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López-Catalina A, Reverter A, Alexandre PA, Nguyen LT, González-Recio O. Stress-induced epigenetic effects driven by maternal lactation in dairy cattle: a comethylation network approach. Epigenetics 2024; 19:2381856. [PMID: 39044410 PMCID: PMC11271077 DOI: 10.1080/15592294.2024.2381856] [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: 04/18/2024] [Accepted: 07/14/2024] [Indexed: 07/25/2024] Open
Abstract
Epigenetic marks do not follow the Mendelian laws of inheritance. The environment can alter the epigenotype of an individual when exposed to different external stressors. In lactating cows, the first stages of gestation overlap with the lactation peak, creating a negative energy balance that is difficult to overcome with diet. This negative energy balance could affect early embryo development that must compete with the mammary tissue for nutrients. We hypothesize that the methylation profiles of calves born to nonlactating heifers are different from those of calves born to lactating cows. We found 50,277 differentially methylated cytosines and 2,281 differentially methylated regions between these two groups of animals. A comethylation network was constructed to study the correlation between the phenotypes of the mothers and the epigenome of the calves, revealing 265 regions associated with the phenotypes. Our study revealed the presence of DMCs and DMRs in calves gestated by heifers and lactating cows, which were linked to the dam's lactation and the calves' ICAP and milk EBV. Gene-specific analysis highlighted associations with vasculature and organ morphogenesis and cell communication and signalling. These finding support the hypothesis that calves gestated by nonlactating mothers have a different methylation profile than those gestated by lactating cows.
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Affiliation(s)
- Adrián López-Catalina
- Departamento de Mejora Genética Animal, Instituto Nacional de Investigación y Tecnología Agraria y Alimentaria (INIA), CSIC, Crta. de la Coruña km 7.5, Madrid, Spain
- Departamento de Producción Agraria, Escuela Técnica Superior de Ingeniería Agronómica, Alimentaria y de Biosistemas, Universidad Politécnica de Madrid, Ciudad Universitaria s/n, Madrid, Spain
- CSIRO Agriculture & Food, Queensland Bioscience Precinct, Brisbane, Queensland, Australia
| | - Antonio Reverter
- CSIRO Agriculture & Food, Queensland Bioscience Precinct, Brisbane, Queensland, Australia
| | - Pamela A. Alexandre
- CSIRO Agriculture & Food, Queensland Bioscience Precinct, Brisbane, Queensland, Australia
| | - Loan T. Nguyen
- Queensland Alliance for Agriculture and Food Innovation, University of Queensland, St Lucia, QLD, Australia
| | - Oscar González-Recio
- Departamento de Mejora Genética Animal, Instituto Nacional de Investigación y Tecnología Agraria y Alimentaria (INIA), CSIC, Crta. de la Coruña km 7.5, Madrid, Spain
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Segura-Ortiz A, García-Nieto J, Aldana-Montes JF, Navas-Delgado I. Multi-objective context-guided consensus of a massive array of techniques for the inference of Gene Regulatory Networks. Comput Biol Med 2024; 179:108850. [PMID: 39013340 DOI: 10.1016/j.compbiomed.2024.108850] [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: 02/08/2024] [Revised: 07/03/2024] [Accepted: 07/03/2024] [Indexed: 07/18/2024]
Abstract
BACKGROUND AND OBJECTIVE Gene Regulatory Network (GRN) inference is a fundamental task in biology and medicine, as it enables a deeper understanding of the intricate mechanisms of gene expression present in organisms. This bioinformatics problem has been addressed in the literature through multiple computational approaches. Techniques developed for inferring from expression data have employed Bayesian networks, ordinary differential equations (ODEs), machine learning, information theory measures and neural networks, among others. The diversity of implementations and their respective customization have led to the emergence of many tools and multiple specialized domains derived from them, understood as subsets of networks with specific characteristics that are challenging to detect a priori. This specialization has introduced significant uncertainty when choosing the most appropriate technique for a particular dataset. This proposal, named MO-GENECI, builds upon the basic idea of the previous proposal GENECI and optimizes consensus among different inference techniques, through a carefully refined multi-objective evolutionary algorithm guided by various objective functions, linked to the biological context at hand. METHODS MO-GENECI has been tested on an extensive and diverse academic benchmark of 106 gene regulatory networks from multiple sources and sizes. The evaluation of MO-GENECI compared its performance to individual techniques using key metrics (AUROC and AUPR) for gene regulatory network inference. Friedman's statistical ranking provided an ordered classification, followed by non-parametric Holm tests to determine statistical significance. RESULTS MO-GENECI's Pareto front approximation facilitates easy selection of an appropriate solution based on generic input data characteristics. The best solution consistently emerged as the winner in all statistical tests, and in many cases, the median precision solution showed no statistically significant difference compared to the winner. CONCLUSIONS MO-GENECI has not only demonstrated achieving more accurate results than individual techniques, but has also overcome the uncertainty associated with the initial choice due to its flexibility and adaptability. It is shown intelligently to select the most suitable techniques for each case. The source code is hosted in a public repository at GitHub under MIT license: https://github.com/AdrianSeguraOrtiz/MO-GENECI. Moreover, to facilitate its installation and use, the software associated with this implementation has been encapsulated in a Python package available at PyPI: https://pypi.org/project/geneci/.
