1
|
Artimovič P, Špaková I, Macejková E, Pribulová T, Rabajdová M, Mareková M, Zavacká M. The ability of microRNAs to regulate the immune response in ischemia/reperfusion inflammatory pathways. Genes Immun 2024:10.1038/s41435-024-00283-6. [PMID: 38909168 DOI: 10.1038/s41435-024-00283-6] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/10/2023] [Revised: 06/07/2024] [Accepted: 06/11/2024] [Indexed: 06/24/2024]
Abstract
MicroRNAs play a crucial role in regulating the immune responses induced by ischemia/reperfusion injury. Through their ability to modulate gene expression, microRNAs adjust immune responses by targeting specific genes and signaling pathways. This review focuses on the impact of microRNAs on the inflammatory pathways triggered during ischemia/reperfusion injury and highlights their ability to modulate inflammation, playing a critical role in the pathophysiology of ischemia/reperfusion injury. Dysregulated expression of microRNAs contributes to the pathogenesis of ischemia/reperfusion injury, therefore targeting specific microRNAs offers an opportunity to restore immune homeostasis and improve patient outcomes. Understanding the complex network of immunoregulatory microRNAs could provide novel therapeutic interventions aimed at attenuating excessive inflammation and preserving tissue integrity.
Collapse
Affiliation(s)
- Peter Artimovič
- Department of Medical and Clinical Biochemistry, Pavol Jozef Šafárik University in Košice, Faculty of Medicine, Košice, Slovakia
| | - Ivana Špaková
- Department of Medical and Clinical Biochemistry, Pavol Jozef Šafárik University in Košice, Faculty of Medicine, Košice, Slovakia
| | - Ema Macejková
- Department of Vascular Surgery, Pavol Jozef Šafárik University in Košice, Faculty of Medicine, Košice, Slovakia
| | - Timea Pribulová
- Department of Vascular Surgery, Pavol Jozef Šafárik University in Košice, Faculty of Medicine, Košice, Slovakia
| | - Miroslava Rabajdová
- Department of Medical and Clinical Biochemistry, Pavol Jozef Šafárik University in Košice, Faculty of Medicine, Košice, Slovakia
| | - Mária Mareková
- Department of Medical and Clinical Biochemistry, Pavol Jozef Šafárik University in Košice, Faculty of Medicine, Košice, Slovakia
| | - Martina Zavacká
- Department of Vascular Surgery, Pavol Jozef Šafárik University in Košice, Faculty of Medicine, Košice, Slovakia.
| |
Collapse
|
2
|
Guo S, Mao C, Peng J, Xie S, Yang J, Xie W, Li W, Yang H, Guo H, Zhu Z, Zheng Y. Improved lung cancer classification by employing diverse molecular features of microRNAs. Heliyon 2024; 10:e26081. [PMID: 38384512 PMCID: PMC10878959 DOI: 10.1016/j.heliyon.2024.e26081] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/12/2024] [Accepted: 02/07/2024] [Indexed: 02/23/2024] Open
Abstract
MiRNAs are edited or modified in multiple ways during their biogenesis pathways. It was reported that miRNA editing was deregulated in tumors, suggesting the potential value of miRNA editing in cancer classification. Here we extracted three types of miRNA features from 395 LUAD and control samples, including the abundances of original miRNAs, the abundances of edited miRNAs, and the editing levels of miRNA editing sites. Our results show that eight classification algorithms selected generally had better performances on combined features than on the abundances of miRNAs or editing features of miRNAs alone. One feature selection algorithm, i.e., the DFL algorithm, selected only three features, i.e., the frequencies of hsa-miR-135b-5p, hsa-miR-210-3p and hsa-mir-182_48u (an edited miRNA), from 316 training samples. Seven classification algorithms achieved 100% accuracies on these three features for 79 independent testing samples. These results indicate that the additional information of miRNA editing is useful in improving the classification of LUAD samples.
Collapse
Affiliation(s)
- Shiyong Guo
- State Key Laboratory of Primate Biomedical Research; Institute of Primate Translational Medicine, Kunming University of Science and Technology, Kunming, Yunnan 650500, China
- College of Horticulture and Landscape, Yunnan Agricultural University, Kunming, Yunnan, 650201, China
- College of Big Data, Yunnan Agricultural University, Kunming, Yunnan, 650201, China
| | - Chunyi Mao
- State Key Laboratory of Primate Biomedical Research; Institute of Primate Translational Medicine, Kunming University of Science and Technology, Kunming, Yunnan 650500, China
| | - Jun Peng
- Department of Thoracic Surgery, The First People's Hospital of Yunnan Province, i.e., The Affiliated Hospital of Kunming University of Science and Technology, Kunming, Yunnan 650032, China
| | - Shaohui Xie
- College of Computer Science and Software Engineering, Shenzhen University, Shenzhen, Guangdong 518060, China
| | - Jun Yang
- School of Criminal Investigation, Yunnan Police College, Kunming, Yunnan 650223, China
| | - Wenping Xie
- College of Horticulture and Landscape, Yunnan Agricultural University, Kunming, Yunnan, 650201, China
- College of Big Data, Yunnan Agricultural University, Kunming, Yunnan, 650201, China
| | - Wanran Li
- College of Horticulture and Landscape, Yunnan Agricultural University, Kunming, Yunnan, 650201, China
- College of Big Data, Yunnan Agricultural University, Kunming, Yunnan, 650201, China
| | - Huaide Yang
- College of Horticulture and Landscape, Yunnan Agricultural University, Kunming, Yunnan, 650201, China
- College of Big Data, Yunnan Agricultural University, Kunming, Yunnan, 650201, China
| | - Hao Guo
- Department of Cardiology, The First Affiliated Hospital of Kunming Medical University, Kunming, Yunnan 650032, China
| | - Zexuan Zhu
- National Engineering Laboratory for Big Data System Computing Technology, Shenzhen University, Shenzhen, Guangdong 518060, China
| | - Yun Zheng
- College of Horticulture and Landscape, Yunnan Agricultural University, Kunming, Yunnan, 650201, China
- College of Big Data, Yunnan Agricultural University, Kunming, Yunnan, 650201, China
| |
Collapse
|
3
|
Bensussen A, Torres-Magallanes JA, Álvarez-Buylla ER, de Álvarez-Buylla ER. Hybrid lineages of CD4 + T cells: a handbook update. Front Immunol 2024; 15:1344078. [PMID: 38312841 PMCID: PMC10834732 DOI: 10.3389/fimmu.2024.1344078] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/24/2023] [Accepted: 01/04/2024] [Indexed: 02/06/2024] Open
Abstract
CD4+ T lymphocytes have been classified into several lineages, according to their gene expression profiles and their effector responses. Interestingly, recent evidence is showing that many lineages could yield hybrid phenotypes with unique properties and functions. It has been reported that such hybrid lineages might underlie pathologies or may function as effector cells with protection capacities against molecular threats. In this work, we reviewed the characteristics of the hybrid lineages reported in the literature, in order to identify the expression profiles that characterize them and the markers that could be used to identify them. We also review the differentiation cues that elicit their hybrid origin and what is known about their physiological roles.
Collapse
Affiliation(s)
- Antonio Bensussen
- Laboratorio de Neuroendocrinología, Centro Universitario de Investigaciones Biomédicas, Universidad de Colima, Colima, Mexico
| | - José Antonio Torres-Magallanes
- Laboratorio de Neuroendocrinología, Centro Universitario de Investigaciones Biomédicas, Universidad de Colima, Colima, Mexico
| | - Elena R. Álvarez-Buylla
- Laboratorio de Genética Molecular, Epigenética, Desarrollo y Evolución de Plantas, Instituto de Ecología, Universidad Nacional Autónoma de México, Ciudad de México, Mexico
- Centro de Ciencias de la Complejidad (C3), Universidad Nacional Autónoma de México, Ciudad de México, Mexico
| | - Elena Roces de Álvarez-Buylla
- Laboratorio de Neuroendocrinología, Centro Universitario de Investigaciones Biomédicas, Universidad de Colima, Colima, Mexico
| |
Collapse
|
4
|
Liu Y, Guo S, Xie W, Yang H, Li W, Zhou N, Yang J, Zhou G, Mao C, Zheng Y. Identification of microRNA editing sites in clear cell renal cell carcinoma. Sci Rep 2023; 13:15117. [PMID: 37704698 PMCID: PMC10499803 DOI: 10.1038/s41598-023-42302-y] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/15/2023] [Accepted: 09/07/2023] [Indexed: 09/15/2023] Open
Abstract
Clear cell renal cell carcinoma (ccRCC) is a malignant tumor originating from the renal tubular epithelium. Although the microRNAs (miRNAs) transcriptome of ccRCC has been extensively studied, the role of miRNAs editing in ccRCC is largely unknown. By analyzing small RNA sequencing profiles of renal tissues of 154 ccRCC patients and 22 normal controls, we identified 1025 miRNA editing sites from 246 pre-miRNAs. There were 122 editing events with significantly different editing levels in ccRCC compared to normal samples, which include two A-to-I editing events in the seed regions of hsa-mir-376a-3p and hsa-mir-376c-3p, respectively, and one C-to-U editing event in the seed region of hsa-mir-29c-3p. After comparing the targets of the original and edited miRNAs, we found that hsa-mir-376a-1_49g, hsa-mir-376c_48g and hsa-mir-29c_59u had many new targets, respectively. Many of these new targets were deregulated in ccRCC, which might be related to the different editing levels of hsa-mir-376a-3p, hsa-mir-376c-3p, hsa-mir-29c-3p in ccRCC compared to normal controls. Our study sheds new light on miRNA editing events and their potential biological functions in ccRCC.
Collapse
Affiliation(s)
- Yulong Liu
- State Key Laboratory of Primate Biomedical Research, Institute of Primate Translational Medicine, Kunming University of Science and Technology, Kunming, 650500, Yunnan, China
| | - Shiyong Guo
- College of Landscape and Horticulture, Yunnan Agricultural University, Kunming, 650201, Yunnan, China
| | - Wenping Xie
- College of Landscape and Horticulture, Yunnan Agricultural University, Kunming, 650201, Yunnan, China
- Faculty of Life Science and Technology, Kunming University of Science and Technology, Kunming, 650500, Yunnan, China
| | - Huaide Yang
- College of Landscape and Horticulture, Yunnan Agricultural University, Kunming, 650201, Yunnan, China
- Faculty of Information Engineering and Automation, Kunming University of Science and Technology, Kunming, 650500, Yunnan, China
| | - Wanran Li
- State Key Laboratory of Primate Biomedical Research, Institute of Primate Translational Medicine, Kunming University of Science and Technology, Kunming, 650500, Yunnan, China
- College of Landscape and Horticulture, Yunnan Agricultural University, Kunming, 650201, Yunnan, China
| | - Nan Zhou
- College of Landscape and Horticulture, Yunnan Agricultural University, Kunming, 650201, Yunnan, China
| | - Jun Yang
- School of Criminal Investigation, Yunnan Police College, Kunming, 650223, Yunnan, China
| | - Guangchen Zhou
- College of Landscape and Horticulture, Yunnan Agricultural University, Kunming, 650201, Yunnan, China
| | - Chunyi Mao
- State Key Laboratory of Primate Biomedical Research, Institute of Primate Translational Medicine, Kunming University of Science and Technology, Kunming, 650500, Yunnan, China
- College of Landscape and Horticulture, Yunnan Agricultural University, Kunming, 650201, Yunnan, China
| | - Yun Zheng
- College of Landscape and Horticulture, Yunnan Agricultural University, Kunming, 650201, Yunnan, China.
| |
Collapse
|
5
|
Wu X, Yang H, Lin H, Suo A, Wu S, Xie W, Zhou N, Guo S, Ding H, Zhou G, Qiu Z, Shi H, Yang J, Zheng Y. Characterizing microRNA editing and mutation sites in Autism Spectrum Disorder. Front Mol Neurosci 2023; 15:1105278. [PMID: 36743290 PMCID: PMC9895120 DOI: 10.3389/fnmol.2022.1105278] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/22/2022] [Accepted: 12/30/2022] [Indexed: 01/21/2023] Open
Abstract
Autism Spectrum Disorder (ASD) is a neurodevelopmental disorder whose pathogenesis is still unclear. MicroRNAs (miRNAs) are a kind of endogenous small non-coding RNAs that play important roles in the post-transcriptional regulation of genes. Recent researches show that miRNAs are edited in multiple ways especially in central nervous systems. A-to-I editing of RNA catalyzed by Adenosine deaminases acting on RNA (ADARs) happens intensively in brain and is also noticed in other organs and tissues. Although miRNAs are widely edited in human brain, miRNA editing in ASD is still largely unexplored. In order to reveal the editing events of miRNAs in ASD, we analyzed 131 miRNA-seq samples from 8 different brain regions of ASD patients and normal controls. We identified 834 editing sites with significant editing levels, of which 70 sites showed significantly different editing levels in the superior frontal gyrus samples of ASD patients (ASD-SFG) when compared with those of control samples. The editing level of an A-to-I editing site in hsa-mir-376a-1 (hsa-mir-376a-1_9_A_g) in ASD-SFG is higher than that of normal controls, and the difference is exaggerated in individuals under 10 years. The increased expression of ADAR1 is consistent with the increased editing level of hsa-mir-376a-1_9_A_g in ASD-SFG samples compared to normal SFG samples. Furthermore, we verify that A-to-I edited hsa-mir-376a-5p directly represses GPR85 and NAPB, which may contribute to the abnormal neuronal development of ASD patients. These results provide new insights into the mechanism of ASD.
