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Han L, Hao P, Wang W, Wu Y, Ruan S, Gao C, Tian W, Tian Y, Li X, Wang L, Zhang W, Wang H, Chang Y, Ding J. Molecular mechanisms that regulate the heat stress response in sea urchins (Strongylocentrotus intermedius) by comparative heat tolerance performance and whole-transcriptome RNA sequencing. THE SCIENCE OF THE TOTAL ENVIRONMENT 2023; 901:165846. [PMID: 37541492 DOI: 10.1016/j.scitotenv.2023.165846] [Citation(s) in RCA: 2] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Subscribe] [Scholar Register] [Received: 04/25/2023] [Revised: 06/07/2023] [Accepted: 07/26/2023] [Indexed: 08/06/2023]
Abstract
In the context of climate change and extreme high temperature, the commercially important sea urchin Strongylocentrotus intermedius suffers high mortality during summer in Northern China. How sea urchins respond to high temperatures is of great concern to academia and industry. How to understand the heat tolerance of sea urchin from the whole transcriptome level. In this study, the heat-resistant S. intermedius bred by our team and its control group were used as the research objects, then we applied whole-transcriptome RNA sequencing to detect differentially expressed mRNAs, microRNAs, long noncoding RNAs that respond to heat stress in the heat-resistant and control S. intermedius. A competitive endogenous RNA (ceRNA) regulatory network was constructed with predicted pairs of differentially expressed mRNAs and noncoding RNAs and revealed the molecular regulatory mechanisms in S. intermedius responding to heat stress. A functional analysis suggested that the ceRNAs were involved in basal metabolism, calcium ion transport, endoplasmic reticulum stress, and apoptosis. This is the whole-transcriptomic analysis of S. intermedius under heat stress to propose ceRNA networks that will provide a basis for studying the potential functions of long noncoding RNAs and miRNAs in the heat stress response in S. intermedius and provide a theoretical basis for the study of the molecular mechanism of sea urchins in response to environmental changes.
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Affiliation(s)
- Lingshu Han
- Key Laboratory of Northern Aquatic Germplasm Resources and Genetic Breeding in Liaoning Province, Dalian 116023, China; Key Laboratory of Mariculture & Stock Enhancement in North China's Sea, Ministry of Agriculture and Rural Affairs, Dalian Ocean University, Dalian, Liaoning, 116023, China; School of Marine Sciences, Ningbo University, Ningbo 315211, China
| | - Pengfei Hao
- Key Laboratory of Northern Aquatic Germplasm Resources and Genetic Breeding in Liaoning Province, Dalian 116023, China; Key Laboratory of Mariculture & Stock Enhancement in North China's Sea, Ministry of Agriculture and Rural Affairs, Dalian Ocean University, Dalian, Liaoning, 116023, China
| | - Wenpei Wang
- Key Laboratory of Northern Aquatic Germplasm Resources and Genetic Breeding in Liaoning Province, Dalian 116023, China; Key Laboratory of Mariculture & Stock Enhancement in North China's Sea, Ministry of Agriculture and Rural Affairs, Dalian Ocean University, Dalian, Liaoning, 116023, China
| | - Yanglei Wu
- Key Laboratory of Northern Aquatic Germplasm Resources and Genetic Breeding in Liaoning Province, Dalian 116023, China; Key Laboratory of Mariculture & Stock Enhancement in North China's Sea, Ministry of Agriculture and Rural Affairs, Dalian Ocean University, Dalian, Liaoning, 116023, China
| | - Shuchao Ruan
- Key Laboratory of Northern Aquatic Germplasm Resources and Genetic Breeding in Liaoning Province, Dalian 116023, China; Key Laboratory of Mariculture & Stock Enhancement in North China's Sea, Ministry of Agriculture and Rural Affairs, Dalian Ocean University, Dalian, Liaoning, 116023, China
| | - Chuang Gao
- Key Laboratory of Northern Aquatic Germplasm Resources and Genetic Breeding in Liaoning Province, Dalian 116023, China; Key Laboratory of Mariculture & Stock Enhancement in North China's Sea, Ministry of Agriculture and Rural Affairs, Dalian Ocean University, Dalian, Liaoning, 116023, China
| | - Wanrong Tian
