypic autoimmune disease characterized by the production of an array of pathogenic autoantibodies, including high-affinity anti-dsDNA IgG antibodies, which play an important role in disease development and progression. Lupus preferentially affects women during their reproductive years. The pathogenesis of lupus is contributed by both genetic factors and epigenetic modifications that arise from exposure to the environment. Epigenetic marks, including DNA methylation, histone post-translational modifications and microRNAs (miRNAs), interact with genetic programs to regulate immune responses. Epigenetic modifications influence gene expression and modulate B cell functions, such as class-switch DNA recombination, somatic hypermutation and plasma cell differentiation, thereby informing the antibody response. Epigenetic dysregulation can result in aberrant antibody responses to exogenous antigens or self-antigens, such as chromatin, histones and dsDNA in lupus. miRNAs play key roles in the post-transcriptional regulation of most gene-regulatory pathways and regulate both the innate and adaptive immune responses. In mice, dysregulation of miRNAs leads to aberrant immune responses and development of systemic autoimmunity. Altered miRNA expression has been reported in human autoimmune diseases, including lupus. The dysregulation of miRNAs in lupus could be the result of multiple environmental factors, such as sex hormones and viral or bacterial infection. Modulation of miRNA is a potential therapeutic strategy for lupus.
Collapse
Affiliation(s)
- Hong Zan
- Department of Microbiology and Immunology, School of Medicine, University of Texas Health Science Center , San Antonio, TX , USA
| | | | | |
Collapse
|
38
|
Schmid M, Smith J, Burt DW, Aken BL, Antin PB, Archibald AL, Ashwell C, Blackshear PJ, Boschiero C, Brown CT, Burgess SC, Cheng HH, Chow W, Coble DJ, Cooksey A, Crooijmans RPMA, Damas J, Davis RVN, de Koning DJ, Delany ME, Derrien T, Desta TT, Dunn IC, Dunn M, Ellegren H, Eöry L, Erb I, Farré M, Fasold M, Fleming D, Flicek P, Fowler KE, Frésard L, Froman DP, Garceau V, Gardner PP, Gheyas AA, Griffin DK, Groenen MAM, Haaf T, Hanotte O, Hart A, Häsler J, Hedges SB, Hertel J, Howe K, Hubbard A, Hume DA, Kaiser P, Kedra D, Kemp SJ, Klopp C, Kniel KE, Kuo R, Lagarrigue S, Lamont SJ, Larkin DM, Lawal RA, Markland SM, McCarthy F, McCormack HA, McPherson MC, Motegi A, Muljo SA, Münsterberg A, Nag R, Nanda I, Neuberger M, Nitsche A, Notredame C, Noyes H, O'Connor R, O'Hare EA, Oler AJ, Ommeh SC, Pais H, Persia M, Pitel F, Preeyanon L, Prieto Barja P, Pritchett EM, Rhoads DD, Robinson CM, Romanov MN, Rothschild M, Roux PF, Schmidt CJ, Schneider AS, Schwartz MG, Searle SM, Skinner MA, Smith CA, Stadler PF, Steeves TE, Steinlein C, Sun L, Takata M, Ulitsky I, Wang Q, Wang Y, Warren WC, Wood JMD, Wragg D, Zhou H. Third Report on Chicken Genes and Chromosomes 2015. Cytogenet Genome Res 2015; 145:78-179. [PMID: 26282327 PMCID: PMC5120589 DOI: 10.1159/000430927] [Citation(s) in RCA: 65] [Impact Index Per Article: 7.2] [Reference Citation Analysis] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/19/2022] Open
Affiliation(s)
- Michael Schmid
- Department of Human Genetics, University of Würzburg, Würzburg, Germany
| | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | |
Collapse
|
39
|
Porstner M, Winkelmann R, Daum P, Schmid J, Pracht K, Côrte-Real J, Schreiber S, Haftmann C, Brandl A, Mashreghi MF, Gelse K, Hauke M, Wirries I, Zwick M, Roth E, Radbruch A, Wittmann J, Jäck HM. miR-148a promotes plasma cell differentiation and targets the germinal center transcription factors Mitf and Bach2. Eur J Immunol 2015; 45:1206-15. [PMID: 25678371 DOI: 10.1002/eji.201444637] [Citation(s) in RCA: 63] [Impact Index Per Article: 7.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/08/2014] [Revised: 01/09/2015] [Accepted: 02/09/2015] [Indexed: 12/18/2022]
Abstract
