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Storti M, Faietti ML, Murgia X, Catozzi C, Minato I, Tatoni D, Cantarella S, Ravanetti F, Ragionieri L, Ciccimarra R, Zoboli M, Vilanova M, Sánchez-Jiménez E, Gay M, Vilaseca M, Villetti G, Pioselli B, Salomone F, Ottonello S, Montanini B, Ricci F. Time-resolved transcriptomic profiling of the developing rabbit's lungs: impact of premature birth and implications for modelling bronchopulmonary dysplasia. Respir Res 2023; 24:80. [PMID: 36922832 PMCID: PMC10015812 DOI: 10.1186/s12931-023-02380-y] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/11/2022] [Accepted: 03/03/2023] [Indexed: 03/17/2023] Open
Abstract
BACKGROUND Premature birth, perinatal inflammation, and life-saving therapies such as postnatal oxygen and mechanical ventilation are strongly associated with the development of bronchopulmonary dysplasia (BPD); these risk factors, alone or combined, cause lung inflammation and alter programmed molecular patterns of normal lung development. The current knowledge on the molecular regulation of lung development mainly derives from mechanistic studies conducted in newborn rodents exposed to postnatal hyperoxia, which have been proven useful but have some limitations. METHODS Here, we used the rabbit model of BPD as a cost-effective alternative model that mirrors human lung development and, in addition, enables investigating the impact of premature birth per se on the pathophysiology of BPD without further perinatal insults (e.g., hyperoxia, LPS-induced inflammation). First, we characterized the rabbit's normal lung development along the distinct stages (i.e., pseudoglandular, canalicular, saccular, and alveolar phases) using histological, transcriptomic and proteomic analyses. Then, the impact of premature birth was investigated, comparing the sequential transcriptomic profiles of preterm rabbits obtained at different time intervals during their first week of postnatal life with those from age-matched term pups. RESULTS Histological findings showed stage-specific morphological features of the developing rabbit's lung and validated the selected time intervals for the transcriptomic profiling. Cell cycle and embryo development, oxidative phosphorylation, and WNT signaling, among others, showed high gene expression in the pseudoglandular phase. Autophagy, epithelial morphogenesis, response to transforming growth factor β, angiogenesis, epithelium/endothelial cells development, and epithelium/endothelial cells migration pathways appeared upregulated from the 28th day of gestation (early saccular phase), which represents the starting point of the premature rabbit model. Premature birth caused a significant dysregulation of the inflammatory response. TNF-responsive, NF-κB regulated genes were significantly upregulated at premature delivery and triggered downstream inflammatory pathways such as leukocyte activation and cytokine signaling, which persisted upregulated during the first week of life. Preterm birth also dysregulated relevant pathways for normal lung development, such as blood vessel morphogenesis and epithelial-mesenchymal transition. CONCLUSION These findings establish the 28-day gestation premature rabbit as a suitable model for mechanistic and pharmacological studies in the context of BPD.
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Affiliation(s)
- Matteo Storti
- Department of Experimental Pharmacology and Translational Science, R&D, Chiesi Farmaceutici S.P.A., 43122, Parma, Italy
| | - Maria Laura Faietti
- Department of Analytic and Early Formulations, Chiesi Farmaceutici S.P.A., R&D, 43122, Parma, Italy
| | | | - Chiara Catozzi
- Department of Experimental Pharmacology and Translational Science, R&D, Chiesi Farmaceutici S.P.A., 43122, Parma, Italy
| | - Ilaria Minato
- Laboratory of Biochemistry and Molecular Biology, Department of Chemistry, Life Sciences and Environmental Sustainability, University of Parma, 43124, Parma, Italy.,Interdepartmental Research Centre Biopharmanet-Tec, University of Parma, 43124, Parma, Italy
| | - Danilo Tatoni
- Laboratory of Biochemistry and Molecular Biology, Department of Chemistry, Life Sciences and Environmental Sustainability, University of Parma, 43124, Parma, Italy.,Department of Medical Biotechnologies, University of Siena, 53100, Siena, Italy
| | - Simona Cantarella
- Laboratory of Biochemistry and Molecular Biology, Department of Chemistry, Life Sciences and Environmental Sustainability, University of Parma, 43124, Parma, Italy.,Division of RNA Biology and Cancer, German Cancer Research Center (DKFZ), 69120, Heidelberg, Germany
| | | | - Luisa Ragionieri
- Department of Veterinary Sciences, University of Parma, 43124, Parma, Italy
| | - Roberta Ciccimarra
- Department of Veterinary Sciences, University of Parma, 43124, Parma, Italy
| | - Matteo Zoboli
- Department of Veterinary Sciences, University of Parma, 43124, Parma, Italy
| | - Mar Vilanova
- Institute for Research in Biomedicine (IRB Barcelona), The Barcelona Institute of Science and Technology, Baldiri Reixac, 10, 08028, Barcelona, Spain
| | - Ester Sánchez-Jiménez
- Institute for Research in Biomedicine (IRB Barcelona), The Barcelona Institute of Science and Technology, Baldiri Reixac, 10, 08028, Barcelona, Spain
| | - Marina Gay
- Institute for Research in Biomedicine (IRB Barcelona), The Barcelona Institute of Science and Technology, Baldiri Reixac, 10, 08028, Barcelona, Spain
| | - Marta Vilaseca
- Institute for Research in Biomedicine (IRB Barcelona), The Barcelona Institute of Science and Technology, Baldiri Reixac, 10, 08028, Barcelona, Spain
| | - Gino Villetti
- Department of Experimental Pharmacology and Translational Science, R&D, Chiesi Farmaceutici S.P.A., 43122, Parma, Italy
| | - Barbara Pioselli
- Department of Analytic and Early Formulations, Chiesi Farmaceutici S.P.A., R&D, 43122, Parma, Italy
| | - Fabrizio Salomone
- Department of Experimental Pharmacology and Translational Science, R&D, Chiesi Farmaceutici S.P.A., 43122, Parma, Italy
| | - Simone Ottonello
- Laboratory of Biochemistry and Molecular Biology, Department of Chemistry, Life Sciences and Environmental Sustainability, University of Parma, 43124, Parma, Italy.,Interdepartmental Research Centre Biopharmanet-Tec, University of Parma, 43124, Parma, Italy
| | - Barbara Montanini
- Laboratory of Biochemistry and Molecular Biology, Department of Chemistry, Life Sciences and Environmental Sustainability, University of Parma, 43124, Parma, Italy. .,Interdepartmental Research Centre Biopharmanet-Tec, University of Parma, 43124, Parma, Italy.