- Key Laboratory of Northern Aquatic Germplasm Resources and Genetic Breeding in Liaoning Province, Dalian 116023, China; Key Laboratory of Mariculture & Stock Enhancement in North China's Sea, Ministry of Agriculture and Rural Affairs, Dalian Ocean University, Dalian, Liaoning, 116023, China
| | - Ye Tian
- Key Laboratory of Northern Aquatic Germplasm Resources and Genetic Breeding in Liaoning Province, Dalian 116023, China; Key Laboratory of Mariculture & Stock Enhancement in North China's Sea, Ministry of Agriculture and Rural Affairs, Dalian Ocean University, Dalian, Liaoning, 116023, China
| | - Xiaonan Li
- Key Laboratory of Northern Aquatic Germplasm Resources and Genetic Breeding in Liaoning Province, Dalian 116023, China; Key Laboratory of Mariculture & Stock Enhancement in North China's Sea, Ministry of Agriculture and Rural Affairs, Dalian Ocean University, Dalian, Liaoning, 116023, China
| | - Luo Wang
- Key Laboratory of Northern Aquatic Germplasm Resources and Genetic Breeding in Liaoning Province, Dalian 116023, China; Key Laboratory of Mariculture & Stock Enhancement in North China's Sea, Ministry of Agriculture and Rural Affairs, Dalian Ocean University, Dalian, Liaoning, 116023, China
| | - Weijie Zhang
- Key Laboratory of Northern Aquatic Germplasm Resources and Genetic Breeding in Liaoning Province, Dalian 116023, China; Key Laboratory of Mariculture & Stock Enhancement in North China's Sea, Ministry of Agriculture and Rural Affairs, Dalian Ocean University, Dalian, Liaoning, 116023, China
| | - Heng Wang
- Key Laboratory of Northern Aquatic Germplasm Resources and Genetic Breeding in Liaoning Province, Dalian 116023, China; Key Laboratory of Mariculture & Stock Enhancement in North China's Sea, Ministry of Agriculture and Rural Affairs, Dalian Ocean University, Dalian, Liaoning, 116023, China
| | - Yaqing Chang
- Key Laboratory of Northern Aquatic Germplasm Resources and Genetic Breeding in Liaoning Province, Dalian 116023, China; Key Laboratory of Mariculture & Stock Enhancement in North China's Sea, Ministry of Agriculture and Rural Affairs, Dalian Ocean University, Dalian, Liaoning, 116023, China
| | - Jun Ding
- Key Laboratory of Northern Aquatic Germplasm Resources and Genetic Breeding in Liaoning Province, Dalian 116023, China; Key Laboratory of Mariculture & Stock Enhancement in North China's Sea, Ministry of Agriculture and Rural Affairs, Dalian Ocean University, Dalian, Liaoning, 116023, China.
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Li H, Zhao S, Jiang M, Zhu T, Liu J, Feng G, Lu L, Dong J, Wu X, Chen X, Zhao Y, Fan S. Biomodified Extracellular Vesicles Remodel the Intestinal Microenvironment to Overcome Radiation Enteritis. ACS NANO 2023; 17:14079-14098. [PMID: 37399352 DOI: 10.1021/acsnano.3c04578] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 07/05/2023]
Abstract
Ionizing radiation (IR) is associated with the occurrence of enteritis, and protecting the whole intestine from radiation-induced gut injury remains an unmet clinical need. Circulating extracellular vesicles (EVs) are proven to be vital factors in the establishment of tissue and cell microenvironments. In this study, we aimed to investigate a radioprotective strategy mediated by small EVs (exosomes) in the context of irradiation-induced intestinal injury. We found that exosomes derived from donor mice exposed to total body irradiation (TBI) could protect recipient mice against TBI-induced lethality and alleviate radiation-induced gastrointestinal (GI) tract toxicity. To enhance the protective effect of EVs, profilings of mouse and human exosomal microRNAs (miRNAs) were performed to identify the functional molecule in exosomes. We found that miRNA-142-5p was highly expressed in exosomes from both donor mice exposed to TBI and patients after radiotherapy (RT). Moreover, miR-142 protected intestinal epithelial cells from irradiation-induced apoptosis and death and mediated EV protection against radiation enteritis by ameliorating the intestinal microenvironment. Then, biomodification of EVs was accomplished via enhancing miR-142 expression and intestinal specificity of exosomes, and thus improved EV-mediated protection from radiation enteritis. Our findings provide an effective approach for protecting against GI syndrome in people exposed to irradiation.
