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Chengcheng L, Raza SHA, Zhimei Y, Sihu W, Shengchen Y, Aloufi BH, Bingzhi L, Zan L. Bta-miR-181d and Bta-miR-196a mediated proliferation, differentiation, and apoptosis in Bovine Myogenic Cells. J Anim Sci 2024; 102:skae142. [PMID: 38766769 PMCID: PMC11161902 DOI: 10.1093/jas/skae142] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/21/2023] [Accepted: 05/17/2024] [Indexed: 05/22/2024] Open
Abstract
Skeletal muscle is an important component of livestock and poultry organisms. The proliferation and differentiation of myoblasts are highly coordinated processes, which rely on the regulation of miRNA. MiRNAs are widely present in organisms and play roles in various biological processes, including cell proliferation, differentiation, and apoptosis. MiR-181d and miR-196a, identified as tumor suppressors, have been found to be involved in cell proliferation, apoptosis, directed differentiation, and cancer cell invasion. However, their role in beef cattle skeletal muscle metabolism remains unclear. In this study, we discovered that overexpression of bta-miR-181d and bta-miR-196a in Qinchuan cattle myoblasts inhibited proliferation and apoptosis while promoting myogenic differentiation through EDU staining, flow cytometry analysis, immunofluorescence staining, and Western blotting. RNA-seq analysis of differential gene expression revealed that after overexpression of bta-miR-181d and bta-miR-196a, the differentially expressed genes were mainly enriched in the PI3K-Akt and MAPK signaling pathways. Furthermore, the phosphorylation levels of key proteins p-AKT in the PI3K signaling pathway and p-MAPK in the MAPK signaling pathway were significantly decreased after overexpression of bta-miR-181d and bta-miR-196a. Overall, this study provides preliminary evidence that bta-miR-181d and bta-miR-196a may regulate proliferation, apoptosis, and differentiation processes in Qinchuan cattle myoblasts by affecting the phosphorylation status of key proteins in PI3K-Akt and MAPK-ERK signaling pathways.
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Affiliation(s)
- Liang Chengcheng
- College of Animal Science and Technology, Xinyang Agriculture and Forestry University, Xinyang, Henan 464000, P.R. China
- College of Animal Science and Technology, Northwest A&F University, Yangling, Shaanxi, 712100, P.R. China
| | - Sayed Haidar Abbas Raza
- College of Animal Science and Technology, Northwest A&F University, Yangling, Shaanxi, 712100, P.R. China
- Guangdong Provincial Key Laboratory of Food Quality and Safety/Nation-Local Joint Engineering Research Center for Machining and Safety of Livestock and Poultry Products, South China Agricultural University, Guangzhou 510642, P.R. China
| | - Yang Zhimei
- College of Animal Science and Technology, Northwest A&F University, Yangling, Shaanxi, 712100, P.R. China
| | - Wang Sihu
- College of Animal Science and Technology, Northwest A&F University, Yangling, Shaanxi, 712100, P.R. China
| | - Yu Shengchen
- College of Animal Science and Technology, Northwest A&F University, Yangling, Shaanxi, 712100, P.R. China
| | - Bandar Hamad Aloufi
- Biology Department, Faculty of Science, University of Ha'il, Ha'il, Saudi Arabia
| | - Li Bingzhi
- College of Animal Science and Technology, Northwest A&F University, Yangling, Shaanxi, 712100, P.R. China
| | - Linsen Zan
- College of Animal Science and Technology, Northwest A&F University, Yangling, Shaanxi, 712100, P.R. China
- National Beef Cattle Improvement Center, Northwest A&F University, Yangling, 712100, China
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2
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Miller A, Dasen JS. Establishing and maintaining Hox profiles during spinal cord development. Semin Cell Dev Biol 2024; 152-153:44-57. [PMID: 37029058 PMCID: PMC10524138 DOI: 10.1016/j.semcdb.2023.03.014] [Citation(s) in RCA: 3] [Impact Index Per Article: 3.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/22/2022] [Revised: 01/18/2023] [Accepted: 03/30/2023] [Indexed: 04/09/2023]
Abstract
The chromosomally-arrayed Hox gene family plays central roles in embryonic patterning and the specification of cell identities throughout the animal kingdom. In vertebrates, the relatively large number of Hox genes and pervasive expression throughout the body has hindered understanding of their biological roles during differentiation. Studies on the subtype diversification of spinal motor neurons (MNs) have provided a tractable system to explore the function of Hox genes during differentiation, and have provided an entry point to explore how neuronal fate determinants contribute to motor circuit assembly. Recent work, using both in vitro and in vivo models of MN subtype differentiation, have revealed how patterning morphogens and regulation of chromatin structure determine cell-type specific programs of gene expression. These studies have not only shed light on basic mechanisms of rostrocaudal patterning in vertebrates, but also have illuminated mechanistic principles of gene regulation that likely operate in the development and maintenance of terminal fates in other systems.
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Affiliation(s)
- Alexander Miller
- NYU Neuroscience Institute and Developmental Genetics Programs, Department of Neuroscience and Physiology, NYU School of Medicine, New York, NY 10016, USA.
| | - Jeremy S Dasen
- NYU Neuroscience Institute and Developmental Genetics Programs, Department of Neuroscience and Physiology, NYU School of Medicine, New York, NY 10016, USA.
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3
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MicroRNAs in Medicinal Plants. Int J Mol Sci 2022; 23:ijms231810477. [PMID: 36142389 PMCID: PMC9500639 DOI: 10.3390/ijms231810477] [Citation(s) in RCA: 11] [Impact Index Per Article: 5.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/11/2022] [Revised: 09/06/2022] [Accepted: 09/07/2022] [Indexed: 11/16/2022] Open
Abstract
Medicinal plant microRNAs (miRNAs) are an endogenous class of small RNA central to the posttranscriptional regulation of gene expression. Biosynthetic research has shown that the mature miRNAs in medicinal plants can be produced from either the standard messenger RNA splicing mechanism or the pre-ribosomal RNA splicing process. The medicinal plant miRNA function is separated into two levels: (1) the cross-kingdom level, which is the regulation of disease-related genes in animal cells by oral intake, and (2) the intra-kingdom level, which is the participation of metabolism, development, and stress adaptation in homologous or heterologous plants. Increasing research continues to enrich the biosynthesis and function of medicinal plant miRNAs. In this review, peer-reviewed papers on medicinal plant miRNAs published on the Web of Science were discussed, covering a total of 78 species. The feasibility of the emerging role of medicinal plant miRNAs in regulating animal gene function was critically evaluated. Staged progress in intra-kingdom miRNA research has only been found in a few medicinal plants, which may be mainly inhibited by their long growth cycle, high demand for growth environment, immature genetic transformation, and difficult RNA extraction. The present review clarifies the research significance, opportunities, and challenges of medicinal plant miRNAs in drug development and agricultural production. The discussion of the latest results furthers the understanding of medicinal plant miRNAs and helps the rational design of the corresponding miRNA/target genes functional modules.
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First Genome of Rock Lizard Darevskia valentini Involved in Formation of Several Parthenogenetic Species. Genes (Basel) 2022; 13:genes13091569. [PMID: 36140737 PMCID: PMC9498476 DOI: 10.3390/genes13091569] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/24/2022] [Revised: 08/22/2022] [Accepted: 08/27/2022] [Indexed: 11/22/2022] Open
Abstract
The extant reptiles are one of the most diverse clades among terrestrial vertebrates and one of a few groups with instances of parthenogenesis. Due to the hybrid origin of parthenogenetic species, reference genomes of the parental species as well as of the parthenogenetic progeny are indispensable to explore the genetic foundations of parthenogenetic reproduction. Here, we report on the first genome assembly of rock lizard Darevskia valentini, a paternal species for several parthenogenetic lineages. The novel genome was used in the reconstruction of the comprehensive phylogeny of Squamata inferred independently from 7369 trees of single-copy orthologs and a supermatrix of 378 conserved proteins. We also investigated Hox clusters, the loci that are often regarded as playing an important role in the speciation of animal groups with drastically diverse morphology. We demonstrated that Hox clusters of D. valentini are invaded with transposons and contain the HoxC1 gene that has been considered to be lost in the amniote ancestor. This study provides confirmation for previous works and releases new genomic data that will contribute to future discoveries on the mechanisms of parthenogenesis as well as support comparative studies among reptiles.
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5
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Integrated computational analysis reveals HOX genes cluster as oncogenic drivers in head and neck squamous cell carcinoma. Sci Rep 2022; 12:7952. [PMID: 35562533 PMCID: PMC9106698 DOI: 10.1038/s41598-022-11590-1] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/27/2021] [Accepted: 04/04/2022] [Indexed: 11/23/2022] Open
Abstract
Alterations in homeobox (HOX) gene expression are involved in the progression of several cancer types including head and neck squamous cell carcinoma (HNSCC). However, regulation of the entire HOX cluster in the pathophysiology of HNSCC is still elusive. By using different comprehensive databases, we have identified the significance of differentially expressed HOX genes (DEHGs) in stage stratification and HPV status in the cancer genome atlas (TCGA)-HNSCC datasets. The genetic and epigenetic alterations, druggable genes, their associated functional pathways and their possible association with cancer hallmarks were identified. We have performed extensive analysis to identify the target genes of DEHGs driving HNSCC. The differentially expressed HOX cluster-embedded microRNAs (DEHMs) in HNSCC and their association with HOX-target genes were evaluated to construct a regulatory network of the HOX cluster in HNSCC. Our analysis identified sixteen DEHGs in HNSCC and determined their importance in stage stratification and HPV infection. We found a total of 55 HNSCC driver genes that were identified as targets of DEHGs. The involvement of DEHGs and their targets in cancer-associated signaling mechanisms have confirmed their role in pathophysiology. Further, we found that their oncogenic nature could be targeted by using the novel and approved anti-neoplastic drugs in HNSCC. Construction of the regulatory network depicted the interaction between DEHGs, DEHMs and their targets genes in HNSCC. Hence, aberrantly expressed HOX cluster genes function in a coordinated manner to drive HNSCC. It could provide a broad perspective to carry out the experimental investigation, to understand the underlying oncogenic mechanism and allow the discovery of new clinical biomarkers for HNSCC.
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6
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Liu C, Gao W, Shi Y, Lv L, Tang W. Association between miR-146a rs2910164, miR-196a2 rs11614913, and miR-499 rs3746444 polymorphisms and the risk of esophageal carcinoma: A case-control study. Cancer Med 2022; 11:3949-3959. [PMID: 35499218 PMCID: PMC9636501 DOI: 10.1002/cam4.4729] [Citation(s) in RCA: 2] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/16/2021] [Revised: 03/10/2022] [Accepted: 03/17/2022] [Indexed: 12/03/2022] Open
Abstract
MicroRNAs (miRNAs) are a group of small, non‐coding, and endogenous RNAs that regulate gene expression and over 50% of them are located at cancer‐related genomic regions or fragile sites. According to previous studies there is significant association of miRNA single nucleotide polymorphisms (SNPs) with tumorigenesis (e.g., esophageal cancer, hepatocellular cancer, gastric cancer, bladder cancer, breast cancer, lung cancer, and colon cancer), however, the conclusions have been inconsistent. To investigate the relationship between miR‐146a rs2910164 C > G, miR‐196a2 rs11614913 T > C, and miR‐499 rs3746444 A > G polymorphisms and the susceptibility to esophageal squamous cell cancer (ESCC) in the Chinese Han nationality, we recruited 829 cases and 1522 controls in our study. In this case–control study, our results suggest that the rs3746444 GG genotype increased ESCC risk [homozygote model: adjusted odds ratio (OR), 2.26; 95% CI, 1.33–3.83; p = 0.003, recessive model: adjusted OR, 2.34; 95% CI, 1.38–3.96; p = 0.002], which remained consistent after Bonferroni correction. There was no association of rs11614913 and rs2910164 polymorphisms with ESCC. After adjusting by age, sex, smoking, and drinking status and body mass index (BMI), the multiple logistic analysis suggested that rs11614913 T → C variation reduced ESCC susceptibility in females and in the ≥63 years old subgroups, while rs2910164 C → G variation increased ESCC risk in both two BMI subgroups.
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Affiliation(s)
- Chao Liu
- Department of Cardiothoracic Surgery, Affiliated People's Hospital of Jiangsu University (Zhenjiang First People's Hospital), Jiangsu Province, China
| | - Wenhui Gao
- School of Medicine, Jiangsu University, Jiangsu Province, China
| | - Yijun Shi
- Department of Cardiothoracic Surgery, Affiliated People's Hospital of Jiangsu University (Zhenjiang First People's Hospital), Jiangsu Province, China
| | - Lu Lv
- Department of Cardiothoracic Surgery, Affiliated People's Hospital of Jiangsu University (Zhenjiang First People's Hospital), Jiangsu Province, China
| | - Weifeng Tang
- Department of Cardiothoracic Surgery, Nanjing Drum Tower Hospital Clinical College of Jiangsu University, Jiangsu Province, China
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7
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Shenoy US, Adiga D, Kabekkodu SP, Hunter KD, Radhakrishnan R. Molecular implications of HOX genes targeting multiple signaling pathways in cancer. Cell Biol Toxicol 2022; 38:1-30. [PMID: 34617205 PMCID: PMC8789642 DOI: 10.1007/s10565-021-09657-2] [Citation(s) in RCA: 8] [Impact Index Per Article: 4.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/03/2021] [Accepted: 09/10/2021] [Indexed: 11/17/2022]
Abstract
Homeobox (HOX) genes encode highly conserved homeotic transcription factors that play a crucial role in organogenesis and tissue homeostasis. Their deregulation impacts the function of several regulatory molecules contributing to tumor initiation and progression. A functional bridge exists between altered gene expression of individual HOX genes and tumorigenesis. This review focuses on how deregulation in the HOX-associated signaling pathways contributes to the metastatic progression in cancer. We discuss their functional significance, clinical implications and ascertain their role as a diagnostic and prognostic biomarker in the various cancer types. Besides, the mechanism of understanding the theoretical underpinning that affects HOX-mediated therapy resistance in cancers has been outlined. The knowledge gained shall pave the way for newer insights into the treatment of cancer.
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Affiliation(s)
- U Sangeetha Shenoy
- Department of Cell and Molecular Biology, Manipal School of Life Sciences, Manipal Academy of Higher Education, Manipal, Karnataka, 576104, India
| | - Divya Adiga
- Department of Cell and Molecular Biology, Manipal School of Life Sciences, Manipal Academy of Higher Education, Manipal, Karnataka, 576104, India
| | - Shama Prasada Kabekkodu
- Department of Cell and Molecular Biology, Manipal School of Life Sciences, Manipal Academy of Higher Education, Manipal, Karnataka, 576104, India
| | - Keith D Hunter
- Academic Unit of Oral and Maxillofacial Medicine and Pathology, School of Clinical Dentistry, University of Sheffield, Sheffield, S10 2TA, UK
| | - Raghu Radhakrishnan
- Department of Oral Pathology, Manipal College of Dental Sciences, Manipal, Manipal Academy of Higher Education, Manipal, 576104, India.