| | - Francesca Ricci
- Department of Experimental Pharmacology and Translational Science, R&D, Chiesi Farmaceutici S.P.A., 43122, Parma, Italy. .,Head of Neonatology and Pulmonary Rare Disease, Preclinical Pharmacology, Chiesi Farmaceutici S.P.A., 43122, Parma, Italy.
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Gao G, Hu S, Zhang K, Wang H, Xie Y, Zhang C, Wu R, Zhao X, Zhang H, Wang Q. Genome-Wide Gene Expression Profiles Reveal Distinct Molecular Characteristics of the Goose Granulosa Cells. Front Genet 2021; 12:786287. [PMID: 34992633 PMCID: PMC8725158 DOI: 10.3389/fgene.2021.786287] [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: 10/01/2021] [Accepted: 11/30/2021] [Indexed: 11/24/2022] Open
Abstract
Granulosa cells (GCs) are decisive players in follicular development. In this study, the follicle tissues and GCs were isolated from the goose during the peak-laying period to perform hematoxylin-eosin staining and RNA-seq, respectively. Moreover, the dynamic mRNA and lncRNA expression profiles and mRNA-lncRNA network analysis were integrated to identify the important genes and lncRNAs. The morphological analysis showed that the size of the GCs did not significantly change, but the thickness of the granulosa layer cells differed significantly across the developmental stages. Subsequently, 14,286 mRNAs, 3,956 lncRNAs, and 1,329 TUCPs (transcripts with unknown coding potential) were detected in the GCs. We identified 37 common DEGs in the pre-hierarchical and hierarchical follicle stages, respectively, which might be critical for follicle development. Moreover, 3,089 significant time-course DEGs (Differentially expressed genes) and 13 core genes in 4 clusters were screened during goose GCs development. Finally, the network lncRNA G8399 with CADH5 and KLF2, and lncRNA G8399 with LARP6 and EOMES were found to be important for follicular development in GCs. Thus, the results would provide a rich resource for elucidating the reproductive biology of geese and accelerate the improvement of the egg-laying performance of geese.
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Affiliation(s)
- Guangliang Gao
- Chongqing Academy of Animal Sciences, Chongqing, China
- Institute of Animal Genetics and Breeding, College of Animal Science and Technology, Sichuan Agricultural University, Chengdu, China
- Chongqing Engineering Research Center of Goose Genetic Improvement, Chongqing, China
- *Correspondence: Guangliang Gao, ; Hongmei Zhang, ; Qigui Wang,
| | - Silu Hu
- Institute of Animal Genetics and Breeding, College of Animal Science and Technology, Sichuan Agricultural University, Chengdu, China
| | - Keshan Zhang
- Chongqing Academy of Animal Sciences, Chongqing, China
- Chongqing Engineering Research Center of Goose Genetic Improvement, Chongqing, China
| | - Haiwei Wang
- Chongqing Academy of Animal Sciences, Chongqing, China
- Chongqing Engineering Research Center of Goose Genetic Improvement, Chongqing, China
| | - Youhui Xie
- Chongqing Academy of Animal Sciences, Chongqing, China
- Chongqing Engineering Research Center of Goose Genetic Improvement, Chongqing, China
| | - Changlian Zhang
- Chongqing Academy of Animal Sciences, Chongqing, China
- Chongqing Engineering Research Center of Goose Genetic Improvement, Chongqing, China
| | - Rui Wu
- Chongqing Academy of Animal Sciences, Chongqing, China
| | - Xianzhi Zhao
- Chongqing Academy of Animal Sciences, Chongqing, China
- Chongqing Engineering Research Center of Goose Genetic Improvement, Chongqing, China
| | - Hongmei Zhang
- Department of Cardiovascular Ultrasound and Non-invasive Cardiology, Sichuan Academy of Medical Sciences and Sichuan Provincial People’s Hospital, Chengdu, China
- Ultrasound in Cardiac Electrophysiology and Biomechanics Key Laboratory of Sichuan Province, Chengdu, China
- *Correspondence: Guangliang Gao, ; Hongmei Zhang, ; Qigui Wang,
| | - Qigui Wang
- Chongqing Academy of Animal Sciences, Chongqing, China
- Chongqing Engineering Research Center of Goose Genetic Improvement, Chongqing, China
- *Correspondence: Guangliang Gao, ; Hongmei Zhang, ; Qigui Wang,