B cells undergo affinity maturation and class switch recombination of their immunoglobulin receptors during a germinal center (GC) reaction, before they differentiate into long-lived antibody-secreting plasma cells (PCs). Transcription factors such as Bach2 and Mitf are essential during this process, as they delay premature differentiation of GC B cells by repressing Blimp-1 and IRF4, two transcription factors required for terminal PC differentiation. Therefore, Bach2 and Mitf expression must be attenuated in activated B cells to allow terminal PC differentiation, but the precise mechanism remains enigmatic. Here, we provide evidence that miR-148a, a small noncoding microRNA, fosters PC differentiation and survival. Next-generation sequencing revealed that miR-148a is the most abundant microRNA in primary human and murine PCs, and its expression is upregulated in activated murine B cells and coincides with Blimp-1 synthesis. miR-148a targets Bach2, Mitf and proapoptotic factors such as PTEN and Bim. When prematurely expressed, miR-148a promotes the differentiation and survival of plasmablasts and reduces frequencies of IgG1(+) cells in primary B-cell cultures. In summary, we propose that miR-148a is a new player in the regulatory network controlling terminal PC differentiation and could, therefore, be a therapeutic target for interfering with PC differentiation and survival.
Collapse
Affiliation(s)
- Martina Porstner
- Division of Molecular Immunology, Department of Internal Medicine III, Nikolaus-Fiebiger-Center for Molecular Medicine, University of Erlangen-Nürnberg, Erlangen, Germany
| | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | |
Collapse
|
40
|
Abstract
Chronic lymphocytic leukemia (CLL) is characterized by a typical defect in apoptosis and is still an incurable disease. Numerous apoptosis inducers have been described. These synthetic compounds and natural products (mainly derived from plants) display antileukemic properties in vitro and in vivo and some have even been tested in the clinic in CLL. They act through several different mechanisms. Most of them involve proteins of the Bcl-2 family, which are the key regulators in triggering the mitochondrial pathway of caspase-dependent apoptosis. Thus, the Mcl-1/Noxa axis appeared as a target. Here I overview natural and synthetic apoptosis inducers and their mechanisms of action in CLL cells. Opportunities for developing novel, apoptosis-based therapeutics are presented.
Collapse
Affiliation(s)
- Christian Billard
- INSERM U 872, Centre de Recherche des Cordeliers, Equipe 18, Paris, France
| |
Collapse
|
41
|
Marques SC, Laursen MB, Bødker JS, Kjeldsen MK, Falgreen S, Schmitz A, Bøgsted M, Johnsen HE, Dybkaer K. MicroRNAs in B-cells: from normal differentiation to treatment of malignancies. Oncotarget 2015; 6:7-25. [PMID: 25622103 PMCID: PMC4381575 DOI: 10.18632/oncotarget.3057] [Citation(s) in RCA: 23] [Impact Index Per Article: 2.6] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/16/2014] [Accepted: 12/09/2014] [Indexed: 12/12/2022] Open
Abstract
MicroRNAs (miRNAs) are small non-coding RNAs that play important post-transcriptional regulatory roles in a wide range of biological processes. They are fundamental to the normal development of cells, and evidence suggests that the deregulation of specific miRNAs is involved in malignant transformation due to their function as oncogenes or tumor suppressors. We know that miRNAs are involved in the development of normal B-cells and that different B-cell subsets express specific miRNA profiles according to their degree of differentiation. B-cell-derived malignancies contain transcription signatures reminiscent of their cell of origin. Therefore, we believe that normal and malignant B-cells share features of regulatory networks controlling differentiation and the ability to respond to treatment. The involvement of miRNAs in these processes makes them good biomarker candidates. B-cell malignancies are highly prevalent, and the poor overall survival of patients with these malignancies demands an improvement in stratification according to prognosis and therapy response, wherein we believe miRNAs may be of great importance. We have critically reviewed the literature, and here we sum up the findings of miRNA studies in hematological cancers, from the development and progression of the disease to the response to treatment, with a particular emphasis on B-cell malignancies.