Collapse
Affiliation(s)
- Xingwang Wu
- State Key Laboratory of Primate Biomedical Research, Kunming University of Science and Technology, Kunming, Yunnan, China,Institute of Primate Translational Medicine, Kunming University of Science and Technology, Kunming, Yunnan, China
| | - Huaide Yang
- Faculty of Information Engineering and Automation, Kunming University of Science and Technology, Kunming, Yunnan, China
| | - Han Lin
- Department of Urology, The First Affiliated Hospital of Kunming Medical University, Kunming, Yunnan, China
| | - Angbaji Suo
- State Key Laboratory of Primate Biomedical Research, Kunming University of Science and Technology, Kunming, Yunnan, China,Institute of Primate Translational Medicine, Kunming University of Science and Technology, Kunming, Yunnan, China
| | - Shuai Wu
- State Key Laboratory of Primate Biomedical Research, Kunming University of Science and Technology, Kunming, Yunnan, China,Institute of Primate Translational Medicine, Kunming University of Science and Technology, Kunming, Yunnan, China
| | - Wenping Xie
- State Key Laboratory of Primate Biomedical Research, Kunming University of Science and Technology, Kunming, Yunnan, China,Institute of Primate Translational Medicine, Kunming University of Science and Technology, Kunming, Yunnan, China
| | - Nan Zhou
- Faculty of Information Engineering and Automation, Kunming University of Science and Technology, Kunming, Yunnan, China
| | - Shiyong Guo
- State Key Laboratory of Primate Biomedical Research, Kunming University of Science and Technology, Kunming, Yunnan, China,Institute of Primate Translational Medicine, Kunming University of Science and Technology, Kunming, Yunnan, China
| | - Hao Ding
- Faculty of Information Engineering and Automation, Kunming University of Science and Technology, Kunming, Yunnan, China
| | - Guangchen Zhou
- Faculty of Information Engineering and Automation, Kunming University of Science and Technology, Kunming, Yunnan, China
| | - Zhichao Qiu
- State Key Laboratory of Primate Biomedical Research, Kunming University of Science and Technology, Kunming, Yunnan, China,Institute of Primate Translational Medicine, Kunming University of Science and Technology, Kunming, Yunnan, China
| | - Hong Shi
- State Key Laboratory of Primate Biomedical Research, Kunming University of Science and Technology, Kunming, Yunnan, China,Institute of Primate Translational Medicine, Kunming University of Science and Technology, Kunming, Yunnan, China
| | - Jun Yang
- School of Criminal Investigation, Yunnan Police College, Kunming, Yunnan, China
| | - Yun Zheng
- State Key Laboratory of Primate Biomedical Research, Kunming University of Science and Technology, Kunming, Yunnan, China,Institute of Primate Translational Medicine, Kunming University of Science and Technology, Kunming, Yunnan, China,Faculty of Information Engineering and Automation, Kunming University of Science and Technology, Kunming, Yunnan, China,College of Landscape and Horticulture, Yunnan Agricultural University, Kunming, Yunnan, China,*Correspondence: Yun Zheng ✉
| |
Collapse
|
6
|
MiR-100 rs1834306 A>G Increases Biliary Atresia Risk in Southern Han Chinese Children. BIOMED RESEARCH INTERNATIONAL 2023; 2023:4835839. [PMID: 36644163 PMCID: PMC9833893 DOI: 10.1155/2023/4835839] [Citation(s) in RCA: 2] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Subscribe] [Scholar Register] [Received: 09/19/2022] [Revised: 11/29/2022] [Accepted: 12/24/2022] [Indexed: 01/06/2023]
Abstract
Background Biliary atresia (BA) is a type of severe cholestatic childhood disease that may have a genetic component. miR-100 plays a key role in regulating cell apoptosis, proliferation, and inflammatory reactions. A single-nucleotide polymorphism in miR-100 has been proven to modulate susceptibility to various diseases. Methods We conducted a case-control retrospective study to explore the correlation between miR-100 gene polymorphism (rs1834306 A>G) and biliary atresia susceptibility in 484 Chinese patients and 1445 matched control subjects. Results Our results showed that rs1834306 A>G was correlated with a significantly increased risk for BA (GG vs. AA: adjusted odds ratio (OR) = 1.44, 95%confidence interval (CI) = 1.02-2.03, p = 0.041; and GG vs. AA/AG: adjusted OR = 1.39, 95%CI = 1.02-1.89, p = 0.036). Conclusions Our results showed that the rs1834306 A>G polymorphism is associated with an increased risk for BA and contributes to BA susceptibility.
Collapse
|
7
|
ADAR1-dependent miR-3144-3p editing simultaneously induces MSI2 expression and suppresses SLC38A4 expression in liver cancer. Exp Mol Med 2023; 55:95-107. [PMID: 36599932 PMCID: PMC9898302 DOI: 10.1038/s12276-022-00916-8] [Citation(s) in RCA: 4] [Impact Index Per Article: 4.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/25/2022] [Revised: 10/26/2022] [Accepted: 11/07/2022] [Indexed: 01/06/2023] Open
Abstract
Aberrant adenosine-to-inosine (A-to-I) RNA editing, catalyzed by adenosine deaminase acting on double-stranded RNA (ADAR), has been implicated in various cancers, but the mechanisms by which microRNA (miRNA) editing contributes to cancer development are largely unknown. Our multistage hepatocellular carcinogenesis transcriptome data analyses, together with publicly available data, indicated that ADAR1 was the most profoundly dysregulated gene among RNA-editing enzyme family members in liver cancer. Targeted inactivation of ADAR1 inhibited the in vitro tumorigenesis of liver cancer cells. An integrative computational analyses of RNA-edited hotspots and the known editing frequency of miRNAs suggested that the miRNA miR-3144-3p was edited by ADAR1 during liver cancer progression. Specifically, ADAR1 promoted A-to-I editing of canonical miR-3144-3p to replace the adenosine at Position 3 in the seed region with a guanine (ED_miR-3144-3p(3_A < G)) in liver cancer cells. We then demonstrated that Musashi RNA-binding protein 2 (MSI2) was a specific target of miR-3144-3p and that MSI2 overexpression was due to excessive ADAR1-dependent over-editing of canonical miR-3144-3p in liver cancer. In addition, target prediction analyses and validation experiments identified solute carrier family 38 member 4 (SLC38A4) as a specific gene target of ED_miR-3144-3p(3_A < G). The ectopic expression of both ADAR1 and the ED_miR-3144-3p(3_A < G) mimic enhanced mitotic activities, and ADAR1 suppressed SLC38A4 expression in liver cancer cells. Treatments with mouse-specific ADAR1-, MSI2-siRNA-, or SLC38A4-expressing plasmids suppressed tumorigenesis and tumor growth in a mouse model of spontaneous liver cancer. Our findings suggest that the aberrant regulation of ADAR1 augments oncogenic MSI2 effects by excessively editing canonical miR-3144-3p and that the resultant ED_miR-3144-3p(3_A < G) simultaneously suppresses tumor suppressor SLC38A4 expression, contributing to hepatocellular carcinogenesis.
Collapse
|
8
|
Bensussen A, Torres-Magallanes JA, Roces de Álvarez-Buylla E. Molecular tracking of insulin resistance and inflammation development on visceral adipose tissue. Front Immunol 2023; 14:1014778. [PMID: 37026009 PMCID: PMC10070947 DOI: 10.3389/fimmu.2023.1014778] [Citation(s) in RCA: 2] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/08/2022] [Accepted: 02/27/2023] [Indexed: 04/08/2023] Open
Abstract
Background Visceral adipose tissue (VAT) is one of the most important sources of proinflammatory molecules in obese people and it conditions the appearance of insulin resistance and diabetes. Thus, understanding the synergies between adipocytes and VAT-resident immune cells is essential for the treatment of insulin resistance and diabetes. Methods We collected information available on databases and specialized literature to construct regulatory networks of VAT resident cells, such as adipocytes, CD4+ T lymphocytes and macrophages. These networks were used to build stochastic models based on Markov chains to visualize phenotypic changes on VAT resident cells under several physiological contexts, including obesity and diabetes mellitus. Results Stochastic models showed that in lean people, insulin produces inflammation in adipocytes as a homeostatic mechanism to downregulate glucose intake. However, when the VAT tolerance to inflammation is exceeded, adipocytes lose insulin sensitivity according to severity of the inflammatory condition. Molecularly, insulin resistance is initiated by inflammatory pathways and sustained by intracellular ceramide signaling. Furthermore, our data show that insulin resistance potentiates the effector response of immune cells, which suggests its role in the mechanism of nutrient redirection. Finally, our models show that insulin resistance cannot be inhibited by anti-inflammatory therapies alone. Conclusion Insulin resistance controls adipocyte glucose intake under homeostatic conditions. However, metabolic alterations such as obesity, enhances insulin resistance in adipocytes, redirecting nutrients to immune cells, permanently sustaining local inflammation in the VAT.
Collapse
Affiliation(s)
- Antonio Bensussen
- *Correspondence: Antonio Bensussen, ; Elena Roces de Álvarez-Buylla,
| | | | | |
Collapse
|
9
|
microRNAs: Critical Players during Helminth Infections. Microorganisms 2022; 11:microorganisms11010061. [PMID: 36677353 PMCID: PMC9861972 DOI: 10.3390/microorganisms11010061] [Citation(s) in RCA: 5] [Impact Index Per Article: 2.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/20/2022] [Revised: 12/19/2022] [Accepted: 12/22/2022] [Indexed: 12/28/2022] Open
Abstract
microRNAs (miRNAs) are a group of small non-coding RNAs that regulate gene expression post-transcriptionally through their interaction with the 3' untranslated regions (3' UTR) of target mRNAs, affecting their stability and/or translation. Therefore, miRNAs regulate biological processes such as signal transduction, cell death, autophagy, metabolism, development, cellular proliferation, and differentiation. Dysregulated expression of microRNAs is associated with infectious diseases, where miRNAs modulate important aspects of the parasite-host interaction. Helminths are parasitic worms that cause various neglected tropical diseases affecting millions worldwide. These parasites have sophisticated mechanisms that give them a surprising immunomodulatory capacity favoring parasite persistence and establishment of infection. In this review, we analyze miRNAs in infections caused by helminths, emphasizing their role in immune regulation and its implication in diagnosis, prognosis, and the development of therapeutic strategies.
Collapse
|
10
|
Characterizing Relevant MicroRNA Editing Sites in Parkinson's Disease. Cells 2022; 12:cells12010075. [PMID: 36611869 PMCID: PMC9818192 DOI: 10.3390/cells12010075] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/13/2022] [Revised: 12/07/2022] [Accepted: 12/10/2022] [Indexed: 12/28/2022] Open
Abstract
MicroRNAs (miRNAs) are extensively edited in human brains. However, the functional relevance of the miRNA editome is largely unknown in Parkinson's disease (PD). By analyzing small RNA sequencing profiles of brain tissues of 43 PD patients and 88 normal controls, we found that the editing levels of five A-to-I and two C-to-U editing sites are significantly correlated with the ages of normal controls, which is disrupted in PD patients. We totally identified 362 miRNA editing sites with significantly different editing levels in prefrontal cortices of PD patients (PD-PC) compared to results of normal controls. We experimentally validated that A-to-I edited miR-497-5p, with significantly higher expression levels in PD-PC compared to normal controls, directly represses OPA1 and VAPB. Furthermore, overexpression of A-to-I edited miR-497-5p downregulates OPA1 and VAPB in two cell lines, and inhibits proliferation of glioma cells. These results suggest that the hyperediting of miR-497-5p in PD contributes to enhanced progressive neurodegeneration of PD patients. Our results provide new insights into the mechanistic understanding, novel diagnostics, and therapeutic clues of PD.