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3
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Jia X, He Y, Chen SY, Wang J, Hu S, Lai SJ. Genome-wide identification and characterisation of long non-coding RNAs in two Chinese cattle breeds. ITALIAN JOURNAL OF ANIMAL SCIENCE 2020. [DOI: 10.1080/1828051x.2020.1735266] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 12/19/2022]
Affiliation(s)
- Xianbo Jia
- Farm Animal Genetic Resources Exploration and Innovation Key Laboratory of Sichuan Province, Sichuan Agricultural University, Chengdu, China
| | - Yang He
- Farm Animal Genetic Resources Exploration and Innovation Key Laboratory of Sichuan Province, Sichuan Agricultural University, Chengdu, China
| | - Shi-Yi Chen
- Farm Animal Genetic Resources Exploration and Innovation Key Laboratory of Sichuan Province, Sichuan Agricultural University, Chengdu, China
| | - Jie Wang
- Farm Animal Genetic Resources Exploration and Innovation Key Laboratory of Sichuan Province, Sichuan Agricultural University, Chengdu, China
| | - Shenqiang Hu
- Farm Animal Genetic Resources Exploration and Innovation Key Laboratory of Sichuan Province, Sichuan Agricultural University, Chengdu, China
| | - Song-Jia Lai
- Farm Animal Genetic Resources Exploration and Innovation Key Laboratory of Sichuan Province, Sichuan Agricultural University, Chengdu, China
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4
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Zhang J, Ma J, Zhou X, Hu S, Ge L, Sun J, Li P, Long K, Jin L, Tang Q, Liu L, Li X, Shuai S, Li M. Comprehensive Analysis of mRNA and lncRNA Transcriptomes Reveals the Differentially Hypoxic Response of Preadipocytes During Adipogenesis. Front Genet 2020; 11:845. [PMID: 32849828 PMCID: PMC7425071 DOI: 10.3389/fgene.2020.00845] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/03/2020] [Accepted: 07/13/2020] [Indexed: 11/28/2022] Open
Abstract
Local hypoxia has recently been reported to occur in the white adipose tissue (WAT) microenvironment during obesity. Adipocytes have a unique life cycle that reflects the different stages of adipogenesis in the WAT niche. Long non-coding RNAs (lncRNAs) play an important role in the cellular response to hypoxia. However, the differentially hypoxic responses of preadipocytes during adipogenesis and the potential role of lncRNAs in this process remain to be elucidated. Here, we evaluated the differentially hypoxic responses of primary hamster preadipocytes during adipogenesis and analyzed mRNA and lncRNA expression in same Ribo-Zero RNA-seq libraries. Hypoxia induced HIF-1α protein during adipogenesis and caused divergent changes of cell phenotypes. A total of 10,318 mRNAs were identified to be expressed in twenty libraries (five timepoints), and 3,198 differentially expressed mRNAs (DE mRNAs) were detected at five timepoints (hypoxia vs. normoxia). Functional enrichment analysis revealed the shared and specific hypoxia response pathways in the different stages of adipogenesis. Hypoxia differentially modulated the expression profile of adipose-associated genes, including adipokines, lipogenesis, lipolysis, hyperplasia, hypertrophy, inflammatory, and extracellular matrix. We also identified 4,296 lncRNAs that were expressed substantially and detected 1,431 DE lncRNAs at five timepoints. Two, 3, 5, 13, and 50 DE mRNAs at D0, D1, D3, D7, and D11, respectively, were highly correlated and locus-nearby DE lncRNAs and mainly involved in the cell cycle, vesicle-mediated transport, and mitochondrion organization. We identified 28 one-to-one lncRNA-mRNA pairs that might be closely related to adipocyte functions, such as ENSCGRT00015041780-Hilpda, TU2105-Cdsn, and TU17588-Ltbp3. These lncRNAs may represent the crucial regulation axis in the cellular response to hypoxia during adipogenesis. This study dissected the effects of hypoxia in the cell during adipogenesis, uncovered novel regulators potentially associated with WAT function, and may provide a new viewpoint for interpretation and treatment of obesity.