Collapse
Affiliation(s)
- Sara Correia Marques
- Department of Haematology, Aalborg University Hospital, Aalborg, Denmark
- Department of Clinical Medicine, Aarhus University, Denmark
| | - Maria Bach Laursen
- Department of Haematology, Aalborg University Hospital, Aalborg, Denmark
| | - Julie Støve Bødker
- Department of Haematology, Aalborg University Hospital, Aalborg, Denmark
| | | | - Steffen Falgreen
- Department of Haematology, Aalborg University Hospital, Aalborg, Denmark
| | - Alexander Schmitz
- Department of Haematology, Aalborg University Hospital, Aalborg, Denmark
| | - Martin Bøgsted
- Department of Haematology, Aalborg University Hospital, Aalborg, Denmark
- Department of Clinical Medicine, Aalborg University, Denmark
| | - Hans Erik Johnsen
- Department of Haematology, Aalborg University Hospital, Aalborg, Denmark
- Department of Clinical Medicine, Aalborg University, Denmark
- Clinical Cancer Research Center, Aalborg University Hospital, Denmark
| | - Karen Dybkaer
- Department of Haematology, Aalborg University Hospital, Aalborg, Denmark
- Department of Clinical Medicine, Aalborg University, Denmark
| |
Collapse
|
42
|
Rivina L, Davoren M, Schiestl RH. Radiation-induced myeloid leukemia in murine models. Hum Genomics 2014; 8:13. [PMID: 25062865 PMCID: PMC4128013 DOI: 10.1186/1479-7364-8-13] [Citation(s) in RCA: 20] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/02/2014] [Accepted: 06/26/2014] [Indexed: 12/18/2022] Open
Abstract
The use of radiation therapy is a cornerstone of modern cancer treatment. The number of patients that undergo radiation as a part of their therapy regimen is only increasing every year, but this does not come without cost. As this number increases, so too does the incidence of secondary, radiation-induced neoplasias, creating a need for therapeutic agents targeted specifically towards incidence reduction and treatment of these cancers. Development and efficacy testing of these agents requires not only extensive in vitro testing but also a set of reliable animal models to accurately recreate the complex situations of radiation-induced carcinogenesis. As radiation-induced leukemic progression often involves genomic changes such as rearrangements, deletions, and changes in methylation, the laboratory mouse Mus musculus, with its fully sequenced genome, is a powerful tool in cancer research. This fact, combined with the molecular and physiological similarities it shares with man and its small size and high rate of breeding in captivity, makes it the most relevant model to use in radiation-induced leukemia research. In this work, we review relevant M. musculus inbred and F1 hybrid animal models, as well as methods of induction of radiation-induced myeloid leukemia. Associated molecular pathologies are also included.
Collapse
Affiliation(s)
| | - Michael Davoren
- Department of Environmental Health Sciences, University of California, Los Angeles, 650 Charles E, Young Dr, South, CHS 71-295, Los Angeles, CA 90095, USA.
| | | |
Collapse
|
43
|
Altered expression pattern of miR-29a, miR-29b and the target genes in myeloid leukemia. Exp Hematol Oncol 2014; 3:17. [PMID: 25006537 PMCID: PMC4086441 DOI: 10.1186/2162-3619-3-17] [Citation(s) in RCA: 49] [Impact Index Per Article: 4.9] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/11/2014] [Accepted: 05/31/2014] [Indexed: 01/07/2023] Open
Abstract
Objectives The miR-29 family have been demonstrated acting as vital tumor suppressor in multiple cancers as well as regulators in the adaptive immune system. Little is known about their role in leukemogenesis. The purpose of this study is to analyze the expression pattern of miR-29a/29b and its target genes Mcl-1 (myeloid cell leukemia sequence 1) and B-cell lymphoma 2 (Bcl-2) in myeloid leukemia. Methods Quantitative real-time PCR was used for detecting genes expression level in peripheral blood mononuclear cells (PBMCs) from 10 cases with newly diagnosed, untreated acute myeloid leukemia (AML) and 14 cases with newly diagnosed, untreated chronic myeloid leukemia (CML) in chronic phase, and 14 healthy individual (HI) served as controls. Correlation between the relative expression levels of different genes have been analyzed. Results Significant lower expression of miR-29a/29b and higher expression level of two potential target genes Bcl-2 and Mcl-1 were found in PBMCs from AML and CML patients compared with HI group. In addtion, miR-29a expression in AML was significantly lower than that in CML. Moreover, negative correlation between miR-29a/29b and its target genes have been found. While, positive correlation between relative expression level of miR-29a and miR-29b or Bcl-2 and Mcl-1 were presented in the total 38 research objects. Conclusion Down-regulated miR-29a and miR-29b, and accompanying up-regulated Bcl-2 and Mcl-1 are the common feature in myeloid leukemias. These data further support the role for miR-29a/29b dysregulation in myeloid leukemogenesis and the therapeutic promise of regulating miR-29a/29b expression for myeloid leukemia in the future.