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Affiliation(s)
- Adrián Segura-Ortiz
- Department de Lenguajes y Ciencias de la Computación, ITIS Software, Universidad de Málaga, Málaga, 29071, Spain.
| | - José García-Nieto
- Department de Lenguajes y Ciencias de la Computación, ITIS Software, Universidad de Málaga, Málaga, 29071, Spain; Biomedical Research Institute of Málaga (IBIMA), Universidad de Málaga, Málaga, Spain
| | - José F Aldana-Montes
- Department de Lenguajes y Ciencias de la Computación, ITIS Software, Universidad de Málaga, Málaga, 29071, Spain; Biomedical Research Institute of Málaga (IBIMA), Universidad de Málaga, Málaga, Spain
| | - Ismael Navas-Delgado
- Department de Lenguajes y Ciencias de la Computación, ITIS Software, Universidad de Málaga, Málaga, 29071, Spain; Biomedical Research Institute of Málaga (IBIMA), Universidad de Málaga, Málaga, Spain
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Tan WLA, Hudson NJ, Porto Neto LR, Reverter A, Afonso J, Fortes MRS. An association weight matrix identified biological pathways associated with bull fertility traits in a multi-breed population. Anim Genet 2024; 55:495-510. [PMID: 38692842 DOI: 10.1111/age.13431] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/16/2023] [Revised: 02/26/2024] [Accepted: 04/01/2024] [Indexed: 05/03/2024]
Abstract
Using seven indicator traits, we investigated the genetic basis of bull fertility and predicted gene interactions from SNP associations. We used percent normal sperm as the key phenotype for the association weight matrix-partial correlation information theory (AWM-PCIT) approach. Beyond a simple list of candidate genes, AWM-PCIT predicts significant gene interactions and associations for the selected traits. These interactions formed a network of 537 genes: 38 genes were transcription cofactors, and 41 genes were transcription factors. The network displayed two distinct clusters, one with 294 genes and another with 243 genes. The network is enriched in fertility-associated pathways: steroid biosynthesis, p53 signalling, and the pentose phosphate pathway. Enrichment analysis also highlighted gene ontology terms associated with 'regulation of neurotransmitter secretion' and 'chromatin formation'. Our network recapitulates some genes previously implicated in another network built with lower-density genotypes. Sequence-level data also highlights additional candidate genes relevant to bull fertility, such as FOXO4, FOXP3, GATA1, CYP27B1, and EBP. A trio of regulatory genes-KDM5C, LRRK2, and PME-was deemed core to the network because of their overarching connections. This trio probably influences bull fertility through their interaction with genes, both known and unknown as to their role in male fertility. Future studies may target the trio and their target genes to enrich our understanding of male fertility further.