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Affiliation(s)
- Hang Li
- Tianjin Key Laboratory of Radiation Medicine and Molecular Nuclear Medicine, Institute of Radiation Medicine, Chinese Academy of Medical Sciences and Peking Union Medical College, Tianjin 300192, P.R. China
| | - Shuya Zhao
- Tianjin Key Laboratory of Radiation Medicine and Molecular Nuclear Medicine, Institute of Radiation Medicine, Chinese Academy of Medical Sciences and Peking Union Medical College, Tianjin 300192, P.R. China
| | - Mian Jiang
- Tianjin Key Laboratory of Radiation Medicine and Molecular Nuclear Medicine, Institute of Radiation Medicine, Chinese Academy of Medical Sciences and Peking Union Medical College, Tianjin 300192, P.R. China
| | - Tong Zhu
- Tianjin Key Laboratory of Radiation Medicine and Molecular Nuclear Medicine, Institute of Radiation Medicine, Chinese Academy of Medical Sciences and Peking Union Medical College, Tianjin 300192, P.R. China
| | - Jinjian Liu
- Tianjin Key Laboratory of Radiation Medicine and Molecular Nuclear Medicine, Institute of Radiation Medicine, Chinese Academy of Medical Sciences and Peking Union Medical College, Tianjin 300192, P.R. China
| | - Guoxing Feng
- Tianjin Key Laboratory of Radiation Medicine and Molecular Nuclear Medicine, Institute of Radiation Medicine, Chinese Academy of Medical Sciences and Peking Union Medical College, Tianjin 300192, P.R. China
| | - Lu Lu
- Tianjin Key Laboratory of Radiation Medicine and Molecular Nuclear Medicine, Institute of Radiation Medicine, Chinese Academy of Medical Sciences and Peking Union Medical College, Tianjin 300192, P.R. China
| | - Jiali Dong
- Tianjin Key Laboratory of Radiation Medicine and Molecular Nuclear Medicine, Institute of Radiation Medicine, Chinese Academy of Medical Sciences and Peking Union Medical College, Tianjin 300192, P.R. China
| | - Xin Wu
- Tianjin Key Laboratory of Radiation Medicine and Molecular Nuclear Medicine, Institute of Radiation Medicine, Chinese Academy of Medical Sciences and Peking Union Medical College, Tianjin 300192, P.R. China
| | - Xin Chen
- Department of Oncology, Renmin Hospital of Wuhan University, Wuhan 430060, Hubei Province China
| | - Yu Zhao
- Tianjin Key Laboratory of Radiation Medicine and Molecular Nuclear Medicine, Institute of Radiation Medicine, Chinese Academy of Medical Sciences and Peking Union Medical College, Tianjin 300192, P.R. China
| | - Saijun Fan
- Tianjin Key Laboratory of Radiation Medicine and Molecular Nuclear Medicine, Institute of Radiation Medicine, Chinese Academy of Medical Sciences and Peking Union Medical College, Tianjin 300192, P.R. China
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Zhuo L, Pan S, Li J, Fu X. Predicting miRNA-lncRNA interactions on plant datasets based on bipartite network embedding method. Methods 2022; 207:97-102. [PMID: 36155251 DOI: 10.1016/j.ymeth.2022.09.002] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/16/2022] [Revised: 09/04/2022] [Accepted: 09/08/2022] [Indexed: 11/15/2022] Open
Abstract
The research of miRNA-lncRNA interactions (MLIs) has received great attention recently due to their vital roles in microbiology and profound significance in diseases. Currently, many related studies mainly focus on animals and the link prediction problem on plants is rarely discussed comprehensively. Motivated by this, we achieve link prediction task based on the concept of bipartite graph and verify encouraging performance of our conclusions by conducting experiments on plant datasets. In this work, we firstly extract attribute information and structure information as base features and further process these information for network embedding. Intra-partition and inter-partition proximity modelling are conducted to construct the loss function, which facilitates the training of parameters. Finally, the superiority of our presented approach is shown by carrying out experiments on four plant datasets, which reflects the significance of this work to the research of microbiology and disease.
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Affiliation(s)
- Linlin Zhuo
- School of Data Science and Artificial Intelligence, Wenzhou University of Technology, Wenzhou, Zhejiang 325035, China
| | - Shiyao Pan
- School of Data Science and Artificial Intelligence, Wenzhou University of Technology, Wenzhou, Zhejiang 325035, China.
| | - Jing Li
- School of Data Science and Artificial Intelligence, Wenzhou University of Technology, Wenzhou, Zhejiang 325035, China
| | - Xiangzheng Fu
- College of Computer Science and Electronic Engineering, Hunan University, Changsha, Hunan 410012, China.