Collapse
|
11
|
Lamana A, Castro-Vázquez D, de la Fuente H, Triguero-Martínez A, Martínez-Hernández R, Revenga M, Villanueva-Romero R, Llamas-Velasco M, Chicharro P, Juarranz Y, Marazuela M, Sales-Sanz M, García-Vicuña R, Tomero E, González-Álvaro I, Martínez C, Gomariz RP. VIP/VPAC Axis Expression in Immune-Mediated Inflammatory Disorders: Associated miRNA Signatures. Int J Mol Sci 2022; 23:ijms23158578. [PMID: 35955723 PMCID: PMC9369218 DOI: 10.3390/ijms23158578] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/07/2022] [Revised: 07/27/2022] [Accepted: 07/29/2022] [Indexed: 12/04/2022] Open
Abstract
Few studies have considered immune-mediated inflammatory disorders (IMID) together, which is necessary to adequately understand them given they share common mechanisms. Our goal was to investigate the expression of vasoactive intestinal peptide (VIP) and its receptors VPAC1 and VPAC2 in selected IMID, analyze the effect of biological therapies on them, and identify miRNA signatures associated with their expression. Serum VIP levels and mRNA of VPAC and miRNA expression in peripheral blood mononuclear cells were analyzed from 52 patients with psoriasis, rheumatoid arthritis, Graves’ disease, or spondyloarthritis and from 38 healthy subjects. IMID patients showed higher levels of VIP and increased expression of VPAC2 compared to controls (p < 0.0001 and p < 0.0192, respectively). Receiver operating characteristic curve analysis showed that the levels of VIP or VPAC2 expression were adequate discriminators capable of identifying IMID. Treatment of IMID patients with anti-TNFα and anti-IL12/23 significantly affected serum VIP levels. We identified miRNA signatures associated with levels of serum VIP and VPAC2 expression, which correlated with IMID diagnosis of the patients. The results indicate that the expression of VIP/VPAC2 is able of identify IMIDs and open up a line of research based on the association between the VIP/VPAC axis and miRNA signatures in immune-mediated diseases.
Collapse
Affiliation(s)
- Amalia Lamana
- Department of Cell Biology, Facultad de Biología y Facultad de Medicina, Universidad Complutense de Madrid, 28040 Madrid, Spain; (A.L.); (D.C.-V.); (R.V.-R.); (Y.J.)
| | - David Castro-Vázquez
- Department of Cell Biology, Facultad de Biología y Facultad de Medicina, Universidad Complutense de Madrid, 28040 Madrid, Spain; (A.L.); (D.C.-V.); (R.V.-R.); (Y.J.)
| | - Hortensia de la Fuente
- Department of Immunology, Instituto de Investigación Princesa, Hospital Universitario de La Princesa, 28006 Madrid, Spain;
| | - Ana Triguero-Martínez
- Department of Rheumatology, Instituto de Investigación Princesa Madrid, Hospital Universitario de La Princesa, 28006 Madrid, Spain; (A.T.-M.); (R.G.-V.); (E.T.); (I.G.-Á.)
| | - Rebeca Martínez-Hernández
- Department of Endocrinology, Instituto de Investigación Princesa, Hospital Universitario de La Princesa, 28006 Madrid, Spain; (R.M.-H.); (M.M.)
| | - Marcelino Revenga
- Department of Rheumatology, Hospital Universitario Ramón y Cajal, 28034 Madrid, Spain;
- Department of Medicine and Medical Specialties, Universidad de Alcalá, 28805 Alcalá de Henares, Spain
| | - Raúl Villanueva-Romero
- Department of Cell Biology, Facultad de Biología y Facultad de Medicina, Universidad Complutense de Madrid, 28040 Madrid, Spain; (A.L.); (D.C.-V.); (R.V.-R.); (Y.J.)
| | - Mar Llamas-Velasco
- Department of Dermatology, Instituto de Investigación Princesa, Hospital Universitario de La Princesa, 28006 Madrid, Spain; (M.L.-V.); (P.C.)
| | - Pablo Chicharro
- Department of Dermatology, Instituto de Investigación Princesa, Hospital Universitario de La Princesa, 28006 Madrid, Spain; (M.L.-V.); (P.C.)
| | - Yasmina Juarranz
- Department of Cell Biology, Facultad de Biología y Facultad de Medicina, Universidad Complutense de Madrid, 28040 Madrid, Spain; (A.L.); (D.C.-V.); (R.V.-R.); (Y.J.)
| | - Mónica Marazuela
- Department of Endocrinology, Instituto de Investigación Princesa, Hospital Universitario de La Princesa, 28006 Madrid, Spain; (R.M.-H.); (M.M.)
| | - Marco Sales-Sanz
- Department of Ophthalmology, Hospital Universitario Ramón y Cajal-IRYCIS, 28034 Madrid, Spain;
| | - Rosario García-Vicuña
- Department of Rheumatology, Instituto de Investigación Princesa Madrid, Hospital Universitario de La Princesa, 28006 Madrid, Spain; (A.T.-M.); (R.G.-V.); (E.T.); (I.G.-Á.)
| | - Eva Tomero
- Department of Rheumatology, Instituto de Investigación Princesa Madrid, Hospital Universitario de La Princesa, 28006 Madrid, Spain; (A.T.-M.); (R.G.-V.); (E.T.); (I.G.-Á.)
| | - Isidoro González-Álvaro
- Department of Rheumatology, Instituto de Investigación Princesa Madrid, Hospital Universitario de La Princesa, 28006 Madrid, Spain; (A.T.-M.); (R.G.-V.); (E.T.); (I.G.-Á.)
| | - Carmen Martínez
- Department of Cell Biology, Facultad de Biología y Facultad de Medicina, Universidad Complutense de Madrid, 28040 Madrid, Spain; (A.L.); (D.C.-V.); (R.V.-R.); (Y.J.)
- Correspondence: (C.M.); (R.P.G.); Tel.: +34-91-3944971 (R.P.G.)
| | - Rosa P. Gomariz
- Department of Cell Biology, Facultad de Biología y Facultad de Medicina, Universidad Complutense de Madrid, 28040 Madrid, Spain; (A.L.); (D.C.-V.); (R.V.-R.); (Y.J.)
- Correspondence: (C.M.); (R.P.G.); Tel.: +34-91-3944971 (R.P.G.)
| |
Collapse
|
12
|
Machida K, Tahara SM. Immunotherapy and Microbiota for Targeting of Liver Tumor-Initiating Stem-like Cells. Cancers (Basel) 2022; 14:2381. [PMID: 35625986 PMCID: PMC9139909 DOI: 10.3390/cancers14102381] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/10/2022] [Revised: 05/04/2022] [Accepted: 05/06/2022] [Indexed: 02/08/2023] Open
Abstract
Cancer contains tumor-initiating stem-like cells (TICs) that are resistant to therapies. Hepatocellular carcinoma (HCC) incidence has increased twice over the past few decades, while the incidence of other cancer types has trended downward globally. Therefore, an understanding of HCC development and therapy resistance mechanisms is needed for this incurable malignancy. This review article describes links between immunotherapies and microbiota in tumor-initiating stem-like cells (TICs), which have stem cell characteristics with self-renewal ability and express pluripotency transcription factors such as NANOG, SOX2, and OCT4. This review discusses (1) how immunotherapies fail and (2) how gut dysbiosis inhibits immunotherapy efficacy. Gut dysbiosis promotes resistance to immunotherapies by breaking gut immune tolerance and activating suppressor immune cells. Unfortunately, this leads to incurable recurrence/metastasis development. Personalized medicine approaches targeting these mechanisms of TIC/metastasis-initiating cells are emerging targets for HCC immunotherapy and microbiota modulation therapy.
Collapse
Affiliation(s)
- Keigo Machida
- Southern California Research Center for ALPD and Cirrhosis, Department of Molecular Microbiology and Immunology, Keck School of Medicine, University of Southern California, 2011 Zonal Ave., 503C-HMR, Los Angeles, CA 90033, USA;
| | | |
Collapse
|
13
|
Leal DFDVB, Santana da Silva MN, Pastana LF, Fernandes MR, de Athayde ADSC, Fernandes Porchera DCR, da Silva CA, Modesto AAC, De Assumpcão PP, dos Santos SEB, dos Santos NPC. Genetic Variants of MicroRNA and DROSHA Genes in Association With the Risk of Tuberculosis in the Amazon Population. Front Genet 2022; 13:850058. [PMID: 35309115 PMCID: PMC8924412 DOI: 10.3389/fgene.2022.850058] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/07/2022] [Accepted: 01/28/2022] [Indexed: 11/17/2022] Open
Abstract
Tuberculosis (TB) is a chronic infection caused by Mycobacterium tuberculosis (Mtb) with high incidence and mortality. Studies reported that host genetic variants might be associated with the risk of tuberculosis. The aim of this study was to perform an association study between 26 single nucleotide polymorphisms (SNPs) and tuberculosis and evaluate whether these SNPs may confer risk factors to tuberculosis in the Amazon population. There were 52 males and 126 females, with total of 178 healthy controls. Genotyping was performed using TaqMan Open Array Genotyping. Ancestry-informative markers were used to estimate the ancestral proportions of the individuals in the case and control groups. The results indicated that the SNPs rs10035440 (DROSHA), rs7372209 (miR26-a1), rs1834306 (miR100), rs4919510 (miR608), and rs10739971 (pri-let-7a-1) were significantly associated with high risk and rs3746444 (miR499) and rs6505162 (miR423), with low risk of developing tuberculosis in the Amazon population. Our study concluded that seven miRNA polymorphisms were associated with tuberculosis. Our study contributes to a better understanding of TB pathogenesis and may promote the development of new diagnostic tools against M. tuberculosis infection.
Collapse
Affiliation(s)
| | | | | | - Marianne Rodrigues Fernandes
- Núcleo de Pesquisa em Oncologia, Universidade Federal do Pará, Belém, Brazil
- *Correspondence: Marianne Rodrigues Fernandes,
| | | | | | | | | | | | - Sidney Emanuel Batista dos Santos
- Núcleo de Pesquisa em Oncologia, Universidade Federal do Pará, Belém, Brazil
- Laboratório de Genética Humana e Médica, Instituto de Ciências Biológicas, Universidade Federal do Pará, Belém, Brazil
| | | |
Collapse
|
14
|
Abstract
Huntington’s disease (HD) is a neurodegenerative disease. MicroRNAs (miRNAs) are small non-coding RNAs that mediate post-transcriptional regulation of target genes. Although miRNAs are extensively edited in human brains, the editome of miRNAs in brains of HD patients is largely unknown. By analyzing the small RNA sequencing profiles of brain tissues of 28 HD patients and 83 normal controls, 1182 miRNA editing sites with significant editing levels were identified. In addition to 27 A-to-I editing sites, we identified 3 conserved C-to-U editing sites in miRNAs of HD patients. 30 SNPs in the miRNAs of HD patients were also identified. Furthermore, 129 miRNA editing events demonstrated significantly different editing levels in prefrontal cortex samples of HD patients (HD-PC) when compared to those of healthy controls. We found that hsa-mir-10b-5p was edited to have an additional cytosine at 5’-end in HD-PC, and the edited hsa-mir-10b repressed GTPBP10 that was often downregulated in HD. The down-regulation of GTPBP10 might contribute to the progression of HD by causing gradual loss of function of mitochondrial. These results provide the first endeavor to characterize the miRNA editing events in HD and their potential functions.
Collapse
|
15
|
Marceca GP, Distefano R, Tomasello L, Lagana A, Russo F, Calore F, Romano G, Bagnoli M, Gasparini P, Ferro A, Acunzo M, Ma Q, Croce CM, Nigita G. MiREDiBase, a manually curated database of validated and putative editing events in microRNAs. Sci Data 2021; 8:199. [PMID: 34349127 PMCID: PMC8338996 DOI: 10.1038/s41597-021-00979-8] [Citation(s) in RCA: 13] [Impact Index Per Article: 4.3] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/11/2021] [Accepted: 06/10/2021] [Indexed: 11/08/2022] Open
Abstract
MicroRNAs (miRNAs) are regulatory small non-coding RNAs that function as translational repressors. MiRNAs are involved in most cellular processes, and their expression and function are presided by several factors. Amongst, miRNA editing is an epitranscriptional modification that alters the original nucleotide sequence of selected miRNAs, possibly influencing their biogenesis and target-binding ability. A-to-I and C-to-U RNA editing are recognized as the canonical types, with the A-to-I type being the predominant one. Albeit some bioinformatics resources have been implemented to collect RNA editing data, it still lacks a comprehensive resource explicitly dedicated to miRNA editing. Here, we present MiREDiBase, a manually curated catalog of editing events in miRNAs. The current version includes 3,059 unique validated and putative editing sites from 626 pre-miRNAs in humans and three primates. Editing events in mature human miRNAs are supplied with miRNA-target predictions and enrichment analysis, while minimum free energy structures are inferred for edited pre-miRNAs. MiREDiBase represents a valuable tool for cell biology and biomedical research and will be continuously updated and expanded at https://ncrnaome.osumc.edu/miredibase .
