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Dorant Y, Quillien V, Le Luyer J, Ky CL. Comparative transcriptomics identifies genes underlying growth performance of the Pacific black-lipped pearl oyster Pinctada margaritifera. BMC Genomics 2024; 25:717. [PMID: 39049022 PMCID: PMC11270918 DOI: 10.1186/s12864-024-10636-0] [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: 04/04/2024] [Accepted: 07/19/2024] [Indexed: 07/27/2024] Open
Abstract
BACKGROUND In bivalves, the rate at which organisms grow is a major functional trait underlying many aspects of their commercial production. Growth is a highly polygenic trait, which is typically regulated by many genes with small to moderate effects. Due to its complexity, growth variability in such shellfish remains poorly understood. In this study, we aimed to investigate differential gene expression among spat of the pearl oyster Pinctada margaritifera with distinct growth phenotypes. RESULTS We selected two groups of P. margaritifera spat belonging to the same F2 cohort based on their growth performance at 5.5 months old. Transcriptome profile analysis identified a total of 394 differentially expressed genes between these Fast-growing (F) and Slow-growing (S) phenotypes. According to functional enrichment analysis, S oysters overexpressed genes associated with stress-pathways and regulation of innate immune responses. In contrast, F oysters up-regulated genes associated with cytoskeleton activity, cell proliferation, and apoptosis. Analysis of genome polymorphism identified 16 single nucleotide polymorphisms (SNPs) significantly associated with the growth phenotypes. SNP effect categorization revealed one SNP identified for high effect and annotated for a stop codon gained mutation. Interestingly, this SNP is located within a gene annotated for scavenger receptor class F member 1 (SRF1), which is known to modulate apoptosis. Our analyses also revealed that all F oysters showed up-regulation for this gene and were homozygous for the stop-codon mutation. Conversely, S oysters had a heterozygous genotype and a reduced expression of this gene. CONCLUSIONS Altogether, our findings suggest that differences in growth among the same oyster cohort may be explained by contrasted metabolic allocation between regulatory pathways for growth and the immune system. This study provides a valuable contribution towards our understanding of the molecular components associated with growth performance in the pearl oyster P. margaritifera and bivalves in general.
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Affiliation(s)
- Y Dorant
- Ifremer, ILM, IRD, UPF, UMR 241 SECOPOL, Polynésie française, Taravao, Tahiti, France.
- IHPE, UMR 5244, Université de Montpellier, CNRS, Université de Perpignan Via Domitia, Ifremer, Montpellier, France.
| | - V Quillien
- Ifremer, ILM, IRD, UPF, UMR 241 SECOPOL, Polynésie française, Taravao, Tahiti, France
- Ifremer, Univ Brest, CNRS, IRD, UMR 6539, LEMAR, Plouzane, F-29280, France
| | - J Le Luyer
- Ifremer, ILM, IRD, UPF, UMR 241 SECOPOL, Polynésie française, Taravao, Tahiti, France
- Ifremer, Univ Brest, CNRS, IRD, UMR 6539, LEMAR, Plouzane, F-29280, France
| | - C L Ky
- Ifremer, ILM, IRD, UPF, UMR 241 SECOPOL, Polynésie française, Taravao, Tahiti, France
- IHPE, UMR 5244, Université de Montpellier, CNRS, Université de Perpignan Via Domitia, Ifremer, Montpellier, France
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Xu D, Zhang S, Zhang S, Liu H, Li P, Yu L, Shang H, Hou Y, Tian Y. NOD2 maybe a biomarker for the survival of kidney cancer patients. Oncotarget 2017; 8:101489-101499. [PMID: 29254180 PMCID: PMC5731890 DOI: 10.18632/oncotarget.21547] [Citation(s) in RCA: 13] [Impact Index Per Article: 1.9] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/02/2017] [Accepted: 09/20/2017] [Indexed: 12/17/2022] Open
Abstract
Background Nucleotide-binding oligomerization domain-containing protein 2 (NOD2) may play an important role in the outcome of kidney cancer patients. To explore the relationship between NOD2 and the prognosis of kidney cancer patients, a databank-based reanalysis was conducted. Materials and Methods Data related to kidney cancer patients at least with survival information, was obtained mainly from The Cancer Genome Atlas (TCGA). Some clinical data, not available online, was collected by personal email to the author. Then, we reanalyzed all the data in order to make a conclusion about the relationship between NOD2 gene and the prognosis of kidney cancer patients. Results A total of 1953 samples with NOD2 information from four databanks of The Cancer Genome Atlas (TCGA) were enrolled in this study. The results of KIPAN showed the Kaplan-Meier curve for risk groups, concordance index, and p-value of the log-rank testing equality of survival curves ( Concordance Index = 56.57, Log−Rank Equal Curves p=0.0009006, R^2 = 0.036/0.953, Risk Groups Hazard Ratio = 1.61 (conf. int. 1.21 ~ 2.13), p = 0.001005) , while a box plot across risk groups, including the p-value testing for difference using t-test (or f-test for more than two groups) was shown. There was a statistical significance for the p value of the result (p < 0.01 ). The similar results could be seen in KIRC and the fourth data (including 468 samples). Conclusions The status of NOD2 gene maybe a biomarker for the survival of kidney cancer patients.
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Affiliation(s)
- Deguo Xu
- Department of Radiation Oncology, Shandong Provincial Qianfoshan Hospital, Shandong University, Jinan, Shandong Province 250014, P.R. China
| | - Shuisheng Zhang
- Department of Abdominal Surgical Oncology, National Cancer Center/Cancer Hospital, Chinese Academy of Medical Sciences and Peking Union Medical College, Beijing 100021, P.R. China
| | - Shenfeng Zhang
- Department of Oncology, Zaozhuang Municipal Hospital of Shandong Province, Shizhong District, Zaozhuang, Shandong Province 277101, P.R. China
| | - Hongmei Liu
- Department of Radiation Oncology, Shandong Provincial Qianfoshan Hospital, Shandong University, Jinan, Shandong Province 250014, P.R. China
| | - Paiyun Li
- Key Laboratory of Carcinogenesis and Translational Research (Ministry of Education/Beijing), Department of Aetiology, Peking University Cancer Hospital and Institute, Beijing 100142, P.R. China
| | - Lili Yu
- Department of Radiation Oncology, Shandong Provincial Qianfoshan Hospital, Shandong University, Jinan, Shandong Province 250014, P.R. China
| | - Heli Shang
- Department of Radiation Oncology, Shandong Provincial Qianfoshan Hospital, Shandong University, Jinan, Shandong Province 250014, P.R. China
| | - Yong Hou
- Department of Radiation Oncology, Shandong Provincial Qianfoshan Hospital, Shandong University, Jinan, Shandong Province 250014, P.R. China
| | - Yuan Tian
- Department of Radiation Oncology, Shandong Provincial Qianfoshan Hospital, Shandong University, Jinan, Shandong Province 250014, P.R. China
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