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8
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Zuo H, Liu X, Luo M, Yang L, Zhu Z, Weng S, He J, Xu X. miR-10c Facilitates White Spot Syndrome Virus Infection by Targeting Toll3 in Litopenaeus vannemei. Front Immunol 2021; 12:733730. [PMID: 34950131 PMCID: PMC8688535 DOI: 10.3389/fimmu.2021.733730] [Citation(s) in RCA: 10] [Impact Index Per Article: 3.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/30/2021] [Accepted: 10/14/2021] [Indexed: 12/03/2022] Open
Abstract
Toll-like receptors (TLRs) are canonical cell membrane receptors functioning to recognize pathogens and transduce signals to activate immune responses. It has been known that Toll3 in Pacific white shrimp Litopenaeus vannamei (LvToll3) plays a critical role in antiviral immunity by inducing the transcription of interferon regulatory factor (IRF), which mediates a signaling axis that is similar to the interferon system of vertebrates. However, the regulatory mechanism of the Toll3-IRF signaling is still unclear. In this study, a novel microRNA (miRNA) of miR-10 family, temporarily named as miR-10c, was identified from L. vannamei. miR-10c may play a nonnegligible regulatory role in shrimp immune responses since it was constitutively expressed in all detected tissues and transcriptionally induced by immune stimulation. Functional analysis validated that miR-10c could target LvToll3 to inhibit its expression, through which miR-10c blocked the nuclear translocation of IRF and facilitated white spot syndrome virus (WSSV) infection. To our knowledge, the present study revealed the first report of a Toll targeted by miRNA in crustaceans and provided a solid evidence base for supporting the role of LvToll3 in antiviral defense by activating IRF signaling in L. vannamei. Identification of the miR-10c/Toll3/IRF regulatory axis in shrimp provides new insights into the participation of miRNA in the regulation of immune responses and contributes to in-depth understanding of the mechanisms of Toll-induced immune responses in L. vannamei.
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Affiliation(s)
- Hongliang Zuo
- State Key Laboratory of Biocontrol, School of Life Sciences, Sun Yat-Sen University, Guangzhou, China.,Southern Marine Science and Engineering Guangdong Laboratory (Zhuhai), Zhuhai, China.,Institute of Aquatic Economic Animals and Guangdong Province Key Laboratory for Aquatic Economic Animals, Sun Yat-Sen University, Guangzhou, China
| | - Xinxin Liu
- State Key Laboratory of Biocontrol, School of Life Sciences, Sun Yat-Sen University, Guangzhou, China
| | - Mengting Luo
- State Key Laboratory of Biocontrol, School of Life Sciences, Sun Yat-Sen University, Guangzhou, China
| | - Linwei Yang
- State Key Laboratory of Biocontrol, School of Life Sciences, Sun Yat-Sen University, Guangzhou, China.,Southern Marine Science and Engineering Guangdong Laboratory (Zhuhai), Zhuhai, China.,Institute of Aquatic Economic Animals and Guangdong Province Key Laboratory for Aquatic Economic Animals, Sun Yat-Sen University, Guangzhou, China
| | - Zhiming Zhu
- Southern Marine Science and Engineering Guangdong Laboratory (Zhuhai), Zhuhai, China
| | - Shaoping Weng
- State Key Laboratory of Biocontrol, School of Life Sciences, Sun Yat-Sen University, Guangzhou, China.,Southern Marine Science and Engineering Guangdong Laboratory (Zhuhai), Zhuhai, China.,Institute of Aquatic Economic Animals and Guangdong Province Key Laboratory for Aquatic Economic Animals, Sun Yat-Sen University, Guangzhou, China
| | - Jianguo He
- State Key Laboratory of Biocontrol, School of Life Sciences, Sun Yat-Sen University, Guangzhou, China.,Southern Marine Science and Engineering Guangdong Laboratory (Zhuhai), Zhuhai, China.,Institute of Aquatic Economic Animals and Guangdong Province Key Laboratory for Aquatic Economic Animals, Sun Yat-Sen University, Guangzhou, China
| | - Xiaopeng Xu
- State Key Laboratory of Biocontrol, School of Life Sciences, Sun Yat-Sen University, Guangzhou, China.,Southern Marine Science and Engineering Guangdong Laboratory (Zhuhai), Zhuhai, China.,Institute of Aquatic Economic Animals and Guangdong Province Key Laboratory for Aquatic Economic Animals, Sun Yat-Sen University, Guangzhou, China
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9
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Wu C, Wu Z, Wang L, Chen Y, Huang X, Wang Z, Tian B. The Modulating Mechanisms of miRNA-196 in Malignancies and Its Prognostic Value: A Systematic Review and Meta-Analysis. Nutr Cancer 2021; 74:423-436. [PMID: 34435522 DOI: 10.1080/01635581.2021.1922718] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 02/08/2023]
Abstract
Accumulating studies have revealed that up- or downregulated miRNA-196 expression correlates with the prognostic value in various malignancies; however, existing single studies lack robust evidence to elucidate the role of miRNA-196 in malignancy. The pooled results showed that the upregulation of miRNA-196 expression was significantly correlated with unfavorable OS [HR 2.14; 95% confidence interval (CI), 1.78-2.57; p < 0.001)] and worse PFS (HR 2.84; 95% CI, 1.29-6.23, P = 0.01) in various malignancies. According to the regulatory mechanisms, studies shown that multiple tumors associated with transcription processes could be modulated by the miRNA-196 family; correspondingly, the miRNA-196 family exerted biological functions that could be regulated by various molecules. The upregulation of miRNA-196a, miRNA-196b and miRNA-196 expression is correlated with significantly unfavorable OS in multiple malignancies; similarly, miRNA-196 overexpression predicts poor PFS in multiple malignancies. Taken together, these findings indicate that miRNA-196a and miRNA-196b may serve as oncogenic molecules and may be potential prognostic biomarkers in multiple malignancies.
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Affiliation(s)
- Chao Wu
- Department of Pancreatic Surgery, West China Hospital, Sichuan University, Chengdu, China
| | - Zuowei Wu
- Department of Pancreatic Surgery, West China Hospital, Sichuan University, Chengdu, China
| | - Li Wang
- Department of Pancreatic Surgery, West China Hospital, Sichuan University, Chengdu, China
| | - Yang Chen
- Department of Pancreatic Surgery, West China Hospital, Sichuan University, Chengdu, China
| | - Xing Huang
- Department of Pancreatic Surgery, West China Hospital, Sichuan University, Chengdu, China
| | - Zihe Wang
- Department of Pancreatic Surgery, West China Hospital, Sichuan University, Chengdu, China
| | - Bole Tian
- Department of Pancreatic Surgery, West China Hospital, Sichuan University, Chengdu, China
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10
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Chakraborty A, Viswanath A, Malipatil R, Rathore A, Thirunavukkarasu N. Structural and Functional Characteristics of miRNAs in Five Strategic Millet Species and Their Utility in Drought Tolerance. Front Genet 2020; 11:608421. [PMID: 33363575 PMCID: PMC7753210 DOI: 10.3389/fgene.2020.608421] [Citation(s) in RCA: 9] [Impact Index Per Article: 2.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/20/2020] [Accepted: 11/05/2020] [Indexed: 11/13/2022] Open
Abstract
Millets are the strategic food crops in arid and drought-prone ecologies. Millets, by virtue of nature, are very well-adapted to drought conditions and able to produce sustainable yield. Millets have important nutrients that can help prevent micro-nutrient malnutrition. As a result of the adverse effect of climate change and widespread malnutrition, millets have attained a strategic position to sustain food and nutritional security. Although millets can adapt well to the drought ecologies where other cereals fail completely, the yield level is very low under stress. There is a tremendous opportunity to increase the genetic potential of millet crops in dry lands when the genetics of the drought-tolerance mechanism is fully explained. MicroRNAs (miRNAs) are the class of small RNAs that control trait expression. They are part of the gene regulation but little studied in millets. In the present study, novel miRNAs and gene targets were identified from the genomic resources of pearl millet, sorghum, foxtail millet, finger millet, and proso millet through in silico approaches. A total of 1,002 miRNAs from 280 families regulating 23,158 targets were identified using different filtration criteria in five millet species. The unique as well as conserved structural features and functional characteristics of miRNA across millets were explained. About 84 miRNAs were conserved across millets in different species combinations, which explained the evolutionary relationship of the millets. Further, 215 miRNAs controlling 155 unique major drought-responsive genes, transcription factors, and protein families revealed the genetics of drought tolerance that are accumulated in the millet genomes. The miRNAs regulating the drought stress through specific targets or multiple targets showed through a network analysis. The identified genes regulated by miRNA genes could be useful in developing functional markers and used for yield improvement under drought in millets as well as in other crops.
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Affiliation(s)
- Animikha Chakraborty
- Genomics and Molecular Breeding Lab, Indian Council of Agricultural Research-Indian Institute of Millets Research, Hyderabad, India
| | - Aswini Viswanath
- Genomics and Molecular Breeding Lab, Indian Council of Agricultural Research-Indian Institute of Millets Research, Hyderabad, India
| | - Renuka Malipatil
- Genomics and Molecular Breeding Lab, Indian Council of Agricultural Research-Indian Institute of Millets Research, Hyderabad, India
| | - Abhishek Rathore
- Statistics, Bioinformatics and Data Management, International Crops Research Institute for the Semi-Arid Tropics, Hyderabad, India
| | - Nepolean Thirunavukkarasu
- Genomics and Molecular Breeding Lab, Indian Council of Agricultural Research-Indian Institute of Millets Research, Hyderabad, India
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11
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Paço A, Aparecida de Bessa Garcia S, Leitão Castro J, Costa-Pinto AR, Freitas R. Roles of the HOX Proteins in Cancer Invasion and Metastasis. Cancers (Basel) 2020; 13:E10. [PMID: 33375038 PMCID: PMC7792759 DOI: 10.3390/cancers13010010] [Citation(s) in RCA: 30] [Impact Index Per Article: 7.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/16/2020] [Revised: 12/16/2020] [Accepted: 12/17/2020] [Indexed: 02/06/2023] Open
Abstract
Invasion and metastasis correspond to the foremost cause of cancer-related death, and the molecular networks behind these two processes are extremely complex and dependent on the intra- and extracellular conditions along with the prime of the premetastatic niche. Currently, several studies suggest an association between the levels of HOX genes expression and cancer cell invasion and metastasis, which favour the formation of novel tumour masses. The deregulation of HOX genes by HMGA2/TET1 signalling and the regulatory effect of noncoding RNAs generated by the HOX loci can also promote invasion and metastasis, interfering with the expression of HOX genes or other genes relevant to these processes. In this review, we present five molecular mechanisms of HOX deregulation by which the HOX clusters products may affect invasion and metastatic processes in solid tumours.
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Affiliation(s)
- Ana Paço
- BLC3—Biomassa Lenho-Celulósica de 3ª Geração, Campus of Technology and Innovation, 3405-169 Oliveira do Hospital, Portugal
| | - Simone Aparecida de Bessa Garcia
- I3S—Institute for Innovation & Health Research, University of Porto, 4200-135 Porto, Portugal; (S.A.d.B.G.); (J.L.C.); (A.R.C.-P.); (R.F.)
| | - Joana Leitão Castro
- I3S—Institute for Innovation & Health Research, University of Porto, 4200-135 Porto, Portugal; (S.A.d.B.G.); (J.L.C.); (A.R.C.-P.); (R.F.)
| | - Ana Rita Costa-Pinto
- I3S—Institute for Innovation & Health Research, University of Porto, 4200-135 Porto, Portugal; (S.A.d.B.G.); (J.L.C.); (A.R.C.-P.); (R.F.)
| | - Renata Freitas
- I3S—Institute for Innovation & Health Research, University of Porto, 4200-135 Porto, Portugal; (S.A.d.B.G.); (J.L.C.); (A.R.C.-P.); (R.F.)
- ICBAS—Institute of Biomedical Sciences Abel Salazar, University of Porto, 4050-313 Porto, Portugal
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12
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Bhardwaj E, Lal M, Anand S, Das S. Independent recurrent evolution of MICRORNA genes converging onto similar non-canonical organisation across green plant lineages is driven by local and segmental duplication events in species, family and lineages. PLANT SCIENCE : AN INTERNATIONAL JOURNAL OF EXPERIMENTAL PLANT BIOLOGY 2020; 301:110661. [PMID: 33218629 DOI: 10.1016/j.plantsci.2020.110661] [Citation(s) in RCA: 3] [Impact Index Per Article: 0.8] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 06/25/2020] [Revised: 09/02/2020] [Accepted: 09/02/2020] [Indexed: 06/11/2023]
Abstract
The relationship between evolutionary history, organisation and transcriptional regulation of genes are intrinsically linked. These have been well studied in canonically organised protein-coding genes but not of MIRNAs. In the present study, we investigated the non-canonical arrangement of MIRNAs across taxonomic boundaries from algae to angiosperms employing a combination of genome organization, phylogeny and synteny. We retrieved the complete dataset of MIRNA from twenty-five species to identify and classify based on organisational patterns. The median size of cluster was between 2-5 kb and between 1-20 % of all MIRNAs are organized in head-to-head (with bidirectional promoter), head-to-tail (tandem), and overlapping manner. Although majority of the clusters are composed of MIRNA homologs, 25% of all clusters comprises of non-homologous genes with a potential of generating functional and regulatory complexity. A comparison of phylogeny and organizational patterns revealed that multiple independent events, some of which are species-specific, and some ancient, in different lineages, are responsible for non-canonical organization. Detailed investigation of MIR395 family across the plants revealed a complex origin of non-canonical arrangement through ancient and recent, segmental and local duplications; analysis of MIR399 family revealed major expansion occurred prior to monocot-dicot split, with few lineage-specific events. Evolution of "convergent" organization pattern of non-canonical arrangement originating from independent loci through recurrent event highlights our poor understanding of evolutionary process of MIRNA genes. The present investigation thus paves way for comparative functional genomics to understand the role of non-canonical organization on transcriptional regulation and regulatory diversity in MIRNA gene families.
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Affiliation(s)
- Ekta Bhardwaj
- Department of Botany, University of Delhi, Delhi, 110 007, India
| | - Mukund Lal
- Department of Botany, University of Delhi, Delhi, 110 007, India
| | - S Anand
- Department of Botany, University of Delhi, Delhi, 110 007, India
| | - Sandip Das
- Department of Botany, University of Delhi, Delhi, 110 007, India.
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13
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Zhang Z, Xu L, Hu Z, Yang B, Xu J. MicroRNA-196b promotes cell growth and metastasis of ovarian cancer by targeting ZMYND11. Minerva Med 2020; 113:707-717. [PMID: 32512976 DOI: 10.23736/s0026-4806.20.06654-9] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/08/2022]
Abstract
BACKGROUND The purpose of this study was to explore the mechanism by which microRNA-196b exerts a tumor promotion effect on ovarian cancer (OCa). METHODS Quantitative real-time polymerase chain reaction (qRT-PCR) was performed to examine the expression of microRNA-196b in 60 pairs of tumor samples and paracancerous ones collected from patients with ovarian cancer, meanwhile, microRNA-196b expression in human ovarian cancer cell lines and normal ovarian epithelial cell lines were also analyzed by qRT-PCR. Bioinformatics methods suggested that ZMYND11 was predicted the target gene of microRNA-196b and its binding relationship was verified by dual luciferase reporter gene experiment. Then cell counting kit (CCK-8) and 5-Ethynyl-2'- deoxyuridine (EdU) assay were performed to analyze the influence of microRNA-196b overexpression on OCa cell proliferation. RESULTS QRT-PCR results showed that microRNA-196b level in OCa tissues was remarkably higher than that in normal ovarian tissues, which was closely relevant to the poor prognosis of tumors. The dual luciferase reporter gene experiments confirmed that microRNA-196b could directly bind to the 3'-UTR of ZMYND11. Overexpression of microRNA-196b remarkably enhanced the proliferation, invasiveness and migratory ability of OCa cells. Meanwhile, overexpression of microRNA-196b significantly decreased ZMYND11 mRNA and protein expression. In addition, ZMYND11 level was also significantly increased in ovarian cancer cells. Compared with the miRNA-NC group, microRNA-196b-mimics + ZMYND11-OE treatment reversed the effect of microRNA-196b-mimics on OCa cell functions. CONCLUSIONS MicroRNA-196b was highly expressed in OCa tissues, which can promote the proliferation, invasiveness and migratory ability of OCa cells by targeting ZMYND11. In addition, the expression disorder of microRNA-196b was associated with the malignant development of OCa.