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Affiliation(s)
- Wei Liang Andre Tan
- School of Chemistry and Molecular Bioscience, The University of Queensland, St Lucia, Queensland, Australia
| | - Nicholas James Hudson
- School of Agriculture and Food Sustainability, The University of Queensland, Gatton, Queensland, Australia
| | | | | | - Juliana Afonso
- School of Chemistry and Molecular Bioscience, The University of Queensland, St Lucia, Queensland, Australia
- Empresa Brasileira de Pesquisa Agropecuária, Pecuária Sudeste, São Carlos, São Paulo, Brazil
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4
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Yang Y, Zhang F, Yu X, Wang L, Wang Z. Integrating microbial 16S rRNA sequencing and non-targeted metabolomics to reveal sexual dimorphism of the chicken cecal microbiome and serum metabolome. Front Microbiol 2024; 15:1403166. [PMID: 39101039 PMCID: PMC11294938 DOI: 10.3389/fmicb.2024.1403166] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/18/2024] [Accepted: 06/24/2024] [Indexed: 08/06/2024] Open
Abstract
Background The gut microbiome plays a key role in the formation of livestock and poultry traits via serum metabolites, and empirical evidence has indicated these traits are sex-linked. Methods We examined 106 chickens (54 male chickens and 52 female chickens) and analyzed cecal content samples and serum samples by 16S rRNA gene sequencing and non-targeted metabolomics, respectively. Results The cecal microbiome of female chickens was more stable and more complex than that of the male chickens. Lactobacillus and Family XIII UCG-001 were enriched in male chickens, while Eubacterium_nodatum_group, Blautia, unclassified_Anaerovoraceae, Romboutsia, Lachnoclostridium, and norank_Muribaculaceae were enriched in female chickens. Thirty-seven differential metabolites were identified in positive mode and 13 in negative mode, showing sex differences. Sphingomyelin metabolites possessed the strongest association with cecal microbes, while 11β-hydroxytestosterone showed a negative correlation with Blautia. Conclusion These results support the role of sexual dimorphism of the cecal microbiome and metabolome and implicate specific gender factors associated with production performance in chickens.
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Affiliation(s)
| | | | | | | | - Zhong Wang
- Key Laboratory of Animal Genetics, Breeding and Reproduction in the Plateau Mountainous Region, Ministry of Education, Guizhou University, Guiyang, China
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Fernandes AC, Reverter A, Keogh K, Alexandre PA, Afonso J, Palhares JCP, Cardoso TF, Malheiros JM, Bruscadin JJ, de Oliveira PSN, Mourão GB, de Almeida Regitano LC, Coutinho LL. Transcriptional response to an alternative diet on liver, muscle, and rumen of beef cattle. Sci Rep 2024; 14:13682. [PMID: 38871745 PMCID: PMC11176196 DOI: 10.1038/s41598-024-63619-2] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/05/2023] [Accepted: 05/30/2024] [Indexed: 06/15/2024] Open
Abstract
Feed cost represents a major economic determinant within cattle production, amounting to an estimated 75% of the total variable costs. Consequently, comprehensive approaches such as optimizing feed utilization through alternative feed sources, alongside the selection of feed-efficient animals, are of great significance. Here, we investigate the effect of two diets, traditional corn-grain fed and alternative by-product based, on 14 phenotypes related to feed, methane emission and production efficiency and on multi-tissue transcriptomics data from liver, muscle, and rumen wall, derived from 52 Nellore bulls, 26 on each diet. To this end, diets were contrasted at the level of phenotype, gene expression, and gene-phenotype network connectivity. As regards the phenotypic level, at a P value < 0.05, significant differences were found in favour of the alternative diet for average daily weight gain at finishing, dry matter intake at finishing, methane emission, carcass yield and subcutaneous fat thickness at the rib-eye muscle area. In terms of the transcriptional level of the 14,776 genes expressed across the examined tissues, we found 487, 484, and 499 genes differentially expressed due to diet in liver, muscle, and rumen, respectively (P value < 0.01). To explore differentially connected phenotypes across both diet-based networks, we focused on the phenotypes with the largest change in average number of connections within diets and tissues, namely methane emission and carcass yield, highlighting, in particular, gene expression changes involving SREBF2, and revealing the largest differential connectivity in rumen and muscle, respectively. Similarly, from examination of differentially connected genes across diets, the top-ranked most differentially connected regulators within each tissue were MEOX1, PTTG1, and BASP1 in liver, muscle, and rumen, respectively. Changes in gene co-expression patterns suggest activation or suppression of specific biological processes and pathways in response to dietary interventions, consequently impacting the phenotype. The identification of genes that respond differently to diets and their associated phenotypic effects serves as a crucial stepping stone for further investigations, aiming to build upon our discoveries. Ultimately, such advancements hold the promise of improving animal welfare, productivity, and sustainability in livestock farming.