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The potency of lncRNA MALAT1/miR-155/CTLA4 axis in altering Th1/Th2 balance of asthma. Biosci Rep 2021; 40:221794. [PMID: 31909418 PMCID: PMC7024843 DOI: 10.1042/bsr20190397] [Citation(s) in RCA: 45] [Impact Index Per Article: 15.0] [Reference Citation Analysis] [Abstract] [Key Words] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/15/2019] [Revised: 11/14/2019] [Accepted: 11/15/2019] [Indexed: 12/14/2022] Open
Abstract
Objectives: The present study examined if the metastasis-associated lung adenocarcinoma transcript 1 (MALAT1)/miR-155/CTLA-4 axis was involved in modifying Th1/Th2 balance, a critical indicator for asthma progression. Methods: Altogether 772 asthma patients and 441 healthy controls were recruited, and their blood samples were collected to determine expressional levels of MALAT1, miR-155, CTLA-4, T-bet, GATA3, Th1-type cytokines and Th2-type cytokines. The CD4+ T cells were administered with pcDNA3.1-MALAT1, si-MALAT1, miR-155 mimic and miR-155 inhibitor to assess their effects on cytokine release. The luciferase reporter gene assay was also adopted to evaluate the sponging relationships between MALAT1 and miR-155, as well as between miR-155 and CTLA-4. Results: Over-expressed MALAT1 and under-expressed miR-155 were more frequently detected among asthma patients who showed traits of reduced forced expiratory failure volume in 1 s (FEV1), FEV1/forced vital capacity (FVC) and FEV1% of predicted (P<0.05). Moreover, MALAT1 expression was negatively expressed with the Th1/Th2 and T-bet/GATA3 ratios, yet miR-155 expression displayed a positively correlation with the ratios (P<0.05). Additionally, the IFN-γ, IL-2 and T-bet levels were reduced under the influence of pcDNA3.1-MALAT1 and miR-155 inhibitor, while levels of IL-4, IL-10 and GATA3 were raised under identical settings (P<0.05). Furthermore, MALAT1 constrained expression of miR-155 within CD4+ T cells by sponging it, and CTLA-4 could interfere with the effects of MALAT1 and miR-155 on Th1/Th2 balance and T-bet/Gata3 ratio (P<0.05). Conclusion: MALAT1 sponging miR-155 was involved with regulation of Th1/Th2 balance within CD4+ T cells, which might aid to develop therapies for amelioration of asthmatic inflammation.
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Jayasuriya R, Ramkumar KM. Role of long non-coding RNAs on the regulation of Nrf2 in chronic diseases. Life Sci 2021; 270:119025. [PMID: 33450255 DOI: 10.1016/j.lfs.2021.119025] [Citation(s) in RCA: 4] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/25/2020] [Revised: 01/03/2021] [Accepted: 01/06/2021] [Indexed: 12/21/2022]
Abstract
Studies have identified dysregulated long non-coding RNA (lncRNA) in several diseases at transcriptional, translational, and post-translational levels. Although our mechanistic knowledge on the regulation of lncRNAs is still limited, one of the mechanisms of action attributed is binding and regulating transcription factors, thus controlling gene expression and protein function. One such transcription factor is nuclear factor erythroid 2-related factor 2 (Nrf2), which plays a critical biological role in maintaining cellular homeostasis at multiple levels in physiological and pathophysiological conditions. The levels of Nrf2 were found to be down-regulated in many chronic diseases, signifying that Nrf2 can be a key therapeutic target. Few lncRNAs like lncRNA ROR, ENSMUST00000125413, lncRNA ODRUL, Nrf2-lncRNA have been associated with the Nrf2 signaling pathway in response to various stimuli, including stress. This review discusses the regulation of Nrf2 in different responses and the potential role of specific lncRNA in modulating its transcriptional activities. This review further helps to enhance our knowledge on the regulatory role of the critical antioxidant transcription factor, Nrf2.
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Affiliation(s)
- Ravichandran Jayasuriya
- SRM Research Institute and Department of Biotechnology, School of bioengineering, SRM Institute of Science and Technology, Kattankulathur, 603 203, Tamil Nadu, India
| | - Kunka Mohanram Ramkumar
- SRM Research Institute and Department of Biotechnology, School of bioengineering, SRM Institute of Science and Technology, Kattankulathur, 603 203, Tamil Nadu, India.
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Zheng Z, Li W, Xu J, Xie B, Yang M, Huang H, Li H, Wang Q. LncMSEN1, a mantle-specific LncRNA participating in nacre formation and response to polyI:C stimulation in pearl oyster Pinctada fucata martensii. FISH & SHELLFISH IMMUNOLOGY 2020; 96:330-335. [PMID: 31830566 DOI: 10.1016/j.fsi.2019.12.015] [Citation(s) in RCA: 8] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 10/04/2019] [Revised: 12/02/2019] [Accepted: 12/08/2019] [Indexed: 06/10/2023]
Abstract
Long noncoding RNA (LncRNA) regulates various life processes, including biomineralization and innate immune response through complex mechanisms. In this research, we identified a LncRNA named LncMSEN1 from pearl oyster Pinctada fucata martensii. LncMSEN1 sequence was validated by PCR, and its expression was high in mantle tissues according to qRT-PCR. LncMSEN1 was co-located with the nacre matrix protein N-U8 and fibrinogen domain-containing protein. And LncMSEN1 and N-U8 expression levels in the mantle were positively correlated. RNA interference was used to detect its effect on nacre formation in shells. Results showed that the decreased LncMSEN1 expression in mantle can cause the disordered growth of crystals on the inner surface of nacre in the shells, as well as the decrease expression of N-U8. In addition, the LncMSEN1 expression level significantly increased at 24 h after polyI:C stimulation in the mantle (P < 0.05). These findings suggested the involvement of LncMSEN1 in the formation of nacre in shells and related to innate immune response in pearl oyster, which provided additional insights into the roles of LncRNAs in pearl oysters.