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Affiliation(s)
- Jinwei Zhang
- Farm Animal Genetic Resource Exploration and Innovation Key Laboratory of Sichuan Province, Sichuan Agricultural University, Chengdu, China
| | - Jideng Ma
- Farm Animal Genetic Resource Exploration and Innovation Key Laboratory of Sichuan Province, Sichuan Agricultural University, Chengdu, China
| | - Xiankun Zhou
- Farm Animal Genetic Resource Exploration and Innovation Key Laboratory of Sichuan Province, Sichuan Agricultural University, Chengdu, China
| | - Silu Hu
- Farm Animal Genetic Resource Exploration and Innovation Key Laboratory of Sichuan Province, Sichuan Agricultural University, Chengdu, China
| | - Liangpeng Ge
- Chongqing Academy of Animal Sciences, Chongqing, China.,Key Laboratory of Pig Industry Sciences, Ministry of Agriculture, Chongqing, China.,Chongqing Key Laboratory of Pig Industry Sciences, Chongqing, China
| | - Jing Sun
- Chongqing Academy of Animal Sciences, Chongqing, China.,Key Laboratory of Pig Industry Sciences, Ministry of Agriculture, Chongqing, China.,Chongqing Key Laboratory of Pig Industry Sciences, Chongqing, China
| | - Penghao Li
- Jinxin Research Institute for Reproductive Medicine and Genetics, Chengdu Xi Nan Gynecological Hospital, Chengdu, China
| | - Keren Long
- Farm Animal Genetic Resource Exploration and Innovation Key Laboratory of Sichuan Province, Sichuan Agricultural University, Chengdu, China
| | - Long Jin
- Farm Animal Genetic Resource Exploration and Innovation Key Laboratory of Sichuan Province, Sichuan Agricultural University, Chengdu, China
| | - Qianzi Tang
- Farm Animal Genetic Resource Exploration and Innovation Key Laboratory of Sichuan Province, Sichuan Agricultural University, Chengdu, China
| | - Lingyan Liu
- Farm Animal Genetic Resource Exploration and Innovation Key Laboratory of Sichuan Province, Sichuan Agricultural University, Chengdu, China
| | - Xuewei Li
- Farm Animal Genetic Resource Exploration and Innovation Key Laboratory of Sichuan Province, Sichuan Agricultural University, Chengdu, China
| | - Surong Shuai
- Farm Animal Genetic Resource Exploration and Innovation Key Laboratory of Sichuan Province, Sichuan Agricultural University, Chengdu, China
| | - Mingzhou Li
- Farm Animal Genetic Resource Exploration and Innovation Key Laboratory of Sichuan Province, Sichuan Agricultural University, Chengdu, China
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5
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Ning C, Ma T, Hu S, Xu Z, Zhang P, Zhao X, Wang Y, Yin H, Hu Y, Fan X, Zeng B, Yang M, Yang D, Ni Q, Li Y, Zhang M, Xu H, Yao Y, Zhu Q, Li D. Long Non-coding RNA and mRNA Profile of Liver Tissue During Four Developmental Stages in the Chicken. Front Genet 2020; 11:574. [PMID: 32612636 PMCID: PMC7309962 DOI: 10.3389/fgene.2020.00574] [Citation(s) in RCA: 10] [Impact Index Per Article: 2.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/09/2019] [Accepted: 05/11/2020] [Indexed: 12/17/2022] Open
Abstract
The liver is the major organ of lipid biosynthesis in the chicken. In laying hens, the liver synthesizes most of the yolk precursors and transports them to developing follicles to produce eggs. However, a systematic investigation of the long non-coding RNA (lncRNA) and mRNA transcriptome in liver across developmental stages is needed. Here, we constructed 12 RNA libraries from liver tissue during four developmental stages: juvenile (day 60), sexual maturity (day 133), peak laying (day 220), and broodiness (day 400). A total of 16,930 putative lncRNAs and 18,260 mRNAs were identified. More than half (53.70%) of the lncRNAs were intergenic lncRNAs. The temporal expression pattern showed that lncRNAs were more restricted than mRNAs. We identified numerous differentially expressed lncRNAs and mRNAs by pairwise comparison between the four developmental stages and found that VTG2, RBP, and a novel protein-coding gene were differentially expressed in all stages. Time-series analysis showed that the modules with upregulated genes were involved in lipid metabolism processes. Co-expression networks suggested functional relatedness between mRNAs and lncRNAs; the DE-lncRNAs were mainly involved in lipid biosynthesis and metabolism processes. We showed that the liver transcriptome varies across different developmental stages. Our results improve our understanding of the molecular mechanisms underlying liver development in chickens.