Collapse
|
44
|
Wang X, Zhu B, Huang Z, Chen L, He Z, Zhang H. MicroRNAs as biomarkers in leukemia. Stem Cell Investig 2014; 1:11. [PMID: 27358857 DOI: 10.3978/j.issn.2306-9759.2014.04.01] [Citation(s) in RCA: 4] [Impact Index Per Article: 0.4] [Reference Citation Analysis] [Abstract] [Key Words] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/15/2013] [Accepted: 04/20/2014] [Indexed: 12/19/2022]
Abstract
Current diagnostic and prognostic markers still exhibit biological limitation and seeking novel molecular biomarkers is crucial for early clinical diagnosis and in the development of novel strategies for leukemia therapy. Emerging evidence showed that dysregulated microRNAs (miRNAs) play important roles in cancer including leukemia. In this review, we summarized recent progress on the role of miRNAs in leukemia, mainly focusing on recent findings that suggest the potential of miRNAs as biomarkers for diagnosis and prognosis. Notably, the circulating miRNAs were also discussed for the fact that they can be detected in body fluids, and thus represent a novel source of promising biomarkers that may be applied to clinical settings.
Collapse
Affiliation(s)
- Xinxin Wang
- China-America Cancer Research Institute, Key Laboratory for Medical Molecular Diagnostics of Guangdong Province, Guangdong Medical College, Dongguan 523808, China
| | - Baohua Zhu
- China-America Cancer Research Institute, Key Laboratory for Medical Molecular Diagnostics of Guangdong Province, Guangdong Medical College, Dongguan 523808, China
| | - Zunnan Huang
- China-America Cancer Research Institute, Key Laboratory for Medical Molecular Diagnostics of Guangdong Province, Guangdong Medical College, Dongguan 523808, China
| | - Liyong Chen
- China-America Cancer Research Institute, Key Laboratory for Medical Molecular Diagnostics of Guangdong Province, Guangdong Medical College, Dongguan 523808, China
| | - Zhiwei He
- China-America Cancer Research Institute, Key Laboratory for Medical Molecular Diagnostics of Guangdong Province, Guangdong Medical College, Dongguan 523808, China
| | - Hua Zhang
- China-America Cancer Research Institute, Key Laboratory for Medical Molecular Diagnostics of Guangdong Province, Guangdong Medical College, Dongguan 523808, China
| |
Collapse
|
45
|
Lymphohematopoietic cancers induced by chemicals and other agents and their implications for risk evaluation: An overview. MUTATION RESEARCH-REVIEWS IN MUTATION RESEARCH 2014; 761:40-64. [PMID: 24731989 DOI: 10.1016/j.mrrev.2014.04.001] [Citation(s) in RCA: 26] [Impact Index Per Article: 2.6] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Subscribe] [Scholar Register] [Received: 09/05/2013] [Revised: 04/02/2014] [Accepted: 04/03/2014] [Indexed: 12/13/2022]
Abstract
Lymphohematopoietic neoplasia are one of the most common types of cancer induced by therapeutic and environmental agents. Of the more than 100 human carcinogens identified by the International Agency for Research on Cancer, approximately 25% induce leukemias or lymphomas. The objective of this review is to provide an introduction into the origins and mechanisms underlying lymphohematopoietic cancers induced by xenobiotics in humans with an emphasis on acute myeloid leukemia, and discuss the implications of this information for risk assessment. Among the agents causing lymphohematopoietic cancers, a number of patterns were observed. Most physical and chemical leukemia-inducing agents such as the therapeutic alkylating agents, topoisomerase II inhibitors, and ionizing radiation induce mainly acute myeloid leukemia through DNA-damaging mechanisms that result in either gene or chromosomal mutations. In contrast, biological agents and a few immunosuppressive chemicals induce primarily lymphoid neoplasms through mechanisms that involve alterations in immune response. Among the environmental agents examined, benzene was clearly associated with acute myeloid leukemia in humans, with increasing but still limited evidence for an association with lymphoid neoplasms. Ethylene oxide and 1,3-butadiene were linked primarily to lymphoid cancers. Although the association between formaldehyde and leukemia remains controversial, several recent evaluations have indicated a potential link between formaldehyde and acute myeloid leukemia. The four environmental agents examined in detail were all genotoxic, inducing gene mutations, chromosomal alterations, and/or micronuclei in vivo. Although it is clear that rapid progress has been made in recent years in our understanding of leukemogenesis, many questions remain for future research regarding chemically induced leukemias and lymphomas, including the mechanisms by which the environmental agents reviewed here induce these diseases and the risks associated with exposures to such agents.