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Affiliation(s)
- Zhiling Zhang
- Department of Obstetrics and Gynecology, Central Hospital of Minhang District, Shanghai, China
| | - Ling Xu
- Department of Obstetrics and Gynecology, Central Hospital of Minhang District, Shanghai, China
| | - Zheng Hu
- Department of Obstetrics and Gynecology, Central Hospital of Minhang District, Shanghai, China
| | - Baohua Yang
- Department of Obstetrics and Gynecology, Central Hospital of Minhang District, Shanghai, China
| | - Jun Xu
- Department of Obstetrics and Gynecology, Central Hospital of Minhang District, Shanghai, China -
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14
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Zhang Y, Zhou L, Zhang Z, Ren F, Chen L, Lan Z. miR‑10a‑5p inhibits osteogenic differentiation of bone marrow‑derived mesenchymal stem cells. Mol Med Rep 2020; 22:135-144. [PMID: 32377690 PMCID: PMC7248527 DOI: 10.3892/mmr.2020.11110] [Citation(s) in RCA: 9] [Impact Index Per Article: 2.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/27/2019] [Accepted: 03/02/2020] [Indexed: 12/17/2022] Open
Abstract
The use of human bone marrow mesenchymal stem cells (hBMSCs) as a tissue engineering application for individuals affected by osteoporosis and other types of bone loss diseases has been well studied in recent years. The osteogenic differentiation of hBMSCs can be regulated by a number of cues. MicroRNAs (miRNAs/miRs) serve as the key regulators of various biological processes; however, to the best of our knowledge, no information exists with regards to the specific modulatory effects of miR-10a-5p on osteogenic differentiation of hBMSCs. The aim of the present study was to investigate the relationship between hBMSCs and miR-10a-5p and, ultimately, to determine how miR-10a-5p affects the osteogenic differentiation process of hBMSCs in vitro and in vivo. The hBMSCs used in the present study were transfected with mirVana™ miRNA inhibitors and mimics, and transfection efficiency was assessed by fluorescence microscopy and reverse transcription-quantitative PCR (RT-qPCR). Viability of hBMSCs following transfection was analyzed using a Cell Counting Kit-8 assay. The mRNA expression levels of specific osteoblast markers, including alkaline phosphatase (ALP) and runt-related transcription factor 2 (RUNX2) were measured using RT-qPCR and western blot analysis. New bone formation was evaluated by Goldner's trichrome staining and micro-CT analysis in vivo. No significant difference in cell viability was observed among the different groups 24 h post-transfection. Overexpression of miR-10a-5p inhibited the expression of osteoblast makers in hBMSCs, whereas inhibition of miR-10a-5p upregulated the expression of ALP and RUNX2 in vitro. Furthermore, miR-10a-5p acted as a suppressor during the process of new bone formation in vivo. In conclusion, the findings of the present study suggested that miR-10a-5p served as a negative regulatory factor during osteoblast differentiation of hBMSCs and may be utilized in a treatment approach for bone repair in osteogenic-related diseases.
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Affiliation(s)
- Yingjie Zhang
- Department of Orthodontics, Stomatological Hospital, Southern Medical University, Guangzhou, Guangdong 510280, P.R. China
| | - Lishu Zhou
- Department of Orthodontics, Stomatological Hospital, Southern Medical University, Guangzhou, Guangdong 510280, P.R. China
| | - Zhaoqiang Zhang
- Department of Oral and Maxillofacial Surgery, Stomatological Hospital, Southern Medical University, Guangzhou, Guangdong 510280, P.R. China
| | - Fei Ren
- Department of Oral Medicine, Stomatological Hospital, Southern Medical University, Guangzhou, Guangdong 510280, P.R. China
| | - Liangjiao Chen
- Department of Orthodontics, Stomatological Hospital, Guangzhou Medical University, Guangzhou, Guangdong 510140, P.R. China
| | - Zedong Lan
- Department of Orthodontics, Shenzhen Stomatological Hospital, Southern Medical University, Shenzhen, Guangdong 518001, P.R. China
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15
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Jin L, Ma XM, Wang TT, Yang Y, Zhang N, Zeng N, Bai ZG, Yin J, Zhang J, Ding GQ, Zhang ZT. Psoralen Suppresses Cisplatin-Mediated Resistance and Induces Apoptosis of Gastric Adenocarcinoma by Disruption of the miR196a-HOXB7-HER2 Axis. Cancer Manag Res 2020; 12:2803-2827. [PMID: 32368152 PMCID: PMC7185648 DOI: 10.2147/cmar.s248094] [Citation(s) in RCA: 7] [Impact Index Per Article: 1.8] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/02/2020] [Accepted: 04/02/2020] [Indexed: 12/19/2022] Open
Abstract
Purpose The present study aimed to investigate the impact of psoralen on miR-196a-5p expression and function, and to reveal the mechanism underlying miR-196a-5p-mediated inhibition and the reversal of cisplatin (DDP) resistance. Methods Serum samples were collected from 50 patients with gastric cancer (GC), and the association between miR-196a-5p expression and the response to chemotherapy was assessed. A DDP-resistant GC cell line was also established to determine the effects of miR-196a-5p and psoralen on DDP resistance. MGC803 cells were transfected with miR-196a-5p mimic and inhibitor vectors for the overexpression and downregulation of miR-196a-5p, respectively. Results Clinical data analysis showed that the lower expression levels of miR-196a-5p were significantly associated with chemoresistance in patients with GC. Upregulation of miR-196a-5p significantly enhanced the anti-proliferative effect, apoptosis and sensitivity to DDP by regulating the protein expression levels of HOXB7, HER2, Bcl-2 and G1/S-specific cyclin-D1 (CCND1). Furthermore, psoralen reversed miR-196a-5p-induced DDP resistance and reduced the expression levels of HOXB7, HER2, Bcl-2 and CCND1. Conclusion miR-196a-5p may be a novel biomarker of chemotherapeutic success in patients with GC and may also influence the sensitivity of GC cells to DDP. Moreover, psoralen can increase chemotherapeutic sensitivity by upregulating miR-196a-5p and then downregulating HOXB7-HER2 signaling axis.
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Affiliation(s)
- Lei Jin
- Department of General Surgery, Beijing Friendship Hospital, Capital Medical University, Beijing, People's Republic of China.,National Clinical Research Center for Digestive Diseases, Beijing, People's Republic of China
| | - Xue-Mei Ma
- Department of General Surgery, Beijing Friendship Hospital, Capital Medical University, Beijing, People's Republic of China.,National Clinical Research Center for Digestive Diseases, Beijing, People's Republic of China
| | - Ting-Ting Wang
- Department of General Surgery, Beijing Friendship Hospital, Capital Medical University, Beijing, People's Republic of China.,National Clinical Research Center for Digestive Diseases, Beijing, People's Republic of China
| | - Yao Yang
- Department of General Surgery, Beijing Friendship Hospital, Capital Medical University, Beijing, People's Republic of China.,National Clinical Research Center for Digestive Diseases, Beijing, People's Republic of China
| | - Nan Zhang
- National Clinical Research Center for Digestive Diseases, Beijing, People's Republic of China.,Department of Radiology, Beijing Friendship Hospital, Capital Medical University, Beijing, People's Republic of China
| | - Na Zeng
- National Clinical Research Center for Digestive Diseases, Beijing, People's Republic of China.,Clinical Epidemiology and EBM Center, Beijing Friendship Hospital, Capital Medical University, Beijing, People's Republic of China
| | - Zhi-Gang Bai
- Department of General Surgery, Beijing Friendship Hospital, Capital Medical University, Beijing, People's Republic of China.,National Clinical Research Center for Digestive Diseases, Beijing, People's Republic of China
| | - Jie Yin
- Department of General Surgery, Beijing Friendship Hospital, Capital Medical University, Beijing, People's Republic of China.,National Clinical Research Center for Digestive Diseases, Beijing, People's Republic of China
| | - Jun Zhang
- Department of General Surgery, Beijing Friendship Hospital, Capital Medical University, Beijing, People's Republic of China.,National Clinical Research Center for Digestive Diseases, Beijing, People's Republic of China
| | - Guo-Qian Ding
- Department of General Surgery, Beijing Friendship Hospital, Capital Medical University, Beijing, People's Republic of China.,National Clinical Research Center for Digestive Diseases, Beijing, People's Republic of China
| | - Zhong-Tao Zhang
- Department of General Surgery, Beijing Friendship Hospital, Capital Medical University, Beijing, People's Republic of China.,National Clinical Research Center for Digestive Diseases, Beijing, People's Republic of China
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16
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Shao J, Wang L, Liu Y, Qi Q, Wang B, Lu S, Liu C. Identification of milRNAs and their target genes in Ganoderma lucidum by high-throughput sequencing and degradome analysis. Fungal Genet Biol 2020; 136:103313. [DOI: 10.1016/j.fgb.2019.103313] [Citation(s) in RCA: 7] [Impact Index Per Article: 1.8] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/05/2018] [Revised: 08/09/2019] [Accepted: 11/15/2019] [Indexed: 12/15/2022]
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17
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Answer to Controversy: miR-10a Replacement Approaches Do Not Offer Protection against Chemotherapy-Induced Gonadotoxicity in Mouse Model. Int J Mol Sci 2019; 20:ijms20194958. [PMID: 31597292 PMCID: PMC6801898 DOI: 10.3390/ijms20194958] [Citation(s) in RCA: 4] [Impact Index Per Article: 0.8] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/10/2019] [Revised: 09/30/2019] [Accepted: 10/03/2019] [Indexed: 12/15/2022] Open
Abstract
It is well known that chemotherapeutic agents may lead to premature ovarian failure and infertility. Therefore, fertility preservation is highly recommended for female cancer survivors. Despite the currently available techniques, new, non-invasive methods need to be developed to protect the ovarian follicles during oncological treatments. MicroRNAs can be effective tools in this field, as they alter their expression during chemotherapy exposure, and hence they can be useful to minimize the off-target toxicity. Previously, we identified several miRNAs with an important role in newborn mouse ovaries exposed to chemotherapy; among them, the miR-10a was one of the most downregulated miRNAs. Given the controversial role of miR-10a in the ovarian function, we decided to investigate its implication in chemotherapy-induced gonadotoxicity. The downregulated levels of miR-10a were restored by a liposome system conjugated with a mimic miR-10a, and the overexpressed miR-10a prevented the upregulation of the targeted gene, phosphatase and tensin homolog (Pten). The apoptosis was evaluated by terminal deoxynucleotidyl transferase dUTP nick end labeling (TUNEL) Assay and Bax expression quantification, while histological studies were also performed to evaluate the follicle count and development. Our results showed that the miR-10a replacement could not protect the ovaries from chemotherapy-induced apoptosis, whereas the targeting of Pten may affect the follicle activation via the phosphoinositide 3-kinase (PI3K)/PTEN/protein kinase B (AKT) pathway. Consequently, the application of miR-10a in fertility preservation is not recommended, and the role of miR-10a needs to be further elucidated.
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18
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Zhang L, Luo B, Dang YW, He RQ, Peng ZG, Chen G, Feng ZB. Clinical Significance of microRNA-196b-5p in Hepatocellular Carcinoma and its Potential Molecular Mechanism. J Cancer 2019; 10:5355-5370. [PMID: 31632480 PMCID: PMC6775707 DOI: 10.7150/jca.29293] [Citation(s) in RCA: 11] [Impact Index Per Article: 2.2] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/16/2018] [Accepted: 08/06/2019] [Indexed: 12/18/2022] Open
Abstract
Objective: To enquire into the clinical significance and potential molecular mechanism of microRNA (miRNA)-196b-5p in hepatocellular carcinoma (HCC). Methods: Quantitative reverse transcription and polymerase chain reaction (qRT-PCR) were utilized to examine miR-196b-5p expression level in 67 HCC paraffin embedded tissues and corresponding adjacent tissues. Correlations of miR-196b-5p expression level with clinicopathological characteristics were analyzed in our study. The expression level and clinical significance of miR-196b-5p in HCC were also evaluated in The Cancer Genome Atlas (TCGA) and Gene Expression Omnibus (GEO) database. We made predictions of the target genes of miR-196b-5p by twelve online software and then selected genes predicted by at least 5 software. Subsequently, in order to obtain the potential target genes of miR-196b-5p, we overlapped the predicted target genes and down-regulated mRNAs in HCC based on TCGA database. Then, we performed the Gene Ontology (GO) and the Disease Ontology (DO) functional annotation, Kyoto Encyclopedia of Genes and Genomes (KEGG) pathway enrichment analysis and Protein-Protein Interaction (PPI) network construction of those miR-196b-5p potential target genes. Results: Higher expression level of miR-196b-5p was seen in HCC tissues than in the corresponding adjacent tissues based on qRT-PCR (P = 0.0007). The expression level of miR-196b-5p was linked with tumor size (P = 0.03), tumor node (P = 0.024), vascular invasion (P = 0.029) and capsular invasion (P = 0.026) in HCC patients. Comprehensive meta-analysis of miR-196b-5p expression based on TCGA, GEO and qRT-PCR verified that higher expression level of miR-196b-5p was observed in HCC tissues than in normal control liver tissues (SMD = 0.56, 95%CI: 0.39-0.72, Pheterogeneity = 0.275, I2 = 18.3%). GO annotation revealed that the top terms in biological process, cellular component and molecular function were single-organism catabolic process, neuronal cell body and transmembrane receptor protein kinase activity, respectively. The most relevant disease in DO annotation was arteriosclerosis. The tryptophan metabolism pathway ranked first in KEGG pathway enrichment analysis. The PPI network showed that IGF1, FOXO1, AR and FOS were mostly likely to become the core genes of miR-196b-5p potential target genes, which however required further experiments for validation. Conclusion: The miR-196b-5p was observed to show higher expression in HCC tissues than in normal control liver tissues. Moreover, the miR-196b-5p expression level had correlations with the clinicopathological parameters such as vascular invasion of HCC, but the molecular mechanisms of miR-196b-5p in HCC still need further elucidation and verification.
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Affiliation(s)
- Lu Zhang
- Department of Pathology, First Affiliated Hospital of Guangxi Medical University, No. 6 Shuangyong Road, Nanning, Guangxi Zhuang Autonomous Region 530021, P. R. China
| | - Bin Luo
- Department of Medical Oncology, First Affiliated Hospital of Guangxi Medical University, No. 6 Shuangyong Road, Nanning, Guangxi Zhuang Autonomous Region 530021, P. R. China
| | - Yi-Wu Dang
- Department of Pathology, First Affiliated Hospital of Guangxi Medical University, No. 6 Shuangyong Road, Nanning, Guangxi Zhuang Autonomous Region 530021, P. R. China
| | - Rong-Quan He
- Department of Medical Oncology, First Affiliated Hospital of Guangxi Medical University, No. 6 Shuangyong Road, Nanning, Guangxi Zhuang Autonomous Region 530021, P. R. China
| | - Zhi-Gang Peng
- Department of Medical Oncology, First Affiliated Hospital of Guangxi Medical University, No. 6 Shuangyong Road, Nanning, Guangxi Zhuang Autonomous Region 530021, P. R. China
| | - Gang Chen
- Department of Pathology, First Affiliated Hospital of Guangxi Medical University, No. 6 Shuangyong Road, Nanning, Guangxi Zhuang Autonomous Region 530021, P. R. China
| | - Zhen-Bo Feng
- Department of Pathology, First Affiliated Hospital of Guangxi Medical University, No. 6 Shuangyong Road, Nanning, Guangxi Zhuang Autonomous Region 530021, P. R. China
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19
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Simões A, Chen L, Chen Z, Zhao Y, Gao S, Marucha PT, Dai Y, DiPietro LA, Zhou X. Differential microRNA profile underlies the divergent healing responses in skin and oral mucosal wounds. Sci Rep 2019; 9:7160. [PMID: 31073224 PMCID: PMC6509259 DOI: 10.1038/s41598-019-43682-w] [Citation(s) in RCA: 23] [Impact Index Per Article: 4.6] [Reference Citation Analysis] [Abstract] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/04/2018] [Accepted: 04/27/2019] [Indexed: 12/31/2022] Open
Abstract
Oral mucosal wounds heal faster than skin wounds, yet the role of microRNAs in this differential healing has never been examined. To delineate the role of microRNAs in this site-specific injury response, we first compared the microRNAome of uninjured skin and oral mucosa in mice. A total of 53 tissue-specific microRNAs for skin and oral mucosa epithelium were identified. The most striking difference was the high abundance of miR-10a/b in skin (accounting for 21.10% of the skin microRNAome) as compared to their low expression in oral mucosa (2.87%). We further examined the dynamic changes of microRNAome throughout the time course of skin and oral mucosal wound healing. More differentially expressed microRNAs were identified in skin wounds than oral wounds (200 and 33, respectively). More specifically, miR-10a/b was significantly down-regulated in skin but not oral wounds. In contrast, up-regulation of miR-21 was observed in both skin and oral wounds. The therapeutic potential of miR-10b and miR-21 in accelerating wound closure was demonstrated in in vitro assays and in a murine skin wound model. Thus, we provided the first site-specific microRNA profile of skin and oral mucosal wound healing, and demonstrate the feasibility of a microRNA-based therapy for promoting wound closure.