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Affiliation(s)
- Zhe Zheng
- Fishery College, Guangdong Ocean University, Zhanjiang, 524025, China
| | - Wenhui Li
- Fishery College, Guangdong Ocean University, Zhanjiang, 524025, China
| | - Jiehua Xu
- Fishery College, Guangdong Ocean University, Zhanjiang, 524025, China
| | - Bingyi Xie
- Fishery College, Guangdong Ocean University, Zhanjiang, 524025, China
| | - Modong Yang
- Fishery College, Guangdong Ocean University, Zhanjiang, 524025, China
| | - Huajie Huang
- Fishery College, Guangdong Ocean University, Zhanjiang, 524025, China
| | - Huishan Li
- Fishery College, Guangdong Ocean University, Zhanjiang, 524025, China
| | - Qingheng Wang
- Fishery College, Guangdong Ocean University, Zhanjiang, 524025, China.
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Yan H, Bombarely A, Xu B, Frazier TP, Wang C, Chen P, Chen J, Hasing T, Cui C, Zhang X, Zhao B, Huang L. siRNAs regulate DNA methylation and interfere with gene and lncRNA expression in the heterozygous polyploid switchgrass. BIOTECHNOLOGY FOR BIOFUELS 2018; 11:208. [PMID: 30061930 PMCID: PMC6058383 DOI: 10.1186/s13068-018-1202-0] [Citation(s) in RCA: 6] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 03/20/2018] [Accepted: 07/10/2018] [Indexed: 05/14/2023]
Abstract
BACKGROUND Understanding the DNA methylome and its relationship with non-coding RNAs, including microRNAs (miRNAs) and long non-coding RNAs (lncRNAs), is essential for elucidating the molecular mechanisms underlying key biological processes in plants. Few studies have examined the functional roles of the DNA methylome in grass species with highly heterozygous polyploid genomes. RESULTS We performed genome-wide DNA methylation profiling in the tetraploid switchgrass (Panicum virgatum L.) cultivar 'Alamo' using bisulfite sequencing. Single-base-resolution methylation patterns were observed in switchgrass leaf and root tissues, which allowed for characterization of the relationship between DNA methylation and mRNA, miRNA, and lncRNA populations. The results of this study revealed that siRNAs positively regulate DNA methylation of the mCHH sites surrounding genes, and that DNA methylation interferes with gene and lncRNA expression in switchgrass. Ninety-six genes covered by differentially methylated regions (DMRs) were annotated by GO analysis as being involved in stimulus-related processes. Functionally, 82% (79/96) of these genes were found to be hypomethylated in switchgrass root tissue. Sequencing analysis of lncRNAs identified two lncRNAs that are potential precursors of miRNAs, which are predicted to target genes that function in cellulose biosynthesis, stress regulation, and stem and root development. CONCLUSIONS This study characterized the DNA methylome in switchgrass and elucidated its relevance to gene and non-coding RNAs. These results provide valuable genomic resources and references that will aid further epigenetic research in this important biofuel crop.
