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Ulloa PE, Jilberto F, Lam N, Rincón G, Valenzuela L, Cordova-Alarcón V, Hernández AJ, Dantagnan P, Ravanal MC, Elgueta S, Araneda C. Identification of Single-Nucleotide Polymorphisms in Differentially Expressed Genes Favoring Soybean Meal Tolerance in Higher-Growth Zebrafish (Danio rerio). MARINE BIOTECHNOLOGY (NEW YORK, N.Y.) 2024; 26:754-765. [PMID: 38958822 DOI: 10.1007/s10126-024-10343-7] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 04/05/2024] [Accepted: 06/25/2024] [Indexed: 07/04/2024]
Abstract
Genetic variability within the same fish species could confer soybean meal (SBM) tolerance in some individuals, thus favoring growth. This study investigates the single-nucleotide polymorphisms (SNPs) in differentially expressed genes (DEGs) favoring SBM tolerance in higher-growth zebrafish (Danio rerio). In a previous work, nineteen families of zebrafish were fed a fish meal diet (100FM control diet) or SBM-based diets supplemented with saponin (50SBM + 2SPN-experimental diet), from juvenile to adult stages. Individuals were selected from families with a genotype-by-environment interaction higher (170 ± 18 mg) or lower (76 ± 10 mg) weight gain on 50SBM + 2SPN in relation to 100FM. Intestinal transcriptomic analysis using RNA-seq revealed six hundred and sixty-five differentially expressed genes in higher-growth fish fed 50SBM + 2SPN diet. In this work, using these results, 47 SNPs in DEGs were selected. These SNPs were genotyped by Sequenom in 340 zebrafish that were fed with a 50SBM + 2SPN diet or with 100FM diet. Marker-trait analysis revealed 4 SNPs associated with growth in 3 immunity-related genes (aif1l, arid3c, and cst14b.2) in response to the 50SBM + 2SPN diet (p-value < 0.05). Two SNPs belonging to aif1l y arid3c produce a positive (+19 mg) and negative (-26 mg) effect on fish growth, respectively. These SNPs can be used as markers to improve the early selection of tolerant fish to SBM diet or other plant-based diets. These genes can be used as biomarkers to identify SNPs in commercial fish, thus contributing to the aquaculture sustainability.
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Affiliation(s)
- Pilar E Ulloa
- Núcleo de Investigaciones Aplicadas en Ciencias Veterinarias y Agronómicas, Universidad de Las Américas, Avenida Manuel Montt 948, Santiago, 7500975, Chile.
| | - Felipe Jilberto
- Food Quality Research Center, Universidad de Chile, Avenida Santa Rosa 11315, Santiago, 8820808, Chile
- Laboratorio de Genética y Biotecnología en Acuicultura, Departamento de Producción Animal, Facultad de Ciencias Agronómicas, Universidad de Chile, Avenida Santa Rosa 11315, Santiago, 8820808, Chile
| | - Natalia Lam
- Food Quality Research Center, Universidad de Chile, Avenida Santa Rosa 11315, Santiago, 8820808, Chile
- Laboratorio de Genética y Biotecnología en Acuicultura, Departamento de Producción Animal, Facultad de Ciencias Agronómicas, Universidad de Chile, Avenida Santa Rosa 11315, Santiago, 8820808, Chile
| | | | - Luis Valenzuela
- INRIA Chile, Avenida Apoquindo 2827, piso 12, Santiago, 7550312, Chile
| | - Valentina Cordova-Alarcón
- Food Quality Research Center, Universidad de Chile, Avenida Santa Rosa 11315, Santiago, 8820808, Chile
- Laboratorio de Genética y Biotecnología en Acuicultura, Departamento de Producción Animal, Facultad de Ciencias Agronómicas, Universidad de Chile, Avenida Santa Rosa 11315, Santiago, 8820808, Chile