Collapse
|
46
|
Kaucsár T, Révész C, Godó M, Krenács T, Albert M, Szalay CI, Rosivall L, Benyó Z, Bátkai S, Thum T, Szénási G, Hamar P. Activation of the miR-17 family and miR-21 during murine kidney ischemia-reperfusion injury. Nucleic Acid Ther 2014; 23:344-54. [PMID: 23988020 DOI: 10.1089/nat.2013.0438] [Citation(s) in RCA: 46] [Impact Index Per Article: 4.6] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/17/2022] Open
Abstract
BACKGROUND Ischemia-reperfusion (I/R) is the main cause of acute kidney injury (AKI) in patients. We investigated renal microRNA (miRNA) expression profiles and the time course of changes in selected miRNA expressions after renal I/R to characterize the miRNA network activated during development and recovery from AKI. METHODS AND RESULTS One day after lethal (30 minutes) and sublethal (20 minutes) renal ischemia, AKI was verified by renal histology (tubular necrosis, regeneration), blood urea nitrogen (BUN) level, renal mRNA expression, and plasma concentration of neutrophil gelatinase-associated lipocalin (NGAL) in C57BL/6J mice. On the first day after 30-minute, lethal I/R miR-21, miR-17-5p, and miR-106a were elevated out of the 21 miRNAs successfully profiled on the Luminex multiplex assay. After 20-minute, sublethal I/R, renal miR-17-5p and miR-106a expressions were elevated on the first and second days of reperfusion, while miR-21 expression increased later and lasted longer. Renal miR-17-5p and miR-21 expressions correlated with each other. Renal function returned to normal on the fourth day after sublethal I/R. CONCLUSIONS Our results demonstrate that besides miR-21, miR-17-5p, and miR-106a are additionally activated during the maintenance and recovery phases of renal I/R injury. Furthermore, a correlation between renal miR-17-5p and miR-21 expressions warrants further investigation of how they may influence each other and the outcome of renal ischemia-reperfusion injury.
Collapse
Affiliation(s)
- Tamás Kaucsár
- Institute of Pathophysiology, Semmelweis University, Budapest, Hungary
| | | | | | | | | | | | | | | | | | | | | | | |
Collapse
|
47
|
Chen H, Lu Q, Zhang Y, Zhang C, Zhang H, Xu H. Overexpression of SLC25A38 protein on acute lymphoblastic leukemia cells. Oncol Lett 2014; 7:1422-1426. [PMID: 24765149 PMCID: PMC3997699 DOI: 10.3892/ol.2014.1947] [Citation(s) in RCA: 4] [Impact Index Per Article: 0.4] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/02/2013] [Accepted: 02/11/2014] [Indexed: 01/19/2023] Open
Abstract
SLC25A38 is a recently identified protein that belongs to the mitochondrial solute carrier family, SLC25. Previous studies have shown that it is a pro-apoptotic protein, which regulates intrinsic caspase-dependent apoptosis. In order to clarify the effect of SLC25A38 protein expression on acute lymphoblastic leukemia (ALL) cells, we detected the expression of SLC25A38 in various cell lines (RPMI 8226, U266, Molt-4 and Jurkat) by western blot analysis. The results indicate that SLC25A38 is highly expressed in the four cell lines. Among 55 leukemia patients (adult, n=32 and infant, n=23), a high expression of SLC25A38 protein was observed in seven infant (7/23, 30.4%) and 15 adult (15/32, 46.9%) ALL patients. Two adult ALL patients that were positive for SLC25A38 were analyzed and the level of SLC25A38 significantly reduced or disappeared following combined chemotherapy, however, reappeared upon ALL recurrence. The expression level was identified to be associated with the proportion of blast cells in the bone marrow. Additionally, SLC25A38 and Notch1 were co-expressed in the four cell lines and the ALL patient samples. The present results show that expression of SLC25A38 is a common feature of ALL cells and may be a novel biomarker for diagnosis, as well as a potential therapeutic target for ALL.