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Affiliation(s)
- Alyne Simões
- Center for Wound Healing & Tissue Regeneration, Department of Periodontics, College of Dentistry, University of Illinois at Chicago, Chicago, IL, USA.,Oral Biology Laboratory, Department of Biomaterials and Oral Biology, School of Dentistry, University of São Paulo, São Paulo, SP, Brazil
| | - Lin Chen
- Center for Wound Healing & Tissue Regeneration, Department of Periodontics, College of Dentistry, University of Illinois at Chicago, Chicago, IL, USA
| | - Zujian Chen
- Center for Molecular Biology of Oral Diseases, Department of Periodontics, College of Dentistry, University of Illinois at Chicago, Chicago, IL, USA
| | - Yan Zhao
- Center for Wound Healing & Tissue Regeneration, Department of Periodontics, College of Dentistry, University of Illinois at Chicago, Chicago, IL, USA
| | - Shang Gao
- Department of Bioengineering, College of Engineering, University of Illinois at Chicago, Chicago, IL, USA
| | - Phillip T Marucha
- Center for Wound Healing & Tissue Regeneration, Department of Periodontics, College of Dentistry, University of Illinois at Chicago, Chicago, IL, USA.,College of Dentistry, Oregon Health and Sciences University, Portland, OR, USA
| | - Yang Dai
- Department of Bioengineering, College of Engineering, University of Illinois at Chicago, Chicago, IL, USA
| | - Luisa A DiPietro
- Center for Wound Healing & Tissue Regeneration, Department of Periodontics, College of Dentistry, University of Illinois at Chicago, Chicago, IL, USA. .,Graduate College, University of Illinois at Chicago, Chicago, IL, USA.
| | - Xiaofeng Zhou
- Center for Wound Healing & Tissue Regeneration, Department of Periodontics, College of Dentistry, University of Illinois at Chicago, Chicago, IL, USA. .,Center for Molecular Biology of Oral Diseases, Department of Periodontics, College of Dentistry, University of Illinois at Chicago, Chicago, IL, USA. .,Graduate College, University of Illinois at Chicago, Chicago, IL, USA. .,UIC Cancer Center, University of Illinois at Chicago, Chicago, IL, USA.
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20
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Sutliff AK, Watson CJW, Chen G, Lazarus P. Regulation of UGT2A1 by miR-196a-5p and miR-196b-5p. J Pharmacol Exp Ther 2019; 369:234-243. [PMID: 30850392 PMCID: PMC6439457 DOI: 10.1124/jpet.118.255935] [Citation(s) in RCA: 10] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/17/2018] [Accepted: 02/15/2019] [Indexed: 12/15/2022] Open
Abstract
UDP-glucuronosyltransferase (UGT) 2A1 is an important enzyme in the detoxification of polycyclic aromatic hydrocarbons found in cigarette smoke. This enzyme is expressed in aerodigestive tract tissues including lung as both its wild-type and exon 4-deleted splice variant isoforms, with the latter acting as a negative regulator of wild-type UGT2A1 activity. UGT2A1 regulation may also be mediated by microRNA (miRNA). To identify miRNA important in the regulation of UGT2A1, expression analysis in tandem with in silico analysis suggested miR-196a-5p and miR-196b-5p as potential top candidates. Significant reductions in firefly luciferase activity were observed in human embryonic kidney cell line 293 cells cotransfected with the wild-type UGT2A1 3'-untranslated region (UTR)-containing luciferase plasmid and either miR-196a-5p (62%, P = 0.00080) or miR-196b-5p (60%, P = 0.00030) mimics. In pull-down assays, there was a 3.4- and 5.2-fold increase in miR-196a-5p (P = 0.054) and miR-196b-5p (P = 0.035), respectively, using the UGT2A1 3'-UTR biotinylated mRNA probe as compared with the β-actin coding region control mRNA probe. UGT2A1 mRNA was reduced by 25% (P = 0.058) and 35% (P = 0.023) in H146 and H1944 cells, respectively, after overexpression of the miR196a-5p mimic. A similar 32% (P = 0.030) and 41% (P = 0.016) reduction was observed after over-expression of the miR-196b-5p mimic. In H146 cells transfected with miRNA mimic together with a small interfering RNA (siRNA) specific for the UGT2A1 splice variant, a significant reduction in 3-hydroxy-benzo[a]pyrene-glucuronide formation was observed. The miR-196a-5p- and miR-196b-55p-treated cells exhibited reductions of 35% (P = 0.047) and 44% (P = 0.0063), respectively. These data suggest that miR-196a-5p and miR-196b-5p play an important role in UGT2A1 regulation within the lung and potentially other aerodigestive tract tissues.
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Affiliation(s)
- Aimee K Sutliff
- Department of Pharmaceutical Sciences, College of Pharmacy and Pharmaceutical Sciences, Washington State University, Spokane, Washington
| | - Christy J W Watson
- Department of Pharmaceutical Sciences, College of Pharmacy and Pharmaceutical Sciences, Washington State University, Spokane, Washington
| | - Gang Chen
- Department of Pharmaceutical Sciences, College of Pharmacy and Pharmaceutical Sciences, Washington State University, Spokane, Washington
| | - Philip Lazarus
- Department of Pharmaceutical Sciences, College of Pharmacy and Pharmaceutical Sciences, Washington State University, Spokane, Washington
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21
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22
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Zhang S, Guo J, Liang M, Qi J, Wang Z, Jian X, Zhang Z, Sun B, Li Z. miR-196a Promotes Proliferation and Inhibits Apoptosis of Immature Porcine Sertoli Cells. DNA Cell Biol 2019; 38:41-48. [DOI: 10.1089/dna.2018.4387] [Citation(s) in RCA: 17] [Impact Index Per Article: 3.4] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/09/2023] Open
Affiliation(s)
- Shaoxuan Zhang
- College of Animal Science, Jilin University, Changchun, Jilin, P.R. China
- Branch of Animal Husbandry, Jilin Academy of Agricultural Science, Gongzhuling, Jilin, China
| | - Jia Guo
- College of Animal Science, Jilin University, Changchun, Jilin, P.R. China
| | - Mengdi Liang
- College of Animal Science, Jilin University, Changchun, Jilin, P.R. China
| | - Jiajia Qi
- College of Animal Science, Jilin University, Changchun, Jilin, P.R. China
| | - Zhenbo Wang
- College of Animal Science, Jilin University, Changchun, Jilin, P.R. China
| | - Xinrui Jian
- Branch of Animal Husbandry, Jilin Academy of Agricultural Science, Gongzhuling, Jilin, China
| | - Zhibin Zhang
- Branch of Animal Husbandry, Jilin Academy of Agricultural Science, Gongzhuling, Jilin, China
| | - Boxing Sun
- College of Animal Science, Jilin University, Changchun, Jilin, P.R. China
| | - Zhaohua Li
- College of Animal Science, Jilin University, Changchun, Jilin, P.R. China
- Branch of Animal Husbandry, Jilin Academy of Agricultural Science, Gongzhuling, Jilin, China
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23
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Romney ALT, Podrabsky JE. Small noncoding RNA profiles along alternative developmental trajectories in an annual killifish. Sci Rep 2018; 8:13364. [PMID: 30190591 PMCID: PMC6127099 DOI: 10.1038/s41598-018-31466-7] [Citation(s) in RCA: 6] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/22/2018] [Accepted: 08/13/2018] [Indexed: 11/24/2022] Open
Abstract
Embryonic development of Austrofundulus limnaeus can occur along two phenotypic trajectories that are physiologically and biochemically distinct. Phenotype appears to be influenced by maternal provisioning based on the observation that young females produce predominately non-diapausing embryos and older females produce mostly diapausing embryos. Embryonic incubation temperature can override this pattern and alter trajectory. We hypothesized that temperature-induced phenotypic plasticity may be regulated by post-transcriptional modification via noncoding RNAs. As a first step to exploring this possibility, RNA-seq was used to generate transcriptomic profiles of small noncoding RNAs in embryos developing along the two alternative trajectories. We find distinct profiles of mature sequences belonging to the miR-10 family expressed in increasing abundance during development and mature sequences of miR-430 that follow the opposite pattern. Furthermore, miR-430 sequences are enriched in escape trajectory embryos. MiR-430 family members are known to target maternally provisioned mRNAs in zebrafish and may operate similarly in A. limnaeus in the context of normal development, and also by targeting trajectory-specific mRNAs. This expression pattern and function for miR-430 presents a potentially novel model for maternal-embryonic conflict in gene regulation that provides the embryo the ability to override maternal programming in the face of altered environmental conditions.
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Affiliation(s)
- Amie L T Romney
- Department of Biology, Portland State University, P.O. Box 751, Portland, OR, 97207, USA.
- Department of Anatomy, Physiology & Cell Biology, University of California at Davis School of Veterinary Medicine, One Shields Ave, Davis, CA, 95616, USA.
| | - Jason E Podrabsky
- Department of Biology, Portland State University, P.O. Box 751, Portland, OR, 97207, USA.
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24
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Botti G, De Chiara A, Di Bonito M, Cerrone M, Malzone MG, Collina F, Cantile M. Noncoding RNAs within the
HOX
gene network in tumor pathogenesis and progression. J Cell Physiol 2018; 234:395-413. [DOI: 10.1002/jcp.27036] [Citation(s) in RCA: 16] [Impact Index Per Article: 2.7] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/21/2018] [Accepted: 06/25/2018] [Indexed: 12/19/2022]
Affiliation(s)
- Gerardo Botti
- Department of Support for Oncological Pathways Diagnostic Area, Pathology Unit, Istituto Nazionale Tumori Fondazione “G. Pascale” Napoli Italy
| | - Anna De Chiara
- Department of Support for Oncological Pathways Diagnostic Area, Pathology Unit, Istituto Nazionale Tumori Fondazione “G. Pascale” Napoli Italy
| | - Maurizio Di Bonito
- Department of Support for Oncological Pathways Diagnostic Area, Pathology Unit, Istituto Nazionale Tumori Fondazione “G. Pascale” Napoli Italy
| | - Margherita Cerrone
- Department of Support for Oncological Pathways Diagnostic Area, Pathology Unit, Istituto Nazionale Tumori Fondazione “G. Pascale” Napoli Italy
| | - Maria Gabriella Malzone
- Department of Support for Oncological Pathways Diagnostic Area, Pathology Unit, Istituto Nazionale Tumori Fondazione “G. Pascale” Napoli Italy
| | - Francesca Collina
- Department of Support for Oncological Pathways Diagnostic Area, Pathology Unit, Istituto Nazionale Tumori Fondazione “G. Pascale” Napoli Italy
| | - Monica Cantile
- Department of Support for Oncological Pathways Diagnostic Area, Pathology Unit, Istituto Nazionale Tumori Fondazione “G. Pascale” Napoli Italy
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Davoodi Mastakani F, Pagheh G, Rashidi Monfared S, Shams-Bakhsh M. Identification and expression analysis of a microRNA cluster derived from pre-ribosomal RNA in Papaver somniferum L. and Papaver bracteatum L. PLoS One 2018; 13:e0199673. [PMID: 30067748 PMCID: PMC6070170 DOI: 10.1371/journal.pone.0199673] [Citation(s) in RCA: 7] [Impact Index Per Article: 1.2] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/09/2017] [Accepted: 06/12/2018] [Indexed: 11/19/2022] Open
Abstract
Opium poppy (Papaver somniferum L.) is one of the ancient medical crops, which produces several important alkaloids such as morphine, noscapine, sanguinarine and codeine. MicroRNAs are endogenous non-coding RNAs that play important regulatory roles in plant diverse biological processes. Many plant miRNAs are encoded as single transcriptional units, in contrast to animal miRNAs, which are often clustered. Herein, using computational approaches, a total of 22 miRNA precursors were identified, which five of them were located as a clustered in pre-ribosomal RNA. Afterward, the transcript level of the precursor and the mature of clustered miRNAs in two species of the Papaveraceae family, i.e. P. somniferum L. and P. bracteatum L, were quantified by RT-PCR. With respect to obtained results, these clustered miRNAs were expressed differentially in different tissues of these species. Moreover, using target prediction and Gene Ontology (GO)-based on functional classification indicated that these miRNAs might play crucial roles in various biological processes as well as metabolic pathways. In this study, we discovered the clustered miRNA derived from pre-rRNA, which may shed some light on the importance of miRNAs in the plant kingdom.
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Affiliation(s)
- Farshad Davoodi Mastakani
- Department of Agricultural Biotechnology, Faculty of Agriculture, Tarbiat Modares University, Tehran, Iran
| | - Gabriel Pagheh
- Department of Agricultural Biotechnology, Faculty of Agriculture, Tarbiat Modares University, Tehran, Iran
| | - Sajad Rashidi Monfared
- Department of Agricultural Biotechnology, Faculty of Agriculture, Tarbiat Modares University, Tehran, Iran
| | - Masoud Shams-Bakhsh
- Department of Plant Pathology, Faculty of Agriculture, Tarbiat Modares University, Tehran, Iran
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Dysregulation of Mir-196b in Head and Neck Cancers Leads to Pleiotropic Effects in the Tumor Cells and Surrounding Stromal Fibroblasts. Sci Rep 2017; 7:17785. [PMID: 29259267 PMCID: PMC5736577 DOI: 10.1038/s41598-017-18138-8] [Citation(s) in RCA: 22] [Impact Index Per Article: 3.1] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/30/2017] [Accepted: 11/24/2017] [Indexed: 02/07/2023] Open
Abstract
The miR-196 family members have been found dysregulated in different cancers. Therefore, they have been proposed as promising biomarkers and therapeutic targets. This study is the first to investigate the role of miR-196b in the development and progression of head and neck squamous cell carcinomas (HNSCC), and also the impact on the surrounding tumor microenvironment. Increased miR-196b levels were detected in 95% of primary tumors and precancerous lesions, although no significant differences were observed between non-progressing versus progressing dysplasias. Furthermore, increased levels of both miR-196a and miR-196b were successfully detected in saliva samples from HNSCC patients. The functional consequences of altered miR-196 expression were investigated in both HNSCC cell lines and cancer-associated fibroblasts (CAFs) by transfection with specific pre-miR precursors. Results showed that both miR-196a and miR-196b elicit cell-specific responses in target genes and downstream regulatory pathways, and have a distinctive impact on cell proliferation, migration and invasion. These data reveal the early occurrence and prevalence of miR-196b dysregulation in HNSCC tumorigenesis, suggesting its utility for early diagnosis and/or disease surveillance and also as a non-invasive biomarker in saliva. The pleiotropic effects of miR-196a/b in HNSCC cell subpopulations and surrounding CAFs may complicate a possible therapeutic application.
