1
|
Nian Q, Li Y, Li J, Zhao L, Rodrigues Lima F, Zeng J, Liu R, Ye Z. U2AF1 in various neoplastic diseases and relevant targeted therapies for malignant cancers with complex mutations (Review). Oncol Rep 2024; 51:5. [PMID: 37975232 PMCID: PMC10688450 DOI: 10.3892/or.2023.8664] [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: 10/03/2023] [Accepted: 11/03/2023] [Indexed: 11/19/2023] Open
Abstract
U2 small nuclear RNA auxiliary factor 1 (U2AF1) is a multifunctional protein that plays a crucial role in the regulation of RNA splicing during eukaryotic gene expression. U2AF1 belongs to the SR family of splicing factors and is involved in the removal of introns from mRNAs and exon-exon binding. Mutations in U2AF1 are frequently observed in myelodysplastic syndrome, primary myelofibrosis, chronic myelomonocytic leukaemia, hairy cell leukaemia and other solid tumours, particularly in lung, pancreatic, and ovarian carcinomas. Therefore, targeting U2AF1 for therapeutic interventions may be a viable strategy for treating malignant diseases. In the present review, the pathogenic mechanisms associated with U2AF1 in different malignant diseases were summarized, and the potential of related targeting agents was discussed. Additionally, the feasibility of natural product-based therapies directed against U2AF1 was explored.
Collapse
Affiliation(s)
- Qing Nian
- Department of Transfusion, Sichuan Provincial People's Hospital, University of Electronic Science and Technology of China, Chengdu, Sichuan 610072, P.R. China
| | - Yihui Li
- Beijing Institute of Ophthalmology, Beijing Tongren Eye Center, Beijing Tongren Hospital, Capital Medical University, Beijing Ophthalmology and Visual Sciences Key Laboratory, Beijing 100730, P.R. China
| | - Jingwei Li
- Department of Transfusion, Sichuan Provincial People's Hospital, University of Electronic Science and Technology of China, Chengdu, Sichuan 610072, P.R. China
| | - Liyun Zhao
- Department of Pharmacy, Personalized Drug Therapy Key Laboratory of Sichuan, Sichuan Academy of Medical Sciences and Sichuan Provincial People's Hospital, School of Medicine, University of Electronic Science and Technology of China, Chengdu, Sichuan 610072, P.R. China
| | - Fernando Rodrigues Lima
- Université Paris Cité, CNRS, Unité de Biologie Fonctionnelle et Adaptative, 75013 Paris, France
| | - Jinhao Zeng
- Department of Gastroenterology, Hospital of Chengdu University of Traditional Chinese Medicine, Chengdu, Sichuan 610000, P.R. China
| | - Rongxing Liu
- Department of Pharmacy, The Second Affiliated Hospital, Army Medical University, Chongqing 400000, P.R. China
| | - Zhijun Ye
- Department of Clinical Nutrition, Sichuan Provincial People's Hospital, University of Electronic Science and Technology of China, Chengdu, Sichuan 610072, P.R. China
| |
Collapse
|
2
|
Du Y, Cao L, Wang S, Guo L, Tan L, Liu H, Feng Y, Wu W. Differences in alternative splicing and their potential underlying factors between animals and plants. J Adv Res 2023:S2090-1232(23)00354-5. [PMID: 37981087 DOI: 10.1016/j.jare.2023.11.017] [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: 05/07/2023] [Revised: 08/16/2023] [Accepted: 11/14/2023] [Indexed: 11/21/2023] Open
Abstract
BACKGROUND Alternative splicing (AS), a posttranscriptional process, contributes to the complexity of transcripts from a limited number of genes in a genome, and AS is considered a great source of genetic and phenotypic diversity in eukaryotes. In animals, AS is tightly regulated during the processes of cell growth and differentiation, and its dysregulation is involved in many diseases, including cancers. Likewise, in plants, AS occurs in all stages of plant growth and development, and it seems to play important roles in the rapid reprogramming of genes in response to environmental stressors. To date, the prevalence and functional roles of AS have been extensively reviewed in animals and plants. However, AS differences between animals and plants, especially their underlying molecular mechanisms and impact factors, are anecdotal and rarely reviewed. AIM OF REVIEW This review aims to broaden our understanding of AS roles in a variety of biological processes and provide insights into the underlying mechanisms and impact factors likely leading to AS differences between animals and plants. KEY SCIENTIFIC CONCEPTS OF REVIEW We briefly summarize the roles of AS regulation in physiological and biochemical activities in animals and plants. Then, we underline the differences in the process of AS between plants and animals and especially analyze the potential impact factors, such as gene exon/intron architecture, 5'/3' untranslated regions (UTRs), spliceosome components, chromatin dynamics and transcription speeds, splicing factors [serine/arginine-rich (SR) proteins and heterogeneous nuclear ribonucleoproteins (hnRNPs)], noncoding RNAs, and environmental stimuli, which might lead to the differences. Moreover, we compare the nonsense-mediated mRNA decay (NMD)-mediated turnover of the transcripts with a premature termination codon (PTC) in animals and plants. Finally, we summarize the current AS knowledge published in animals versus plants and discuss the potential development of disease therapies and superior crops in the future.
Collapse
Affiliation(s)
- Yunfei Du
- State Key Laboratory of Subtropical Silviculture, Zhejiang A&F University, Lin'an, 311300, Hangzhou, China
| | - Lu Cao
- State Key Laboratory of Subtropical Silviculture, Zhejiang A&F University, Lin'an, 311300, Hangzhou, China
| | - Shuo Wang
- State Key Laboratory of Subtropical Silviculture, Zhejiang A&F University, Lin'an, 311300, Hangzhou, China
| | - Liangyu Guo
- State Key Laboratory of Subtropical Silviculture, Zhejiang A&F University, Lin'an, 311300, Hangzhou, China
| | - Lingling Tan
- State Key Laboratory of Subtropical Silviculture, Zhejiang A&F University, Lin'an, 311300, Hangzhou, China
| | - Hua Liu
- State Key Laboratory of Subtropical Silviculture, Zhejiang A&F University, Lin'an, 311300, Hangzhou, China
| | - Ying Feng
- Key Laboratory of Nutrition, Metabolism and Food Safety, Shanghai Institute of Nutrition and Health (SINH), Chinese Academy of Sciences (CAS), Shanghai 200032, China.
| | - Wenwu Wu
- State Key Laboratory of Subtropical Silviculture, Zhejiang A&F University, Lin'an, 311300, Hangzhou, China.
| |
Collapse
|
3
|
Gomez-Verjan JC, Esparza-Aguilar M, Martin-Martin V, Salazar-Perez C, Cadena-Trejo C, Gutierrez-Robledo LM, Arroyo P. DNA methylation profile of a rural cohort exposed to early-adversity and malnutrition: An exploratory analysis. Exp Gerontol 2022; 167:111899. [PMID: 35907475 DOI: 10.1016/j.exger.2022.111899] [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: 07/11/2021] [Revised: 02/08/2022] [Accepted: 07/13/2022] [Indexed: 11/04/2022]
Abstract
Barker's hypothesis affirms that undernourishment in early-life induces metabolic reprogramming that compromises organism functions later in life, leading to age-related diseases. We are exposed to environmental and social conditions that impact our life trajectories, leading to ageing phenotypes as we grow. Epigenetic mechanisms constitute the link between both external stimuli and genetic programming. Studies have focused on describing the effect of early adverse events such as trauma, famines, or childhood labor on epigenetic markers in adulthood and the elderly. However, we lack information on epigenetic programming in individuals born in rural communities from underdeveloped countries, exposed to negative influences during fetal and postnatal development, particularly chronic malnutrition. Hence, in this exploratory analysis, we characterize the epigenome of individuals and some parents from Tlaltizapan (a rural community in Mexico originally studied almost 50 years ago) and collect anthropometric data on growth and development, as well on the living conditions of the families. Our results help build a biological hypothesis indicating that most of the epigenetic age measures of the subjects are significantly different among them. Interestingly, the most affected methylated regions correspond to pathways involved in neuronal system development, reproductive behaviour, learning and memory regulation.