Collapse
Affiliation(s)
- Huaying Chen
- Department of Hematology, Zhongshan Hospital of Xiamen University, Xiamen, Fujian 361004, P.R. China
| | - Quanyi Lu
- Department of Hematology, Zhongshan Hospital of Xiamen University, Xiamen, Fujian 361004, P.R. China
| | - Yunwu Zhang
- Fujian Provincial Key Laboratory of Neurodegenerative Disease and Aging Research, College of Medicine, Xiamen, Fujian 361000, P.R. China
| | - Cuilin Zhang
- Fujian Provincial Key Laboratory of Neurodegenerative Disease and Aging Research, College of Medicine, Xiamen, Fujian 361000, P.R. China ; School of Pharmaceutical Sciences, Xiamen University, Xiamen, Fujian 361000, P.R. China
| | - Han Zhang
- Fujian Provincial Key Laboratory of Neurodegenerative Disease and Aging Research, College of Medicine, Xiamen, Fujian 361000, P.R. China
| | - Huaxi Xu
- Fujian Provincial Key Laboratory of Neurodegenerative Disease and Aging Research, College of Medicine, Xiamen, Fujian 361000, P.R. China
| |
Collapse
|
48
|
Zhang L, Li X, Ke Z, Huang L, Liang Y, Wu J, Zhang X, Chen Y, Zhang H, Luo X. MiR-99a may serve as a potential oncogene in pediatric myeloid leukemia. Cancer Cell Int 2013; 13:110. [PMID: 24191888 PMCID: PMC4176743 DOI: 10.1186/1475-2867-13-110] [Citation(s) in RCA: 23] [Impact Index Per Article: 2.1] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/04/2013] [Accepted: 11/01/2013] [Indexed: 12/19/2022] Open
Abstract
Background Leukemia is the most common malignant proliferative disease in children. Our previous study found that miR-99a was up-regulated in pediatric primary AML using microRNA expression profiles. Up to date, although there is a certain number of reports on microRNA expression features and functions in pediatric acute myeloid leukemia (AML) and chronic myeloid leukemia (CML), the expression and function of miR-99a in these diseases remain to be investigated. Methods qRT-PCR was performed to measure the expression level of miR-99a in 88 samples including 68 pediatric acute myeloid leukemia patients, 8 chronic myeloid leukemia patients and 12 pediatric controls. MTT assay, apoptosis assay, dual-luciferase reporter transfection assay and western blot analysis were used to investigate the function of miR-99a. Results MiR-99a was highly expressed in pediatric-onset AML (M1-M5) and CML, while significantly lowly expressed during complete remission of these diseases. MTT assay indicated that the proliferations of K562 and HL60 cells were significantly promoted by miR-99a, and apoptosis assessment by Annexin V/propidium iodide staining demonstrated that the apoptosis of these cells was inhibited by miR-99a. Additionally, dual-luciferase reporter transfection assay and western blot analysis indicated that miR-99a may target CTDSPL and TRIB2, which are two tumor suppressor genes. Conclusions This study revealed that miR-99a may play a potential oncogenic role in pediatric myeloid leukemia including AML and CML via regulating tumor suppressors CTDSPL and TRIB2, suggesting that these two leukemias might share some common biological pathways involved in the generation and development of disease and miR-99a could be a common therapeutic target for myeloid leukemias treatment.