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Affiliation(s)
- Anna Carolina Fernandes
- Department of Animal Science, Luiz de Queiroz College of Agriculture, University of São Paulo (ESALQ-USP), Piracicaba, São Paulo, Brazil
- CSIRO Agriculture & Food, Queensland Bioscience Precinct, 306 Carmody Rd., St. Lucia, Brisbane, QLD, 4067, Australia
| | - Antonio Reverter
- CSIRO Agriculture & Food, Queensland Bioscience Precinct, 306 Carmody Rd., St. Lucia, Brisbane, QLD, 4067, Australia
| | - Kate Keogh
- CSIRO Agriculture & Food, Queensland Bioscience Precinct, 306 Carmody Rd., St. Lucia, Brisbane, QLD, 4067, Australia
- Animal and Bioscience Research Department, Teagasc, Animal & Grassland Research and Innovation Centre, Grange, Dunsany, Co. Meath, Ireland
| | - Pâmela Almeida Alexandre
- CSIRO Agriculture & Food, Queensland Bioscience Precinct, 306 Carmody Rd., St. Lucia, Brisbane, QLD, 4067, Australia
| | - Juliana Afonso
- Brazilian Agricultural Research Corporation, Embrapa Pecuária Sudeste, São Carlos, São Paulo, Brazil
| | | | - Tainã Figueiredo Cardoso
- Brazilian Agricultural Research Corporation, Embrapa Pecuária Sudeste, São Carlos, São Paulo, Brazil
| | - Jessica Moraes Malheiros
- Brazilian Agricultural Research Corporation, Embrapa Pecuária Sudeste, São Carlos, São Paulo, Brazil
- Beef Cattle Research Center, Animal Science Institute (IZ), Sertãozinho, São Paulo, Brazil
| | - Jennifer Jessica Bruscadin
- Center of Biological and Health Sciences, Federal University of São Carlos, São Carlos, São Paulo, Brazil
| | | | - Gerson Barreto Mourão
- Department of Animal Science, Luiz de Queiroz College of Agriculture, University of São Paulo (ESALQ-USP), Piracicaba, São Paulo, Brazil
| | | | - Luiz Lehmann Coutinho
- Department of Animal Science, Luiz de Queiroz College of Agriculture, University of São Paulo (ESALQ-USP), Piracicaba, São Paulo, Brazil.
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Hudson NJ, Cramp RL, Franklin CE. Dramatic genome-wide reprogramming of mRNA in hypometabolic muscle. Comp Biochem Physiol B Biochem Mol Biol 2024; 272:110952. [PMID: 38355035 DOI: 10.1016/j.cbpb.2024.110952] [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: 11/16/2023] [Revised: 01/17/2024] [Accepted: 02/10/2024] [Indexed: 02/16/2024]
Abstract
In response to seasonal droughts, the green striped burrowing frog Cyclorana alboguttata enters a reversible hypometabolic state called aestivation where heart rate and oxygen consumption can be reduced despite warm (>25C°) ambient temperatures. With a view to understanding molecular mechanisms we profiled aestivating versus control gastrocnemius muscle using mRNA sequencing. This indicated an extensive metabolic reprogramming, with nearly a quarter of the entire transcriptome (3996 of 16,960 mRNA) exhibiting a nominal >2-fold change. Consistent with a physiological adaptation to spare carbohydrate reserves, carbohydrate catabolism was systemically downregulated. A 630-fold downregulation of ENO3 encoding the enolase enzyme was most striking. The 590 frog orthologs of mRNA encoding the mitoproteome were, viewed as a population, significantly downregulated during aestivation, although not to the same extent as mRNA encoding carbohydrate catabolism. Prominent examples include members of the TCA cycle (IDH2), electron transport chain (NDUFA6), the ATP synthase complex (ATP5F1B) and ADP/ATP intracellular transport (SLC25A4). Moreover, mRNA derived from the mt genome itself (e.g. mt-ND1) were also downregulated. Most prominent among the upregulated mRNA are those encoding aspects of regulated proteolysis including the proteosome (e.g. PSME4L), peptidases (USP25), atrogins (FBXO32) and ubiquitination (VCP). Finally, we note the ∼5-fold upregulation of the mRNA EIFG3 that encodes part of the EIF4F complex. This possesses global control of protein synthesis. Given protein synthesis is repressed in aestivating frogs this indicates the skeletal musculature is poised for accelerated translation of mRNA upon emergence, supporting a strategy to rapidly restore function when the summer rains come.