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Sekigami Y, Kobayashi T, Omi A, Nishitsuji K, Ikuta T, Fujiyama A, Satoh N, Saiga H. Hox gene cluster of the ascidian, Halocynthia roretzi, reveals multiple ancient steps of cluster disintegration during ascidian evolution. ZOOLOGICAL LETTERS 2017; 3:17. [PMID: 28932414 PMCID: PMC5602962 DOI: 10.1186/s40851-017-0078-3] [Citation(s) in RCA: 13] [Impact Index Per Article: 1.9] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Figures] [Subscribe] [Scholar Register] [Received: 06/12/2017] [Accepted: 09/12/2017] [Indexed: 06/07/2023]
Abstract
BACKGROUND Hox gene clusters with at least 13 paralog group (PG) members are common in vertebrate genomes and in that of amphioxus. Ascidians, which belong to the subphylum Tunicata (Urochordata), are phylogenetically positioned between vertebrates and amphioxus, and traditionally divided into two groups: the Pleurogona and the Enterogona. An enterogonan ascidian, Ciona intestinalis (Ci), possesses nine Hox genes localized on two chromosomes; thus, the Hox gene cluster is disintegrated. We investigated the Hox gene cluster of a pleurogonan ascidian, Halocynthia roretzi (Hr) to investigate whether Hox gene cluster disintegration is common among ascidians, and if so, how such disintegration occurred during ascidian or tunicate evolution. RESULTS Our phylogenetic analysis reveals that the Hr Hox gene complement comprises nine members, including one with a relatively divergent Hox homeodomain sequence. Eight of nine Hr Hox genes were orthologous to Ci-Hox1, 2, 3, 4, 5, 10, 12 and 13. Following the phylogenetic classification into 13 PGs, we designated Hr Hox genes as Hox1, 2, 3, 4, 5, 10, 11/12/13.a, 11/12/13.b and HoxX. To address the chromosomal arrangement of the nine Hox genes, we performed two-color chromosomal fluorescent in situ hybridization, which revealed that the nine Hox genes are localized on a single chromosome in Hr, distinct from their arrangement in Ci. We further examined the order of the nine Hox genes on the chromosome by chromosome/scaffold walking. This analysis suggested a gene order of Hox1, 11/12/13.b, 11/12/13.a, 10, 5, X, followed by either Hox4, 3, 2 or Hox2, 3, 4 on the chromosome. Based on the present results and those previously reported in Ci, we discuss the establishment of the Hox gene complement and disintegration of Hox gene clusters during the course of ascidian or tunicate evolution. CONCLUSIONS The Hox gene cluster and the genome must have experienced extensive reorganization during the course of evolution from the ancestral tunicate to Hr and Ci. Nevertheless, some features are shared in Hox gene components and gene arrangement on the chromosomes, suggesting that Hox gene cluster disintegration in ascidians involved early events common to tunicates as well as later ascidian lineage-specific events.
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Affiliation(s)
- Yuka Sekigami
- Department of Biological Sciences and Technology, Tokyo Metropolitan University, 1-1 Minamiohsawa, Hachiohji, Tokyo, 192-0397 Japan
| | - Takuya Kobayashi
- Department of Biological Sciences and Technology, Tokyo Metropolitan University, 1-1 Minamiohsawa, Hachiohji, Tokyo, 192-0397 Japan
| | - Ai Omi
- Department of Biological Sciences and Technology, Tokyo Metropolitan University, 1-1 Minamiohsawa, Hachiohji, Tokyo, 192-0397 Japan
| | - Koki Nishitsuji
- Marine Genomics Unit, Okinawa Institute of Science and Technology Graduate University, Onna, Okinawa, 904-0495 Japan
| | - Tetsuro Ikuta
- Department of Biological Sciences and Technology, Tokyo Metropolitan University, 1-1 Minamiohsawa, Hachiohji, Tokyo, 192-0397 Japan
| | - Asao Fujiyama
- National Institute of Genetics, 1111 Yata, Mishima, Shizuoka, 411-8540 Japan
| | - Noriyuki Satoh
- Marine Genomics Unit, Okinawa Institute of Science and Technology Graduate University, Onna, Okinawa, 904-0495 Japan
| | - Hidetoshi Saiga
- Department of Biological Sciences and Technology, Tokyo Metropolitan University, 1-1 Minamiohsawa, Hachiohji, Tokyo, 192-0397 Japan
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Divoux A, Xie H, Li JL, Karastergiou K, Perera RJ, Chang RJ, Fried SK, Smith SR. MicroRNA-196 Regulates HOX Gene Expression in Human Gluteal Adipose Tissue. Obesity (Silver Spring) 2017; 25. [PMID: 28649807 PMCID: PMC5551414 DOI: 10.1002/oby.21896] [Citation(s) in RCA: 18] [Impact Index Per Article: 2.6] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Indexed: 01/19/2023]
Abstract
OBJECTIVE Lower body fat is associated with diminishing cardiometabolic risk. Physiological differences between gluteofemoral and abdominal subcutaneous adipocyte functions are known, but the molecular basis for depot differences in adipocyte function is poorly understood. The objective of this study was to identify depot differences in microRNA (miRNA) expression in human abdominal and gluteofemoral subcutaneous adipose tissues and their implication in gene regulation. METHODS Abdominal and gluteofemoral adipose tissue aspirates obtained from 18 participants (9 male and 9 female, age 30 ± 1.5 y, BMI 27.3 ± 1.23 kg/m2 ) were analyzed for miRNA expression profiles by next-generation DNA sequencing. The raw reads were mapped to miRBase 17, and differentially expressed miRNAs were confirmed by qRT-PCR. The hsa-mimic-miR196a was transfected into cultured abdominal preadipocytes isolated from five women with obesity. Target gene expression was evaluated by RT-qPCR. RESULTS Among the 640 miRNAs detected in adipose tissue, miR196a2, miR196a1, miR196b, and miR204 showed a higher expression in the gluteofemoral depot (fold change = 2.7, 2.3, 1.7, and 2.3, respectively) independent of sex. Bioinformatic analyses and human primary preadipocyte transfection with miR196 suggested that the differentially expressed miRNAs could directly or indirectly modulate homeobox (HOX) gene expression. CONCLUSIONS The miR196 gene family could play an important role in the regulation of HOX gene expression in subcutaneous adipose tissue and in fat distribution variation.
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Affiliation(s)
- Adeline Divoux
- Translational Research Institute for Metabolism and Diabetes, Florida Hospital, Sanford Burnham Prebys Medical Discovery Institute, Orlando, Florida, USA
- Center for Metabolic Origins of Disease, Sanford Burnham Prebys Medical Discovery Institute, Orlando, Florida, USA
| | - Hui Xie
- Translational Research Institute for Metabolism and Diabetes, Florida Hospital, Sanford Burnham Prebys Medical Discovery Institute, Orlando, Florida, USA
- Center for Metabolic Origins of Disease, Sanford Burnham Prebys Medical Discovery Institute, Orlando, Florida, USA
| | - Jian-Liang Li
- Center for Metabolic Origins of Disease, Sanford Burnham Prebys Medical Discovery Institute, Orlando, Florida, USA
| | - Kalypso Karastergiou
- Obesity Center, Department of Medicine, Boston University School of Medicine, Boston, Massachusetts, USA
| | - Ranjan J Perera
- Center for Metabolic Origins of Disease, Sanford Burnham Prebys Medical Discovery Institute, Orlando, Florida, USA
| | - R Jeffrey Chang
- Division of Reproductive Endocrinology, Department of Reproductive Medicine, University of California, San Diego, La Jolla, California, USA
| | - Susan K Fried
- Obesity Center, Department of Medicine, Boston University School of Medicine, Boston, Massachusetts, USA
| | - Steven R Smith
- Translational Research Institute for Metabolism and Diabetes, Florida Hospital, Sanford Burnham Prebys Medical Discovery Institute, Orlando, Florida, USA
- Center for Metabolic Origins of Disease, Sanford Burnham Prebys Medical Discovery Institute, Orlando, Florida, USA
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Jo A, Im J, Lee HE, Jang D, Nam GH, Mishra A, Kim WJ, Kim W, Cha HJ, Kim HS. Evolutionary conservation and expression of miR-10a-3p in olive flounder and rock bream. Gene 2017; 628:16-23. [PMID: 28698161 DOI: 10.1016/j.gene.2017.07.020] [Citation(s) in RCA: 11] [Impact Index Per Article: 1.6] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/29/2017] [Revised: 07/01/2017] [Accepted: 07/07/2017] [Indexed: 12/19/2022]
Abstract
MicroRNAs (miRNAs) are small non-coding RNAs (ncRNAs) that mainly bind to the seed sequences located within the 3' untranslated region (3' UTR) of target genes. They perform an important biological function as regulators of gene expression. Different genes can be regulated by the same miRNA, whilst different miRNAs can be regulated by the same genes. Here, the evolutionary conservation and expression pattern of miR-10a-3p in olive flounder and rock bream was examined. Binding sites (AAAUUC) to seed region of the 3' UTR of target genes were highly conserved in various species. The expression pattern of miR-10a-3p was ubiquitous in the examined tissues, whilst its expression level was decreased in gill tissues infected by viral hemorrhagic septicemia virus (VHSV) compared to the normal control. In the case of rock bream, the spleen, kidney, and liver tissues showed dominant expression levels of miR-10a-3p. Only the liver tissues in the rock bream samples infected by the iridovirus indicated a dominant miR-10a-3p expression. The gene ontology (GO) analysis of predicted target genes for miR-10a-3p revealed that multiple genes are related to binding activity, catalytic activity, cell components as well as cellular and metabolic process. Overall the results imply that the miR-10a-3p could be used as a biomarker to detect VHSV infection in olive flounder and iridovirus infection in rock bream. In addition, the data provides fundamental information for further study of the complex interaction between miR-10a-3p and gene expression.
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Affiliation(s)
- Ara Jo
- Department of Biological Sciences, College of Natural Sciences, Pusan National University, Busan 46241, Republic of Korea; Genetic Engineering Institute, Pusan National University, Busan 46241, Republic of Korea
| | - Jennifer Im
- Department of Biological Sciences, College of Natural Sciences, Pusan National University, Busan 46241, Republic of Korea
| | - Hee-Eun Lee
- Department of Biological Sciences, College of Natural Sciences, Pusan National University, Busan 46241, Republic of Korea; Genetic Engineering Institute, Pusan National University, Busan 46241, Republic of Korea
| | - Dongmin Jang
- Department of Biological Sciences, College of Natural Sciences, Pusan National University, Busan 46241, Republic of Korea
| | - Gyu-Hwi Nam
- Department of Biological Sciences, College of Natural Sciences, Pusan National University, Busan 46241, Republic of Korea; Genetic Engineering Institute, Pusan National University, Busan 46241, Republic of Korea
| | - Anshuman Mishra
- Department of Biological Sciences, College of Natural Sciences, Pusan National University, Busan 46241, Republic of Korea; Genetic Engineering Institute, Pusan National University, Busan 46241, Republic of Korea
| | - Woo-Jin Kim
- Genetics and Breeding Research Center, National Institute of Fisheries Science, Geoje 53334, Republic of Korea
| | - Won Kim
- School of Biological Sciences, Seoul National University, Seoul 08824, Republic of Korea
| | - Hee-Jae Cha
- Departments of Parasitology and Genetics, College of Medicine, Kosin University, Busan 49267, Republic of Korea
| | - Heui-Soo Kim
- Department of Biological Sciences, College of Natural Sciences, Pusan National University, Busan 46241, Republic of Korea; Genetic Engineering Institute, Pusan National University, Busan 46241, Republic of Korea.
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Xin J, Li J, Feng Y, Wang L, Zhang Y, Yang R. Downregulation of long noncoding RNA HOTAIRM1 promotes monocyte/dendritic cell differentiation through competitively binding to endogenous miR-3960. Onco Targets Ther 2017; 10:1307-1315. [PMID: 28280365 PMCID: PMC5338958 DOI: 10.2147/ott.s124201] [Citation(s) in RCA: 50] [Impact Index Per Article: 7.1] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/20/2023] Open
Abstract
Myeloid differentiation is controlled by a multilayered regulatory circuitry consisting of various elements, including histone modifications, transcription factors, and posttranscriptional regulators such as miRNAs, long noncoding RNAs, and circular RNAs. However, the molecular mechanism underlying this biological process remains unclear. In this study, through epigenetic profiling analysis using chromatin immunoprecipitation (ChIP) followed by sequencing (ChIP-seq), we identified an lncRNA, HOTAIRM1, with a critical role in myeloid development. Further ChIP-chip analysis showed obvious H3K4me3 and H3K27me3 histone modification peak changes in the promoter region of HOTAIRM1 during the process of monocyte to dendritic cell (DC) differentiation. In line with this observation, HOTAIRM1 RNA expression was downregulated when monocytes differentiated into DCs. Moreover, we found that HOTAIRM1 RNA was regulated by epigenetic factors such as RBBP4 and RBBP7. Mechanistically, we found that the silencing of HOTAIRM1 caused changes in the expression of several monocyte differentiation markers such as CD14 and B7H2. In addition, based on the “competing endogenous RNA” hypothesis, we discovered miR-3960 targeting both HOTAIRM1 and the DC differentiation repression gene, HOXA1, by most possibly constructing a potential competing endogenous RNA network. Increased miR-3960 expression could downregulate both of these two long RNAs and finally lead peripheral blood cells to differentiate into DCs. In summary, our study demonstrates that HOTAIRM1 competitively binds to miR-3960 and finally regulates the process of hematopoiesis, which reveals a novel regulatory mechanism of lncRNA function.
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Affiliation(s)
- Jiaxuan Xin
- State Key Laboratory of Medicinal Chemical Biology, Nankai University, Tianjin, People's Republic of China
| | - Jing Li
- State Key Laboratory of Medicinal Chemical Biology, Nankai University, Tianjin, People's Republic of China
| | - Yue Feng
- State Key Laboratory of Medicinal Chemical Biology, Nankai University, Tianjin, People's Republic of China
| | - Liyang Wang
- Faculty of Medicine, University of Southampton, Southampton, UK
| | - Yuan Zhang
- State Key Laboratory of Medicinal Chemical Biology, Nankai University, Tianjin, People's Republic of China
| | - Rongcun Yang
- State Key Laboratory of Medicinal Chemical Biology, Nankai University, Tianjin, People's Republic of China; Key Laboratory of Bioactive Materials, Ministry of Education; Department of Immunology, Nankai University School of Medicine, Nankai University, Tianjin, People's Republic of China
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Gomes F, Watanabe L, Nozawa S, Oliveira L, Cardoso J, Vianez J, Nunes M, Schneider H, Sampaio I. Identification and characterization of the expression profile of the microRNAs in the Amazon species Colossoma macropomum by next generation sequencing. Genomics 2017; 109:67-74. [PMID: 28192178 DOI: 10.1016/j.ygeno.2017.02.001] [Citation(s) in RCA: 13] [Impact Index Per Article: 1.9] [Reference Citation Analysis] [Abstract] [Key Words] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/03/2016] [Revised: 02/06/2017] [Accepted: 02/08/2017] [Indexed: 01/20/2023]
Abstract
Colossoma macropomum is a resistant species native of Amazonas and Orinoco river basins. It is regarded as the second largest finfish of Solimões and Amazon rivers, representing a major fishery resource in Amazonas and an important species in tropical aquaculture. MicroRNAs are non-coding endogenous riboregulators of nearly 22 nucleotides that play a key role in post-transcriptional gene regulation of several organisms. We analyzed samples of liver and skin from specimens of C. macropomum using next generation sequencing. The dataset was evaluated using computational programs to check the quality of sequences, identification of miRNAs, as well as to evaluate the expression levels of these microRNAs and interaction of target genes. We identified 279 conserved miRNAs, being 257 from liver and 272 from skin, with several miRNAs shared between tissues, with divergence in the number of reads. The strands miR-5p and miR-3p were observed in 72 miRNAs, some of them presenting a higher number of 3p reads. The functional annotation of the most expressed miRNAs resulted in 27 pathways for the liver and skin mainly related to the "biological processes" domain. Based on the identified pathways, we visualized a large gene network, suggesting the regulation of selected miRNA over this interactive dataset. We were able to identify and characterize the expression levels of miRNAs in two tissues of great activity in C. macropomum, which stands out as the beginning of several studies that can be carried out to elucidate the influence of miRNAs in this species and their applicability as biotechnological tools.