Collapse
Affiliation(s)
| | | | | | | | | | | | | | | | - Hua Zhang
- Department of Pediatric, The First Affiliated Hospital of Sun Yat-Sen University, Zhongshan Er Lu, Guangzhou 510080, China.
| | | |
Collapse
|
49
|
Wang SH, Lin SY. Tumor dormancy: potential therapeutic target in tumor recurrence and metastasis prevention. Exp Hematol Oncol 2013; 2:29. [PMID: 24502434 PMCID: PMC4176492 DOI: 10.1186/2162-3619-2-29] [Citation(s) in RCA: 37] [Impact Index Per Article: 3.4] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/10/2013] [Accepted: 10/12/2013] [Indexed: 12/14/2022] Open
Abstract
In past decades, cancer patient survival has been improved with earlier detection and advancements in therapy. However, many patients who exhibit no clinical symptoms after frontline therapy subsequently suffer, often many years later, aggressive tumor recurrence. Cancer recurrence represents a critical clinical challenge in effectively treating malignancies and for patients’ quality of life. Tumor cell dormancy may help to explain treatment resistance and recurrence or metastatic reactivation. Understanding the dormant stage of tumor cells may help in discovering ways to maintain the dormant state or permanently eliminate dormant residual disseminated tumor cells. Over the past decade, numerous studies indicate that various mechanisms of tumor dormancy exist, including cellular dormancy (quiescence), angiogenic dormancy, and immunologic dormancy. In this short review, we summarize recent experimental and clinical evidence for these three mechanisms and other possible tumor microenvironment mechanisms that may influence tumor dormancy.
Collapse
Affiliation(s)
| | - Shiaw-Yih Lin
- Department of Systems Biology, Unit 950, The University of Texas MD Anderson Cancer Center, 1515 Holcombe Blvd,, Houston, TX 77054, USA.
| |
Collapse
|
50
|
Xu Y, Li W, Liu X, Ma H, Tu Z, Dai Y. Analysis of microRNA expression profile by small RNA sequencing in Down syndrome fetuses. Int J Mol Med 2013; 32:1115-25. [PMID: 24071828 DOI: 10.3892/ijmm.2013.1499] [Citation(s) in RCA: 29] [Impact Index Per Article: 2.6] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/19/2013] [Accepted: 08/22/2013] [Indexed: 11/06/2022] Open
Abstract
Down syndrome (DS) is caused by trisomy of human chromosome 21 (Hsa21) and is associated with numerous deleterious phenotypes, including cognitive impairment, childhood leukemia and immune defects. Five Hsa21‑derived microRNAs (i.e., hsa-miR-99a, let-7c, miR-125b-2, miR-155 and miR-802) are involved in variable phenotypes of DS. However, the changes involved in the genome-wide microRNA expression of DS fetuses under the influence of trisomy 21 have yet to be determined. To investigate the expression characteristic of microRNAs during the development of DS fetuses and identify whether another microRNA gene resides in the Hsa21, Illumina high-throughput sequencing technology was employed to comprehensively characterize the microRNA expression profiles of the DS and normal fetal cord blood mononuclear cells (CBMCs). In total, 149 of 395 identified microRNAs were significantly differentially expressed (fold change >2.0 and P<0.001) and 2 of 181 candidate novel microRNAs were identified as residing within the ̔DS critical region̓ of human chromosome 21 (chr21q22.2‑22.3). Additionally, 7 of 14 Hsa21-derived microRNAs were detected, although not all seven were overexpressed in DS CBMCs compared with the control. Gene ontology enrichment analyses revealed that a set of abnormally expressed microRNAs were involved in the regulation of transcription, gene expression, cellular biosynthetic process and nucleic acid metabolic process. Significantly, most of the mRNA targets in these categories were associated with immune modulation (i.e., SOD1, MXD4, PBX1, BCLAF1 and FOXO1). Findings of the present study provided a considerable insight into understanding the expression characteristic of microRNAs in the DS fetal CBMCs. To the best of our knowledge, this is the first study to examine genome-wide microRNA expression profiles in the DS fetus. Differentially expressed microRNAs may be involved in hemopoietic abnormalities and the immune defects of DS fetuses and newborns.
Collapse
Affiliation(s)
- Yong Xu
- Clinical Medical Research Center, Pingshan People's Hospital, Shenzhen, Guangdong 518118, P.R. China
| | | | | | | | | | | |
Collapse
|