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Affiliation(s)
- Nicholas J Hudson
- School of Agriculture and Food Sustainability, The University of Queensland, Gatton, Queensland 4343, Australia.
| | - Rebecca L Cramp
- School of the Environment, The University of Queensland, St. Lucia, Queensland 4072, Australia
| | - Craig E Franklin
- School of the Environment, The University of Queensland, St. Lucia, Queensland 4072, Australia. https://twitter.com/Franklin_EcoLab
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Zhang ZY, Sun ZJ, Gao D, Hao YD, Lin H, Liu F. Excavation of gene markers associated with pancreatic ductal adenocarcinoma based on interrelationships of gene expression. IET Syst Biol 2024. [PMID: 38530028 DOI: 10.1049/syb2.12090] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/20/2023] [Revised: 02/06/2024] [Accepted: 03/10/2024] [Indexed: 03/27/2024] Open
Abstract
Pancreatic ductal adenocarcinoma (PDAC) accounts for 95% of all pancreatic cancer cases, posing grave challenges to its diagnosis and treatment. Timely diagnosis is pivotal for improving patient survival, necessitating the discovery of precise biomarkers. An innovative approach was introduced to identify gene markers for precision PDAC detection. The core idea of our method is to discover gene pairs that display consistent opposite relative expression and differential co-expression patterns between PDAC and normal samples. Reversal gene pair analysis and differential partial correlation analysis were performed to determine reversal differential partial correlation (RDC) gene pairs. Using incremental feature selection, the authors refined the selected gene set and constructed a machine-learning model for PDAC recognition. As a result, the approach identified 10 RDC gene pairs. And the model could achieve a remarkable accuracy of 96.1% during cross-validation, surpassing gene expression-based models. The experiment on independent validation data confirmed the model's performance. Enrichment analysis revealed the involvement of these genes in essential biological processes and shed light on their potential roles in PDAC pathogenesis. Overall, the findings highlight the potential of these 10 RDC gene pairs as effective diagnostic markers for early PDAC detection, bringing hope for improving patient prognosis and survival.