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Affiliation(s)
- Haidong Yan
- Department of Grassland Science, Animal Science and Technology College, Sichuan Agricultural University, Chengdu, 611130 China
- Department of Horticulture, Virginia Tech, Blacksburg, VA 24061 USA
| | | | - Bin Xu
- College of Grassland Science, Nanjing Agricultural University, Nanjing, 210095 China
| | - Taylor P. Frazier
- Department of Plant Sciences, University of Tennessee, Knoxville, TN 37996 USA
| | - Chengran Wang
- Department of Grassland Science, Animal Science and Technology College, Sichuan Agricultural University, Chengdu, 611130 China
| | - Peilin Chen
- Department of Grassland Science, Animal Science and Technology College, Sichuan Agricultural University, Chengdu, 611130 China
| | - Jing Chen
- Department of Grassland Science, Animal Science and Technology College, Sichuan Agricultural University, Chengdu, 611130 China
| | - Tomas Hasing
- Department of Horticulture, Virginia Tech, Blacksburg, VA 24061 USA
| | - Chenming Cui
- Department of Plant Pathology, Physiology, and Weed Science, Virginia Tech, Blacksburg, VA 24061 USA
| | - Xinquan Zhang
- Department of Grassland Science, Animal Science and Technology College, Sichuan Agricultural University, Chengdu, 611130 China
| | - Bingyu Zhao
- Department of Horticulture, Virginia Tech, Blacksburg, VA 24061 USA
| | - Linkai Huang
- Department of Grassland Science, Animal Science and Technology College, Sichuan Agricultural University, Chengdu, 611130 China
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Pacheco-Marín R, Melendez-Zajgla J, Castillo-Rojas G, Mandujano-Tinoco E, Garcia-Venzor A, Uribe-Carvajal S, Cabrera-Orefice A, Gonzalez-Torres C, Gaytan-Cervantes J, Mitre-Aguilar IB, Maldonado V. Transcriptome profile of the early stages of breast cancer tumoral spheroids. Sci Rep 2016; 6:23373. [PMID: 27021602 PMCID: PMC4810430 DOI: 10.1038/srep23373] [Citation(s) in RCA: 16] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/10/2015] [Accepted: 03/02/2016] [Indexed: 12/15/2022] Open
Abstract
Oxygen or nutrient deprivation of early stage tumoral spheroids can be used to reliably mimic the initial growth of primary and metastatic cancer cells. However, cancer cell growth during the initial stages has not been fully explored using a genome-wide approach. Thus, in the present study, we investigated the transcriptome of breast cancer cells during the initial stages of tumoral growth using RNAseq in a model of Multicellular Tumor Spheroids (MTS). Network analyses showed that a metastatic signature was enriched as several adhesion molecules were deregulated, including EPCAM, E-cadherin, integrins and syndecans, which were further supported by an increase in cell migration. Interestingly, we also found that the cancer cells at this stage of growth exhibited a paradoxical hyperactivation of oxidative mitochondrial metabolism. In addition, we found a large number of regulated (long non coding RNA) lncRNAs, several of which were co-regulated with neighboring genes. The regulatory role of some of these lncRNAs on mRNA expression was demonstrated with gain of function assays. This is the first report of an early-stage MTS transcriptome, which not only reveals a complex expression landscape, but points toward an important contribution of long non-coding RNAs in the final phenotype of three-dimensional cellular models.
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Affiliation(s)
- Rosario Pacheco-Marín
- Epigenetics, National Institute of Genomic Medicine, Periférico Sur No. 4809, Col Arenal Tepepan, Delegación Tlalpan, México, D.F., C.P 14610.,Posgraduate Program in Biological Sciences, Faculty of Medicine (UNAM), University City Avenue 3000 C.P. 04510, Coyoacan, Mexico City
| | - Jorge Melendez-Zajgla
- Functional Genomics laboratories, National Institute of Genomic Medicine, Periférico Sur No. 4809, Col Arenal Tepepan, Delegación Tlalpan, México, D.F., C.P 14610
| | - Gonzalo Castillo-Rojas
- Microbial Molecular Immunology Program, Department of Microbiology and Parasitology, Faculty of Medicine, National Autonomous University of Mexico (UNAM), University City Avenue 3000 C.P. 04510, Coyoacan, Mexico City
| | - Edna Mandujano-Tinoco
- Functional Genomics laboratories, National Institute of Genomic Medicine, Periférico Sur No. 4809, Col Arenal Tepepan, Delegación Tlalpan, México, D.F., C.P 14610
| | - Alfredo Garcia-Venzor
- Functional Genomics laboratories, National Institute of Genomic Medicine, Periférico Sur No. 4809, Col Arenal Tepepan, Delegación Tlalpan, México, D.F., C.P 14610
| | - Salvador Uribe-Carvajal
- Department of Molecular Genetics, Institute of Cellular Physiology (UNAM), University City Avenue 3000 C.P. 04510, Coyoacan, Mexico City
| | - Alfredo Cabrera-Orefice
- Department of Molecular Genetics, Institute of Cellular Physiology (UNAM), University City Avenue 3000 C.P. 04510, Coyoacan, Mexico City