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Affiliation(s)
- Chunyou Ning
- Farm Animal Genetic Resources Exploration and Innovation Key Laboratory of Sichuan Province, College of Animal Science and Technology, Sichuan Agricultural University, Chengdu, China
| | - Tianyuan Ma
- Farm Animal Genetic Resources Exploration and Innovation Key Laboratory of Sichuan Province, College of Animal Science and Technology, Sichuan Agricultural University, Chengdu, China
| | - Silu Hu
- Farm Animal Genetic Resources Exploration and Innovation Key Laboratory of Sichuan Province, College of Animal Science and Technology, Sichuan Agricultural University, Chengdu, China
| | - Zhongxian Xu
- Farm Animal Genetic Resources Exploration and Innovation Key Laboratory of Sichuan Province, College of Animal Science and Technology, Sichuan Agricultural University, Chengdu, China
| | - Pu Zhang
- Farm Animal Genetic Resources Exploration and Innovation Key Laboratory of Sichuan Province, College of Animal Science and Technology, Sichuan Agricultural University, Chengdu, China
| | - Xiaoling Zhao
- Farm Animal Genetic Resources Exploration and Innovation Key Laboratory of Sichuan Province, College of Animal Science and Technology, Sichuan Agricultural University, Chengdu, China
| | - Yan Wang
- Farm Animal Genetic Resources Exploration and Innovation Key Laboratory of Sichuan Province, College of Animal Science and Technology, Sichuan Agricultural University, Chengdu, China
| | - Huadong Yin
- Farm Animal Genetic Resources Exploration and Innovation Key Laboratory of Sichuan Province, College of Animal Science and Technology, Sichuan Agricultural University, Chengdu, China
| | - Yaodong Hu
- Farm Animal Genetic Resources Exploration and Innovation Key Laboratory of Sichuan Province, College of Animal Science and Technology, Sichuan Agricultural University, Chengdu, China
| | - Xiaolan Fan
- Farm Animal Genetic Resources Exploration and Innovation Key Laboratory of Sichuan Province, College of Animal Science and Technology, Sichuan Agricultural University, Chengdu, China
| | - Bo Zeng
- Farm Animal Genetic Resources Exploration and Innovation Key Laboratory of Sichuan Province, College of Animal Science and Technology, Sichuan Agricultural University, Chengdu, China
| | - Mingyao Yang
- Farm Animal Genetic Resources Exploration and Innovation Key Laboratory of Sichuan Province, College of Animal Science and Technology, Sichuan Agricultural University, Chengdu, China
| | - Deying Yang
- Farm Animal Genetic Resources Exploration and Innovation Key Laboratory of Sichuan Province, College of Animal Science and Technology, Sichuan Agricultural University, Chengdu, China
| | - Qingyong Ni
- Farm Animal Genetic Resources Exploration and Innovation Key Laboratory of Sichuan Province, College of Animal Science and Technology, Sichuan Agricultural University, Chengdu, China
| | - Yan Li
- Farm Animal Genetic Resources Exploration and Innovation Key Laboratory of Sichuan Province, College of Animal Science and Technology, Sichuan Agricultural University, Chengdu, China
| | - Mingwang Zhang
- Farm Animal Genetic Resources Exploration and Innovation Key Laboratory of Sichuan Province, College of Animal Science and Technology, Sichuan Agricultural University, Chengdu, China
| | - Huailiang Xu
- College of Life Science, Sichuan Agricultural University, Ya'an, China
| | - Yongfang Yao
- College of Life Science, Sichuan Agricultural University, Ya'an, China
| | - Qing Zhu
- Farm Animal Genetic Resources Exploration and Innovation Key Laboratory of Sichuan Province, College of Animal Science and Technology, Sichuan Agricultural University, Chengdu, China
| | - Diyan Li
- Farm Animal Genetic Resources Exploration and Innovation Key Laboratory of Sichuan Province, College of Animal Science and Technology, Sichuan Agricultural University, Chengdu, China
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6
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Nolte W, Weikard R, Brunner RM, Albrecht E, Hammon HM, Reverter A, Kühn C. Identification and Annotation of Potential Function of Regulatory Antisense Long Non-Coding RNAs Related to Feed Efficiency in Bos taurus Bulls. Int J Mol Sci 2020; 21:E3292. [PMID: 32384694 PMCID: PMC7247587 DOI: 10.3390/ijms21093292] [Citation(s) in RCA: 6] [Impact Index Per Article: 1.5] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/14/2020] [Revised: 05/02/2020] [Accepted: 05/04/2020] [Indexed: 12/18/2022] Open
Abstract
Long non-coding RNAs (lncRNAs) can influence transcriptional and translational processes in mammalian cells and are associated with various developmental, physiological and phenotypic conditions. However, they remain poorly understood and annotated in livestock species. We combined phenotypic, metabolomics and liver transcriptomic data of bulls divergent for residual feed intake (RFI) and fat accretion. Based on a project-specific transcriptome annotation for the bovine reference genome ARS-UCD.1.2 and multiple-tissue total RNA sequencing data, we predicted 3590 loci to be lncRNAs. To identify lncRNAs with potential regulatory influence on phenotype and gene expression, we applied the regulatory impact factor algorithm on a functionally prioritized set of loci (n = 4666). Applying the algorithm of partial correlation and information theory, significant and independent pairwise correlations were calculated and co-expression networks were established, including plasma metabolites correlated with lncRNAs. The network hub lncRNAs were assessed for potential cis-actions and subjected to biological pathway enrichment analyses. Our results reveal a prevalence of antisense lncRNAs positively correlated with adjacent protein-coding genes and suggest their participation in mitochondrial function, acute phase response signalling, TCA-cycle, fatty acid β-oxidation and presumably gluconeogenesis. These antisense lncRNAs indicate a stabilizing function for their cis-correlated genes and a putative regulatory role in gene expression.