Collapse
Affiliation(s)
- J C Gomez-Verjan
- Direccion de Investigación, Instituto Nacional de Geriatría, INGER, Mexico City, Mexico.
| | | | | | | | - C Cadena-Trejo
- Direccion de Investigación, Instituto Nacional de Geriatría, INGER, Mexico City, Mexico
| | | | - P Arroyo
- Direccion de Investigación, Instituto Nacional de Geriatría, INGER, Mexico City, Mexico
| |
Collapse
|
4
|
Proteomic analysis of adipose tissue revealing differentially abundant proteins in highly efficient mid-lactating dairy cows. Sci Rep 2022; 12:9721. [PMID: 35697844 PMCID: PMC9192684 DOI: 10.1038/s41598-022-13964-x] [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: 10/31/2021] [Accepted: 05/31/2022] [Indexed: 11/26/2022] Open
Abstract
The improvement of nutrient utilization efficiency in dairy cows represents an important task in view of the current rising demand for animal products and sustainable resource usage. In this perspective, the identification of appropriate markers to identify the most efficient animals for dairy production becomes a crucial factor. Residual feed intake (RFI), which represents the difference between predicted and actual intake, is used to define the efficiency of cows. In this study, subcutaneous adipose tissue (AT) was collected from five high efficient (HEF) and five low efficient (LEF) mid-lactation Holstein dairy cows, that represented subgroups of the 20% lowest RFI values (HEF) and highest 20% RFI values (LEF), out of a cohort of 155 cows that were examined for feed efficiency at the individual dairy barn at Volcani Institute, Israel. Adipose samples were examined for proteomic analysis by nano-LC/MS–MS and gene expression by RT-PCR. A total of 101 differential proteins (P ≤ 0.05 and fold change ± 1.5) and two protein networks related to feed efficiency were found between HEF and LEF cows. Among the enriched top canonical pathways, FAT10 signaling, EIF2 signaling, Sirtuin signaling, Acute phase response signaling, Protein ubiquitination and mTOR signaling pathways were related to feed efficiency in AT. Furthermore, abundance of transferrin (TF; FC = 78.35, P = 0.02) enriched pathways, including mTOR signaling, LXR/RXR and FXR/RXR activation was found in AT of HEF cows. Relative mRNA expression of RBM39, which is involved in energy metabolism, was decreased in AT of HEF versus LEF. The relationship found between the AT proteins and/or metabolic pathways and the feed efficiency demonstrates that AT may reflect metabolic adaptations to high efficiency, and suggests that these proteins together with their metabolic mechanisms are suitable candidates as biomarkers to identify efficient cows for dairy production.
Collapse
|
5
|
Malhan D, Basti A, Relógio A. Transcriptome analysis of clock disrupted cancer cells reveals differential alternative splicing of cancer hallmarks genes. NPJ Syst Biol Appl 2022; 8:17. [PMID: 35552415 PMCID: PMC9098426 DOI: 10.1038/s41540-022-00225-w] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/08/2021] [Accepted: 04/04/2022] [Indexed: 12/13/2022] Open
Abstract
Emerging evidence points towards a regulatory role of the circadian clock in alternative splicing (AS). Whether alterations in core-clock components may contribute to differential AS events is largely unknown. To address this, we carried out a computational analysis on recently generated time-series RNA-seq datasets from three core-clock knockout (KO) genes (ARNTL, NR1D1, PER2) and WT of a colorectal cancer (CRC) cell line, and time-series RNA-seq datasets for additional CRC and Hodgkin’s lymphoma (HL) cells, murine WT, Arntl KO, and Nr1d1/2 KO, and murine SCN WT tissue. The deletion of individual core-clock genes resulted in the loss of circadian expression in crucial spliceosome components such as SF3A1 (in ARNTLKO), SNW1 (in NR1D1KO), and HNRNPC (in PER2KO), which led to a differential pattern of KO-specific AS events. All HCT116KO cells showed a rhythmicity loss of a crucial spliceosome gene U2AF1, which was also not rhythmic in higher progression stage CRC and HL cancer cells. AS analysis revealed an increase in alternative first exon events specific to PER2 and NR1D1 KO in HCT116 cells, and a KO-specific change in expression and rhythmicity pattern of AS transcripts related to cancer hallmarks genes including FGFR2 in HCT116_ARNTLKO, CD44 in HCT116_NR1D1KO, and MET in HCT116_PER2KO. KO-specific changes in rhythmic properties of known spliced variants of these genes (e.g. FGFR2 IIIb/FGFR2 IIIc) correlated with epithelial-mesenchymal-transition signalling. Altogether, our bioinformatic analysis highlights a role for the circadian clock in the regulation of AS, and reveals a potential impact of clock disruption in aberrant splicing in cancer hallmark genes.
Collapse
Affiliation(s)
- Deeksha Malhan
- Institute for Theoretical Biology (ITB), Charité - Universitätsmedizin Berlin, corporate member of Freie Universität Berlin, Humboldt - Universität zu Berlin, and Berlin Institute of Health, Berlin, 10117, Germany.,Molecular Cancer Research Center (MKFZ), Medical Department of Hematology, Oncology, and Tumor Immunology, Charité - Universitätsmedizin Berlin, corporate member of Freie Universität Berlin Humboldt - Universität zu Berlin, and Berlin Institute of Health, Berlin, 10117, Germany.,Institute for Systems Medicine, Faculty of Human Medicine, MSH Medical School Hamburg, Hamburg, 20457, Germany
| | - Alireza Basti
- Institute for Theoretical Biology (ITB), Charité - Universitätsmedizin Berlin, corporate member of Freie Universität Berlin, Humboldt - Universität zu Berlin, and Berlin Institute of Health, Berlin, 10117, Germany.,Molecular Cancer Research Center (MKFZ), Medical Department of Hematology, Oncology, and Tumor Immunology, Charité - Universitätsmedizin Berlin, corporate member of Freie Universität Berlin Humboldt - Universität zu Berlin, and Berlin Institute of Health, Berlin, 10117, Germany.,Institute for Systems Medicine, Faculty of Human Medicine, MSH Medical School Hamburg, Hamburg, 20457, Germany
| | - Angela Relógio
- Institute for Theoretical Biology (ITB), Charité - Universitätsmedizin Berlin, corporate member of Freie Universität Berlin, Humboldt - Universität zu Berlin, and Berlin Institute of Health, Berlin, 10117, Germany. .,Molecular Cancer Research Center (MKFZ), Medical Department of Hematology, Oncology, and Tumor Immunology, Charité - Universitätsmedizin Berlin, corporate member of Freie Universität Berlin Humboldt - Universität zu Berlin, and Berlin Institute of Health, Berlin, 10117, Germany. .,Institute for Systems Medicine, Faculty of Human Medicine, MSH Medical School Hamburg, Hamburg, 20457, Germany.
| |
Collapse
|
6
|
Wang H, Chan TW, Vashisht AA, Drew BG, Calkin AC, Harris TE, Wohlschlegel JA, Xiao X, Reue K. Lipin 1 modulates mRNA splicing during fasting adaptation in liver. JCI Insight 2021; 6:e150114. [PMID: 34494556 PMCID: PMC8492312 DOI: 10.1172/jci.insight.150114] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.7] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/31/2021] [Accepted: 07/23/2021] [Indexed: 01/03/2023] Open
Abstract
Lipin 1 regulates cellular lipid homeostasis through roles in glycerolipid synthesis (through phosphatidic acid phosphatase activity) and transcriptional coactivation. Lipin 1-deficient individuals exhibit episodic disease symptoms that are triggered by metabolic stress, such as stress caused by prolonged fasting. We sought to identify critical lipin 1 activities during fasting. We determined that lipin 1 deficiency induces widespread alternative mRNA splicing in liver during fasting, much of which is normalized by refeeding. The role of lipin 1 in mRNA splicing was largely independent of its enzymatic function. We identified interactions between lipin 1 and spliceosome proteins, as well as a requirement for lipin 1 to maintain homeostatic levels of spliceosome small nuclear RNAs and specific RNA splicing factors. In fasted Lpin1-/- liver, we identified a correspondence between alternative splicing of phospholipid biosynthetic enzymes and dysregulated phospholipid levels; splicing patterns and phospholipid levels were partly normalized by feeding. Thus, lipin 1 influences hepatic lipid metabolism through mRNA splicing, as well as through enzymatic and transcriptional activities, and fasting exacerbates the deleterious effects of lipin 1 deficiency on metabolic homeostasis.