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Affiliation(s)
- Zhao-Yue Zhang
- School of Life Science and Technology, University of Electronic Science and Technology of China, Chengdu, China
- School of Healthcare Technology, Chengdu Neusoft University, Chengdu, China
| | - Zi-Jie Sun
- School of Life Science and Technology, University of Electronic Science and Technology of China, Chengdu, China
| | - Dong Gao
- School of Life Science and Technology, University of Electronic Science and Technology of China, Chengdu, China
| | - Yu-Duo Hao
- School of Life Science and Technology, University of Electronic Science and Technology of China, Chengdu, China
| | - Hao Lin
- School of Life Science and Technology, University of Electronic Science and Technology of China, Chengdu, China
| | - Fen Liu
- Department of Radiation Oncology, Peking University Cancer Hospital (Inner Mongolia Campus), Affiliated Cancer Hospital of Inner Mongolia Medical University, Inner Mongolia Cancer Hospital, Hohhot, China
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Afonso J, Lima AO, de Sousa MAP, de Athayde FRF, Fortes MRS. Transcription factors and miRNA act as contrary regulators of gene expression in the testis and epididymis of Bos indicus animals. Gene 2024; 899:148133. [PMID: 38181930 DOI: 10.1016/j.gene.2024.148133] [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: 10/17/2023] [Revised: 12/11/2023] [Accepted: 01/02/2024] [Indexed: 01/07/2024]
Abstract
Spermatogenesis is highly conserved among mammalians, but its gene expression and regulatory profile are not entirely known. As transcription factors (TFs) and miRNAs are crucial for gene expression regulation, identifying genes negatively regulated by miRNAs and positively regulated by TFs in the testis and epididymis can provide a deeper understanding of gene expression and regulatory patterns. To do this, we used expression data coming from RNA-Seq and miRNA-Seq experiments made with biopsies from testicular parenchyma, head of the epididymis, and tail of the epididymis of four Brahman bulls. We identified miRNA differentially expressed (DE) by comparing the three distinct tissues. A co-expression analysis combined with a regulatory impact factor approach identified miRNAs and TFs with regulatory impact over gene expression regulation in the Bos indicus tissues studied. We identified 116 DE miRNAs, 206 miRNAs and 237 TFs with a significant regulatory impact on mRNA patterns in the tissues' comparisons. bta-miR-196b was the only DE miRNA for all tissue comparisons and it may be a regulator of spermatogenesis through its links with adipogenesis and insulin biosynthesis. DE genes and TFs involved in contrary regulations between the epididymis head and testis parenchyma were associated with spermatogenesis, sexual reproduction, and sperm motility. Our results provide possible mechanisms, governed by the contrary effect of miRNA and TF, leading to the differential expression between the studied tissues. We have demonstrated that our predictions of miRNAs and TFs co-regulations over target DE genes can retrieve known regulatory mechanisms and predict new ones that merit further validation.
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Affiliation(s)
- Juliana Afonso
- Embrapa Pecuária Sudeste, São Carlos, São Paulo, Brazil; School of Chemistry and Molecular Biosciences, The University of Queensland, Brisbane, Australia.
| | - Andressa Oliveira Lima
- Division of Medical Genetics, Department of Genome Sciences, Department of Medicine, University of Washington, Seattle, WA, USA
| | - Marco Antonio Perpétuo de Sousa
- Departamento de Produção e Saúde Animal, Universidade Estadual Paulista "Júlio de Mesquita Filho" (UNESP), Faculdade de Medicina Veterinária, Araçatuba, Brazil
| | - Flávia Regina Florêncio de Athayde
- Departamento de Produção e Saúde Animal, Universidade Estadual Paulista "Júlio de Mesquita Filho" (UNESP), Faculdade de Medicina Veterinária, Araçatuba, Brazil
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Keogh K, Kenny DA, Alexandre PA, McGee M, Reverter A. An across breed, diet and tissue analysis reveals the transcription factor NR1H3 as a key mediator of residual feed intake in beef cattle. BMC Genomics 2024; 25:234. [PMID: 38438858 PMCID: PMC10910725 DOI: 10.1186/s12864-024-10151-2] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/31/2023] [Accepted: 02/21/2024] [Indexed: 03/06/2024] Open
Abstract
BACKGROUND Provision of feed is a major determinant of overall profitability in beef production systems, accounting for up to 75% of the variable costs. Thus, improving cattle feed efficiency, by way of determining the underlying genomic control and subsequently selecting for feed efficient cattle, provides a method through which feed input costs may be reduced. The objective of this study was to undertake gene co-expression network analysis using RNA-Sequence data generated from Longissimus dorsi and liver tissue samples collected from steers of two contrasting breeds (Charolais and Holstein-Friesian) divergent for residual feed intake (RFI), across two consecutive distinct dietary phases (zero-grazed grass and high-concentrate). Categories including differentially expressed genes (DEGs) based on the contrasts of RFI phenotype, breed and dietary source, as well as key transcription factors and proteins secreted in plasma were utilised as nodes of the gene co-expression network. RESULTS Of the 2,929 DEGs within the network analysis, 1,604 were reported to have statistically significant correlations (≥ 0.80), resulting in a total of 43,876 significant connections between genes. Pathway analysis of clusters of co-expressed genes revealed enrichment of processes related to lipid metabolism (fatty acid biosynthesis, fatty acid β-oxidation, cholesterol biosynthesis), immune function, (complement cascade, coagulation system, acute phase response signalling), and energy production (oxidative phosphorylation, mitochondrial L-carnitine shuttle pathway) based on genes related to RFI, breed and dietary source contrasts. CONCLUSIONS Although similar biological processes were evident across the three factors examined, no one gene node was evident across RFI, breed and diet contrasts in both liver and muscle tissues. However within the liver tissue, the IRX4, NR1H3, HOXA13 and ZNF648 gene nodes, which all encode transcription factors displayed significant connections across the RFI, diet and breed comparisons, indicating a role for these transcription factors towards the RFI phenotype irrespective of diet and breed. Moreover, the NR1H3 gene encodes a protein secreted into plasma from the hepatocytes of the liver, highlighting the potential for this gene to be explored as a robust biomarker for the RFI trait in beef cattle.