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Affiliation(s)
- Wietje Nolte
- Institute of Genome Biology, Leibniz Institute for Farm Animal Biology (FBN), 18196 Dummerstorf, Germany; (W.N.); (R.W.); (R.M.B.)
| | - Rosemarie Weikard
- Institute of Genome Biology, Leibniz Institute for Farm Animal Biology (FBN), 18196 Dummerstorf, Germany; (W.N.); (R.W.); (R.M.B.)
| | - Ronald M. Brunner
- Institute of Genome Biology, Leibniz Institute for Farm Animal Biology (FBN), 18196 Dummerstorf, Germany; (W.N.); (R.W.); (R.M.B.)
| | - Elke Albrecht
- Institute of Muscle Biology and Growth, Leibniz Institute for Farm Animal Biology (FBN), 18196 Dummerstorf, Germany;
| | - Harald M. Hammon
- Institute of Nutritional Physiology “Oskar Kellner”, Leibniz Institute for Farm Animal Biology (FBN), 18196 Dummerstorf, Germany;
| | - Antonio Reverter
- Commonwealth Scientific and Industrial Research Organisation (CSIRO) Agriculture and Food, Queensland Bioscience Precinct, St Lucia 4067 QLD, Australia;
| | - Christa Kühn
- Institute of Genome Biology, Leibniz Institute for Farm Animal Biology (FBN), 18196 Dummerstorf, Germany; (W.N.); (R.W.); (R.M.B.)
- Faculty of Agricultural and Environmental Sciences, University Rostock, 18059 Rostock, Germany
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7
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Lin K, Song LJ, Ma J, Zhang TS, You DY, He YW. Identification of cancer hallmark-associated gene and lncRNA cooperative regulation pairs and dictate lncRNA roles in oral squamous cell carcinoma. J Cell Mol Med 2020; 24:5213-5223. [PMID: 32202050 PMCID: PMC7205782 DOI: 10.1111/jcmm.15174] [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: 08/07/2019] [Revised: 12/17/2019] [Accepted: 03/01/2020] [Indexed: 12/28/2022] Open
Abstract
Oral squamous cell carcinoma (OSCC) is the most common malignant tumour in the oral and maxillofacial region. Numerous cancers share ten common traits ("hallmarks") that govern the transformation of normal cells into cancer cells. Long non-coding RNAs (lncRNAs) are important factors that contribute to tumorigenesis. However, very little is known about the cooperative relationships between lncRNAs and cancer hallmark-associated genes in OSCC. Through integrative analysis of cancer hallmarks, somatic mutations, copy number variants (CNVs) and expression, some OSCC-specific cancer hallmark-associated genes and lncRNAs are identified. A computational framework to identify gene and lncRNA cooperative regulation pairs (GLCRPs) associated with different cancer hallmarks is developed based on the co-expression and co-occurrence of mutations. The distinct and common features of ten cancer hallmarks based on GLCRPs are characterized in OSCC. Cancer hallmark insensitivity to antigrowth signals and self-sufficiency in growth signals are shared by most GLCRPs in OSCC. Some key GLCRPs participate in many cancer hallmarks in OSCC. Cancer hallmark-associated GLCRP networks have complex patterns and specific functions in OSCC. Specially, some key GLCRPs are associated with the prognosis of OSCC patients. In summary, we generate a comprehensive landscape of cancer hallmark-associated GLCRPs that can act as a starting point for future functional explorations, the identification of biomarkers and lncRNA-based targeted therapy in OSCC.
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Affiliation(s)
- Ken Lin
- Department of Otolaryngology, Head and Neck Surgery, The Affiliated Children's Hospital of Kunming Medical University, Kunming, China.,Department of Otolaryngology, Head and Neck Surgery, Kunming Children's Hospital, Kunming, China.,The Affiliated Stomatological Hospital of Kunming Medical University, Kunming, China
| | - Lin-Jing Song
- Department of Oncology, Yan'an Hospital, Kunming, China
| | - Jing Ma
- Department of Otolaryngology, Head and Neck Surgery, Kunming Children's Hospital, Kunming, China
| | - Tie-Song Zhang
- Department of Otolaryngology, Head and Neck Surgery, Kunming Children's Hospital, Kunming, China
| | - Ding-Yun You
- School of Public Health, Kunming Medical University, Kunming, China
| | - Yong-Wen He
- Department of Dental Research, The Affiliated Stomatological Hospital of Kunming Medical University, Kunming, China
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8
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Transcriptional Differences of Coding and Non-Coding Genes Related to the Absence of Melanocyte in Skins of Bama Pig. Genes (Basel) 2019; 11:genes11010047. [PMID: 31905971 PMCID: PMC7017308 DOI: 10.3390/genes11010047] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.2] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/04/2019] [Revised: 12/16/2019] [Accepted: 12/22/2019] [Indexed: 01/31/2023] Open
Abstract
Skin is the body’s largest organ, and the main function of skin is to protect underlying organs from possible external damage. Melanocytes play an important role in skin pigmentation. The Bama pig has a “two-end-black” phenotype with different coat colors across skin regions, e.g., white skin (without melanocytes) and black skin (with melanocytes), which could be a model to investigate skin-related disorders, specifically loss of melanocytes. Here, we generated expression profiles of mRNAs and long noncoding RNAs in Bama pig skins with different coat colors. In total, 14,900 mRNAs and 7549 lncRNAs were expressed. Overall, 2338 mRNAs/113 lncRNAs with FDR-adjusted p-value ≤ 0.05 were considered to be differentially expressed (DE) mRNAs/lncRNAs, with 1305 down-regulated mRNAs and 1033 up-regulated mRNAs in white skin with|log2(fold change)| > 1. The genes down-regulated in white skin were associated with pigmentation, melanocyte–keratinocyte interaction, and keratin, while up-regulated ones were mainly associated with cellular energy metabolisms. Furthermore, those DE lncRNAs were predicted to be implicated in pigmentation, keratin synthesis and cellular energy metabolism. In general, this study provides insight into the transcriptional difference involved in melanocyte-loss-induced keratinocyte changes and promotes the Bama pig as a biomedical model in skin research.
