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Zhao J, He Z, Chen X, Huang Y, Xie J, Qin X, Ni Z, Sun C. Growth trait gene analysis of kuruma shrimp (Marsupenaeus japonicus) by transcriptome study. COMPARATIVE BIOCHEMISTRY AND PHYSIOLOGY D-GENOMICS & PROTEOMICS 2021; 40:100874. [PMID: 34243027 DOI: 10.1016/j.cbd.2021.100874] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.7] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Subscribe] [Scholar Register] [Received: 03/04/2021] [Revised: 05/16/2021] [Accepted: 06/28/2021] [Indexed: 10/21/2022]
Abstract
Growth traits are a vital standard for the animal culture industry. The molecular mechanism of growth traits remains poorly understood, especially in aquaculture, which hinders the development of the selective breeding industry. Genomic resources discovered by next-generation sequencing (NGS) have been widely applied in certain species. However, accurate assembly and downstream analysis by NGS are still major challenges for species without reference genomes. In this study, a comparative transcriptome analysis of an economic crustacean species (Marsupenaeus japonicus) between a fast growth group and slow growth group at different stages was performed by SMRT (single molecule real time) and NGS. A high-quality full-length transcriptome (e.g., mean length of unigenes was longer than those unigenes assembled by Illumina clean reads from previous reports, and annotation rate was higher than Illumina sequencing in the same studies) was generated and analyzed. Several differentially expressed genes (DEGs) related to growth were identified and validated by quantitative real-time PCR (qPCR). The results showed that compared with the late stage, more DEGs were identified at the early stage, indicating that the growth-related physiological activity differences between different individuals at the early stage were higher than at the late stage. Moreover, 215 DEGs were shared between the early stage and late stage, and 109 had divergent functions during development. These 109 genes may play an important role in regulating the specific growth rate (SGR) of kuruma shrimp. In addition, twelve growth-related pathways were shared between the two comparative groups. Among these pathways, the fly Hippo signaling pathway and its key gene Mj14-3-3-like were identified for the first time to be involved in growth traits in crustaceans. Further analysis showed that Mj14-3-3-like was significantly downregulated in the fast growth group at the early stage and late stage; its expression level was reduced to its lowest level at the intermolt stage (C), the most important growth stage in shrimp, suggesting that Mj14-3-3-like may inhibit the growth of kuruma shrimp. Our study helps to elucidate the genes involved in the molecular mechanisms governing growth traits in kuruma shrimp, which is valuable for future shrimp developmental research.
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Affiliation(s)
- Jichen Zhao
- College of Fisheries, Guangdong Ocean University, Zhanjiang, PR China
| | - Zihao He
- College of Fisheries, Guangdong Ocean University, Zhanjiang, PR China
| | - Xieyan Chen
- College of Fisheries, Guangdong Ocean University, Zhanjiang, PR China
| | - Yiyi Huang
- College of Fisheries, Guangdong Ocean University, Zhanjiang, PR China
| | - Jingjing Xie
- College of Fisheries, Guangdong Ocean University, Zhanjiang, PR China
| | - Xuan Qin
- College of Fisheries, Guangdong Ocean University, Zhanjiang, PR China
| | - Zuotao Ni
- Institute of Oceanology, Chinese Academy of Sciences, Qingdao, PR China.
| | - Chengbo Sun
- College of Fisheries, Guangdong Ocean University, Zhanjiang, PR China; Guangdong Provincial Laboratory of Southern Marine Science and Engineering, Zhanjiang, PR China; Guangdong Provincial Key Laboratory of Pathogenic Biology and Epidemiology for Aquatic Economic Animals, Zhanjiang, PR China.
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Dickinson A, Saraswat M, Mäkitie A, Silén R, Hagström J, Haglund C, Joenväärä S, Silén S. Label-free tissue proteomics can classify oral squamous cell carcinoma from healthy tissue in a stage-specific manner. Oral Oncol 2018; 86:206-215. [PMID: 30409303 DOI: 10.1016/j.oraloncology.2018.09.013] [Citation(s) in RCA: 7] [Impact Index Per Article: 1.2] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/06/2018] [Revised: 08/21/2018] [Accepted: 09/13/2018] [Indexed: 10/28/2022]
Abstract
OBJECTIVES No prognostic or predictive biomarkers for oral squamous cell carcinoma (OSCC) exist. We aimed to discover novel proteins, altered in OSCC, to be further investigated as potential biomarkers, and to improve understanding about pathways involved in OSCC. MATERIALS AND METHODS Proteomic signatures of seven paired healthy and OSCC tissue samples were identified using ultra-definition quantitative mass spectrometry, then analysed and compared using Anova, principal component analysis, hierarchical clustering and OPLS-DA modelling. A selection of significant proteins that were also altered in the serum from a previous study (PMID: 28632724) were validated immunohistochemically on an independent cohort (n = 66) to confirm immunopositivity and location within tumour tissue. Ingenuity Pathways Analysis was employed to identify altered pathways. RESULTS Of 829 proteins quantified, 257 were significant and 72 were able to classify healthy vs OSCC using OPLS-DA modelling. We identified 19 proteins not previously known to be upregulated in OSCC, including prosaposin and alpha-taxilin. KIAA1217 and NDRG1 were upregulated in stage IVa compared with stage I tumours. Altered pathways included calcium signalling, cellular movement, haematological system development and function, and immune cell trafficking, and involved NF-kB and MAPK networks. CONCLUSIONS We found a set of proteins reliably separating OSCC tumour from healthy tissue, and multiple proteins differing between stage I and stage IVa OSCC. These potential biomarkers can be studied and validated in larger cohorts.
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Affiliation(s)
- Amy Dickinson
- Transplantation Laboratory, Haartman Institute, University of Helsinki, Haartmaninkatu 3, PO Box 21, 00014, Finland; Department of Otorhinolaryngology - Head and Neck Surgery, University of Helsinki and Helsinki University Hospital, Helsinki, Finland.
| | - Mayank Saraswat
- Transplantation Laboratory, Haartman Institute, University of Helsinki, Haartmaninkatu 3, PO Box 21, 00014, Finland; HUSLAB, Helsinki University Hospital, Helsinki 00290, Finland.
| | - Antti Mäkitie
- Department of Otorhinolaryngology - Head and Neck Surgery, University of Helsinki and Helsinki University Hospital, Helsinki, Finland; Division of Ear, Nose and Throat Diseases, Department of Clinical Sciences, Intervention and Technology, Karolinska Institutet and Karolinska University Hospital, Stockholm, Sweden.
| | - Robert Silén
- Transplantation Laboratory, Haartman Institute, University of Helsinki, Haartmaninkatu 3, PO Box 21, 00014, Finland.
| | - Jaana Hagström
- HUSLAB, Helsinki University Hospital, Helsinki 00290, Finland; Department of Pathology, University of Helsinki, Finland.
| | - Caj Haglund
- Department of Surgery, University of Helsinki and Helsinki, University Hospital, Helsinki, Finland; Research Programs Unit, Translational Cancer Biology, University of Helsinki, Helsinki, Finland.
| | - Sakari Joenväärä
- Transplantation Laboratory, Haartman Institute, University of Helsinki, Haartmaninkatu 3, PO Box 21, 00014, Finland; HUSLAB, Helsinki University Hospital, Helsinki 00290, Finland.
| | - Suvi Silén
- Department of Otorhinolaryngology - Head and Neck Surgery, University of Helsinki and Helsinki University Hospital, Helsinki, Finland; Department of Biosciences and Nutrition, Karolinska Institutet, Stockholm, Sweden.
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