Collapse
Affiliation(s)
- Gioacchino P Marceca
- Department of Clinical and Experimental Medicine, University of Catania, Catania, Italy
| | - Rosario Distefano
- Department of Cancer Biology and Genetics and Comprehensive Cancer Center, The Ohio State University, Columbus, OH, USA
| | - Luisa Tomasello
- Department of Cancer Biology and Genetics and Comprehensive Cancer Center, The Ohio State University, Columbus, OH, USA
| | - Alessandro Lagana
- Department of Genetics and Genomic Sciences, Icahn School of Medicine at Mount Sinai, New York, NY, USA
| | - Francesco Russo
- Section for Clinical Mass Spectrometry, Danish Center for Neonatal Screening, Department of Congenital Disorders, Statens Serum Institut, Copenhagen, Denmark
| | - Federica Calore
- Department of Cancer Biology and Genetics and Comprehensive Cancer Center, The Ohio State University, Columbus, OH, USA
| | - Giulia Romano
- Division of Pulmonary Diseases and Critical Care Medicine, Virginia Commonwealth University, Richmond, VA, USA
| | - Marina Bagnoli
- Fondazione IRCCS Istituto Nazionale dei Tumori (INT), Milan, Italy
| | - Pierluigi Gasparini
- Department of Cancer Biology and Genetics and Comprehensive Cancer Center, The Ohio State University, Columbus, OH, USA
- School of Biomedical Sciences and Pharmacy, College of Health, Medicine and Wellbeing, University of Newcastle, Callaghan, NSW, Australia
- Hunter Medical Research Institute, New Lambton Heights, NSW, Australia
| | - Alfredo Ferro
- Department of Clinical and Experimental Medicine, University of Catania, Catania, Italy
| | - Mario Acunzo
- Division of Pulmonary Diseases and Critical Care Medicine, Virginia Commonwealth University, Richmond, VA, USA
| | - Qin Ma
- Department of Biomedical Informatics, College of Medicine, The Ohio State University, Columbus, OH, USA
| | - Carlo M Croce
- Department of Cancer Biology and Genetics and Comprehensive Cancer Center, The Ohio State University, Columbus, OH, USA.
| | - Giovanni Nigita
- Department of Cancer Biology and Genetics and Comprehensive Cancer Center, The Ohio State University, Columbus, OH, USA.
| |
Collapse
|
16
|
Nazari N, Jafari F, Ghalamfarsa G, Hadinia A, Atapour A, Ahmadi M, Dolati S, Rostamzadeh D. The emerging role of microRNA in regulating the mTOR signaling pathway in immune and inflammatory responses. Immunol Cell Biol 2021; 99:814-832. [PMID: 33988889 DOI: 10.1111/imcb.12477] [Citation(s) in RCA: 19] [Impact Index Per Article: 6.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/17/2020] [Revised: 05/10/2021] [Accepted: 05/10/2021] [Indexed: 01/01/2023]
Abstract
The mechanistic/mammalian target of rapamycin (mTOR) is considered to be an atypical protein kinase that plays a critical role in integrating different cellular and environmental inputs in the form of growth factors, nutrients and energy and, subsequently, in regulating different cellular events, including cell metabolism, survival, homeostasis, growth and cellular differentiation. Immunologically, mTOR is a critical regulator of immune function through integrating numerous signals from the immune microenvironment, which coordinates the functions of immune cells and T cell fate decisions. The crucial role of mTOR in immune responses has been lately even more appreciated. MicroRNAs (miRNAs) are endogenous, small, noncoding single-stranded RNAs that act as molecular regulators involved in multiple processes during immune cells development, homeostasis, activation and effector polarization. Several studies have recently indicated that a range of miRNAs are involved in regulating the phosphoinositide 3-kinase/protein kinase B/mTOR (PI3K/AKT/mTOR) signaling pathway by targeting multiple components of this signaling pathway and modulating the expression and function of these targets. Current evidence has revealed the interplay between miRNAs and the mTOR pathway circuits in various immune cell types. The expression of individual miRNA can affect the function of mTOR signaling to determine the cell fate decisions in immune responses through coordinating immune signaling and cell metabolism. Dysregulation of the mTOR pathway/miRNAs crosstalk has been reported in cancers and various immune-related diseases. Thus, expression profiles of dysregulated miRNAs could influence the mTOR pathway, resulting in the promotion of aberrant immunity. This review summarizes the latest information regarding the reciprocal role of the mTOR signaling pathway and miRNAs in orchestrating immune responses.
Collapse
Affiliation(s)
- Nazanin Nazari
- Shiraz Institute for Cancer Research, School of Medicine, Shiraz University of Medical Sciences, Shiraz, Iran
| | - Farzaneh Jafari
- Department of Medical Genetics, School of Medicine, Shiraz University of Medical Sciences, Shiraz, Iran
| | - Ghasem Ghalamfarsa
- Cellular and Molecular Research Center, Yasuj University of Medical Sciences, Yasuj, Iran
| | - Abolghasem Hadinia
- Cellular and Molecular Research Center, Yasuj University of Medical Sciences, Yasuj, Iran
| | - Amir Atapour
- Department of Medical Biotechnology, School of Advanced Medical Sciences and Technologies, Shiraz University of Medical Sciences, Shiraz, Iran
| | - Majid Ahmadi
- Stem Cell Research Center, Tabriz University of Medical Sciences, Tabriz, Iran
| | - Sanam Dolati
- Physical Medicine and Rehabilitation Research Center, Aging Research Institute, Tabriz University of Medical Sciences, Tabriz, Iran
| | - Davood Rostamzadeh
- Cellular and Molecular Research Center, Yasuj University of Medical Sciences, Yasuj, Iran.,Medicinal Plants Research Center, Yasuj University of Medical Sciences, Yasuj, Iran
| |
Collapse
|
17
|
Sengupta P, Bose D, Chatterjee S. The Molecular Tête-à-Tête between G-Quadruplexes and the i-motif in the Human Genome. Chembiochem 2021; 22:1517-1537. [PMID: 33355980 DOI: 10.1002/cbic.202000703] [Citation(s) in RCA: 12] [Impact Index Per Article: 4.0] [Reference Citation Analysis] [Abstract] [Key Words] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/09/2020] [Revised: 12/16/2020] [Indexed: 12/22/2022]
Abstract
G-Quadruplex (GQ) and i-motif structures are the paradigmatic examples of nonclassical tetrastranded nucleic acids having multifarious biological functions and widespread applications in therapeutics and material science. Recently, tetraplexes emerged as promising anticancer targets due to their structural robustness, gene-regulatory roles, and predominant distribution at specific loci of oncogenes. However, it is arguable whether the i-motif evolves in the complementary single-stranded region after GQ formation in its opposite strand and vice versa. In this review, we address the prerequisites and significance of the simultaneous and/or mutually exclusive formation of GQ and i-motif structures at complementary and sequential positions in duplexes in the cellular milieu. We discussed how their dynamic interplay Sets up cellular homeostasis and exacerbates carcinogenesis. The review gives insights into the spatiotemporal formation of GQ and i-motifs that could be harnessed to design different types of reporter systems and diagnostic platforms for potential bioanalytical and therapeutic intervention.
Collapse
Affiliation(s)
- Pallabi Sengupta
- Department of Biophysics, Bose Institute, Centenary Campus, P-1/12, C.I.T. Scheme VIIM, Kankurgachi, Kolkata, 700054, West Bengal, India
| | - Debopriya Bose
- Department of Biophysics, Bose Institute, Centenary Campus, P-1/12, C.I.T. Scheme VIIM, Kankurgachi, Kolkata, 700054, West Bengal, India
| | - Subhrangsu Chatterjee
- Department of Biophysics, Bose Institute, Centenary Campus, P-1/12, C.I.T. Scheme VIIM, Kankurgachi, Kolkata, 700054, West Bengal, India
| |
Collapse
|
18
|
Wang T, Zhou Q, Shang Y. Downregulation of miRNA-451a Promotes the Differentiation of CD4+ T Cells towards Th2 Cells by Upregulating ETS1 in Childhood Asthma. J Innate Immun 2020; 13:38-48. [PMID: 33271553 DOI: 10.1159/000509714] [Citation(s) in RCA: 12] [Impact Index Per Article: 3.0] [Reference Citation Analysis] [Abstract] [Key Words] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/24/2019] [Accepted: 05/21/2020] [Indexed: 12/18/2022] Open
Abstract
Children exposed to common aeroallergens may develop asthma that progresses into adulthood. Inflammation regulated by T helper 2 (Th2) cells, a specific subpopulation of CD4+ T lymphocytes, is involved in asthmatic injury. Herein, our microarray data indicated that microRNA-451a-5p (miRNA-451a) expression decreased by 4.6-fold and ETS proto-oncogene 1 (ETS1) increased by 2.2-fold in the peripheral blood lymphocytes isolated from asthmatic children (n = 4) as compared to control individuals (n = 4). The negative correlation between miRNA-451a and ETS1 was further validated in 40 CD4+ T cell samples (10 healthy vs. 30 asthmatic samples). In vitro, naïve CD4+ T cells isolated from control individuals were cultured under Th2 cell polarizing condition. miRNA-451a expression decreased while ETS1 increased in CD4+ T cells in the setting of Th2 cell polarization. Moreover, miRNA-451a knockdown enhanced Th2 cell polarization - cells positive for both GATA3 (GATA binding protein 3, a Th2-transcription factor) and CD4 increased, and the generation of Th2 cell cytokines, interleukin (IL)5 and IL13, increased. In contrast, miRNA-451a overexpression inhibited Th2 cell differentiation. Interestingly, dual-Luciferase assay proved ETS1 as a novel target of miRNA-451a. Moreover, enforced expression of ETS1 partially restored miRNA-451a-induced inhibition of IL5 and IL13, and increased the GATA3+CD4+ cell population. Collectively, our work demonstrates that downregulation of miRNA-451a upregulates ETS1 expression in CD4+ T cells, which may contribute to Th2 cell differentiation in pediatric asthma.
Collapse
Affiliation(s)
- Tianyue Wang
- Department of Pediatrics, Shengjing Hospital of China Medical University, Shenyang, China
| | - Qianlan Zhou
- Department of Pediatrics, Shengjing Hospital of China Medical University, Shenyang, China
| | - Yunxiao Shang
- Department of Pediatrics, Shengjing Hospital of China Medical University, Shenyang, China,
| |
Collapse
|
19
|
Eniafe J, Jiang S. MicroRNA-99 family in cancer and immunity. WILEY INTERDISCIPLINARY REVIEWS-RNA 2020; 12:e1635. [PMID: 33230974 DOI: 10.1002/wrna.1635] [Citation(s) in RCA: 24] [Impact Index Per Article: 6.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Subscribe] [Scholar Register] [Received: 07/31/2020] [Revised: 11/02/2020] [Accepted: 11/04/2020] [Indexed: 12/19/2022]
Abstract
The microRNA (miR)-99 family comprising miR-99a, miR-99b, and miR-100 is an evolutionarily conserved family with existence dating prior to the bilaterians. Members are typically oncogenic in leukemia while their functional roles in other cancers alternate between that of a tumor suppressor and a tumor promoter. Targets of the miR-99 family rank in the lists of oncogenes and tumor suppressors, thereby illustrating the dual role of this miR family as oncogenic miRs (oncomiRs) and tumor suppressing miRs (TSmiRs) in different cellular contexts. In addition to their functional roles in cancers, miR-99 family is implicated in the modulation of macrophage inflammatory responses and T-cell subsets biology, thereby exerting critical roles in the maintenance of tissue homeostasis, establishment of peripheral tolerance as well as resolution of an inflammatory reaction. Here, we review emerging knowledge of this miR family and discuss remaining concerns linked to their activities. A better dissection of the functional roles of miR-99 family members in cancer and immunity will help in the development of novel miR-99-based therapeutics for the treatment of human cancer and immune-related diseases. This article is categorized under: RNA in Disease and Development > RNA in Disease.