Collapse
Affiliation(s)
- Huan Wang
- Human Genetics, David Geffen School of Medicine at UCLA
| | | | - Ajay A Vashisht
- Biological Chemistry, University of California, Los Angeles, California, USA
| | - Brian G Drew
- Baker Heart and Diabetes Institute, Melbourne, Victoria, Australia
| | - Anna C Calkin
- Baker Heart and Diabetes Institute, Melbourne, Victoria, Australia.,Central Clinical School, Monash University, Melbourne, Victoria, Australia.,Baker Department of Cardiometabolic Health, University of Melbourne, Parkville, Victoria, Australia
| | - Thurl E Harris
- Pharmacology, University of Virginia, Charlottesville, Virginia, USA
| | - James A Wohlschlegel
- Biological Chemistry, University of California, Los Angeles, California, USA.,Molecular Biology Institute and
| | - Xinshu Xiao
- Bioinformatics Interdepartmental Program and.,Molecular Biology Institute and.,Integrative Biology and Physiology, University of California, Los Angeles, California, USA
| | - Karen Reue
- Human Genetics, David Geffen School of Medicine at UCLA,,Molecular Biology Institute and
| |
Collapse
|
7
|
Ponce de León C, Lorite P, López-Casado MÁ, Barro F, Palomeque T, Torres MI. Significance of PD1 Alternative Splicing in Celiac Disease as a Novel Source for Diagnostic and Therapeutic Target. Front Immunol 2021; 12:678400. [PMID: 34220824 PMCID: PMC8242946 DOI: 10.3389/fimmu.2021.678400] [Citation(s) in RCA: 6] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/09/2021] [Accepted: 05/26/2021] [Indexed: 02/05/2023] Open
Abstract
Background We have focused on the alteration of the PD-1/PD-L1 pathway in celiac disease and discussed the roles of the PD1 pathway in regulating the immune response. We explored the idea that the altered mRNA splicing process in key regulatory proteins could represent a novel source to identify diagnostic, prognostic, and therapeutic targets in celiac disease. Methods We characterized the PD1 mRNA variants' profile in CD patients and in response to gluten peptides' incubation after in vitro experiments. Total RNA from whole blood was isolated, and the coding region of the human PD-1 mRNA was amplified by cDNA PCR. Results PCR amplification of the human PD-1 coding sequence revealed an association between the over-expression of the sPD-1 protein and the PD-1Δex3 transcript in celiac disease. Thus, we have found three novel alternative spliced isoforms, two of which result in a truncated protein and the other isoform with a loss of 14 aa of exon 2 and complete exon 3 (Δ3) which could encode a new soluble form of PD1 (sPD-1). Conclusions Our study provides evidence that dietary gluten can modulate processes required for cell homeostasis through the splicing of pre-mRNAs encoding key regulatory proteins, which represents an adaptive mechanism in response to different nutritional conditions.
Collapse
Affiliation(s)
| | - Pedro Lorite
- Department of Experimental Biology, Faculty of Health Sciences, University of Jaén, Jaén, Spain
| | | | - Francisco Barro
- Department of Plant Genetic Improvement, Institute for Sustainable Agriculture, Spanish National Research Council (CSIC), Córdoba, Spain
| | - Teresa Palomeque
- Department of Experimental Biology, Faculty of Health Sciences, University of Jaén, Jaén, Spain
| | - María Isabel Torres
- Department of Experimental Biology, Faculty of Health Sciences, University of Jaén, Jaén, Spain
| |
Collapse
|
8
|
Sugawara K, Ishizaki S, Kikuchi S, Kuramitz H, Kadoya T. Construction of Protein Probe with a His‐tag and an Electron‐transfer Peptide for a Target Protein Sensing. ELECTROANAL 2020. [DOI: 10.1002/elan.202060338] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/09/2022]
Affiliation(s)
| | - Sora Ishizaki
- Maebashi Institute of Technology Gunma 371-0816 Japan
| | - Soya Kikuchi
- Maebashi Institute of Technology Gunma 371-0816 Japan
| | - Hideki Kuramitz
- Department of Environmental Biology and Chemistry, Graduate School of Science and Engineering for Research University of Toyama Toyama 930-8555 Japan
| | | |
Collapse
|
9
|
del Río-Moreno M, Luque RM, Rangel-Zúñiga OA, Alors-Pérez E, Alcalá-Diaz JF, Roncero-Ramos I, Camargo A, Gahete MD, López-Miranda J, Castaño JP. Dietary Intervention Modulates the Expression of Splicing Machinery in Cardiovascular Patients at High Risk of Type 2 Diabetes Development: From the CORDIOPREV Study. Nutrients 2020; 12:E3528. [PMID: 33212780 PMCID: PMC7696699 DOI: 10.3390/nu12113528] [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: 10/13/2020] [Revised: 11/03/2020] [Accepted: 11/12/2020] [Indexed: 12/11/2022] Open
Abstract
Type-2 diabetes mellitus (T2DM) has become a major health problem worldwide. T2DM risk can be reduced with healthy dietary interventions, but the precise molecular underpinnings behind this association are still incompletely understood. We recently discovered that the expression profile of the splicing machinery is associated with the risk of T2DM development. Thus, the aim of this work was to evaluate the influence of 3-year dietary intervention in the expression pattern of the splicing machinery components in peripheral blood mononuclear cells (PBMCs) from patients within the CORDIOPREV study. Expression of splicing machinery components was determined in PBMCs, at baseline and after 3 years of follow-up, from all patients who developed T2DM (Incident-T2DM, n = 107) and 108 randomly selected non-T2DM subjects, who were randomly enrolled in two healthy dietary patterns (Mediterranean or low-fat diets). Dietary intervention modulated the expression of key splicing machinery components (i.e., up-regulation of SPFQ/RMB45/RNU6, etc., down-regulation of RNU2/SRSF6) after three years, independently of the type of healthy diet. Some of these changes (SPFQ/RMB45/SRSF6) were associated with key clinical features and were differentially induced in Incident-T2DM patients and non-T2DM subjects. This study reveals that splicing machinery can be modulated by long-term dietary intervention, and could become a valuable tool to screen the progression of T2DM.