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Gu Y, Zhou R, Jin L, Tao X, Zhong Z, Yang X, Liang Y, Yang Y, Wang Y, Chen X, Gong J, He Z, Li M, Lv X. Temporal expression profiling of long noncoding RNA and mRNA in the peripheral blood during porcine development. ASIAN-AUSTRALASIAN JOURNAL OF ANIMAL SCIENCES 2019; 33:836-847. [PMID: 31480157 PMCID: PMC7206404 DOI: 10.5713/ajas.19.0313] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.2] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Subscribe] [Scholar Register] [Received: 04/12/2019] [Accepted: 07/23/2019] [Indexed: 12/15/2022]
Abstract
Objective We investigated the temporal expression profiles of long noncoding RNA (lncRNA) and mRNA in the peripheral blood of pigs during development and identified the lncRNAs that are related to the blood-based immune system. Methods Peripheral blood samples were obtained from the pigs at 0, 7, 28, and 180 days and 2 years of age. RNA sequencing was performed to survey the lncRNA and mRNA transcriptomes in the samples. Short time-series expression miner (STEM) was used to show temporal expression patterns in the mRNAs and lncRNAs. Gene ontology and Kyoto encyclopedia of genes and genomes analyses were performed to assess the genes’ biological relevance. To predict the functions of the identified lncRNAs, we extracted mRNAs that were nearby loci and highly correlated with the lncRNAs. Results In total of 5,946 lncRNA and 12,354 mRNA transcripts were identified among the samples. STEM showed that most lncRNAs and mRNAs had similar temporal expression patterns during development, indicating the expressional correlation and functional relatedness between them. The five stages were divided into two classes: the suckling period and the late developmental stage. Most genes were expressed at low level during the suckling period, but at higher level during the late stages. Expression of several T-cell-related genes increased continuously during the suckling period, indicating that these genes are crucial for establishing the adaptive immune system in piglets at this stage. Notably, lncRNA TCONS-00086451 may promote blood-based immune system development by upregulating nuclear factor of activated T-cells cytoplasmic 2 expression. Conclusion This study provides a catalog of porcine peripheral blood-related lncRNAs and mRNAs and reveals the characteristics and temporal expression profiles of these lncRNAs and mRNAs during peripheral blood development from the newborn to adult stages in pigs.
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Affiliation(s)
- Yiren Gu
- Animal Breeding and Genetics Key Laboratory of Sichuan Province, Sichuan Animal Science Academy, Chengdu, Sichuan 610066, China.,Farm Animal Genetic Resources Exploration and Innovation Key Laboratory of Sichuan Province, Sichuan Agricultural University, Chengdu, Sichuan 611130, China
| | - Rui Zhou
- Farm Animal Genetic Resources Exploration and Innovation Key Laboratory of Sichuan Province, Sichuan Agricultural University, Chengdu, Sichuan 611130, China
| | - Long Jin
- Farm Animal Genetic Resources Exploration and Innovation Key Laboratory of Sichuan Province, Sichuan Agricultural University, Chengdu, Sichuan 611130, China
| | - Xuan Tao
- Animal Breeding and Genetics Key Laboratory of Sichuan Province, Sichuan Animal Science Academy, Chengdu, Sichuan 610066, China
| | - Zhijun Zhong
- Animal Breeding and Genetics Key Laboratory of Sichuan Province, Sichuan Animal Science Academy, Chengdu, Sichuan 610066, China
| | - Xuemei Yang
- Animal Breeding and Genetics Key Laboratory of Sichuan Province, Sichuan Animal Science Academy, Chengdu, Sichuan 610066, China
| | - Yan Liang
- Animal Breeding and Genetics Key Laboratory of Sichuan Province, Sichuan Animal Science Academy, Chengdu, Sichuan 610066, China
| | - Yuekui Yang
- Animal Breeding and Genetics Key Laboratory of Sichuan Province, Sichuan Animal Science Academy, Chengdu, Sichuan 610066, China
| | - Yan Wang
- Animal Breeding and Genetics Key Laboratory of Sichuan Province, Sichuan Animal Science Academy, Chengdu, Sichuan 610066, China
| | - Xiaohui Chen
- Animal Breeding and Genetics Key Laboratory of Sichuan Province, Sichuan Animal Science Academy, Chengdu, Sichuan 610066, China
| | - Jianjun Gong
- Animal Breeding and Genetics Key Laboratory of Sichuan Province, Sichuan Animal Science Academy, Chengdu, Sichuan 610066, China
| | - Zhiping He
- Animal Breeding and Genetics Key Laboratory of Sichuan Province, Sichuan Animal Science Academy, Chengdu, Sichuan 610066, China
| | - Mingzhou Li
- Farm Animal Genetic Resources Exploration and Innovation Key Laboratory of Sichuan Province, Sichuan Agricultural University, Chengdu, Sichuan 611130, China