| | - Adrián J Hernández
- Núcleo de Investigación en Producción Alimentaria, Departamento de Ciencias Agropecuarias y Acuícolas, Facultad de Recursos Naturales, Universidad Católica de Temuco, Temuco, 4780000, Chile
| | - Patricio Dantagnan
- Núcleo de Investigación en Producción Alimentaria, Departamento de Ciencias Agropecuarias y Acuícolas, Facultad de Recursos Naturales, Universidad Católica de Temuco, Temuco, 4780000, Chile
| | - Maria Cristina Ravanal
- Instituto de Ciencia y Tecnología de los Alimentos (ICYTAL), Facultad de Ciencias Agrarias y Alimentarias, Universidad Austral de Chile, Isla Teja, Avda. Julio Sarrazín s/n, Valdivia, 5090000, Chile
| | - Sebastian Elgueta
- Facultad de Ciencias Para El Cuidado de La Salud, Universidad San Sebastian, Sede Los Leones, Santiago, Chile
| | - Cristian Araneda
- Food Quality Research Center, Universidad de Chile, Avenida Santa Rosa 11315, Santiago, 8820808, Chile
- Laboratorio de Genética y Biotecnología en Acuicultura, Departamento de Producción Animal, Facultad de Ciencias Agronómicas, Universidad de Chile, Avenida Santa Rosa 11315, Santiago, 8820808, Chile
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Wang M, Yan X, Dong Y, Li X, Gao B. Machine learning and multi-omics data reveal driver gene-based molecular subtypes in hepatocellular carcinoma for precision treatment. PLoS Comput Biol 2024; 20:e1012113. [PMID: 38728362 PMCID: PMC11230636 DOI: 10.1371/journal.pcbi.1012113] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/02/2024] [Revised: 07/08/2024] [Accepted: 04/24/2024] [Indexed: 05/12/2024] Open
Abstract
The heterogeneity of Hepatocellular Carcinoma (HCC) poses a barrier to effective treatment. Stratifying highly heterogeneous HCC into molecular subtypes with similar features is crucial for personalized anti-tumor therapies. Although driver genes play pivotal roles in cancer progression, their potential in HCC subtyping has been largely overlooked. This study aims to utilize driver genes to construct HCC subtype models and unravel their molecular mechanisms. Utilizing a novel computational framework, we expanded the initially identified 96 driver genes to 1192 based on mutational aspects and an additional 233 considering driver dysregulation. These genes were subsequently employed as stratification markers for further analyses. A novel multi-omics subtype classification algorithm was developed, leveraging mutation and expression data of the identified stratification genes. This algorithm successfully categorized HCC into two distinct subtypes, CLASS A and CLASS B, demonstrating significant differences in survival outcomes. Integrating multi-omics and single-cell data unveiled substantial distinctions between these subtypes regarding transcriptomics, mutations, copy number variations, and epigenomics. Moreover, our prognostic model exhibited excellent predictive performance in training and external validation cohorts. Finally, a 10-gene classification model for these subtypes identified TTK as a promising therapeutic target with robust classification capabilities. This comprehensive study provides a novel perspective on HCC stratification, offering crucial insights for a deeper understanding of its pathogenesis and the development of promising treatment strategies.