Collapse
Grants
- PIE14/00005 Instituto de Salud Carlos III
- PIE14/00031 Instituto de Salud Carlos III
- PI16/00264 Instituto de Salud Carlos III
- CP15/00156 Instituto de Salud Carlos III
- PI17/002287 Instituto de Salud Carlos III
- BFU2016-80360-R Ministerio de Economía, Industria y Competitividad, Gobierno de España
- TIN2017-83445-P Ministerio de Economía, Industria y Competitividad, Gobierno de España
- PI13/00023 Ministerio de Economía, Industria y Competitividad, Gobierno de España
- AGL2012/39615 Ministerio de Economía, Industria y Competitividad, Gobierno de España
- AGL2015-67896-P Ministerio de Economía, Industria y Competitividad, Gobierno de España
- BIO-0139 Junta de Andalucía
- CTS-1406 Junta de Andalucía
- CTS-525 Junta de Andalucía
- PI-0541-2013 Junta de Andalucía
- CVI-7450 Junta de Andalucía
Collapse
Affiliation(s)
- Mercedes del Río-Moreno
- Maimonides Institute for Biomedical Research of Cordoba (IMIBIC), 14004 Córdoba, Spain; (M.d.R.-M.); (O.A.R.-Z.); (E.A.-P.); (J.F.A.-D.); (I.R.-R.); (A.C.)
- Department of Cell Biology, University of Córdoba, 14004 Córdoba, Spain
- Reina Sofia University Hospital, 14004 Córdoba, Spain
- CIBER Fisiopatología de la Obesidad y Nutrición (CIBERobn), 14004 Córdoba, Spain
| | - Raúl M. Luque
- Maimonides Institute for Biomedical Research of Cordoba (IMIBIC), 14004 Córdoba, Spain; (M.d.R.-M.); (O.A.R.-Z.); (E.A.-P.); (J.F.A.-D.); (I.R.-R.); (A.C.)
- Department of Cell Biology, University of Córdoba, 14004 Córdoba, Spain
- Reina Sofia University Hospital, 14004 Córdoba, Spain
- CIBER Fisiopatología de la Obesidad y Nutrición (CIBERobn), 14004 Córdoba, Spain
| | - Oriol A. Rangel-Zúñiga
- Maimonides Institute for Biomedical Research of Cordoba (IMIBIC), 14004 Córdoba, Spain; (M.d.R.-M.); (O.A.R.-Z.); (E.A.-P.); (J.F.A.-D.); (I.R.-R.); (A.C.)
- CIBER Fisiopatología de la Obesidad y Nutrición (CIBERobn), 14004 Córdoba, Spain
- Lipid and Atherosclerosis Unit, Department of Medicine, Reina Sofia University Hospital, University of Córdoba, 14004 Córdoba, Spain
| | - Emilia Alors-Pérez
- Maimonides Institute for Biomedical Research of Cordoba (IMIBIC), 14004 Córdoba, Spain; (M.d.R.-M.); (O.A.R.-Z.); (E.A.-P.); (J.F.A.-D.); (I.R.-R.); (A.C.)
- Department of Cell Biology, University of Córdoba, 14004 Córdoba, Spain
- Reina Sofia University Hospital, 14004 Córdoba, Spain
- CIBER Fisiopatología de la Obesidad y Nutrición (CIBERobn), 14004 Córdoba, Spain
| | - Juan F. Alcalá-Diaz
- Maimonides Institute for Biomedical Research of Cordoba (IMIBIC), 14004 Córdoba, Spain; (M.d.R.-M.); (O.A.R.-Z.); (E.A.-P.); (J.F.A.-D.); (I.R.-R.); (A.C.)
- CIBER Fisiopatología de la Obesidad y Nutrición (CIBERobn), 14004 Córdoba, Spain
- Lipid and Atherosclerosis Unit, Department of Medicine, Reina Sofia University Hospital, University of Córdoba, 14004 Córdoba, Spain
| | - Irene Roncero-Ramos
- Maimonides Institute for Biomedical Research of Cordoba (IMIBIC), 14004 Córdoba, Spain; (M.d.R.-M.); (O.A.R.-Z.); (E.A.-P.); (J.F.A.-D.); (I.R.-R.); (A.C.)
- CIBER Fisiopatología de la Obesidad y Nutrición (CIBERobn), 14004 Córdoba, Spain
- Lipid and Atherosclerosis Unit, Department of Medicine, Reina Sofia University Hospital, University of Córdoba, 14004 Córdoba, Spain
| | - Antonio Camargo
- Maimonides Institute for Biomedical Research of Cordoba (IMIBIC), 14004 Córdoba, Spain; (M.d.R.-M.); (O.A.R.-Z.); (E.A.-P.); (J.F.A.-D.); (I.R.-R.); (A.C.)
- CIBER Fisiopatología de la Obesidad y Nutrición (CIBERobn), 14004 Córdoba, Spain
- Lipid and Atherosclerosis Unit, Department of Medicine, Reina Sofia University Hospital, University of Córdoba, 14004 Córdoba, Spain
| | - Manuel D. Gahete
- Maimonides Institute for Biomedical Research of Cordoba (IMIBIC), 14004 Córdoba, Spain; (M.d.R.-M.); (O.A.R.-Z.); (E.A.-P.); (J.F.A.-D.); (I.R.-R.); (A.C.)
- Department of Cell Biology, University of Córdoba, 14004 Córdoba, Spain
- Reina Sofia University Hospital, 14004 Córdoba, Spain
- CIBER Fisiopatología de la Obesidad y Nutrición (CIBERobn), 14004 Córdoba, Spain
| | - José López-Miranda
- Maimonides Institute for Biomedical Research of Cordoba (IMIBIC), 14004 Córdoba, Spain; (M.d.R.-M.); (O.A.R.-Z.); (E.A.-P.); (J.F.A.-D.); (I.R.-R.); (A.C.)
- CIBER Fisiopatología de la Obesidad y Nutrición (CIBERobn), 14004 Córdoba, Spain
- Lipid and Atherosclerosis Unit, Department of Medicine, Reina Sofia University Hospital, University of Córdoba, 14004 Córdoba, Spain
| | - Justo P. Castaño
- Maimonides Institute for Biomedical Research of Cordoba (IMIBIC), 14004 Córdoba, Spain; (M.d.R.-M.); (O.A.R.-Z.); (E.A.-P.); (J.F.A.-D.); (I.R.-R.); (A.C.)
- Department of Cell Biology, University of Córdoba, 14004 Córdoba, Spain
- Reina Sofia University Hospital, 14004 Córdoba, Spain
- CIBER Fisiopatología de la Obesidad y Nutrición (CIBERobn), 14004 Córdoba, Spain
| |
Collapse
|
10
|
Banerjee P, Carmelo VAO, Kadarmideen HN. Integrative Analysis of Metabolomic and Transcriptomic Profiles Uncovers Biological Pathways of Feed Efficiency in Pigs. Metabolites 2020; 10:E275. [PMID: 32640603 PMCID: PMC7408121 DOI: 10.3390/metabo10070275] [Citation(s) in RCA: 5] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/21/2020] [Revised: 06/24/2020] [Accepted: 07/04/2020] [Indexed: 12/12/2022] Open
Abstract
Feed efficiency (FE) is an economically important trait. Thus, reliable predictors would help to reduce the production cost and provide sustainability to the pig industry. We carried out metabolome-transcriptome integration analysis on 40 purebred Duroc and Landrace uncastrated male pigs to identify potential gene-metabolite interactions and explore the molecular mechanisms underlying FE. To this end, we applied untargeted metabolomics and RNA-seq approaches to the same animals. After data quality control, we used a linear model approach to integrate the data and find significant differently correlated gene-metabolite pairs separately for the breeds (Duroc and Landrace) and FE groups (low and high FE) followed by a pathway over-representation analysis. We identified 21 and 12 significant gene-metabolite pairs for each group. The valine-leucine-isoleucine biosynthesis/degradation and arginine-proline metabolism pathways were associated with unique metabolites. The unique genes obtained from significant metabolite-gene pairs were associated with sphingolipid catabolism, multicellular organismal process, cGMP, and purine metabolic processes. While some of the genes and metabolites identified were known for their association with FE, others are novel and provide new avenues for further research. Further validation of genes, metabolites, and gene-metabolite interactions in larger cohorts will elucidate the regulatory mechanisms and pathways underlying FE.