Collapse
Affiliation(s)
- Joseph Eniafe
- Department of Microbiology and Immunology, Louisiana State University Health Sciences Center, Shreveport, Louisiana, USA
| | - Shuai Jiang
- Department of Microbiology and Immunology, Louisiana State University Health Sciences Center, Shreveport, Louisiana, USA
| |
Collapse
|
20
|
Song H, Liu D, Dong S, Zeng L, Wu Z, Zhao P, Zhang L, Chen ZS, Zou C. Epitranscriptomics and epiproteomics in cancer drug resistance: therapeutic implications. Signal Transduct Target Ther 2020; 5:193. [PMID: 32900991 PMCID: PMC7479143 DOI: 10.1038/s41392-020-00300-w] [Citation(s) in RCA: 53] [Impact Index Per Article: 13.3] [Reference Citation Analysis] [Abstract] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/16/2020] [Revised: 07/18/2020] [Accepted: 07/28/2020] [Indexed: 12/24/2022] Open
Abstract
Drug resistance is a major hurdle in cancer treatment and a key cause of poor prognosis. Epitranscriptomics and epiproteomics are crucial in cell proliferation, migration, invasion, and epithelial–mesenchymal transition. In recent years, epitranscriptomic and epiproteomic modification has been investigated on their roles in overcoming drug resistance. In this review article, we summarized the recent progress in overcoming cancer drug resistance in three novel aspects: (i) mRNA modification, which includes alternative splicing, A-to-I modification and mRNA methylation; (ii) noncoding RNAs modification, which involves miRNAs, lncRNAs, and circRNAs; and (iii) posttranslational modification on molecules encompasses drug inactivation/efflux, drug target modifications, DNA damage repair, cell death resistance, EMT, and metastasis. In addition, we discussed the therapeutic implications of targeting some classical chemotherapeutic drugs such as cisplatin, 5-fluorouridine, and gefitinib via these modifications. Taken together, this review highlights the importance of epitranscriptomic and epiproteomic modification in cancer drug resistance and provides new insights on potential therapeutic targets to reverse cancer drug resistance.
Collapse
Affiliation(s)
- Huibin Song
- Shenzhen People's Hospital (The Second Clinical Medical College, Jinan University; The First Affiliated Hospital, Southern University of Science and Technology), Shenzhen, 518001, Guangdong, China
| | - Dongcheng Liu
- Shenzhen People's Hospital (The Second Clinical Medical College, Jinan University; The First Affiliated Hospital, Southern University of Science and Technology), Shenzhen, 518001, Guangdong, China
| | - Shaowei Dong
- Shenzhen People's Hospital (The Second Clinical Medical College, Jinan University; The First Affiliated Hospital, Southern University of Science and Technology), Shenzhen, 518001, Guangdong, China
| | - Leli Zeng
- College of Pharmacy and Health Sciences, St. John's University, Queens, 11439 New York, USA.,Tomas Lindahl Nobel Laureate Laboratory, Research Centre, The Seventh Affiliated Hospital, Sun Yat-sen University, Shenzhen, 518107, Guangdong, China
| | - Zhuoxun Wu
- College of Pharmacy and Health Sciences, St. John's University, Queens, 11439 New York, USA
| | - Pan Zhao
- Shenzhen People's Hospital (The Second Clinical Medical College, Jinan University; The First Affiliated Hospital, Southern University of Science and Technology), Shenzhen, 518001, Guangdong, China
| | - Litu Zhang
- Department of Research, Affiliated Tumor Hospital of Guangxi Medical University, Nanning, 530021, Guangxi, China
| | - Zhe-Sheng Chen
- College of Pharmacy and Health Sciences, St. John's University, Queens, 11439 New York, USA.
| | - Chang Zou
- Shenzhen People's Hospital (The Second Clinical Medical College, Jinan University; The First Affiliated Hospital, Southern University of Science and Technology), Shenzhen, 518001, Guangdong, China. .,Shenzhen Public Service Platform on Tumor Precision Medicine and Molecular Diagnosis, Shenzhen, 518001, Guangdong, China.
| |
Collapse
|
21
|
Daveri E, Vergani E, Shahaj E, Bergamaschi L, La Magra S, Dosi M, Castelli C, Rodolfo M, Rivoltini L, Vallacchi V, Huber V. microRNAs Shape Myeloid Cell-Mediated Resistance to Cancer Immunotherapy. Front Immunol 2020; 11:1214. [PMID: 32793185 PMCID: PMC7387687 DOI: 10.3389/fimmu.2020.01214] [Citation(s) in RCA: 13] [Impact Index Per Article: 3.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/10/2020] [Accepted: 05/15/2020] [Indexed: 12/20/2022] Open
Abstract
Immunotherapy with immune checkpoint inhibitors can achieve long-term tumor control in subsets of patients. However, its effect can be blunted by myeloid-induced resistance mechanisms. Myeloid cells are highly plastic and physiologically devoted to wound healing and to immune homeostasis maintenance. In cancer, their physiological activities can be modulated, leading to an expansion of pro-inflammatory and immunosuppressive cells, the myeloid-derived suppressor cells (MDSCs), with detrimental consequences. The involvement of MDSCs in tumor development and progression has been widely investigated and MDSC-induced immunosuppression is acknowledged as a mechanism hindering effective immune checkpoint blockade. Small non-coding RNA molecules, the microRNAs (miRs), contribute to myeloid cell regulation at different levels, comprising metabolism and function, as well as their skewing to a MDSC phenotype. miR expression can be indirectly induced by cancer-derived factors or through direct miR import via extracellular vesicles. Due to their structural stability and their presence in body fluids miRs represent promising predictive biomarkers of resistance, as we recently found by investigating plasma samples of melanoma patients undergoing immune checkpoint blockade. Dissection of the miR-driven involved mechanisms would pave the way for the identification of new druggable targets. Here, we discuss the role of these miRs in shaping myeloid resistance to immunotherapy with a special focus on immunosuppression and immune escape.
Collapse
Affiliation(s)
- Elena Daveri
- Unit of Immunotherapy of Human Tumors, Department of Research, Fondazione IRCCS Istituto Nazionale dei Tumori, Milan, Italy
| | - Elisabetta Vergani
- Unit of Immunotherapy of Human Tumors, Department of Research, Fondazione IRCCS Istituto Nazionale dei Tumori, Milan, Italy
| | - Eriomina Shahaj
- Unit of Immunotherapy of Human Tumors, Department of Research, Fondazione IRCCS Istituto Nazionale dei Tumori, Milan, Italy
| | - Laura Bergamaschi
- Unit of Immunotherapy of Human Tumors, Department of Research, Fondazione IRCCS Istituto Nazionale dei Tumori, Milan, Italy
| | - Stefano La Magra
- Unit of Immunotherapy of Human Tumors, Department of Research, Fondazione IRCCS Istituto Nazionale dei Tumori, Milan, Italy
| | - Michela Dosi
- Unit of Immunotherapy of Human Tumors, Department of Research, Fondazione IRCCS Istituto Nazionale dei Tumori, Milan, Italy
| | - Chiara Castelli
- Unit of Immunotherapy of Human Tumors, Department of Research, Fondazione IRCCS Istituto Nazionale dei Tumori, Milan, Italy
| | - Monica Rodolfo
- Unit of Immunotherapy of Human Tumors, Department of Research, Fondazione IRCCS Istituto Nazionale dei Tumori, Milan, Italy
| | - Licia Rivoltini
- Unit of Immunotherapy of Human Tumors, Department of Research, Fondazione IRCCS Istituto Nazionale dei Tumori, Milan, Italy
| | - Viviana Vallacchi
- Unit of Immunotherapy of Human Tumors, Department of Research, Fondazione IRCCS Istituto Nazionale dei Tumori, Milan, Italy
| | - Veronica Huber
- Unit of Immunotherapy of Human Tumors, Department of Research, Fondazione IRCCS Istituto Nazionale dei Tumori, Milan, Italy
| |
Collapse
|
22
|
Abstract
PURPOSE OF REVIEW Regulatory T cells (Tregs) are critical contributors to immune homeostasis and their dysregulation can lead to the loss of immune tolerance and autoimmune diseases like type 1 diabetes (T1D). Recent studies have highlighted microRNAs (miRNAs) as important regulators of the immune system, by fine-tuning relevant genes in various immune cell types. In this review article, we discuss recent insights into miRNA regulation of immune tolerance and activation. Specifically, we discuss how the dysregulation of miRNAs in T cells contributes to their aberrant function and the onset of islet autoimmunity, as well as their potential as targets of novel intervention strategies to interfere with autoimmune activation. RECENT FINDINGS Several studies have shown that the dysregulation of individual miRNAs in T cells can contribute to impaired immune tolerance, contributing to onset and progression of islet autoimmunity. Importantly, the targeting of these miRNAs, including miR-92a, miR-142-3p and miR-181a, resulted in relevant effects on downstream pathways, improved Treg function and reduced islet autoimmunity in murine models. miRNAs are critical regulators of immune homeostasis and the dysregulation of individual miRNAs in T cells contributes to aberrant T cell function and autoimmunity. The specific targeting of individual miRNAs could improve Treg homeostasis and therefore limit overshooting T cell activation and islet autoimmunity.
Collapse
Affiliation(s)
- Martin G. Scherm
- Institute of Diabetes Research, Group Immune Tolerance in Type 1 Diabetes, Helmholtz Diabetes Center at Helmholtz Zentrum München, Heidemannstrasse 1, 80939 Munich, Germany
- Deutsches Zentrum für Diabetesforschung (DZD), Ingolstaedter Landstrasse 1, 85764 Munich-, Neuherberg, Germany
| | - Carolin Daniel
- Institute of Diabetes Research, Group Immune Tolerance in Type 1 Diabetes, Helmholtz Diabetes Center at Helmholtz Zentrum München, Heidemannstrasse 1, 80939 Munich, Germany
- Deutsches Zentrum für Diabetesforschung (DZD), Ingolstaedter Landstrasse 1, 85764 Munich-, Neuherberg, Germany
- Division of Clinical Pharmacology, Department of Medicine IV, Ludwig-Maximilians-Universität München, 80337 Munich, Germany
| |
Collapse
|
23
|
Queiroz FR, Portilho LG, Jeremias WDJ, Babá ÉH, do Amaral LR, Silva LM, Coelho PMZ, Caldeira RL, Gomes MDS. Deep sequencing of small RNAs reveals the repertoire of miRNAs and piRNAs in Biomphalaria glabrata. Mem Inst Oswaldo Cruz 2020; 115:e190498. [PMID: 32609280 PMCID: PMC7328434 DOI: 10.1590/0074-02760190498] [Citation(s) in RCA: 5] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/23/2019] [Accepted: 05/22/2020] [Indexed: 01/27/2023] Open
Abstract
BACKGROUND Biomphalaria glabrata snails are widely distributed in schistosomiasis endemic areas like America and Caribe, displaying high susceptibility to infection by Schistosoma mansoni. After the availability of B. glabrata genome and transcriptome data, studies focusing on genetic markers and small non-coding RNAs have become more relevant. The small RNAs have been considered important through their ability to finely regulate the gene expression in several organisms, thus controlling the functions like cell growth, metabolism, and susceptibility/resistance to infection. OBJECTIVE The present study aims on identification and characterisation of the repertoire of small non-coding RNAs in B. glabrata (Bgl-small RNAs). METHODS By using small RNA sequencing, bioinformatics tools and quantitative reverse transcription polymerase chain reaction (RT-qPCR), we identified, characterised, and validated the presence of small RNAs in B. glabrata. FINDINGS 89 mature miRNAs were identified and five of them were classified as Mollusk-specific. When compared to model organisms, sequences of B. glabrata miRNAs showed a high degree of conservation. In addition, several target genes were predicted for all the mature miRNAs identified. Furthermore, piRNAs were identified in the genome of B. glabrata for the first time. The B. glabrata piRNAs showed strong conservation of uridine as first nucleotide at 5’ end, besides adenine at 10th position. Our results showed that B. glabrata has diverse repertoire of circulating ncRNAs, several which might be involved in mollusk susceptibility to infection, due to their potential roles in the regulation of S. mansoni development. MAIN CONCLUSIONS Further studies are necessary in order to confirm the role of the Bgl-small RNAs in the parasite/host relationship thus opening new perspectives on interference of small RNAs in the organism development and susceptibility to infection.