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Affiliation(s)
- Meng Wang
- Faculty of Environment and Life of Beijing University of Technology, Beijing, China
| | - Xinyue Yan
- Faculty of Environment and Life of Beijing University of Technology, Beijing, China
| | - Yanan Dong
- Faculty of Environment and Life of Beijing University of Technology, Beijing, China
| | - Xiaoqin Li
- Faculty of Environment and Life of Beijing University of Technology, Beijing, China
| | - Bin Gao
- Faculty of Environment and Life of Beijing University of Technology, Beijing, China
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The Prognostic Value of AT-Rich Interaction Domain (ARID) Family Members in Patients with Hepatocellular Carcinoma. EVIDENCE-BASED COMPLEMENTARY AND ALTERNATIVE MEDICINE 2022; 2022:1150390. [PMID: 36034939 PMCID: PMC9410793 DOI: 10.1155/2022/1150390] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Subscribe] [Scholar Register] [Received: 06/15/2022] [Accepted: 07/19/2022] [Indexed: 12/24/2022]
Abstract
Objective Hepatocellular carcinoma (HCC) is one of the most lethal malignancies with a poor prognosis. The AT-rich interaction domain (ARID) family plays an essential regulatory role in the pathogenesis and progression of cancers. This study aims to evaluate the prognostic value and clinical significance of human ARID family genes in HCC. Methods ONCOMINE and The Cancer Genome Atlas (TCGA) databases were employed to retrieve ARIDs expression profile and clinicopathological information of HCC. Kaplan–Meier plotter and MethSurv were applied to the survival analysis of patients with HCC. CBioPortal was used to analyze genetic mutations of ARIDs. Gene Expression Profiling Interactive Analysis (GEPIA) and Metascape were used to perform hub gene identification and functional enrichment. Results Expression levels of 11 ARIDs were upregulated in HCC, and 2 ARIDs were downregulated. Also, 4 ARIDs and 5 ARIDs were correlated with pathologic stages and histologic grades, respectively. Furthermore, higher expression of ARID1A, ARID1B, ARID2, ARID3A, ARID3B, ARID5B, KDM5A, KDM5B, KDM5C, and JARID2 was remarkably correlated with worse overall survival of patients with HCC, and the high ARID3C/KDM5D expression was related to longer overall survival. Multivariate Cox analysis indicated that ARID3A, KDM5C, and KDM5D were independent risk factors for HCC prognosis. Moreover, ARIDs mutations and 127 CpGs methylation in all ARIDs were observed to be significantly associated with the prognosis of HCC patients. Besides, our data showed that ARIDs could regulate tumor-related pathways and distinct immune cells in the HCC microenvironment. Conclusions ARIDs present the potential prognostic value for HCC. Our findings suggest that ARID3A, KDM5C, and KDM5D may be the prognostic biomarkers for patients with HCC.
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Comprehensive Landscape of ARID Family Members and Their Association with Prognosis and Tumor Microenvironment in Hepatocellular Carcinoma. J Immunol Res 2022; 2022:1688460. [PMID: 35402625 PMCID: PMC8986425 DOI: 10.1155/2022/1688460] [Citation(s) in RCA: 2] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/09/2022] [Revised: 03/02/2022] [Accepted: 03/07/2022] [Indexed: 02/05/2023] Open
Abstract
As one of the most lethal forms of cancers, hepatocellular carcinoma (HCC) claims many lives around the world, and it is especially common in China. The ARID family plays key roles in the pathogenesis and development of human cancers. The potential of several functional genes used as novel biomarkers has attracted more and more attention. However, the prognostic values of the ARID family in HCC patients are rarely known by people. In this study, we performed comprehensive analysis using TCGA datasets, finding that the expressions of ARID4B, ARID2, ARID3B, JARID2, ARID1A, ARID1B, and ARID3A were increased in HCC specimens compared to nontumor specimens, while the expressions of ARID4A and ARID3C were decreased in HCC specimens. According to the Pearson correlation data, the methylation levels of the majority of ARID members were negatively correlated. Upregulation of ARID3A, ARID5B, and ARID1A was related to a poor HCC outcome according to the data of multivariate assays. Then, we built a LASSO Cox regression model based on ARID3A, ARID5B, and ARID1A in HCC. Overall survival rates were considerably lower for those with high risk scores compared to those with low risk scores. Finally, we studied the associations between risk scores and several types of infiltrating immune cells. The data revealed that the risk score was positively related to the infiltration of CD8+ T cells, B cell, T cell CD8+, neutrophil, macrophage, and myeloid dendritic cell. This study conducted a thorough analysis of the ARID members, resulting in new insights for further examination of the ARID family members as prospective targets in the treatment of HCC.
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