Collapse
Affiliation(s)
| | | | - Haja N. Kadarmideen
- Quantitative Genomics, Bioinformatics and Computational Biology Group, Department of Applied Mathematics and Computer Science, Technical University of Denmark, 2800 Kongens Lyngby, Denmark; (P.B.); (V.A.O.C.)
| |
Collapse
|
11
|
del Río-Moreno M, Alors-Pérez E, González-Rubio S, Ferrín G, Reyes O, Rodríguez-Perálvarez M, Sánchez-Frías ME, Sánchez-Sánchez R, Ventura S, López-Miranda J, Kineman RD, de la Mata M, Castaño JP, Gahete MD, Luque RM. Dysregulation of the Splicing Machinery Is Associated to the Development of Nonalcoholic Fatty Liver Disease. J Clin Endocrinol Metab 2019; 104:3389-3402. [PMID: 30901032 PMCID: PMC6590982 DOI: 10.1210/jc.2019-00021] [Citation(s) in RCA: 50] [Impact Index Per Article: 10.0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Received: 01/04/2019] [Accepted: 03/18/2019] [Indexed: 02/06/2023]
Abstract
CONTEXT Nonalcoholic fatty liver disease (NAFLD) is a common obesity-associated pathology characterized by hepatic fat accumulation, which can progress to fibrosis, cirrhosis, and hepatocellular carcinoma. Obesity is associated with profound changes in gene-expression patterns of the liver, which could contribute to the onset of comorbidities. OBJECTIVE As these alterations might be linked to a dysregulation of the splicing process, we aimed to determine whether the dysregulation in the expression of splicing machinery components could be associated with NAFLD. PARTICIPANTS We collected 41 liver biopsies from nonalcoholic individuals with obesity, with or without hepatic steatosis, who underwent bariatric surgery. INTERVENTIONS The expression pattern of splicing machinery components was determined using a microfluidic quantitative PCR-based array. An in vitro approximation to determine lipid accumulation using HepG2 cells was also implemented. RESULTS The liver of patients with obesity and steatosis exhibited a severe dysregulation of certain splicing machinery components compared with patients with obesity without steatosis. Nonsupervised clustering analysis allowed the identification of three molecular phenotypes of NAFLD with a unique fingerprint of alterations in splicing machinery components, which also presented distinctive hepatic and clinical-metabolic alterations and a differential response to bariatric surgery after 1 year. In addition, in vitro silencing of certain splicing machinery components (i.e., PTBP1, RBM45, SND1) reduced fat accumulation and modulated the expression of key de novo lipogenesis enzymes, whereas conversely, fat accumulation did not alter spliceosome components expression. CONCLUSION There is a close relationship between splicing machinery dysregulation and NAFLD development, which should be further investigated to identify alternative therapeutic targets.
Collapse
Affiliation(s)
- Mercedes del Río-Moreno
- Maimonides Institute for Biomedical Research of Córdoba, Córdoba, Spain
- Department of Cell Biology, Physiology and Immunology, University of Córdoba, Córdoba, Spain
- Reina Sofia University Hospital, Córdoba, Spain
- Centro de Investigación Biomédica en Red Fisiopatología de la Obesidad y Nutrición, Córdoba, Spain
| | - Emilia Alors-Pérez
- Maimonides Institute for Biomedical Research of Córdoba, Córdoba, Spain
- Department of Cell Biology, Physiology and Immunology, University of Córdoba, Córdoba, Spain
- Reina Sofia University Hospital, Córdoba, Spain
- Centro de Investigación Biomédica en Red Fisiopatología de la Obesidad y Nutrición, Córdoba, Spain
| | - Sandra González-Rubio
- Maimonides Institute for Biomedical Research of Córdoba, Córdoba, Spain
- Reina Sofia University Hospital, Córdoba, Spain
- Centro de Investigación Biomédica en Red Enfermedades Hepáticas y Digestivas, Córdoba, Spain
| | - Gustavo Ferrín
- Maimonides Institute for Biomedical Research of Córdoba, Córdoba, Spain
- Reina Sofia University Hospital, Córdoba, Spain
- Centro de Investigación Biomédica en Red Enfermedades Hepáticas y Digestivas, Córdoba, Spain
| | - Oscar Reyes
- Maimonides Institute for Biomedical Research of Córdoba, Córdoba, Spain
- Department of Computer Sciences, University of Córdoba, Córdoba, Spain
| | - Manuel Rodríguez-Perálvarez
- Maimonides Institute for Biomedical Research of Córdoba, Córdoba, Spain
- Reina Sofia University Hospital, Córdoba, Spain
- Centro de Investigación Biomédica en Red Enfermedades Hepáticas y Digestivas, Córdoba, Spain
| | - Marina E Sánchez-Frías
- Maimonides Institute for Biomedical Research of Córdoba, Córdoba, Spain
- Reina Sofia University Hospital, Córdoba, Spain
- Anatomical Pathology Service, Reina Sofia University Hospital, Córdoba, Spain
| | - Rafael Sánchez-Sánchez
- Maimonides Institute for Biomedical Research of Córdoba, Córdoba, Spain
- Reina Sofia University Hospital, Córdoba, Spain
- Anatomical Pathology Service, Reina Sofia University Hospital, Córdoba, Spain
| | - Sebastián Ventura
- Maimonides Institute for Biomedical Research of Córdoba, Córdoba, Spain
- Department of Computer Sciences, University of Córdoba, Córdoba, Spain
- Department of Information Systems, King Abdulaziz University, Jeddah, Saudi Arabia Kingdom
| | - José López-Miranda
- Maimonides Institute for Biomedical Research of Córdoba, Córdoba, Spain
- Reina Sofia University Hospital, Córdoba, Spain
- Centro de Investigación Biomédica en Red Fisiopatología de la Obesidad y Nutrición, Córdoba, Spain
- Lipids and Atherosclerosis Unit, Reina Sofia University Hospital, Córdoba, Spain
| | - Rhonda D Kineman
- Research and Development Division, Jesse Brown Veterans Affairs Medical Center, Chicago, Illinois
- Section of Endocrinology, Diabetes, and Metabolism, Department of Medicine, University of Illinois at Chicago, Chicago, Illinois
| | - Manuel de la Mata
- Maimonides Institute for Biomedical Research of Córdoba, Córdoba, Spain
- Reina Sofia University Hospital, Córdoba, Spain
- Centro de Investigación Biomédica en Red Enfermedades Hepáticas y Digestivas, Córdoba, Spain
| | - Justo P Castaño
- Maimonides Institute for Biomedical Research of Córdoba, Córdoba, Spain
- Department of Cell Biology, Physiology and Immunology, University of Córdoba, Córdoba, Spain
- Reina Sofia University Hospital, Córdoba, Spain
- Centro de Investigación Biomédica en Red Fisiopatología de la Obesidad y Nutrición, Córdoba, Spain
| | - Manuel D Gahete
- Maimonides Institute for Biomedical Research of Córdoba, Córdoba, Spain
- Department of Cell Biology, Physiology and Immunology, University of Córdoba, Córdoba, Spain
- Reina Sofia University Hospital, Córdoba, Spain
- Centro de Investigación Biomédica en Red Fisiopatología de la Obesidad y Nutrición, Córdoba, Spain
| | - Raúl M Luque
- Maimonides Institute for Biomedical Research of Córdoba, Córdoba, Spain
- Department of Cell Biology, Physiology and Immunology, University of Córdoba, Córdoba, Spain
- Reina Sofia University Hospital, Córdoba, Spain
- Centro de Investigación Biomédica en Red Fisiopatología de la Obesidad y Nutrición, Córdoba, Spain
| |
Collapse
|
12
|
Vitali M, Sirri R, Zappaterra M, Zambonelli P, Giannini G, Lo Fiego DP, Davoli R. Functional analysis finds differences on the muscle transcriptome of pigs fed an n-3 PUFA-enriched diet with or without antioxidant supplementations. PLoS One 2019; 14:e0212449. [PMID: 30785965 PMCID: PMC6382273 DOI: 10.1371/journal.pone.0212449] [Citation(s) in RCA: 4] [Impact Index Per Article: 0.8] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/19/2018] [Accepted: 02/01/2019] [Indexed: 12/11/2022] Open
Abstract
Supplementing pig diets with n-3 polyunsaturated fatty acids (n-3 PUFA) may produce meat products with an increased n-3 fatty acid content, and the combined antioxidants addition could prevent lipid oxidation in the feed. However, to date, the effects of these bioactive compounds at the molecular level in porcine skeletal muscle are mostly unknown. This study aimed to analyse changes in the Longissimus thoracis transcriptome of 35 pigs fed three diets supplemented with: linseed (L); linseed, vitamin E and Selenium (LES) or linseed and plant-derived polyphenols (LPE). Pigs were reared from 80.8 ± 5.6 kg to 151.8 ± 9.9 kg. After slaughter, RNA-Seq was performed and 1182 differentially expressed genes (DEGs) were submitted to functional analysis. The L vs LES comparison did not show differences, while L vs LPE showed 1102 DEGs and LES vs LPE 80 DEGs. LPE compared to the other groups showed the highest number of up-regulated genes involved in preserving muscle metabolism and structure. Results enlighten that the combined supplementation of bioactive lipids (n-3 PUFA from linseed) with plant extracts as a source of polyphenols increases, compared to the only addition of linseed, the expression of genes involved in mRNA metabolic processes and transcriptional regulation, glucose uptake and, finally, in supporting muscle development and physiology. These results improve the knowledge of the biological effect of bioactive compounds in Longissimus thoracis muscle, and sustain the growing interest over their use in pig production.