Collapse
Affiliation(s)
- Fábio Ribeiro Queiroz
- Fundação Oswaldo Cruz-Fiocruz, Instituto René Rachou, Grupo de Pesquisa em Biologia do Schistosoma mansoni e sua Interação com o Hospedeiro, Belo Horizonte, MG, Brasil
| | - Laysa Gomes Portilho
- Universidade Federal de Uberlândia, Laboratório de Bioinformática e Análises Moleculares, Patos de Minas, MG, Brasil
| | | | - Élio Hideo Babá
- Fundação Oswaldo Cruz-Fiocruz, Instituto René Rachou, Grupo de Pesquisa em Biologia do Schistosoma mansoni e sua Interação com o Hospedeiro, Belo Horizonte, MG, Brasil
| | - Laurence Rodrigues do Amaral
- Universidade Federal de Uberlândia, Laboratório de Bioinformática e Análises Moleculares, Patos de Minas, MG, Brasil.,Universidade Federal de Uberlândia, Rede Multidisciplinar de Pesquisa, Ciência e Tecnologia, Patos de Minas, MG, Brasil
| | - Luciana Maria Silva
- Fundação Ezequiel Dias, Serviço de Biologia Celular do Departamento de Pesquisas e Desenvolvimento, Belo Horizonte, MG, Brasil
| | - Paulo Marcos Zech Coelho
- Fundação Oswaldo Cruz-Fiocruz, Instituto René Rachou, Grupo de Pesquisa em Biologia do Schistosoma mansoni e sua Interação com o Hospedeiro, Belo Horizonte, MG, Brasil
| | - Roberta Lima Caldeira
- Fundação Oswaldo Cruz-Fiocruz, Instituto René Rachou, Grupo de Pesquisa em Helmintologia e Malacologia Médica, Belo Horizonte, MG, Brasil
| | - Matheus de Souza Gomes
- Universidade Federal de Uberlândia, Laboratório de Bioinformática e Análises Moleculares, Patos de Minas, MG, Brasil.,Universidade Federal de Uberlândia, Rede Multidisciplinar de Pesquisa, Ciência e Tecnologia, Patos de Minas, MG, Brasil
| |
Collapse
|
24
|
Human Brain Shows Recurrent Non-Canonical MicroRNA Editing Events Enriched for Seed Sequence with Possible Functional Consequence. Noncoding RNA 2020; 6:ncrna6020021. [PMID: 32498345 PMCID: PMC7345632 DOI: 10.3390/ncrna6020021] [Citation(s) in RCA: 4] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/28/2020] [Revised: 05/25/2020] [Accepted: 05/27/2020] [Indexed: 12/16/2022] Open
Abstract
RNA editing is a post-transcriptional modification, which can provide tissue-specific functions not encoded in DNA. Adenosine-to-inosine is the predominant editing event and, along with cytosine-to-uracil changes, constitutes canonical editing. The rest is non-canonical editing. In this study, we have analysed non-canonical editing of microRNAs in the human brain. We have performed massively parallel small RNA sequencing of frontal cortex (FC) and corpus callosum (CC) pairs from nine normal individuals (post-mortem). We found 113 and 90 unique non-canonical editing events in FC and CC samples, respectively. More than 70% of events were in the miRNA seed sequence—implicating an altered set of target mRNAs and possibly resulting in a functional consequence. Up to 15% of these events were recurring and found in at least three samples, also supporting the biological relevance of such variations. Two specific sequence variations, C-to-A and G-to-U, accounted for over 80% of non-canonical miRNA editing events—and revealed preferred sequence motifs. Our study is one of the first reporting non-canonical editing in miRNAs in the human brain. Our results implicate miRNA non-canonical editing as one of the contributing factors towards transcriptomic diversity in the human brain.
Collapse
|
25
|
Scherm MG, Daniel C. miRNA-Mediated Immune Regulation in Islet Autoimmunity and Type 1 Diabetes. Front Endocrinol (Lausanne) 2020; 11:606322. [PMID: 33329406 PMCID: PMC7731293 DOI: 10.3389/fendo.2020.606322] [Citation(s) in RCA: 8] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Received: 09/14/2020] [Accepted: 10/27/2020] [Indexed: 12/15/2022] Open
Abstract
The important role of microRNAs as major modulators of various physiological processes, including immune regulation and homeostasis, has been increasingly recognized. Consequently, aberrant miRNA expression contributes to the defective regulation of T cell development, differentiation, and function. This can result in immune activation and impaired tolerance mechanisms, which exert a cardinal function for the onset of islet autoimmunity and the progression to T1D. The specific impact of miRNAs for immune regulation and how miRNAs and their downstream targets are involved in the pathogenesis of islet autoimmunity and T1D has been investigated recently. These studies revealed that increased expression of individual miRNAs is involved in several layers of tolerance impairments, such as inefficient Treg induction and Treg instability. The targeted modulation of miRNAs using specific inhibitors, resulting in improved immune homeostasis, as well as improved methods for the targeting of miRNAs, suggest that miRNAs, especially in T cells, are a promising target for the reestablishment of immune tolerance.
Collapse
Affiliation(s)
- Martin G. Scherm
- Institute of Diabetes Research, Group Immune Tolerance in Type 1 Diabetes, Helmholtz Diabetes Center at Helmholtz Zentrum München, Munich, Germany
- Deutsches Zentrum für Diabetesforschung (DZD), Munich-Neuherberg, Germany
| | - Carolin Daniel
- Institute of Diabetes Research, Group Immune Tolerance in Type 1 Diabetes, Helmholtz Diabetes Center at Helmholtz Zentrum München, Munich, Germany
- Deutsches Zentrum für Diabetesforschung (DZD), Munich-Neuherberg, Germany
- Division of Clinical Pharmacology, Department of Medicine IV, Ludwig-Maximilians-Universität München, Munich, Germany
- *Correspondence: Carolin Daniel,
| |
Collapse
|
26
|
Pinto Y, Buchumenski I, Levanon EY, Eisenberg E. Human cancer tissues exhibit reduced A-to-I editing of miRNAs coupled with elevated editing of their targets. Nucleic Acids Res 2019; 46:71-82. [PMID: 29165639 PMCID: PMC5758889 DOI: 10.1093/nar/gkx1176] [Citation(s) in RCA: 59] [Impact Index Per Article: 11.8] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/20/2017] [Accepted: 11/13/2017] [Indexed: 12/17/2022] Open
Abstract
A-to-I RNA editing is an important post-transcriptional modification, known to be altered in tumors. It targets dozens of sites within miRNAs, some of which impact miRNA biogenesis and function, as well as many miRNA recognition sites. However, the full extent of the effect of editing on regulation by miRNAs and its behavior in human cancers is still unknown. Here we systematically characterized miRNA editing in 10 593 human samples across 32 cancer types and normal controls. We find that the majority of previously reported sites show little to no evidence for editing in this dataset, compile a list of 58 reliable miRNA editing sites, and study them across normal and cancer samples. Edited miRNA versions tend to suppress expression of known oncogenes, and, consistently, we observe a clear global tendency for hypo-editing in tumors, in strike contrast to the behavior for mRNA editing, allowing an accurate classification of normal/tumor samples based on their miRNA editing profile. In many cancers this profile correlates with patients' survival. Finally, thousands of miRNA binding sites are differentially edited in cancer. Our study thus establishes the important effect of RNA editing on miRNA-regulation in the tumor cell, with prospects for diagnostic and prognostic applications.
Collapse
Affiliation(s)
- Yishay Pinto
- The Mina and Everard Goodman Faculty of Life Sciences, Bar-Ilan University, 5290002 Ramat-Gan, Israel
| | - Ilana Buchumenski
- The Mina and Everard Goodman Faculty of Life Sciences, Bar-Ilan University, 5290002 Ramat-Gan, Israel
| | - Erez Y Levanon
- The Mina and Everard Goodman Faculty of Life Sciences, Bar-Ilan University, 5290002 Ramat-Gan, Israel
| | - Eli Eisenberg
- Raymond and Beverly Sackler School of Physics and Astronomy and Sagol School of Neuroscience, Tel Aviv University, Tel Aviv 6997801, Israel
| |
Collapse
|
27
|
Identifying microRNAs and Their Editing Sites in Macaca mulatta. Cells 2019; 8:cells8070682. [PMID: 31284505 PMCID: PMC6678584 DOI: 10.3390/cells8070682] [Citation(s) in RCA: 5] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/27/2019] [Revised: 07/01/2019] [Accepted: 07/02/2019] [Indexed: 02/08/2023] Open
Abstract
MicroRNAs (miRNAs) are small non-coding RNAs that are critical in post-transcriptional regulation. Macaca mulatta is an important nonhuman primate that is often used in basic and translational researches. However, the annotation of miRNAs in Macaca mulatta is far from complete, and there are no reports of miRNA editing events in Macaca mulatta, although editing may affect the biogenesis or functions of the miRNAs. To improve miRNA annotation and to reveal editing events of miRNAs in Macaca mulatta, we generated 12 small RNA profiles from eight tissues and performed comprehensive analysis of these profiles. We identified 479 conserved pre-miRNAs that have not been reported in Macaca mulatta and 17 species specific miRNAs. Furthermore, we identified 3386 editing sites with significant editing levels from 471 pre-miRNAs after analyzing the 12 self-generated and 58 additional published sRNA-seq profiles from 17 different types of organs or tissues. In addition to 16 conserved A-to-I editing sites, we identified five conserved C-to-U editing sites in miRNAs of Macaca mulatta and Homo sapiens. We also identified 11 SNPs in the miRNAs of Macaca mulatta. The analysis of the potential targets of 69 miRNAs with editing or mutation events in their seed regions suggest that these editing or mutation events severely changed their targets and their potential functions. These results significantly increase our understanding of miRNAs and their mutation/editing events in Macaca mulatta.
Collapse
|
28
|
Association between the pig genome and its gut microbiota composition. Sci Rep 2019; 9:8791. [PMID: 31217427 PMCID: PMC6584621 DOI: 10.1038/s41598-019-45066-6] [Citation(s) in RCA: 45] [Impact Index Per Article: 9.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/19/2018] [Accepted: 05/30/2019] [Indexed: 12/24/2022] Open
Abstract
The gut microbiota has been evolving with its host along the time creating a symbiotic relationship. In this study, we assess the role of the host genome in the modulation of the microbiota composition in pigs. Gut microbiota compositions were estimated through sequencing the V3-V4 region of the 16S rRNA gene from rectal contents of 285 pigs. A total of 1,261 operational taxonomic units were obtained and grouped in 18 phyla and 101 genera. Firmicutes (45.36%) and Bacteroidetes (37.47%) were the two major phyla obtained, whereas at genus level Prevotella (7.03%) and Treponema (6.29%) were the most abundant. Pigs were also genotyped with a high-throughput method for 45,508 single nucleotide polymorphisms that covered the entire pig genome. Subsequently, genome-wide association studies were made among the genotypes of these pigs and their gut microbiota composition. A total of 52 single-nucleotide polymorphisms distributed in 17 regions along the pig genome were associated with the relative abundance of six genera; Akkermansia, CF231, Phascolarctobacterium, Prevotella, SMB53, and Streptococcus. Our results suggest 39 candidate genes that may be modulating the microbiota composition and manifest the association between host genome and gut microbiota in pigs.
Collapse
|
29
|
Adibzadeh Sereshgi MM, Abdollahpour-Alitappeh M, Mahdavi M, Ranjbar R, Ahmadi K, Taheri RA, Fasihi-Ramandi M. Immunologic balance of regulatory T cell/T helper 17 responses in gastrointestinal infectious diseases: Role of miRNAs. Microb Pathog 2019; 131:135-143. [PMID: 30914387 DOI: 10.1016/j.micpath.2019.03.029] [Citation(s) in RCA: 4] [Impact Index Per Article: 0.8] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/20/2018] [Revised: 03/18/2019] [Accepted: 03/22/2019] [Indexed: 12/22/2022]
Abstract
Gastrointestinal Infectious diseases (GIDs) are the second cause of death worldwide. T helper17 cells (Th17) play an important role in GIDs through production of IL-17A, IL-17F, and IL-22 cytokines. Because of their increased activities in GID, Th17 and its inflammatory cytokines can inhibit the progression and eliminate the infection. Actually, although Th17 have the best performance in the acute phase, regulatory T cells (Treg cells) are enhanced in the chronic phase and infection progress through its suppressive function. In addition, Treg cells prevent undesirable inflammatory damages developed by immune system components. On the other hand, miRNAs have important roles in the regulation of immune responses to eliminate bacterial infections and protect host organisms from harmful effects. Actually, miRNAs can reinforce innate and adaptive immunity to remove infections. Of note, miRNAs can develop a regulatory network with the immune system. Additionally, miRNAs can also serve in favor of bacteria to reduce immune responses. Therefore, balance of immune responses in Treg and Th17 cells can influence outcome of many infectious diseases. In conclusion, there is an imbalance in the Treg/Th17 ratio in GIDs; importantly, sets of miRNAs, particularly miR155 and miR146, were determined to be involved clearly in GIDs.