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Affiliation(s)
- Fátima Gomes
- Institute of Coastal Studies, Laboratory of Genetics and Molecular Biology, Federal University of Pará, Campus of Bragança, 68600-000 Bragança, PA, Brazil.
| | - Luciana Watanabe
- Institute of Coastal Studies, Laboratory of Genetics and Molecular Biology, Federal University of Pará, Campus of Bragança, 68600-000 Bragança, PA, Brazil.
| | - Sérgio Nozawa
- Dow AgroSciences, Av Antonio Diederichsen, 400, - Ribeirão Preto, SP 14020-250, Brazil.
| | - Layanna Oliveira
- Center for Technological Innovation, Evandro Chagas Institute, Ministry of Health, 67030-000 Ananindeua, PA, Brazil.
| | - Jedson Cardoso
- Center for Technological Innovation, Evandro Chagas Institute, Ministry of Health, 67030-000 Ananindeua, PA, Brazil; Postgraduate Program in Virology (PPGV), Evandro Chagas Institute, Ministry of Health, Ananindeua, PA 67030-000, Brazil.
| | - João Vianez
- Center for Technological Innovation, Evandro Chagas Institute, Ministry of Health, 67030-000 Ananindeua, PA, Brazil.
| | - Márcio Nunes
- Center for Technological Innovation, Evandro Chagas Institute, Ministry of Health, 67030-000 Ananindeua, PA, Brazil.
| | - Horacio Schneider
- Institute of Coastal Studies, Laboratory of Genetics and Molecular Biology, Federal University of Pará, Campus of Bragança, 68600-000 Bragança, PA, Brazil.
| | - Iracilda Sampaio
- Institute of Coastal Studies, Laboratory of Genetics and Molecular Biology, Federal University of Pará, Campus of Bragança, 68600-000 Bragança, PA, Brazil.
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Kao D, Lai AG, Stamataki E, Rosic S, Konstantinides N, Jarvis E, Di Donfrancesco A, Pouchkina-Stancheva N, Sémon M, Grillo M, Bruce H, Kumar S, Siwanowicz I, Le A, Lemire A, Eisen MB, Extavour C, Browne WE, Wolff C, Averof M, Patel NH, Sarkies P, Pavlopoulos A, Aboobaker A. The genome of the crustacean Parhyale hawaiensis, a model for animal development, regeneration, immunity and lignocellulose digestion. eLife 2016; 5:20062. [PMID: 27849518 PMCID: PMC5111886 DOI: 10.7554/elife.20062] [Citation(s) in RCA: 115] [Impact Index Per Article: 14.4] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/26/2016] [Accepted: 10/19/2016] [Indexed: 12/17/2022] Open
Abstract
The amphipod crustacean Parhyale hawaiensis is a blossoming model system for studies of developmental mechanisms and more recently regeneration. We have sequenced the genome allowing annotation of all key signaling pathways, transcription factors, and non-coding RNAs that will enhance ongoing functional studies. Parhyale is a member of the Malacostraca clade, which includes crustacean food crop species. We analysed the immunity related genes of Parhyale as an important comparative system for these species, where immunity related aquaculture problems have increased as farming has intensified. We also find that Parhyale and other species within Multicrustacea contain the enzyme sets necessary to perform lignocellulose digestion ('wood eating'), suggesting this ability may predate the diversification of this lineage. Our data provide an essential resource for further development of Parhyale as an experimental model. The first malacostracan genome will underpin ongoing comparative work in food crop species and research investigating lignocellulose as an energy source. DOI:http://dx.doi.org/10.7554/eLife.20062.001 The marine crustacean known as Parhyale hawaiensis is related to prawns, shrimps and crabs and is found at tropical coastlines around the world. This species has recently attracted scientific interest as a possible new model to study how animal embryos develop before birth and, because Parhyale can rapidly regrow lost limbs, how tissues and organs regenerate. Indeed, Parhyale has many characteristics that make it a good model organism, being small, fast-growing and easy to keep and care for in the laboratory. Several research tools have already been developed to make it easier to study Parhyale. This includes the creation of a system for using the popular gene editing technology, CRISPR, in this animal. However, one critical resource that is available for most model organisms was missing; the complete sequence of all the genetic information of this crustacean, also known as its genome, was not available. Kao, Lai, Stamataki et al. have now compiled the Parhyale genome – which is slightly larger than the human genome – and studied its genetics. Analysis revealed that Parhyale has genes that allow it to fully digest plant material. This is unusual because most animals that do this rely upon the help of bacteria. Kao, Lai, Stamataki et al. also identified genes that provide some of the first insights into the immune system of crustaceans, which protects these creatures from diseases. Kao, Lai, Stamataki et al. have provided a resource and findings that could help to establish Parhyale as a popular model organism for studying several ideas in biology, including organ regeneration and embryonic development. Understanding how Parhyale digests plant matter, for example, could progress the biofuel industry towards efficient production of greener energy. Insights from its immune system could also be adapted to make farmed shrimp and prawns more resistant to infections, boosting seafood production. DOI:http://dx.doi.org/10.7554/eLife.20062.002
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Affiliation(s)
- Damian Kao
- Department of Zoology, University of Oxford, Oxford, United Kingdom
| | - Alvina G Lai
- Department of Zoology, University of Oxford, Oxford, United Kingdom
| | - Evangelia Stamataki
- Janelia Research Campus, Howard Hughes Medical Institute, Virginia, United States
| | - Silvana Rosic
- MRC Clinical Sciences Centre, Imperial College London, London, United Kingdom.,Clinical Sciences, Imperial College London, London, United Kingdom
| | - Nikolaos Konstantinides
- Institut de Gé nomique Fonctionnelle de Lyon, Centre National de la Recherche Scientifique (CNRS) and É cole Normale Supé rieure de Lyon, Lyon, France
| | - Erin Jarvis
- Department of Molecular and Cell Biology, University of California, Berkeley, United States
| | | | | | - Marie Sémon
- Institut de Gé nomique Fonctionnelle de Lyon, Centre National de la Recherche Scientifique (CNRS) and É cole Normale Supé rieure de Lyon, Lyon, France
| | - Marco Grillo
- Institut de Gé nomique Fonctionnelle de Lyon, Centre National de la Recherche Scientifique (CNRS) and É cole Normale Supé rieure de Lyon, Lyon, France
| | - Heather Bruce
- Department of Molecular and Cell Biology, University of California, Berkeley, United States
| | - Suyash Kumar
- Janelia Research Campus, Howard Hughes Medical Institute, Virginia, United States
| | - Igor Siwanowicz
- Janelia Research Campus, Howard Hughes Medical Institute, Virginia, United States
| | - Andy Le
- Janelia Research Campus, Howard Hughes Medical Institute, Virginia, United States
| | - Andrew Lemire
- Janelia Research Campus, Howard Hughes Medical Institute, Virginia, United States
| | - Michael B Eisen
- Molecular and Cell Biology, Howard Hughes Medical Institute, University of California, Berkeley, United States
| | - Cassandra Extavour
- Department of Organismic and Evolutionary Biology, Harvard University, Cambridge, United States
| | - William E Browne
- Department of Invertebrate Zoology, Smithsonian National Museum of Natural History, Washington, United States
| | - Carsten Wolff
- Vergleichende Zoologie, Institut fur Biologie,Humboldt-Universitat zu Berlin, Berlin, Germany
| | - Michalis Averof
- Institut de Gé nomique Fonctionnelle de Lyon, Centre National de la Recherche Scientifique (CNRS) and É cole Normale Supé rieure de Lyon, Lyon, France
| | - Nipam H Patel
- Department of Molecular and Cell Biology, University of California, Berkeley, United States
| | - Peter Sarkies
- MRC Clinical Sciences Centre, Imperial College London, London, United Kingdom.,Clinical Sciences, Imperial College London, London, United Kingdom
| | | | - Aziz Aboobaker
- Department of Zoology, University of Oxford, Oxford, United Kingdom
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35
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Functional RNAs control T follicular helper cells. J Hum Genet 2016; 62:81-86. [PMID: 27488442 DOI: 10.1038/jhg.2016.88] [Citation(s) in RCA: 4] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/29/2016] [Revised: 06/08/2016] [Accepted: 06/09/2016] [Indexed: 02/07/2023]
Abstract
T follicular helper cells (Tfh cells), which are a prototypic subset of effector CD4+ T cells, regulate the production of high-affinity antibodies by controlling B cells at initial and recall phases. Since the discovery of Tfh cells in human tonsils, many notable studies focusing on Tfh cells have clarified mechanisms underlying Tfh-cell-related physiological and pathological settings. Results of these studies revealed a chief regulatory function of BCL6 in Tfh cells and the involvement of Tfh cells in the pathogenesis of various disorders including autoimmune diseases, allergies and cancers. Further, accumulating evidence has revealed microRNAs (miRNAs) of functional noncoding RNAs (ncRNAs) to be cardinal regulators of Tfh cells during the processes of development, differentiation and plasticity. In this review article, we summarize and discuss the results of recent studies about miRNAs operating Tfh-cell function and their relationships in diseases. Through the window of such functional ncRNAs, the functional significance of Tfh cells in CD4+ T-cell biology is becoming apparent. Studies to determine the complex background of the genetic program of Tfh cells operated by functional RNAs should lead to an understanding of the manifestations of Tfh cells with unidentified pathophysiological relevance.
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36
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Nitsche A, Stadler PF. Evolutionary clues in lncRNAs. WILEY INTERDISCIPLINARY REVIEWS-RNA 2016; 8. [PMID: 27436689 DOI: 10.1002/wrna.1376] [Citation(s) in RCA: 43] [Impact Index Per Article: 5.4] [Reference Citation Analysis] [Abstract] [Track Full Text] [Subscribe] [Scholar Register] [Received: 02/24/2016] [Revised: 06/06/2016] [Accepted: 06/09/2016] [Indexed: 12/13/2022]
Abstract
The diversity of long non-coding RNAs (lncRNAs) in the human transcriptome is in stark contrast to the sparse exploration of their functions concomitant with their conservation and evolution. The pervasive transcription of the largely non-coding human genome makes the evolutionary age and conservation patterns of lncRNAs to a topic of interest. Yet it is a fairly unexplored field and not that easy to determine as for protein-coding genes. Although there are a few experimentally studied cases, which are conserved at the sequence level, most lncRNAs exhibit weak or untraceable primary sequence conservation. Recent studies shed light on the interspecies conservation of secondary structures among lncRNA homologs by using diverse computational methods. This highlights the importance of structure on functionality of lncRNAs as opposed to the poor impact of primary sequence changes. Further clues in the evolution of lncRNAs are given by selective constraints on non-coding gene structures (e.g., promoters or splice sites) as well as the conservation of prevalent spatio-temporal expression patterns. However, a rapid evolutionary turnover is observable throughout the heterogeneous group of lncRNAs. This still gives rise to questions about its functional meaning. WIREs RNA 2017, 8:e1376. doi: 10.1002/wrna.1376 For further resources related to this article, please visit the WIREs website.
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Affiliation(s)
- Anne Nitsche
- Bioinformatics Group, Department of Computer Science, University Leipzig, Leipzig, Germany.,Institute de Biologie Moléculaire et Cellulaire, Université de Strasbourg, Cedex, France
| | - Peter F Stadler
- Bioinformatics Group, Department of Computer Science, University Leipzig, Leipzig, Germany.,Interdisciplinary Center for Bioinformatics, University Leipzig, Leipzig, Germany.,Max Planck Institute for Mathematics in the Sciences, Leipzig, Germany.,Department of Diagnostics, Fraunhofer Institute for Cell Therapy and Immunology - IZI, Leipzig, Germany.,Center for Non-Coding RNA in Technology and Health, University of Copenhagen, Frederiksberg, Denmark.,Department of Theoretical Chemistry, University of Vienna, Wien, Austria.,Santa Fe Institute, Santa Fe, NM, USA
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37
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Toraih EA, Fawzy MS, Mohammed EA, Hussein MH, EL-Labban MM. MicroRNA-196a2 Biomarker and Targetome Network Analysis in Solid Tumors. Mol Diagn Ther 2016; 20:559-577. [DOI: 10.1007/s40291-016-0223-2] [Citation(s) in RCA: 34] [Impact Index Per Article: 4.3] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/05/2023]
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38
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Giusti J, Pinhal D, Moxon S, Campos CL, Münsterberg A, Martins C. MicroRNA-10 modulates Hox genes expression during Nile tilapia embryonic development. Mech Dev 2016; 140:12-8. [DOI: 10.1016/j.mod.2016.03.002] [Citation(s) in RCA: 16] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/25/2015] [Revised: 02/12/2016] [Accepted: 03/11/2016] [Indexed: 11/16/2022]
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39
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Lu YC, Chang JT, Chan EC, Chao YK, Yeh TS, Chen JS, Cheng AJ. miR-196, an Emerging Cancer Biomarker for Digestive Tract Cancers. J Cancer 2016; 7:650-5. [PMID: 27076845 PMCID: PMC4829550 DOI: 10.7150/jca.13460] [Citation(s) in RCA: 42] [Impact Index Per Article: 5.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/05/2015] [Accepted: 02/11/2016] [Indexed: 12/25/2022] Open
Abstract
Over the past decade, the emergence of microRNA (miRNA) research has firmly established this molecular family as a key component in cells. MiRNAs, which function as negative gene regulators, participate in multiple biological processes and maintain homeostasis in cells. The dysregulation of miRNA may contribute to numerous human disorders, including cancer. Recently, miR-196 was found to be aberrantly expressed in a wide range of malignant diseases, which suggests that it plays important roles in carcinogenesis. Here, we summarize the current knowledge concerning miR-196 family in cancers. This review includes miR-196 gene structure and aberrant expression in various cancers, and current understanding of numerous functions and regulatory targets of miR-196 in specific cancers. Since miR-196 are consistently found over-expressed in digestive tract cancer tissues, we also reviewed the clinical significance and potential applications of miR-196 in these cancers. We highlight that miR-196 may serve as an emerging cancer biomarker for digestive tract cancers.