Collapse
Affiliation(s)
- Marika Vitali
- Interdepartmental Centre for Industrial Agrifood Research (CIRI- AGRO), University of Bologna, Cesena, Italy
| | - Rubina Sirri
- Interdepartmental Centre for Industrial Agrifood Research (CIRI- AGRO), University of Bologna, Cesena, Italy
| | - Martina Zappaterra
- Department of Agricultural and Food Sciences (DISTAL), University of Bologna, Bologna, Italy
| | - Paolo Zambonelli
- Interdepartmental Centre for Industrial Agrifood Research (CIRI- AGRO), University of Bologna, Cesena, Italy
- Department of Agricultural and Food Sciences (DISTAL), University of Bologna, Bologna, Italy
| | - Giulia Giannini
- Department of Agricultural and Food Sciences (DISTAL), University of Bologna, Bologna, Italy
| | - Domenico Pietro Lo Fiego
- Department of Life Sciences, University of Modena and Reggio Emilia, Reggio Emilia, Italy
- Interdepartmental Research Centre for Agri-Food Biological Resources Improvement and Valorisation (BIOGEST-SITEIA), University of Modena and Reggio Emilia, Reggio Emilia, Italy
| | - Roberta Davoli
- Interdepartmental Centre for Industrial Agrifood Research (CIRI- AGRO), University of Bologna, Cesena, Italy
- Department of Agricultural and Food Sciences (DISTAL), University of Bologna, Bologna, Italy
| |
Collapse
|
13
|
Zhang JG, Xu C, Zhang L, Zhu W, Shen H, Deng HW. Identify gene expression pattern change at transcriptional and post-transcriptional levels. Transcription 2019; 10:137-146. [PMID: 30696368 DOI: 10.1080/21541264.2019.1575159] [Citation(s) in RCA: 3] [Impact Index Per Article: 0.6] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/15/2022] Open
Abstract
Gene transcription is regulated with distinct sets of regulatory factors at multiple levels. Transcriptional and post-transcriptional regulation constitute two major regulation modes of gene expression to either activate or repress the initiation of transcription and thereby control the number of proteins synthesized during translation. Disruptions of the proper regulation patterns at transcriptional and post-transcriptional levels are increasingly recognized as causes of human diseases. Consequently, identifying the differential gene expression at transcriptional and post-transcriptional levels respectively is vital to identify potential disease-associated and/or causal genes and understand their roles in the disease development. Here, we proposed a novel method with a linear mixed model that can identify a set of differentially expressed genes at transcriptional and post-transcriptional levels. The simulation and real data analysis showed our method could provide an accurate way to identify genes subject to aberrant transcriptional and post-transcriptional regulation and reveal the potential causal genes that contributed to the diseases.
Collapse
Affiliation(s)
- Ji-Gang Zhang
- a Center of Bioinformatics and Genomics, Department of Global Biostatistics and Data Science , Tulane University , New Orleans , LA , USA.,b Computational Science , The Jackson Laboratory , Bar Harbor , ME , USA
| | - Chao Xu
- a Center of Bioinformatics and Genomics, Department of Global Biostatistics and Data Science , Tulane University , New Orleans , LA , USA.,c Department of Biostatistics and Epidemiology , University of Oklahoma Health Science Center , Oklahoma City , OK , USA
| | - Lan Zhang
- a Center of Bioinformatics and Genomics, Department of Global Biostatistics and Data Science , Tulane University , New Orleans , LA , USA
| | - Wei Zhu
- a Center of Bioinformatics and Genomics, Department of Global Biostatistics and Data Science , Tulane University , New Orleans , LA , USA
| | - Hui Shen
- a Center of Bioinformatics and Genomics, Department of Global Biostatistics and Data Science , Tulane University , New Orleans , LA , USA
| | - Hong-Wen Deng
- a Center of Bioinformatics and Genomics, Department of Global Biostatistics and Data Science , Tulane University , New Orleans , LA , USA.,d School of Basic Medical Science , Central South University , Changsha , China
| |
Collapse
|
14
|
Chen L, Zhang YH, Wang S, Zhang Y, Huang T, Cai YD. Prediction and analysis of essential genes using the enrichments of gene ontology and KEGG pathways. PLoS One 2017; 12:e0184129. [PMID: 28873455 PMCID: PMC5584762 DOI: 10.1371/journal.pone.0184129] [Citation(s) in RCA: 173] [Impact Index Per Article: 24.7] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/16/2017] [Accepted: 08/18/2017] [Indexed: 12/20/2022] Open
Abstract
Identifying essential genes in a given organism is important for research on their fundamental roles in organism survival. Furthermore, if possible, uncovering the links between core functions or pathways with these essential genes will further help us obtain deep insight into the key roles of these genes. In this study, we investigated the essential and non-essential genes reported in a previous study and extracted gene ontology (GO) terms and biological pathways that are important for the determination of essential genes. Through the enrichment theory of GO and KEGG pathways, we encoded each essential/non-essential gene into a vector in which each component represented the relationship between the gene and one GO term or KEGG pathway. To analyze these relationships, the maximum relevance minimum redundancy (mRMR) was adopted. Then, the incremental feature selection (IFS) and support vector machine (SVM) were employed to extract important GO terms and KEGG pathways. A prediction model was built simultaneously using the extracted GO terms and KEGG pathways, which yielded nearly perfect performance, with a Matthews correlation coefficient of 0.951, for distinguishing essential and non-essential genes. To fully investigate the key factors influencing the fundamental roles of essential genes, the 21 most important GO terms and three KEGG pathways were analyzed in detail. In addition, several genes was provided in this study, which were predicted to be essential genes by our prediction model. We suggest that this study provides more functional and pathway information on the essential genes and provides a new way to investigate related problems.