| | - Carolina Gonzalez-Torres
- Functional Genomics laboratories, National Institute of Genomic Medicine, Periférico Sur No. 4809, Col Arenal Tepepan, Delegación Tlalpan, México, D.F., C.P 14610
| | - Javier Gaytan-Cervantes
- Functional Genomics laboratories, National Institute of Genomic Medicine, Periférico Sur No. 4809, Col Arenal Tepepan, Delegación Tlalpan, México, D.F., C.P 14610
| | - Irma B Mitre-Aguilar
- Unit of Biochemistry, National Institute of Medical Sciences and Nutrition Salvador Zubirán (INCMNSZ), Av. Vasco de Quiroga N° 15, Colonia Belisario Domínguez Sección XVI, Delegación Tlalpan. CP.14080, México D. F., México
| | - Vilma Maldonado
- Epigenetics, National Institute of Genomic Medicine, Periférico Sur No. 4809, Col Arenal Tepepan, Delegación Tlalpan, México, D.F., C.P 14610
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Pek JW, Okamura K. Regulatory RNAs discovered in unexpected places. WILEY INTERDISCIPLINARY REVIEWS-RNA 2015; 6:671-86. [DOI: 10.1002/wrna.1309] [Citation(s) in RCA: 14] [Impact Index Per Article: 1.6] [Reference Citation Analysis] [Track Full Text] [Subscribe] [Scholar Register] [Received: 06/17/2015] [Revised: 08/14/2015] [Accepted: 08/21/2015] [Indexed: 12/20/2022]
Affiliation(s)
- Jun Wei Pek
- Temasek Life Sciences Laboratory; 1 Research Link, National University of Singapore; Singapore Singapore
| | - Katsutomo Okamura
- Temasek Life Sciences Laboratory; 1 Research Link, National University of Singapore; Singapore Singapore
- School of Biological Sciences; Nanyang Technological University; Singapore Singapore
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Zhu HQ, Zhou X, Chang H, Li HG, Liu FF, Ma CQ, Lu J. Aberrant Expression of CCAT1 Regulated by c-Myc Predicts the Prognosis of Hepatocellular Carcinoma. Asian Pac J Cancer Prev 2015. [DOI: 10.7314/apjcp.2015.16.13.5181] [Citation(s) in RCA: 50] [Impact Index Per Article: 5.6] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/17/2023] Open
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11
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Hubé F, Francastel C. "Pocket-sized RNA-Seq": A Method to Capture New Mature microRNA Produced from a Genomic Region of Interest. Noncoding RNA 2015; 1:127-138. [PMID: 29861419 PMCID: PMC5932543 DOI: 10.3390/ncrna1020127] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.2] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/11/2015] [Revised: 06/03/2015] [Accepted: 06/23/2015] [Indexed: 12/28/2022] Open
Abstract
Currently, the discovery of new small ncRNAs requires high throughput methods even in the case of focused research on the regulation of specific genes or set of genes. We propose herein a simple, rapid, efficient, and cost effective method to clone and sequence single, yet unknown, small ncRNA. This technique that we called “Pocket-sized RNA-Seq” or psRNA-seq is based on in vitro transcription, RNA pull down and adapted RACE-PCR methods that allow its implementation using either available commercial kits or in-house reagents.
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Affiliation(s)
- Florent Hubé
- University Paris Diderot, Sorbonne Paris Cité, 75205 Paris, France.
- Epigénétique et Destin Cellulaire, CNRS UMR 7216, 75013 Paris, France.
| | - Claire Francastel
- University Paris Diderot, Sorbonne Paris Cité, 75205 Paris, France.
- Epigénétique et Destin Cellulaire, CNRS UMR 7216, 75013 Paris, France.
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Zhu H, Zhou X, Chang H, Li H, Liu F, Ma C, Lu J. CCAT1 promotes hepatocellular carcinoma cell proliferation and invasion. INTERNATIONAL JOURNAL OF CLINICAL AND EXPERIMENTAL PATHOLOGY 2015; 8:5427-5434. [PMID: 26191246 PMCID: PMC4503117] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Subscribe] [Scholar Register] [Received: 03/05/2015] [Accepted: 04/21/2015] [Indexed: 06/04/2023]
Abstract
It has been reported that CCAT1 is involved in the development of malignancies including colon cancer and gastric cancer. However, the role of CCAT1 in HCC still remains unknown. Real-time PCR was performed to test the relative expression of CCAT1 in HCC tissues and cell lines. We performed Chi-Square Analysis to study the correlation between clinical characteristics and CCAT1 expression. Based on the correlation, cell proliferation assay, cell invasion assay, wound healing assay and cell apoptosis assay were conducted in two HCC cell lines to examine the regulatory effect of CCAT1 on the HCC cells. The results indicated that the expression of CCAT1 was significantly increased in HCC tissues and cells compared with controls. We also found that the abnormally expressed CCAT1 could promote cell proliferation, migration and invasion. Taken together, our findings demonstrated that the aberrant expression of CCAT1 promotes hepatocellular carcinoma in vitro.