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Affiliation(s)
- Ya-Ching Lu
- 1. Department of Medical Biotechnology and Laboratory science, College of Medicine, Chang Gung University, Taoyuan 333, Taiwan
| | - Joseph T Chang
- 2. Department of Radiation Oncology, Chang Gung Memorial Hospital, Taoyuan 333, Taiwan
| | - Err-Cheng Chan
- 1. Department of Medical Biotechnology and Laboratory science, College of Medicine, Chang Gung University, Taoyuan 333, Taiwan
| | - Yin-Kai Chao
- 3. Department of Thoracic Surgery, Chang Gung Memorial Hospital, Taoyuan 333, Taiwan
| | - Ta-Sen Yeh
- 4. Department of General Surgery, Chang Gung Memorial Hospital, Taoyuan 333, Taiwan
| | - Jinn-Shiun Chen
- 5. Department of Colorectal Surgery, Chang Gung Memorial Hospital, Taoyuan 333, Taiwan
| | - Ann-Joy Cheng
- 1. Department of Medical Biotechnology and Laboratory science, College of Medicine, Chang Gung University, Taoyuan 333, Taiwan
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40
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Ning X, Liu S, Qiu Y, Li G, Li Y, Li M, Yang G. Expression Profiles and Biological Roles of miR-196a in Swine. Genes (Basel) 2016; 7:genes7020005. [PMID: 26805888 PMCID: PMC4773749 DOI: 10.3390/genes7020005] [Citation(s) in RCA: 7] [Impact Index Per Article: 0.9] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/20/2015] [Revised: 12/30/2015] [Accepted: 01/12/2016] [Indexed: 12/17/2022] Open
Abstract
MicroRNAs (miRNAs) are a class of small non-coding RNA molecules, which play important roles in animals by targeting mRNA transcripts for translational repression. Recent studies have demonstrated that miRNAs are involved in regulation of adipocyte development. The expression of miR-196a in different porcine tissues and developing fat tissues was detected, and gene ontology (GO) term enrichment was then used to predict the expression profiles and potential biological roles of miR-196a in swine. To further verify the roles of miR-196a in porcine adipocyte development, a recombinant adenovirus encoding miR-196a gene (Ad-miR-196a) was constructed and used to study the effect of miR-196a on preadipocyte proliferation and differentiation. Here, our data demonstrate that miR-196a displays a tissue-specific expression pattern and has comprehensive biological roles in swine, especially in adipose development. In addition, overexpression of miR-196a had no effect on preadipocyte proliferation, but induced preadipocyte differentiation by increasing expression of adipocyte specific markers, lipid accumulation and triglyceride content. These data represent the first demonstration of miR-196a expression profiles and roles in swine, thereby providing valuable insight into the functions of miR-196a in adipocyte biology.
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Affiliation(s)
- Xiaomin Ning
- Laboratory of Animal Fat Deposition and Muscle Development, College of Animal Science and Technology, Northwest A & F University, Yangling 712100, China.
| | - Shuai Liu
- Laboratory of Animal Fat Deposition and Muscle Development, College of Animal Science and Technology, Northwest A & F University, Yangling 712100, China.
| | - Yang Qiu
- Laboratory of Animal Fat Deposition and Muscle Development, College of Animal Science and Technology, Northwest A & F University, Yangling 712100, China.
| | - Guoxi Li
- College of Animal Science and Veterinary Medicine, Henan Agricultural University, Zhengzhou 450002, China.
| | - Yanjie Li
- Laboratory of Animal Fat Deposition and Muscle Development, College of Animal Science and Technology, Northwest A & F University, Yangling 712100, China.
| | - Meihang Li
- Laboratory of Animal Fat Deposition and Muscle Development, College of Animal Science and Technology, Northwest A & F University, Yangling 712100, China.
| | - Gongshe Yang
- Laboratory of Animal Fat Deposition and Muscle Development, College of Animal Science and Technology, Northwest A & F University, Yangling 712100, China.
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41
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De Kumar B, Krumlauf R. HOXs and lincRNAs: Two sides of the same coin. SCIENCE ADVANCES 2016; 2:e1501402. [PMID: 27034976 PMCID: PMC4805430 DOI: 10.1126/sciadv.1501402] [Citation(s) in RCA: 39] [Impact Index Per Article: 4.9] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 10/07/2015] [Accepted: 11/28/2015] [Indexed: 05/13/2023]
Abstract
The clustered Hox genes play fundamental roles in regulation of axial patterning and elaboration of the basic body plan in animal development. There are common features in the organization and regulatory landscape of Hox clusters associated with their highly conserved functional roles. The presence of transcribed noncoding sequences embedded within the vertebrate Hox clusters is providing insight into a new layer of regulatory information associated with Hox genes.
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Affiliation(s)
- Bony De Kumar
- Stowers Institute for Medical Research, Kansas City, MO 64110, USA
| | - Robb Krumlauf
- Stowers Institute for Medical Research, Kansas City, MO 64110, USA
- Department of Anatomy and Cell Biology, Kansas University Medical Center, Kansas City, KS 66160, USA
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42
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Mo JS, Alam KJ, Kang IH, Park WC, Seo GS, Choi SC, Kim HS, Moon HB, Yun KJ, Chae SC. MicroRNA 196B regulates FAS-mediated apoptosis in colorectal cancer cells. Oncotarget 2015; 6:2843-55. [PMID: 25605245 PMCID: PMC4413621 DOI: 10.18632/oncotarget.3066] [Citation(s) in RCA: 46] [Impact Index Per Article: 5.1] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/11/2014] [Accepted: 12/22/2014] [Indexed: 01/01/2023] Open
Abstract
Using miRNA microarray analysis, we identified 31 miRNAs that were significantly up-regulated or down-regulated in colon cancer tissues. We chose MIR196B, which was specifically up-regulated in colon cancer, for further study. We identified 18 putative MIR196B target genes by comparing between the mRNAs down-regulated in MIR196B-overexpressed cells and the assumed MIR196B target genes predicted by public bioinformatics tools. The association between MIR196B and FAS was verified in this study. FAS expression was constitutively elevated in normal human colorectal tissues. However, its expression was often reduced in human colorectal cancer. The decrease in FAS expression could be responsible for the reduction of apoptosis in colorectal cancer cells. In colorectal cancer tissue, we showed that MIR196B up-regulation was mutually followed by down regulation of FAS expression. We also showed that MIR196B directly repressed FAS expression in colorectal cells. Furthermore, anti-MIR196B up-regulated FAS expression and increased apoptosis in colorectal cancer cell lines. Our results suggest that the up-regulation of MIR196B modulates apoptosis in colorectal cancer cells by partially repressing FAS expression and that anti-MIR196B could be a potential candidate as an anti-cancer drug in colorectal cancer therapy.
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Affiliation(s)
- Ji-Su Mo
- Department of Pathology, School of Medicine, Wonkwang University, Iksan, Chonbuk, Republic of Korea
| | - Khondoker Jahengir Alam
- Department of Pathology, School of Medicine, Wonkwang University, Iksan, Chonbuk, Republic of Korea
| | - In-Hong Kang
- Department of Pathology, School of Medicine, Wonkwang University, Iksan, Chonbuk, Republic of Korea
| | - Won Cheol Park
- Department of Surgery, School of Medicine, Wonkwang University, Iksan, Chonbuk, Republic of Korea
| | - Geom-Seog Seo
- Digestive Disease Research Institute, Wonkwang University, Iksan, Chonbuk, Republic of Korea
| | - Suck-Chei Choi
- Digestive Disease Research Institute, Wonkwang University, Iksan, Chonbuk, Republic of Korea
| | - Hun-Soo Kim
- Department of Pathology, School of Medicine, Wonkwang University, Iksan, Chonbuk, Republic of Korea
| | - Hyung-Bae Moon
- Department of Pathology, School of Medicine, Wonkwang University, Iksan, Chonbuk, Republic of Korea
| | - Ki-Jung Yun
- Department of Pathology, School of Medicine, Wonkwang University, Iksan, Chonbuk, Republic of Korea.,Digestive Disease Research Institute, Wonkwang University, Iksan, Chonbuk, Republic of Korea
| | - Soo-Cheon Chae
- Department of Pathology, School of Medicine, Wonkwang University, Iksan, Chonbuk, Republic of Korea.,Digestive Disease Research Institute, Wonkwang University, Iksan, Chonbuk, Republic of Korea
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43
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Quah S, Holland PWH. The Hox cluster microRNA miR-615: a case study of intronic microRNA evolution. EvoDevo 2015; 6:31. [PMID: 26451238 PMCID: PMC4597612 DOI: 10.1186/s13227-015-0027-1] [Citation(s) in RCA: 14] [Impact Index Per Article: 1.6] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/31/2015] [Accepted: 09/25/2015] [Indexed: 12/30/2022] Open
Abstract
BACKGROUND Introns represent a potentially rich source of existing transcription for the evolution of novel microRNAs (miRNAs). Within the Hox gene clusters, a miRNA gene, miR-615, is located within the intron of the Hoxc5 gene. This miRNA has a restricted phylogenetic distribution, providing an opportunity to examine the origin and evolution of a new miRNA within the intron of a developmentally-important homeobox gene. RESULTS Alignment and structural analyses show that the sequence is highly conserved across eutherian mammals and absent in non-mammalian tetrapods. Marsupials possess a similar sequence which we predict will not be efficiently processed as a miRNA. Our analyses suggest that transcription of HOXC5 in humans is accompanied by expression of miR-615 in all cases, but that the miRNA can also be transcribed independently of its host gene through the use of an intragenic promoter. We present scenarios for the evolution of miR-615 through intronic exaptation, and speculate on the acquisition of independent transcriptional regulation. Target prediction and transcriptomic analyses suggest that the dominant product of miR-615 is involved in the regulation of growth and a range of developmental processes. CONCLUSIONS The miR-615 gene evolved within the intron of Hoxc5 in the ancestor of placental mammals. Using miR-615 as a case study, we propose a model by which a functional miRNA can emerge within an intron gradually, by selection on secondary structure followed by evolution of an independent miRNA promoter. The location within a Hox gene intron is of particular interest as the miRNA is specific to placental mammals, is co-expressed with its host gene and may share complementary functions.
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Affiliation(s)
- Shan Quah
- Department of Zoology, University of Oxford, South Parks Road, Oxford, OX1 3PS UK
| | - Peter W. H. Holland
- Department of Zoology, University of Oxford, South Parks Road, Oxford, OX1 3PS UK
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44
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Fantini S, Salsi V, Vitobello A, Rijli FM, Zappavigna V. MicroRNA-196b is transcribed from an autonomous promoter and is directly regulated by Cdx2 and by posterior Hox proteins during embryogenesis. BIOCHIMICA ET BIOPHYSICA ACTA-GENE REGULATORY MECHANISMS 2015; 1849:1066-80. [PMID: 26141604 DOI: 10.1016/j.bbagrm.2015.06.014] [Citation(s) in RCA: 19] [Impact Index Per Article: 2.1] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Subscribe] [Scholar Register] [Received: 02/17/2015] [Revised: 06/25/2015] [Accepted: 06/28/2015] [Indexed: 12/26/2022]
Abstract
The miR-196 miRNA gene family located within the Hox gene clusters has been shown to function during embryogenesis and to be aberrantly expressed in various malignancies, including leukaemia, melanoma, and colorectal cancer. Despite its involvement in numerous biological processes, the control of miR-196 expression is still poorly defined. We identified the miR-196b promoter and found that the mature miR-196b originates from a large, non-coding primary transcript, which starts within an autonomous TATA box promoter and is not in physical continuity with either the Hoxa10 or Hoxa9 main primary transcripts. A ~680bp genomic fragment, spanning the pri-miR-196b transcription start site, is sufficient to recapitulate the neural tube expression pattern of miR-196 during embryogenesis. This region contains potential binding sites for Cdx and 5'Hox transcription factors. Two of these sites revealed to be necessary for neural tube expression and were bound in vivo by Cdx2 and Hoxd13. We show that Cdx2 is required for miR-196 expression and that both Cdx2 and 5'Hox, but not 3'Hox, are able to activate the miR-196b promoter. The possible role of Cdx2- and 5'Hox-mediated regulation of miR-196 expression in vertebrate anterior-posterior (AP) axis formation during embryogenesis is discussed.
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Affiliation(s)
- Sebastian Fantini
- Department of Life Sciences, University of Modena and Reggio Emilia, Via G. Campi 213/d, Modena 41125, Italy
| | - Valentina Salsi
- Department of Life Sciences, University of Modena and Reggio Emilia, Via G. Campi 213/d, Modena 41125, Italy
| | - Antonio Vitobello
- Friedrich Miescher Institute for Biomedical Research, Maulbeerstrasse 66, CH-4058 Basel, Switzerland
| | - Filippo M Rijli
- Friedrich Miescher Institute for Biomedical Research, Maulbeerstrasse 66, CH-4058 Basel, Switzerland
| | - Vincenzo Zappavigna
- Department of Life Sciences, University of Modena and Reggio Emilia, Via G. Campi 213/d, Modena 41125, Italy.
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45
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Han Q, Zhou C, Liu F, Xu G, Zheng R, Zhang X. MicroRNA-196a post-transcriptionally upregulates the UBE2C proto-oncogene and promotes cell proliferation in breast cancer. Oncol Rep 2015; 34:877-83. [PMID: 26062455 DOI: 10.3892/or.2015.4049] [Citation(s) in RCA: 22] [Impact Index Per Article: 2.4] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/18/2015] [Accepted: 04/20/2015] [Indexed: 11/06/2022] Open
Abstract
Accumulating evidence has shown that miR-196a plays an important role in tumorigenesis and tumor progression in various types of cancer. miRNA profiling studies have suggested that miR-196a is highly overexpressed in breast cancer. However, the functional mechanism of miR-196a in breast cancer remains unclear. In the present study, we first showed that the expression of miR-196a was significantly upregulated in human breast cancer samples and breast cancer cell lines. Using a loss-of-function approach, we showed that the downregulation of miR-196a inhibited the proliferation of breast cancer cells in vitro and in vivo. Ubiquitin-conjugating enzyme E2C (UBE2C) gene as a cellular proto-oncogene, which was overexpressed and positively correlated with miR-196a expression in breast cancer tissues, was identified as a direct target of miR-196a. Moreover, in order to investigate whether miR-196a regulated cell growth in breast cancer cells by targeting UBE2C, rescue studies were performed in breast cancer cells. The restoration of UBE2C by transfecting UBE2C cDNA in anti-miR-196a-transfected breast cancer cells rescued the suppression of cell proliferation. In conclusion, the present study showed that miR-196a promoted cell proliferation by targeting UBE2C in breast cancer. Thus, miR-196a may be a potential oncogene in breast cancer and a promising therapeutic target in breast cancer treatment.
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Affiliation(s)
- Qinglin Han
- Department of General Surgery, Changhai Hospital, Second Military Medical University, Shanghai 200433, P.R. China
| | - Chun Zhou
- Department of Surgery Research Laboratory, The Affiliated Hospital of Nantong University, Nantong, Jiangsu 226000, P.R. China
| | - Fan Liu
- Department of Surgery Research Laboratory, The Affiliated Hospital of Nantong University, Nantong, Jiangsu 226000, P.R. China
| | - Guanghuan Xu
- Department of General Surgery, Changhai Hospital, Second Military Medical University, Shanghai 200433, P.R. China
| | - Rui Zheng
- Department of General Surgery, Changhai Hospital, Second Military Medical University, Shanghai 200433, P.R. China
| | - Xin Zhang
- Department of General Surgery, Changhai Hospital, Second Military Medical University, Shanghai 200433, P.R. China
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46
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Dunn J, Simmons R, Thabet S, Jo H. The role of epigenetics in the endothelial cell shear stress response and atherosclerosis. Int J Biochem Cell Biol 2015; 67:167-76. [PMID: 25979369 DOI: 10.1016/j.biocel.2015.05.001] [Citation(s) in RCA: 42] [Impact Index Per Article: 4.7] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/07/2015] [Revised: 04/30/2015] [Accepted: 05/02/2015] [Indexed: 12/15/2022]
Abstract
Currently in the field of vascular biology, the role of epigenetics in endothelial cell biology and vascular disease has attracted more in-depth study. Using both in vitro and in vivo models of blood flow, investigators have recently begun to reveal the underlying epigenetic regulation of endothelial gene expression. Recently, our group, along with two other independent groups, have demonstrated that blood flow controls endothelial gene expression by DNA methyltransferases (DNMT1 and 3A). Disturbed flow (d-flow), characterized by low and oscillating shear stress (OS), is pro-atherogenic and induces expression of DNMT1 both in vivo and in vitro. D-flow regulates genome-wide DNA methylation patterns in a DNMT-dependent manner. The DNMT inhibitor 5-Aza-2'deoxycytidine (5Aza) or DNMT1 siRNA reduces OS-induced endothelial inflammation. Moreover, 5Aza inhibits the development of atherosclerosis in ApoE(-/-) mice. Through a systems biological analysis of genome-wide DNA methylation patterns and gene expression data, we found 11 mechanosensitive genes which were suppressed by d-flow in vivo, experienced hypermethylation in their promoter region in response to d-flow, and were rescued by 5Aza treatment. Interestingly, among these mechanosensitive genes, the two transcription factors HoxA5 and Klf3 contain cAMP-response-elements (CRE), which may indicate that methylation of CRE sites could serve as a mechanosensitive master switch in gene expression. These findings provide new insight into the mechanism by which flow controls epigenetic DNA methylation patterns, which in turn alters endothelial gene expression, regulates vascular biology, and induces atherosclerosis. These novel findings have broad implications for understanding the biochemical mechanisms of atherogenesis and provide a basis for identifying potential therapeutic targets for atherosclerosis. This article is part of a Directed Issue entitled: Epigenetics dynamics in development and disease.