Collapse
Affiliation(s)
- Lei Chen
- School of Life Sciences, Shanghai University, Shanghai, People’s Republic of China
- College of Information Engineering, Shanghai Maritime University, Shanghai, People’s Republic of China
| | - Yu-Hang Zhang
- Institute of Health Sciences, Shanghai Institutes for Biological Sciences, Chinese Academy of Sciences, Shanghai, People’s Republic of China
| | - ShaoPeng Wang
- School of Life Sciences, Shanghai University, Shanghai, People’s Republic of China
| | - YunHua Zhang
- Anhui province key lab of farmland ecological conversation and pollution prevention, School of Resources and Environment, Anhui Agricultural University, Hefei, People’s Republic of China
| | - Tao Huang
- Institute of Health Sciences, Shanghai Institutes for Biological Sciences, Chinese Academy of Sciences, Shanghai, People’s Republic of China
| | - Yu-Dong Cai
- School of Life Sciences, Shanghai University, Shanghai, People’s Republic of China
| |
Collapse
|
15
|
Pegolo S, Cecchinato A, Mach N, Babbucci M, Pauletto M, Bargelloni L, Schiavon S, Bittante G. Transcriptomic Changes in Liver of Young Bulls Caused by Diets Low in Mineral and Protein Contents and Supplemented with n-3 Fatty Acids and Conjugated Linoleic Acid. PLoS One 2016; 11:e0167747. [PMID: 27930681 PMCID: PMC5145186 DOI: 10.1371/journal.pone.0167747] [Citation(s) in RCA: 8] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/21/2016] [Accepted: 11/19/2016] [Indexed: 02/04/2023] Open
Abstract
The aim of the present study was to identify transcriptional modifications and regulatory networks accounting for physiological and metabolic responses to specific nutrients in the liver of young Belgian Blue × Holstein bulls using RNA-sequencing. A larger trial has been carried out in which animals were fed with different diets: 1] a conventional diet; 2] a low-protein/low-mineral diet (low-impact diet) and 3] a diet enriched in n-3 fatty acids (FAs), conjugated linoleic acid (CLA) and vitamin E (nutraceutical diet). The initial hypothesis was that the administration of low-impact and nutraceutical diets might influence the transcriptional profiles in bovine liver and the resultant nutrient fluxes, which are essential for optimal liver function and nutrient interconversion. Results showed that the nutraceutical diet significantly reduced subcutaneous fat covering in vivo and liver pH. Dietary treatments did not affect overall liver fat content, but significantly modified the liver profile of 33 FA traits (out of the total 89 identified by gas-chromatography). In bulls fed nutraceutical diet, the percentage of n-3 and CLA FAs increased around 2.5-fold compared with the other diets, whereas the ratio of n6/n3 decreased 2.5-fold. Liver transcriptomic analyses revealed a total of 198 differentially expressed genes (DEGs) when comparing low-impact, nutraceutical and conventional diets, with the nutraceutical diet showing the greatest effects on liver transcriptome. Functional analyses using ClueGo and Ingenuity Pathway Analysis evidenced that DEGs in bovine liver were variously involved in energy reserve metabolic process, glutathione metabolism, and carbohydrate and lipid metabolism. Modifications in feeding strategies affected key transcription factors regulating the expression of several genes involved in fatty acid metabolism, e.g. insulin-induced gene 1, insulin receptor substrate 2, and RAR-related orphan receptor C. This study provides noteworthy insights into the molecular changes occurring as a result of nutrient variation in diets (aimed at reducing the environmental impact and improving human health) and broadens our understanding of the relationship between nutrients variation and phenotypic effects.
Collapse
Affiliation(s)
- Sara Pegolo
- Department of Agronomy, Food, Natural Resources, Animals and Environment (DAFNAE), University of Padova, Legnaro, Padova, Italy
- * E-mail:
| | - Alessio Cecchinato
- Department of Agronomy, Food, Natural Resources, Animals and Environment (DAFNAE), University of Padova, Legnaro, Padova, Italy
| | - Núria Mach
- Animal Genetics and Integrative Biology unit (GABI), INRA, AgroParisTech, Université Paris-Saclay, Jouy-en-Josas, France
| | - Massimiliano Babbucci
- Department of Comparative Biomedicine and Food Science, University of Padova, Legnaro, Padova, Italy
| | - Marianna Pauletto
- Department of Comparative Biomedicine and Food Science, University of Padova, Legnaro, Padova, Italy
| | - Luca Bargelloni
- Department of Comparative Biomedicine and Food Science, University of Padova, Legnaro, Padova, Italy
| | - Stefano Schiavon
- Department of Agronomy, Food, Natural Resources, Animals and Environment (DAFNAE), University of Padova, Legnaro, Padova, Italy
| | - Giovanni Bittante
- Department of Agronomy, Food, Natural Resources, Animals and Environment (DAFNAE), University of Padova, Legnaro, Padova, Italy
| |
Collapse
|
16
|
Watson E, Yilmaz LS, Walhout AJM. Understanding Metabolic Regulation at a Systems Level: Metabolite Sensing, Mathematical Predictions, and Model Organisms. Annu Rev Genet 2016; 49:553-75. [PMID: 26631516 DOI: 10.1146/annurev-genet-112414-055257] [Citation(s) in RCA: 29] [Impact Index Per Article: 3.6] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/09/2022]
Abstract
Metabolic networks are extensively regulated to facilitate tissue-specific metabolic programs and robustly maintain homeostasis in response to dietary changes. Homeostatic metabolic regulation is achieved through metabolite sensing coupled to feedback regulation of metabolic enzyme activity or expression. With a wealth of transcriptomic, proteomic, and metabolomic data available for different cell types across various conditions, we are challenged with understanding global metabolic network regulation and the resulting metabolic outputs. Stoichiometric metabolic network modeling integrated with "omics" data has addressed this challenge by generating nonintuitive, testable hypotheses about metabolic flux rewiring. Model organism studies have also yielded novel insight into metabolic networks. This review covers three topics: the feedback loops inherent in metabolic regulatory networks, metabolic network modeling, and interspecies studies utilizing Caenorhabditis elegans and various bacterial diets that have revealed novel metabolic paradigms.
Collapse
Affiliation(s)
- Emma Watson
- Program in Systems Biology, Program in Molecular Medicine, University of Massachusetts Medical School, Worcester, Massachusetts 01605; , ,
| | - L Safak Yilmaz
- Program in Systems Biology, Program in Molecular Medicine, University of Massachusetts Medical School, Worcester, Massachusetts 01605; , ,
| | - Albertha J M Walhout
- Program in Systems Biology, Program in Molecular Medicine, University of Massachusetts Medical School, Worcester, Massachusetts 01605; , ,
| |
Collapse
|
17
|
Trittmann JK, Gastier-Foster JM, Zmuda EJ, Frick J, Rogers LK, Vieland VJ, Chicoine LG, Nelin LD. A single nucleotide polymorphism in the dimethylarginine dimethylaminohydrolase gene is associated with lower risk of pulmonary hypertension in bronchopulmonary dysplasia. Acta Paediatr 2016; 105:e170-5. [PMID: 26663142 DOI: 10.1111/apa.13296] [Citation(s) in RCA: 17] [Impact Index Per Article: 2.1] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Received: 09/04/2015] [Revised: 11/17/2015] [Accepted: 12/01/2015] [Indexed: 12/30/2022]
Abstract
AIM Pulmonary hypertension (PH) develops in 25-40% of bronchopulmonary dysplasia (BPD) patients, substantially increasing mortality. We have previously found that asymmetric dimethylarginine (ADMA), an endogenous inhibitor of nitric oxide (NO) production, is elevated in patients with BPD-associated PH. ADMA is metabolised by N(ᴳ) ,N(ᴳ) -dimethylarginine dimethylaminohydrolase (DDAH). Presently, we test the hypothesis that there are single nucleotide polymorphisms (SNPs) in DDAH1 and/or DDAH2 associated with the development of PH in BPD patients. METHODS BPD patients were enrolled (n = 98) at Nationwide Children's Hospital. Clinical characteristics and 36 SNPs in DDAH1 and DDAH2 were compared between BPD-associated PH patients (cases) and BPD-alone patients (controls). RESULTS In BPD patients, 25 (26%) had echocardiographic evidence of PH (cases). In this cohort, DDAH1 wild-type rs480414 was 92% sensitive and 53% specific for PH in BPD, and the DDAH1 SNP rs480414 decreased the risk of PH in an additive model of inheritance (OR = 0.39; 95% CI [0.18-0.88], p = 0.01). CONCLUSION The rs480414 SNP in DDAH1 may be protective against the development of PH in patients with BPD. Furthermore, the DDAH1 rs480414 may be a useful biomarker in developing predictive models for PH in patients with BPD.