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Affiliation(s)
- Huaqiang Zhu
- Department of Hepatobiliary Surgery, Provincial Hospital Affiliated to Shandong University (East District) Jinan 250014, Shandong Province, China
| | - Xu Zhou
- Department of Hepatobiliary Surgery, Provincial Hospital Affiliated to Shandong University (East District) Jinan 250014, Shandong Province, China
| | - Hong Chang
- Department of Hepatobiliary Surgery, Provincial Hospital Affiliated to Shandong University (East District) Jinan 250014, Shandong Province, China
| | - Hongguang Li
- Department of Hepatobiliary Surgery, Provincial Hospital Affiliated to Shandong University (East District) Jinan 250014, Shandong Province, China
| | - Fangfeng Liu
- Department of Hepatobiliary Surgery, Provincial Hospital Affiliated to Shandong University (East District) Jinan 250014, Shandong Province, China
| | - Chaoqun Ma
- Department of Hepatobiliary Surgery, Provincial Hospital Affiliated to Shandong University (East District) Jinan 250014, Shandong Province, China
| | - Jun Lu
- Department of Hepatobiliary Surgery, Provincial Hospital Affiliated to Shandong University (East District) Jinan 250014, Shandong Province, China
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Distinct expression pattern of miRNAs in Marek's disease virus infected-chicken splenic tumors and non-tumorous spleen tissues. Res Vet Sci 2014; 97:156-61. [PMID: 24794245 DOI: 10.1016/j.rvsc.2014.04.003] [Citation(s) in RCA: 19] [Impact Index Per Article: 1.9] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/31/2013] [Revised: 04/03/2014] [Accepted: 04/13/2014] [Indexed: 11/24/2022]
Abstract
MicroRNAs (miRNAs) are small RNA molecules that regulate gene expression. Emerging evidence suggests that differential miRNA expression is associated with viral infection and tumorigenesis. Recently discovered microRNAs in the Marek's disease virus (MDV) genome have been suggested to have regulatory roles during MDV oncogenesis. To gain more insight into the molecular mechanisms of the tumorigenesis of MDV, we used microarrays to screen host and viral miRNAs that were sensitive to infection by MDV. Microarray analysis showed significant differential expression of 79 miRNAs, which was confirmed by qRT-PCR analysis. These data suggest that differentially expressed miRNAs may have major roles in MDV-induced tumorigenesis. In addition, we found two clades of chicken miRNAs had increased expression in splenic tumors and non-tumorous spleen tissues from GA-infected chickens. Thus, the expression of these miRNAs can be considered signatures for MDV infection and tumorigenesis.
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Mohammed J, Flynt AS, Siepel A, Lai EC. The impact of age, biogenesis, and genomic clustering on Drosophila microRNA evolution. RNA (NEW YORK, N.Y.) 2013; 19:1295-308. [PMID: 23882112 PMCID: PMC3753935 DOI: 10.1261/rna.039248.113] [Citation(s) in RCA: 22] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 03/20/2013] [Accepted: 06/07/2013] [Indexed: 05/16/2023]
Abstract
The molecular evolutionary signatures of miRNAs inform our understanding of their emergence, biogenesis, and function. The known signatures of miRNA evolution have derived mostly from the analysis of deeply conserved, canonical loci. In this study, we examine the impact of age, biogenesis pathway, and genomic arrangement on the evolutionary properties of Drosophila miRNAs. Crucial to the accuracy of our results was our curation of high-quality miRNA alignments, which included nearly 150 corrections to ortholog calls and nucleotide sequences of the global 12-way Drosophilid alignments currently available. Using these data, we studied primary sequence conservation, normalized free-energy values, and types of structure-preserving substitutions. We expand upon common miRNA evolutionary patterns that reflect fundamental features of miRNAs that are under functional selection. We observe that melanogaster-subgroup-specific miRNAs, although recently emerged and rapidly evolving, nonetheless exhibit evolutionary signatures that are similar to well-conserved miRNAs and distinct from other structured noncoding RNAs and bulk conserved non-miRNA hairpins. This provides evidence that even young miRNAs may be selected for regulatory activities. More strikingly, we observe that mirtrons and clustered miRNAs both exhibit distinct evolutionary properties relative to solo, well-conserved miRNAs, even after controlling for sequence depth. These studies highlight the previously unappreciated impact of biogenesis strategy and genomic location on the evolutionary dynamics of miRNAs, and affirm that miRNAs do not evolve as a unitary class.
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Affiliation(s)
- Jaaved Mohammed
- Department of Biological Statistics and Computational Biology, Cornell University, Ithaca, New York 14853, USA
- Tri-Institutional Training Program in Computational Biology and Medicine, New York, New York 10065, USA
| | - Alex S. Flynt
- Sloan-Kettering Institute, Department of Developmental Biology, New York, New York 10065, USA
| | - Adam Siepel
- Department of Biological Statistics and Computational Biology, Cornell University, Ithaca, New York 14853, USA
| | - Eric C. Lai
- Sloan-Kettering Institute, Department of Developmental Biology, New York, New York 10065, USA
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