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Affiliation(s)
- Jessilyn Dunn
- Wallace H. Coulter Department of Biomedical Engineering, Georgia Institute of Technology and Emory University, USA
| | - Rachel Simmons
- Wallace H. Coulter Department of Biomedical Engineering, Georgia Institute of Technology and Emory University, USA
| | - Salim Thabet
- Division of Cardiology, Georgia Institute of Technology and Emory University, USA
| | - Hanjoong Jo
- Wallace H. Coulter Department of Biomedical Engineering, Georgia Institute of Technology and Emory University, USA; Division of Cardiology, Georgia Institute of Technology and Emory University, USA.
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47
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Dunn J, Thabet S, Jo H. Flow-Dependent Epigenetic DNA Methylation in Endothelial Gene Expression and Atherosclerosis. Arterioscler Thromb Vasc Biol 2015; 35:1562-9. [PMID: 25953647 DOI: 10.1161/atvbaha.115.305042] [Citation(s) in RCA: 66] [Impact Index Per Article: 7.3] [Reference Citation Analysis] [Abstract] [Key Words] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/05/2015] [Accepted: 04/27/2015] [Indexed: 12/31/2022]
Abstract
Epigenetic mechanisms that regulate endothelial cell gene expression are now emerging. DNA methylation is the most stable epigenetic mark that confers persisting changes in gene expression. Not only is DNA methylation important in rendering cell identity by regulating cell type-specific gene expression throughout differentiation, but it is becoming clear that DNA methylation also plays a key role in maintaining endothelial cell homeostasis and in vascular disease development. Disturbed blood flow causes atherosclerosis, whereas stable flow protects against it by differentially regulating gene expression in endothelial cells. Recently, we and others have shown that flow-dependent gene expression and atherosclerosis development are regulated by mechanisms dependent on DNA methyltransferases (1 and 3A). Disturbed blood flow upregulates DNA methyltransferase expression both in vitro and in vivo, which leads to genome-wide DNA methylation alterations and global gene expression changes in a DNA methyltransferase-dependent manner. These studies revealed several mechanosensitive genes, such as HoxA5, Klf3, and Klf4, whose promoters were hypermethylated by disturbed blood flow, but rescued by DNA methyltransferases inhibitors such as 5Aza-2-deoxycytidine. These findings provide new insight into the mechanism by which flow controls epigenomic DNA methylation patterns, which in turn alters endothelial gene expression, regulates vascular biology, and modulates atherosclerosis development.
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Affiliation(s)
- Jessilyn Dunn
- From the Wallace H. Coulter Department of Biomedical Engineering (J.D., S.T., H.J.) and Division of Cardiology, Georgia Institute of Technology and Emory University, Atlanta
| | - Salim Thabet
- From the Wallace H. Coulter Department of Biomedical Engineering (J.D., S.T., H.J.) and Division of Cardiology, Georgia Institute of Technology and Emory University, Atlanta
| | - Hanjoong Jo
- From the Wallace H. Coulter Department of Biomedical Engineering (J.D., S.T., H.J.) and Division of Cardiology, Georgia Institute of Technology and Emory University, Atlanta.
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48
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Dunn J, Qiu H, Kim S, Jjingo D, Hoffman R, Kim CW, Jang I, Son DJ, Kim D, Pan C, Fan Y, Jordan IK, Jo H. Flow-dependent epigenetic DNA methylation regulates endothelial gene expression and atherosclerosis. J Clin Invest 2014; 124:3187-99. [PMID: 24865430 PMCID: PMC4071393 DOI: 10.1172/jci74792] [Citation(s) in RCA: 212] [Impact Index Per Article: 21.2] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/16/2013] [Accepted: 03/28/2014] [Indexed: 12/17/2022] Open
Abstract
In atherosclerosis, plaques preferentially develop in arterial regions of disturbed blood flow (d-flow), which alters endothelial gene expression and function. Here, we determined that d-flow regulates genome-wide DNA methylation patterns in a DNA methyltransferase-dependent (DNMT-dependent) manner. Induction of d-flow by partial carotid ligation surgery in a murine model induced DNMT1 in arterial endothelium. In cultured endothelial cells, DNMT1 was enhanced by oscillatory shear stress (OS), and reduction of DNMT with either the inhibitor 5-aza-2'-deoxycytidine (5Aza) or siRNA markedly reduced OS-induced endothelial inflammation. Moreover, administration of 5Aza reduced lesion formation in 2 mouse models of atherosclerosis. Using both reduced representation bisulfite sequencing (RRBS) and microarray, we determined that d-flow in the carotid artery resulted in hypermethylation within the promoters of 11 mechanosensitive genes and that 5Aza treatment restored normal methylation patterns. Of the identified genes, HoxA5 and Klf3 encode transcription factors that contain cAMP response elements, suggesting that the methylation status of these loci could serve as a mechanosensitive master switch in gene expression. Together, our results demonstrate that d-flow controls epigenomic DNA methylation patterns in a DNMT-dependent manner, which in turn alters endothelial gene expression and induces atherosclerosis.
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MESH Headings
- Animals
- Apolipoproteins E/deficiency
- Apolipoproteins E/genetics
- Atherosclerosis/genetics
- Atherosclerosis/metabolism
- Atherosclerosis/physiopathology
- Azacitidine/analogs & derivatives
- Azacitidine/pharmacology
- DNA (Cytosine-5-)-Methyltransferase 1
- DNA (Cytosine-5-)-Methyltransferases/antagonists & inhibitors
- DNA (Cytosine-5-)-Methyltransferases/genetics
- DNA (Cytosine-5-)-Methyltransferases/metabolism
- DNA Methylation
- Decitabine
- Disease Models, Animal
- Endothelial Cells/drug effects
- Endothelial Cells/metabolism
- Epigenesis, Genetic
- Gene Expression Regulation
- Homeodomain Proteins/genetics
- Human Umbilical Vein Endothelial Cells
- Humans
- Kruppel-Like Transcription Factors/genetics
- Mice
- Mice, Inbred C57BL
- Mice, Knockout
- Phosphoproteins/genetics
- Plaque, Atherosclerotic/etiology
- Plaque, Atherosclerotic/genetics
- Plaque, Atherosclerotic/physiopathology
- Promoter Regions, Genetic
- RNA, Messenger/genetics
- RNA, Messenger/metabolism
- Regional Blood Flow
- Stress, Mechanical
- Transcription Factors
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Affiliation(s)
- Jessilyn Dunn
- Wallace H. Coulter Department of Biomedical Engineering, Georgia Institute of Technology and Emory University, School of Biology, Georgia Institute of Technology, and Division of Cardiology, Department of Medicine, Emory University, Atlanta, Georgia, USA
| | - Haiwei Qiu
- Wallace H. Coulter Department of Biomedical Engineering, Georgia Institute of Technology and Emory University, School of Biology, Georgia Institute of Technology, and Division of Cardiology, Department of Medicine, Emory University, Atlanta, Georgia, USA
| | - Soyeon Kim
- Wallace H. Coulter Department of Biomedical Engineering, Georgia Institute of Technology and Emory University, School of Biology, Georgia Institute of Technology, and Division of Cardiology, Department of Medicine, Emory University, Atlanta, Georgia, USA
| | - Daudi Jjingo
- Wallace H. Coulter Department of Biomedical Engineering, Georgia Institute of Technology and Emory University, School of Biology, Georgia Institute of Technology, and Division of Cardiology, Department of Medicine, Emory University, Atlanta, Georgia, USA
| | - Ryan Hoffman
- Wallace H. Coulter Department of Biomedical Engineering, Georgia Institute of Technology and Emory University, School of Biology, Georgia Institute of Technology, and Division of Cardiology, Department of Medicine, Emory University, Atlanta, Georgia, USA
| | - Chan Woo Kim
- Wallace H. Coulter Department of Biomedical Engineering, Georgia Institute of Technology and Emory University, School of Biology, Georgia Institute of Technology, and Division of Cardiology, Department of Medicine, Emory University, Atlanta, Georgia, USA
| | - Inhwan Jang
- Wallace H. Coulter Department of Biomedical Engineering, Georgia Institute of Technology and Emory University, School of Biology, Georgia Institute of Technology, and Division of Cardiology, Department of Medicine, Emory University, Atlanta, Georgia, USA
| | - Dong Ju Son
- Wallace H. Coulter Department of Biomedical Engineering, Georgia Institute of Technology and Emory University, School of Biology, Georgia Institute of Technology, and Division of Cardiology, Department of Medicine, Emory University, Atlanta, Georgia, USA
| | - Daniel Kim
- Wallace H. Coulter Department of Biomedical Engineering, Georgia Institute of Technology and Emory University, School of Biology, Georgia Institute of Technology, and Division of Cardiology, Department of Medicine, Emory University, Atlanta, Georgia, USA
| | - Chenyi Pan
- Wallace H. Coulter Department of Biomedical Engineering, Georgia Institute of Technology and Emory University, School of Biology, Georgia Institute of Technology, and Division of Cardiology, Department of Medicine, Emory University, Atlanta, Georgia, USA
| | - Yuhong Fan
- Wallace H. Coulter Department of Biomedical Engineering, Georgia Institute of Technology and Emory University, School of Biology, Georgia Institute of Technology, and Division of Cardiology, Department of Medicine, Emory University, Atlanta, Georgia, USA
| | - I. King Jordan
- Wallace H. Coulter Department of Biomedical Engineering, Georgia Institute of Technology and Emory University, School of Biology, Georgia Institute of Technology, and Division of Cardiology, Department of Medicine, Emory University, Atlanta, Georgia, USA
| | - Hanjoong Jo
- Wallace H. Coulter Department of Biomedical Engineering, Georgia Institute of Technology and Emory University, School of Biology, Georgia Institute of Technology, and Division of Cardiology, Department of Medicine, Emory University, Atlanta, Georgia, USA
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Salas-Huetos A, Blanco J, Vidal F, Mercader JM, Garrido N, Anton E. New insights into the expression profile and function of micro-ribonucleic acid in human spermatozoa. Fertil Steril 2014; 102:213-222.e4. [PMID: 24794309 DOI: 10.1016/j.fertnstert.2014.03.040] [Citation(s) in RCA: 55] [Impact Index Per Article: 5.5] [Reference Citation Analysis] [Abstract] [Key Words] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/27/2013] [Revised: 02/28/2014] [Accepted: 03/18/2014] [Indexed: 12/11/2022]
Abstract
OBJECTIVE To characterize the microRNA (miRNA) expression profile in spermatozoa from human fertile individuals and their implications in human fertility. DESIGN The expression levels of 736 miRNAs were evaluated using TaqMan arrays. Ontologic analyses were performed to determine the presence of enriched biological processes among their targets. SETTING University research and clinical institutes. PATIENT(S) Ten individuals with normal seminogram, standard karyotype, and proven fertility. INTERVENTION(S) None. MAIN OUTCOME MEASURE(S) Expression levels of 736 miRNAs, presence of enriched metabolic routes among their targets, homogeneity of the population, influence of demographic features in the results, presence of miRNA stable pairs, and best miRNA normalizing candidates. RESULT(S) A total of 221 miRNAs were consistently present in all individuals, 452 were only detected in some individuals, and 63 did not appear in any sample. The ontologic analysis of the 2,356 potential targets of the ubiquitous miRNAs showed an enrichment of processes related to cell differentiation, development, morphogenesis, and embryogenesis. None of the miRNAs were significantly correlated with age, semen volume, sperm concentration, motility, or morphology. Correlations between samples were statistically significant, indicating a high homogeneity of the population. A set of 48 miRNA pairs displayed a stable expression, a particular behavior that is discussed in relationship to their usefulness as fertility biomarkers. Hsa-miR-532-5p, hsa-miR-374b-5p, and hsa-miR-564 seemed to be the best normalizing miRNA candidates. CONCLUSION(S) Human sperm contain a stable population of miRNAs potentially related to embryogenesis and spermatogenesis.
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Affiliation(s)
- Albert Salas-Huetos
- Unitat de Biologia Cel·lular, Facultat de Biociències, Universitat Autònoma de Barcelona, Bellaterra (Cerdanyola del Vallès), Spain
| | - Joan Blanco
- Unitat de Biologia Cel·lular, Facultat de Biociències, Universitat Autònoma de Barcelona, Bellaterra (Cerdanyola del Vallès), Spain
| | - Francesca Vidal
- Unitat de Biologia Cel·lular, Facultat de Biociències, Universitat Autònoma de Barcelona, Bellaterra (Cerdanyola del Vallès), Spain
| | - Josep M Mercader
- Joint Institution for Research in Biomedicine-Barcelona Supercomputing Center Program on Computational Biology, Barcelona Supercomputing Center, Barcelona, Spain
| | - Nicolás Garrido
- Laboratorio de Andrología y Banco de Semen, Instituto Valenciano de Infertilidad Valencia, Valencia, Spain
| | - Ester Anton
- Unitat de Biologia Cel·lular, Facultat de Biociències, Universitat Autònoma de Barcelona, Bellaterra (Cerdanyola del Vallès), Spain.
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50
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Combined elevation of microRNA-196a and microRNA-196b in sera predicts unfavorable prognosis in patients with osteosarcomas. Int J Mol Sci 2014; 15:6544-55. [PMID: 24747591 PMCID: PMC4013646 DOI: 10.3390/ijms15046544] [Citation(s) in RCA: 54] [Impact Index Per Article: 5.4] [Reference Citation Analysis] [Abstract] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/13/2014] [Revised: 03/28/2014] [Accepted: 04/09/2014] [Indexed: 12/31/2022] Open
Abstract
AIM To investigate whether the aberrant expression of microRNA (miR)-196a and miR-196b can be used as potential prognostic markers of human osteosarcoma. METHODS Quantitative real-time reverse transcriptase-polymerase chain reaction (qRT-PCR) analysis was performed to detect the expression levels of miR-196a and miR-196b in osteosarcoma tissues and patients' sera. RESULTS Expression levels of miR-196a and miR-196b in osteosarcoma tissues were both significantly higher than those in noncancerous bone tissues (both p<0.001), in line with which, the serum levels of the two miRNAs were also markedly upregulated in patients with osteosarcomas compared with healthy controls (both p<0.001). Then, the elevation of serum miR-196a and miR-196b levels both more frequently occurred in osteosarcoma patients with high tumor grade (p=0.008 and 0.01, respectively), positive metastasis (p=0.001 and 0.006, respectively) and recurrence (p=0.001 and 0.006, respectively). Moreover, high serum miR-196a, high serum miR-196b and conjoined expression of miR-196a/miR-196b were all independent prognostic factors for OS (overall survival) and DFS (disease-free survival) of osteosarcoma patients. CONCLUSION Our present data indicate the involvement of miR-196a and miR-196b upregulation in the pathogenesis of osteosarcoma. More importantly, the altered levels of circulating miR-196a and miR-196b might have great potential to serve as novel and non-invasive prognostic factors for this malignancy.
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