Collapse
Affiliation(s)
- Jennifer K. Trittmann
- Ohio Perinatal Research Network; The Research Institute at Nationwide Children's Hospital; Columbus OH USA
- Pulmonary Hypertension Group; Center for Perinatal Research; The Research Institute at Nationwide Children's Hospital; Columbus OH USA
- Department of Pediatrics; The Ohio State University; Columbus OH USA
| | - Julie M. Gastier-Foster
- Department of Pediatrics; The Ohio State University; Columbus OH USA
- Cytogenetics/Molecular Genetics Laboratory at Nationwide Children's Hospital; Columbus OH USA
- Department of Pathology; The Ohio State University; Columbus OH USA
| | - Erik J. Zmuda
- Cytogenetics/Molecular Genetics Laboratory at Nationwide Children's Hospital; Columbus OH USA
- Department of Pathology; The Ohio State University; Columbus OH USA
| | - Jessica Frick
- Cytogenetics/Molecular Genetics Laboratory at Nationwide Children's Hospital; Columbus OH USA
- Department of Pathology; The Ohio State University; Columbus OH USA
| | - Lynette K. Rogers
- Ohio Perinatal Research Network; The Research Institute at Nationwide Children's Hospital; Columbus OH USA
- Pulmonary Hypertension Group; Center for Perinatal Research; The Research Institute at Nationwide Children's Hospital; Columbus OH USA
- Department of Pediatrics; The Ohio State University; Columbus OH USA
| | - Veronica J. Vieland
- Department of Pediatrics; The Ohio State University; Columbus OH USA
- Battelle Center for Mathematical Medicine; The Research Institute at Nationwide Children's Hospital; Columbus OH USA
| | - Louis G. Chicoine
- Pulmonary Hypertension Group; Center for Perinatal Research; The Research Institute at Nationwide Children's Hospital; Columbus OH USA
- Department of Pediatrics; The Ohio State University; Columbus OH USA
| | - Leif D. Nelin
- Ohio Perinatal Research Network; The Research Institute at Nationwide Children's Hospital; Columbus OH USA
- Pulmonary Hypertension Group; Center for Perinatal Research; The Research Institute at Nationwide Children's Hospital; Columbus OH USA
- Department of Pediatrics; The Ohio State University; Columbus OH USA
| |
Collapse
|
18
|
Zhang S, Wu X, Pan C, Lei C, Dang R, Chen H, Lan X. Identification of novel isoforms of dairy goat EEF1D and their mRNA expression characterization. Gene 2016; 581:14-20. [PMID: 26794801 DOI: 10.1016/j.gene.2016.01.013] [Citation(s) in RCA: 5] [Impact Index Per Article: 0.6] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/31/2015] [Revised: 12/21/2015] [Accepted: 01/11/2016] [Indexed: 11/26/2022]
Abstract
Eukaryotic translation elongation factor 1 delta (EEF1D) gene encodes guanine nucleotide exchange protein eEF1Bδ, which participates in the eukaryotic protein synthesis, and plays important roles in regulating cell cycling and milk production. This study firstly focused on detecting the isoforms of dairy goat EEF1D gene and their mRNA expression characterization. Herein, two novel isoforms, EEF1Da and EEF1Dc, were identified in dairy goat. The entire coding sequences of EEF1Da and EEF1Dc isoforms were 843bp and 267bp in length, respectively. Goat EEF1Da had complete conserved domains of elongation factor 1 (EF1) family, and the evolution of goat EEF1Da isoform was agreed with the evolution of species. Expression pattern analysis of different isoforms revealed relatively ubiquitous expression of EEF1D and EEF1Da. While EEF1Dc only expressed in heart, lung, kidney, adipose and muscle. Combining with the analysis results of cloning, qRT-PCR and bioinformatics, EEF1Da is the major alternative splicing form of EEF1D gene. Interestingly, qRT-PCR result showed that the highest expression of EEF1D was in adipose, which is the major component of mammary. This result was consistent with the early research that EEF1D expressed highly in the mammary, which indicated that EEF1D played a potential key role in regulating adipose development and milk production. All these findings would provide a foundation for the further research of EEF1D gene and development of dairy goat industry.
Collapse
Affiliation(s)
- Sihuan Zhang
- College of Animal Science and Technology, Northwest A&F University, Shaanxi Key Laboratory of Molecular Biology for Agriculture, Yangling, Shaanxi 712100, PR China.
| | - Xianfeng Wu
- College of Animal Science and Technology, Northwest A&F University, Shaanxi Key Laboratory of Molecular Biology for Agriculture, Yangling, Shaanxi 712100, PR China.
| | - Chuanying Pan
- College of Animal Science and Technology, Northwest A&F University, Shaanxi Key Laboratory of Molecular Biology for Agriculture, Yangling, Shaanxi 712100, PR China
| | - Chuzhao Lei
- College of Animal Science and Technology, Northwest A&F University, Shaanxi Key Laboratory of Molecular Biology for Agriculture, Yangling, Shaanxi 712100, PR China
| | - Ruihua Dang
- College of Animal Science and Technology, Northwest A&F University, Shaanxi Key Laboratory of Molecular Biology for Agriculture, Yangling, Shaanxi 712100, PR China
| | - Hong Chen
- College of Animal Science and Technology, Northwest A&F University, Shaanxi Key Laboratory of Molecular Biology for Agriculture, Yangling, Shaanxi 712100, PR China
| | - Xianyong Lan
- College of Animal Science and Technology, Northwest A&F University, Shaanxi Key Laboratory of Molecular Biology for Agriculture, Yangling, Shaanxi 712100, PR China.
| |
Collapse
|
19
|
ESRP2 controls an adult splicing programme in hepatocytes to support postnatal liver maturation. Nat Commun 2015; 6:8768. [PMID: 26531099 PMCID: PMC4635967 DOI: 10.1038/ncomms9768] [Citation(s) in RCA: 76] [Impact Index Per Article: 8.4] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/03/2015] [Accepted: 09/25/2015] [Indexed: 12/15/2022] Open
Abstract
Although major genetic networks controlling early liver specification and morphogenesis are known, the mechanisms responsible for postnatal hepatic maturation are poorly understood. Here we employ global analyses of the mouse liver transcriptome to demonstrate that postnatal remodelling of the liver is accompanied by large-scale transcriptional and post-transcriptional transitions that are cell-type-specific and temporally coordinated. Combining detailed expression analyses with gain- and loss-of-function studies, we identify epithelial splicing regulatory protein 2 (ESRP2) as a conserved regulatory factor that controls the neonatal-to-adult switch of ∼20% of splice isoforms in mouse and human hepatocytes. The normal shift in splicing coincides tightly with dramatic postnatal induction of ESRP2 in hepatocytes. We further demonstrate that forced expression of ESRP2 in immature mouse and human hepatocytes is sufficient to drive a reciprocal shift in splicing and causes various physiological abnormalities. These findings define a direct role for ESRP2 in the generation of conserved repertoires of adult splice isoforms that facilitate terminal differentiation and maturation of hepatocytes.
Collapse
|