Collapse
Affiliation(s)
| | | | - Mehdi Mahdavi
- Immunotherapy Group, The Institute of Pharmaceutical Sciences (TIPS), Tehran University of Medical Sciences, Tehran, Iran; Recombinant Vaccine Research Center, Tehran University of Medical Sciences, Tehran, Iran
| | - Reza Ranjbar
- Molecular Biology Research Center, System Biology and Poisoning Institute, Baqiyatallah University of Medical Sciences, Tehran, Iran
| | - Kazem Ahmadi
- Molecular Biology Research Center, System Biology and Poisoning Institute, Baqiyatallah University of Medical Sciences, Tehran, Iran
| | - Ramezan Ali Taheri
- Nanobiotechnology Research Center, Baqiyatallah University of Medical Sciences, Tehran, Iran
| | - Mahdi Fasihi-Ramandi
- Molecular Biology Research Center, System Biology and Poisoning Institute, Baqiyatallah University of Medical Sciences, Tehran, Iran.
| |
Collapse
|
30
|
Anandagoda N, Willis JC, Hertweck A, Roberts LB, Jackson I, Gökmen MR, Jenner RG, Howard JK, Lord GM. microRNA-142-mediated repression of phosphodiesterase 3B critically regulates peripheral immune tolerance. J Clin Invest 2019; 129:1257-1271. [PMID: 30741720 PMCID: PMC6391082 DOI: 10.1172/jci124725] [Citation(s) in RCA: 40] [Impact Index Per Article: 8.0] [Reference Citation Analysis] [Abstract] [Key Words] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/06/2018] [Accepted: 12/21/2018] [Indexed: 01/02/2023] Open
Abstract
Tregs play a fundamental role in immune tolerance via control of self-reactive effector T cells (Teffs). This function is dependent on maintenance of a high intracellular cAMP concentration. A number of microRNAs are implicated in the maintenance of Tregs. In this study, we demonstrate that peripheral immune tolerance is critically dependent on posttranscriptional repression of the cAMP-hydrolyzing enzyme phosphodiesterase-3b (Pde3b) by microRNA-142-5p (miR-142-5p). In this manner, miR-142-5p acts as an immunometabolic regulator of intracellular cAMP, controlling Treg suppressive function. Mir142 was associated with a super enhancer bound by the Treg lineage–determining transcription factor forkhead box P3 (FOXP3), and Treg-specific deletion of miR-142 in mice (TregΔ142) resulted in spontaneous, lethal, multisystem autoimmunity, despite preserved numbers of phenotypically normal Tregs. Pharmacological inhibition and genetic ablation of PDE3B prevented autoimmune disease and reversed the impaired suppressive function of Tregs in TregΔ142 animals. These findings reveal a critical molecular switch, specifying Treg function through the modulation of a highly conserved, cell-intrinsic metabolic pathway. Modulation of this pathway has direct relevance to the pathogenesis and treatment of autoimmunity and cancer.
Collapse
Affiliation(s)
- Nelomi Anandagoda
- School of Immunology and Microbial Sciences, King's College London, London, United Kingdom
| | - Joanna Cd Willis
- School of Immunology and Microbial Sciences, King's College London, London, United Kingdom
| | - Arnulf Hertweck
- School of Immunology and Microbial Sciences, King's College London, London, United Kingdom.,UCL Cancer Institute, University College London, London, United Kingdom
| | - Luke B Roberts
- School of Immunology and Microbial Sciences, King's College London, London, United Kingdom
| | - Ian Jackson
- School of Immunology and Microbial Sciences, King's College London, London, United Kingdom
| | - M Refik Gökmen
- School of Immunology and Microbial Sciences, King's College London, London, United Kingdom
| | - Richard G Jenner
- UCL Cancer Institute, University College London, London, United Kingdom
| | - Jane K Howard
- School of Life Course Sciences, King's College London, London, United Kingdom
| | - Graham M Lord
- School of Immunology and Microbial Sciences, King's College London, London, United Kingdom
| |
Collapse
|
31
|
Abstract
Since their serendipitous discovery in nematodes, microRNAs (miRNAs) have emerged as key regulators of biological processes in animals. These small RNAs form complex networks that regulate cell differentiation, development and homeostasis. Deregulation of miRNA function is associated with an increasing number of human diseases, particularly cancer. Recent discoveries have expanded our understanding of the control of miRNA function. Here, we review the mechanisms that modulate miRNA activity, stability and cellular localization through alternative processing and maturation, sequence editing, post-translational modifications of Argonaute proteins, viral factors, transport from the cytoplasm and regulation of miRNA-target interactions. We conclude by discussing intriguing, unresolved research questions.
Collapse
Affiliation(s)
- Luca F R Gebert
- Department of Integrative Structural and Computational Biology, The Scripps Research Institute, La Jolla, CA, USA
| | - Ian J MacRae
- Department of Integrative Structural and Computational Biology, The Scripps Research Institute, La Jolla, CA, USA.
| |
Collapse
|
32
|
Sinha P, Jaiswal P, Jainarayanan AK, Brahmachari SK. Intronic miRNA mediated gene expression regulation controls protein crowding inside the cell. Gene 2018; 679:172-178. [PMID: 30189267 DOI: 10.1016/j.gene.2018.08.082] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.2] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/22/2018] [Revised: 07/29/2018] [Accepted: 08/30/2018] [Indexed: 01/07/2023]
Abstract
Gene regulatory effects of microRNAs at a posttranscriptional level have been established over the last decade. In this study, we analyze the interaction networks of mRNA translation regulation through intronic miRNA, under various tissue-specific cellular contexts, taking into account the thermodynamic affinity, chemical kinetics, co-localization, concentration levels, network parameters and the presence of competitive interactors. This database, and analysis has been made available through an open-access web-server, miRiam, to promote further exploration. Here we report that expression of genes involved in Apoptosis Processes, Immune System Processes, Translation Regulator Activities, and Molecular Transport Activities within the cell are predominately regulated by miRNA mediation. Our findings further indicate that this regulatory effect has a profound effect in controlling protein crowding inside the cell. A miRNA mediated gene expression regulation serves as a temporal regulator, allowing the cellular machinery to temporarily 'pause' the translation of mRNA, indicating that the miRNA-mRNA interactions may be important for governing the optimal usage of cell volume.
Collapse
Affiliation(s)
- Prashant Sinha
- Cluster Innovation Centre, University of Delhi, Delhi 110007, India
| | - Pragya Jaiswal
- Cluster Innovation Centre, University of Delhi, Delhi 110007, India
| | | | - Samir K Brahmachari
- Cluster Innovation Centre, University of Delhi, Delhi 110007, India; CSIR-Institute of Genomics and Integrative Biology, Delhi 110007, India; Academy of Scientific and Innovative Research, CRRI, New Delhi 110020, India.
| |
Collapse
|
33
|
Moein S, Vaghari-Tabari M, Qujeq D, Majidinia M, Nabavi SM, Yousefi B. MiRNAs and inflammatory bowel disease: An interesting new story. J Cell Physiol 2018; 234:3277-3293. [PMID: 30417350 DOI: 10.1002/jcp.27173] [Citation(s) in RCA: 51] [Impact Index Per Article: 8.5] [Reference Citation Analysis] [Abstract] [Key Words] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/03/2018] [Accepted: 07/17/2018] [Indexed: 02/06/2023]
Abstract
Inflammatory bowel disease (IBD), as a chronic and recurrent inflammatory disorder, is caused by a dysregulated and aberrant immune response to exposed environmental factors in genetically susceptible individuals. Despite huge efforts in determining the molecular pathogenesis of IBD, an increasing worldwide incidence of IBD has been reported. MicroRNAs (miRNAs) are a set of noncoding RNA molecules that are about 22 nucleotides long, and these molecules are involved in the regulation of the gene expression. By clarifying the important role of miRNAs in a number of diseases, their role was also considered in IBD; numerous studies have been performed on this topic. In this review, we attempt to summarize a number of studies and discuss some of the recent developments in the roles of miRNAs in the pathophysiology, diagnosis, and treatment of IBD.
Collapse
Affiliation(s)
- Soheila Moein
- Medicinal Plants Processing Research Center, Shiraz University of Medical Sciences, Shiraz, Iran.,Department of Biochemistry, Faculty of Medicine, Hormozgan University of Medical Sciences, Bandar Abbas, Iran
| | - Mostafa Vaghari-Tabari
- Department of Biochemistry, Faculty of Medicine, Hormozgan University of Medical Sciences, Bandar Abbas, Iran.,Immunology Research Center, Tabriz University of Medical Sciences, Tabriz, Iran
| | - Durdi Qujeq
- Cellular and Molecular Biology Research Center (CMBRC), Health Research Institute, Babol University of Medical Sciences, Babol, Irantab.,Department of Clinical Biochemistry, Babol University of Medical Sciences, Babol, Iran
| | - Maryam Majidinia
- Solid Tumor Research Center, Urmia University of Medical Sciences, Urmia, Iran
| | - Seyed Mohammad Nabavi
- Applied Biotechnology Research Center, Baqiyatallah University of Medical Sciences, Tehran, Iran
| | - Bahman Yousefi
- Liver and Gastrointestinal Diseases Research Center, Tabriz University of Medical Sciences, Tabriz, Iran.,Molecular Medicine Research Center, Tabriz University of Medical Sciences, Tabriz, Iran
| |
Collapse
|
34
|
Wang Y, Liang H. When MicroRNAs Meet RNA Editing in Cancer: A Nucleotide Change Can Make a Difference. Bioessays 2018; 40:10.1002/bies.201700188. [PMID: 29280160 PMCID: PMC5828010 DOI: 10.1002/bies.201700188] [Citation(s) in RCA: 26] [Impact Index Per Article: 4.3] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/03/2017] [Revised: 11/22/2017] [Indexed: 12/20/2022]
Abstract
RNA editing is a major post-transcriptional mechanism that changes specific nucleotides at the RNA level. The most common RNA editing type in humans is adenosine (A) to inosine (I) editing, which is mediated by ADAR enzymes. RNA editing events can not only change amino acids in proteins, but also affect the functions of non-coding RNAs such as miRNAs. Recent studies have characterized thousands of miRNA RNA editing events across different cancer types. Importantly, individual cases of miRNA editing have been reported to play a role in cancer development. In this review, we summarize the current knowledge of miRNA editing in cancer, and discuss the mechanisms on how miRNA-related editing events modulate the initiation and progression of human cancer. Finally, we discuss the challenges and future directions of studying miRNA editing in cancer.
Collapse
Affiliation(s)
- Yumeng Wang
- Graduate Program in Quantitative and Computational Biosciences, Baylor College of Medicine, Houston, TX 77030, USA
- Department of Bioinformatics and Computational Biology, The University of Texas MD Anderson Cancer Center, Houston, TX 77030, USA
| | - Han Liang
- Graduate Program in Quantitative and Computational Biosciences, Baylor College of Medicine, Houston, TX 77030, USA
- Department of Bioinformatics and Computational Biology, The University of Texas MD Anderson Cancer Center, Houston, TX 77030, USA
- Department of Systems Biology, The University of Texas MD Anderson Cancer Center, Houston, TX 77030, USA
| |
Collapse
|
35
|
Hippen KL, Loschi M, Nicholls J, MacDonald KPA, Blazar BR. Effects of MicroRNA on Regulatory T Cells and Implications for Adoptive Cellular Therapy to Ameliorate Graft-versus-Host Disease. Front Immunol 2018; 9:57. [PMID: 29445371 PMCID: PMC5797736 DOI: 10.3389/fimmu.2018.00057] [Citation(s) in RCA: 39] [Impact Index Per Article: 6.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/31/2017] [Accepted: 01/09/2018] [Indexed: 01/15/2023] Open
Abstract
Regulatory T cells (Tregs) are key mediators of the immune system. MicroRNAs (miRNAs) are a family of ~22 nucleotide non-coding RNAs that are processed from longer precursors by the RNases Drosha and Dicer. miRNA regulates protein expression posttranscriptionally through mRNA destabilization or translational silencing. A critical role for miRNA in Treg function was initially discovered when both Dicer and Drosha knockout (KO) mice were found to develop a fatal autoimmune disease phenotypically similar to Foxp3 KO mice.
Collapse
Affiliation(s)
- Keli L Hippen
- Department of Pediatrics, Division of Blood and Marrow Transplantation, University of Minnesota Cancer Center, Minneapolis, MN, United States
| | - Michael Loschi
- Department of Pediatrics, Division of Blood and Marrow Transplantation, University of Minnesota Cancer Center, Minneapolis, MN, United States
| | - Jemma Nicholls
- Department of Pediatrics, Division of Blood and Marrow Transplantation, University of Minnesota Cancer Center, Minneapolis, MN, United States
| | - Kelli P A MacDonald
- The Antigen Presentation and Immunoregulation Laboratory and Bone Marrow Transplantation Laboratory, QIMR Berghofer Medical Research Institute, University of Minnesota Cancer Center, Brisbane, QLD, Australia
| | - Bruce R Blazar
- Department of Pediatrics, Division of Blood and Marrow Transplantation, University of Minnesota Cancer Center, Minneapolis, MN, United States
| |
Collapse
|
36
|
Ma N, Guo P, Zhang J, He T, Kim SW, Zhang G, Ma X. Nutrients Mediate Intestinal Bacteria-Mucosal Immune Crosstalk. Front Immunol 2018; 9:5. [PMID: 29416535 PMCID: PMC5787545 DOI: 10.3389/fimmu.2018.00005] [Citation(s) in RCA: 156] [Impact Index Per Article: 26.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/04/2017] [Accepted: 01/03/2018] [Indexed: 12/20/2022] Open
Abstract
The intestine is the shared site of nutrient digestion, microbiota colonization and immune cell location and this geographic proximity contributes to a large extent to their interaction. The onset and development of a great many diseases, such as inflammatory bowel disease and metabolic syndrome, will be caused due to the imbalance of body immune. As competent assistants, the intestinal bacteria are also critical in disease prevention and control. Moreover, the gut commensal bacteria are essential for development and normal operation of immune system and the pathogens are also closely bound up with physiological disorders and diseases mediated by immune imbalance. Understanding how our diet and nutrient affect bacterial composition and dynamic function, and the innate and adaptive status of our immune system, represents not only a research need but also an opportunity or challenge to improve health. Herein, this review focuses on the recent discoveries about intestinal bacteria–immune crosstalk and nutritional regulation on their interplay, with an aim to provide novel insights that can aid in understanding their interactions.