| | - Xuebin Lv
- Animal Breeding and Genetics Key Laboratory of Sichuan Province, Sichuan Animal Science Academy, Chengdu, Sichuan 610066, China
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Wang J, Li ZX, Yang DD, Liu PQ, Wang ZQ, Zeng YQ, Chen W. Diquat Determines a Deregulation of lncRNA and mRNA Expression in the Liver of Postweaned Piglets. OXIDATIVE MEDICINE AND CELLULAR LONGEVITY 2019; 2019:9148535. [PMID: 31214284 PMCID: PMC6535875 DOI: 10.1155/2019/9148535] [Citation(s) in RCA: 5] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Subscribe] [Scholar Register] [Received: 10/22/2018] [Revised: 02/24/2019] [Accepted: 04/17/2019] [Indexed: 01/01/2023]
Abstract
Oxidative stress is detrimental to animals and can depress the growth performance and regulate the gene expression of animals. However, it remains unclear how oxidative stress regulates the expression of long noncoding RNAs (lncRNAs) and mRNAs. Therefore, the purpose of this article was to explore the profiles of lncRNAs and mRNAs in the liver of piglets under oxidative stress. Here, we constructed a piglet oxidative stress model induced by diquat and evaluated the effects of oxidative stress on the growth performance and antioxidant enzyme activity of piglets. We also used RNA-Seq to examine the global expression of lncRNAs and mRNAs in piglets under oxidative stress. The targets of lncRNAs and mRNAs were enriched in gene ontology (GO) terms and signaling pathways. The results show that the growth performance and activities of antioxidant enzymes were decreased in piglets under oxidative stress. Moreover, eight lncRNAs (6 upregulated and 2 downregulated) and 30 mRNAs (8 upregulated and 22 downregulated) were differentially expressed in the oxidative stress group of piglets compared to the negative control group. According to biological processes in enriched GO terms, the oxoacid metabolic process, intramolecular oxidoreductase activity, and oxidation-reduction process play important roles in oxidative stress. Pathway analysis showed that the signaling pathways involved in insulin and glucose metabolism had a close relationship with oxidative stress. Further in vitro experiments showed that the expression of the upregulated gene GNMT was significantly increased in primary porcine hepatocytes after diquat stimulation. In contrast, the level of the downregulated gene GCK was significantly decreased at 12 h in primary porcine hepatocytes after diquat stimulation. Our results expand our knowledge of the lncRNAs and mRNAs transcribed in the livers of piglets under oxidative stress and provide a basis for future research on the molecular mechanisms mediating oxidative stress and tissue damage.
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Affiliation(s)
- Jin Wang
- Shandong Provincial Key Laboratory of Animal Biotechnology and Disease Control and Prevention, College of Animal Science and Technology, Shandong Agricultural University, No. 61 Daizong Street, Tai'an City, Shandong Province 271018, China
| | - Zhi-xin Li
- Shandong Provincial Key Laboratory of Animal Biotechnology and Disease Control and Prevention, College of Animal Science and Technology, Shandong Agricultural University, No. 61 Daizong Street, Tai'an City, Shandong Province 271018, China
| | - Dan-dan Yang
- Shandong Provincial Key Laboratory of Animal Biotechnology and Disease Control and Prevention, College of Animal Science and Technology, Shandong Agricultural University, No. 61 Daizong Street, Tai'an City, Shandong Province 271018, China
| | - Pei-qi Liu
- Shandong Provincial Key Laboratory of Animal Biotechnology and Disease Control and Prevention, College of Animal Science and Technology, Shandong Agricultural University, No. 61 Daizong Street, Tai'an City, Shandong Province 271018, China
| | - Zhi-qiang Wang
- Shandong Provincial Key Laboratory of Animal Biotechnology and Disease Control and Prevention, College of Animal Science and Technology, Shandong Agricultural University, No. 61 Daizong Street, Tai'an City, Shandong Province 271018, China
| | - Yong-qing Zeng
- Shandong Provincial Key Laboratory of Animal Biotechnology and Disease Control and Prevention, College of Animal Science and Technology, Shandong Agricultural University, No. 61 Daizong Street, Tai'an City, Shandong Province 271018, China
| | - Wei Chen
- Shandong Provincial Key Laboratory of Animal Biotechnology and Disease Control and Prevention, College of Animal Science and Technology, Shandong Agricultural University, No. 61 Daizong Street, Tai'an City, Shandong Province 271018, China
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