Collapse
Affiliation(s)
- Ning Ma
- State Key Laboratory of Animal Nutrition, Department of Animal Nutrition and Feed Science, China Agricultural University, Beijing, China
| | - Pingting Guo
- State Key Laboratory of Animal Nutrition, Department of Animal Nutrition and Feed Science, China Agricultural University, Beijing, China
| | - Jie Zhang
- State Key Laboratory of Animal Nutrition, Department of Animal Nutrition and Feed Science, China Agricultural University, Beijing, China.,Animal Husbandry and Veterinary Department, Beijing Vocational College of Agriculture, Beijing, China
| | - Ting He
- State Key Laboratory of Animal Nutrition, Department of Animal Nutrition and Feed Science, China Agricultural University, Beijing, China
| | - Sung Woo Kim
- Department of Animal Science, North Carolina State University, Raleigh, NC, United States
| | - Guolong Zhang
- Department of Animal Science, Oklahoma State University, Stillwater, OK, United States
| | - Xi Ma
- State Key Laboratory of Animal Nutrition, Department of Animal Nutrition and Feed Science, China Agricultural University, Beijing, China.,Department of Internal Medicine, University of Texas Southwestern Medical Center, Dallas, TX, United States.,Department of Biochemistry, University of Texas Southwestern Medical Center, Dallas, TX, United States
| |
Collapse
|
37
|
The role of A-to-I RNA editing in cancer development. Curr Opin Genet Dev 2017; 48:51-56. [PMID: 29127844 DOI: 10.1016/j.gde.2017.10.009] [Citation(s) in RCA: 54] [Impact Index Per Article: 7.7] [Reference Citation Analysis] [Abstract] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/06/2017] [Revised: 10/10/2017] [Accepted: 10/13/2017] [Indexed: 01/11/2023]
Abstract
Adenosine-to-inosine (A-to-I) RNA editing is the most common type of post-transcriptional nucleotide modification in humans, which is catalyzed in ADAR enzymes. Recent genomic studies have revealed thousands of altered RNA editing events in various cancer tissues, leading to diverse functional consequences. A critical role of individual A-to-I RNA editing events in cancer has been reported. Here, we review the current state of our knowledge on key A-to-I RNA editing events in coding and non-coding regions for their roles in cancer development and discuss their potential clinical utility. A better understanding of A-to-I RNA editing and its oncogenic mechanisms may facilitate the development of novel cancer therapeutic strategies.
Collapse
|
38
|
A-to-I editing in human miRNAs is enriched in seed sequence, influenced by sequence contexts and significantly hypoedited in glioblastoma multiforme. Sci Rep 2017; 7:2466. [PMID: 28550310 PMCID: PMC5446428 DOI: 10.1038/s41598-017-02397-6] [Citation(s) in RCA: 45] [Impact Index Per Article: 6.4] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/01/2017] [Accepted: 04/18/2017] [Indexed: 01/14/2023] Open
Abstract
Editing in microRNAs, particularly in seed can significantly alter the choice of their target genes. We show that out of 13 different human tissues, different regions of brain showed higher adenosine to inosine (A-to-I) editing in mature miRNAs. These events were enriched in seed sequence (73.33%), which was not observed for cytosine to uracil (17.86%) editing. More than half of the edited miRNAs showed increased stability, 72.7% of which had ΔΔG values less than −6.0 Kcal/mole and for all of them the edited adenosines mis-paired with cytosines on the pre-miRNA structure. A seed-editing event in hsa-miR-411 (with A – C mismatch) lead to increased expression of the mature form compared to the unedited version in cell culture experiments. Further, small RNA sequencing of GBM patients identified significant miRNA hypoediting which correlated with downregulation of ADAR2 both in metadata and qRT-PCR based validation. Twenty-two significant (11 novel) A-to-I hypoediting events were identified in GBM samples. This study highlights the importance of specific sequence and structural requirements of pre-miRNA for editing along with a suggestive crucial role for ADAR2. Enrichment of A-to-I editing in seed sequence highlights this as an important layer for genomic regulation in health and disease, especially in human brain.
Collapse
|
39
|
Wang Y, Xu X, Yu S, Jeong KJ, Zhou Z, Han L, Tsang YH, Li J, Chen H, Mangala LS, Yuan Y, Eterovic AK, Lu Y, Sood AK, Scott KL, Mills GB, Liang H. Systematic characterization of A-to-I RNA editing hotspots in microRNAs across human cancers. Genome Res 2017; 27:1112-1125. [PMID: 28411194 PMCID: PMC5495064 DOI: 10.1101/gr.219741.116] [Citation(s) in RCA: 117] [Impact Index Per Article: 16.7] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/15/2016] [Accepted: 04/11/2017] [Indexed: 12/12/2022]
Abstract
RNA editing, a widespread post-transcriptional mechanism, has emerged as a new player in cancer biology. Recent studies have reported key roles for individual miRNA editing events, but a comprehensive picture of miRNA editing in human cancers remains largely unexplored. Here, we systematically characterized the miRNA editing profiles of 8595 samples across 20 cancer types from miRNA sequencing data of The Cancer Genome Atlas and identified 19 adenosine-to-inosine (A-to-I) RNA editing hotspots. We independently validated 15 of them by perturbation experiments in several cancer cell lines. These miRNA editing events show extensive correlations with key clinical variables (e.g., tumor subtype, disease stage, and patient survival time) and other molecular drivers. Focusing on the RNA editing hotspot in miR-200b, a key tumor metastasis suppressor, we found that the miR-200b editing level correlates with patient prognosis opposite to the pattern observed for the wild-type miR-200b expression. We further experimentally showed that, in contrast to wild-type miRNA, the edited miR-200b can promote cell invasion and migration through its impaired ability to inhibit ZEB1/ZEB2 and acquired concomitant ability to repress new targets, including LIFR, a well-characterized metastasis suppressor. Our study highlights the importance of miRNA editing in gene regulation and suggests its potential as a biomarker for cancer prognosis and therapy.
Collapse
Affiliation(s)
- Yumeng Wang
- Graduate Program in Structural and Computational Biology and Molecular Biophysics, Baylor College of Medicine, Houston, Texas 77030, USA.,Department of Bioinformatics and Computational Biology, The University of Texas MD Anderson Cancer Center, Houston, Texas 77030, USA
| | - Xiaoyan Xu
- Department of Bioinformatics and Computational Biology, The University of Texas MD Anderson Cancer Center, Houston, Texas 77030, USA.,Department of Pathophysiology, College of Basic Medicine Science, China Medical University, Shenyang, Liaoning Province 110122, China
| | - Shuangxing Yu
- Department of Systems Biology, The University of Texas MD Anderson Cancer Center, Houston, Texas 77030, USA
| | - Kang Jin Jeong
- Department of Systems Biology, The University of Texas MD Anderson Cancer Center, Houston, Texas 77030, USA
| | - Zhicheng Zhou
- Department of Bioinformatics and Computational Biology, The University of Texas MD Anderson Cancer Center, Houston, Texas 77030, USA.,Department of Systems Biology, The University of Texas MD Anderson Cancer Center, Houston, Texas 77030, USA
| | - Leng Han
- Department of Biochemistry and Molecular Biology, The University of Texas Health Science Center at Houston McGovern Medical School, Houston, Texas 77030, USA
| | - Yiu Huen Tsang
- Department of Molecular and Human Genetics, Baylor College of Medicine, Houston, Texas 77030, USA
| | - Jun Li
- Department of Bioinformatics and Computational Biology, The University of Texas MD Anderson Cancer Center, Houston, Texas 77030, USA
| | - Hu Chen
- Graduate Program in Structural and Computational Biology and Molecular Biophysics, Baylor College of Medicine, Houston, Texas 77030, USA.,Department of Bioinformatics and Computational Biology, The University of Texas MD Anderson Cancer Center, Houston, Texas 77030, USA
| | - Lingegowda S Mangala
- Department of Gynecologic Oncology and Reproductive Medicine, The University of Texas MD Anderson Cancer Center, Houston, Texas 77030, USA.,Center for RNA Interference and Non-Coding RNAs, The University of Texas MD Anderson Cancer Center, Houston, Texas 77030, USA
| | - Yuan Yuan
- Department of Bioinformatics and Computational Biology, The University of Texas MD Anderson Cancer Center, Houston, Texas 77030, USA
| | - A Karina Eterovic
- Department of Systems Biology, The University of Texas MD Anderson Cancer Center, Houston, Texas 77030, USA
| | - Yiling Lu
- Department of Systems Biology, The University of Texas MD Anderson Cancer Center, Houston, Texas 77030, USA
| | - Anil K Sood
- Department of Gynecologic Oncology and Reproductive Medicine, The University of Texas MD Anderson Cancer Center, Houston, Texas 77030, USA.,Center for RNA Interference and Non-Coding RNAs, The University of Texas MD Anderson Cancer Center, Houston, Texas 77030, USA.,Department of Cancer Biology, The University of Texas MD Anderson Cancer Center, Houston, Texas 77030, USA
| | - Kenneth L Scott
- Department of Molecular and Human Genetics, Baylor College of Medicine, Houston, Texas 77030, USA
| | - Gordon B Mills
- Department of Systems Biology, The University of Texas MD Anderson Cancer Center, Houston, Texas 77030, USA
| | - Han Liang
- Graduate Program in Structural and Computational Biology and Molecular Biophysics, Baylor College of Medicine, Houston, Texas 77030, USA.,Department of Bioinformatics and Computational Biology, The University of Texas MD Anderson Cancer Center, Houston, Texas 77030, USA.,Department of Systems Biology, The University of Texas MD Anderson Cancer Center, Houston, Texas 77030, USA
| |
Collapse
|
40
|
Wu YH, Liu W, Xue B, Zhang L, Liu XY, Liu B, Wang Y, Cai Y, Duan R. Upregulated Expression of microRNA-16 Correlates with Th17/Treg Cell Imbalance in Patients with Rheumatoid Arthritis. DNA Cell Biol 2016; 35:853-860. [PMID: 27875659 DOI: 10.1089/dna.2016.3349] [Citation(s) in RCA: 32] [Impact Index Per Article: 4.0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/14/2022] Open
Affiliation(s)
- Yuan-Hao Wu
- Institute of Basic Research in Clinical Medicine, China Academy of Chinese Medical Sciences, Beijing, China
- Department of Rheumatology and Immunology, First Teaching Hospital of Tianjin University of Traditional Chinese Medicine, Tianjin, China
| | - Wei Liu
- Department of Rheumatology and Immunology, First Teaching Hospital of Tianjin University of Traditional Chinese Medicine, Tianjin, China
| | - Bin Xue
- Department of Rheumatology and Immunology, First Teaching Hospital of Tianjin University of Traditional Chinese Medicine, Tianjin, China
| | - Lei Zhang
- Department of Rheumatology and Immunology, First Teaching Hospital of Tianjin University of Traditional Chinese Medicine, Tianjin, China
| | - Xiao-Ya Liu
- Department of Rheumatology and Immunology, First Teaching Hospital of Tianjin University of Traditional Chinese Medicine, Tianjin, China
| | - Bin Liu
- Department of Rheumatology and Immunology, First Teaching Hospital of Tianjin University of Traditional Chinese Medicine, Tianjin, China
| | - Yi Wang
- Department of Rheumatology and Immunology, First Teaching Hospital of Tianjin University of Traditional Chinese Medicine, Tianjin, China
| | - Yue Cai
- Department of Rheumatology and Immunology, First Teaching Hospital of Tianjin University of Traditional Chinese Medicine, Tianjin, China
| | - Ran Duan
- Department of Rheumatology and Immunology, First Teaching Hospital of Tianjin University of Traditional Chinese Medicine, Tianjin, China
| |
Collapse
|