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Affiliation(s)
- Kate Keogh
- Animal and Bioscience Research Department, Teagasc, Animal & Grassland Research and Innovation Centre, Grange, Dunsany, Co. Meath, Ireland.
- Queensland Bioscience Precinct, CSIRO Agriculture & Food, 306 Carmody Rd., St. Lucia, 4067, Brisbane, QLD, Australia.
| | - D A Kenny
- Animal and Bioscience Research Department, Teagasc, Animal & Grassland Research and Innovation Centre, Grange, Dunsany, Co. Meath, Ireland
| | - P A Alexandre
- Queensland Bioscience Precinct, CSIRO Agriculture & Food, 306 Carmody Rd., St. Lucia, 4067, Brisbane, QLD, Australia
| | - M McGee
- Livestock Systems Research Department, Teagasc, Animal & Grassland Research and Innovation Centre, Grange, Dunsany, Co. Meath, Ireland
| | - A Reverter
- Queensland Bioscience Precinct, CSIRO Agriculture & Food, 306 Carmody Rd., St. Lucia, 4067, Brisbane, QLD, Australia
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Mantilla Valdivieso EF, Ross EM, Raza A, Nguyen L, Hayes BJ, Jonsson NN, James P, Tabor AE. Expression network analysis of bovine skin infested with Rhipicephalus australis identifies pro-inflammatory genes contributing to tick susceptibility. Sci Rep 2024; 14:4419. [PMID: 38388834 PMCID: PMC10884027 DOI: 10.1038/s41598-024-54577-w] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/09/2023] [Accepted: 02/14/2024] [Indexed: 02/24/2024] Open
Abstract
The skin is the primary feeding site of ticks that infest livestock animals such as cattle. The highly specialised functions of skin at the molecular level may be a factor contributing to variation in susceptibility to tick infestation; but these remain to be well defined. The aim of this study was to investigate the bovine skin transcriptomic profiles of tick-naïve and tick-infested cattle and to uncover the gene expression networks that influence contrasting phenotypes of host resistance to ticks. RNA-Seq data was obtained from skin of Brangus cattle with high (n = 5) and low (n = 6) host resistance at 0 and 12 weeks following artificial tick challenge with Rhipicephalus australis larvae. No differentially expressed genes were detected pre-infestation between high and low resistance groups, but at 12-weeks there were 229 differentially expressed genes (DEGs; FDR < 0.05), of which 212 were the target of at least 1866 transcription factors (TFs) expressed in skin. Regulatory impact factor (RIF) analysis identified 158 significant TFs (P < 0.05) of which GRHL3, and DTX1 were also DEGs in the experiment. Gene term enrichment showed the significant TFs and DEGs were enriched in processes related to immune response and biological pathways related to host response to infectious diseases. Interferon Type 1-stimulated genes, including MX2, ISG15, MX1, OAS2 were upregulated in low host resistance steers after repeated tick challenge, suggesting dysregulated wound healing and chronic inflammatory skin processes contributing to host susceptibility to ticks. The present study provides an assessment of the bovine skin transcriptome before and after repeated tick challenge and shows that the up-regulation of pro-inflammatory genes is a prominent feature in the skin of tick-susceptible animals. In addition, the identification of transcription factors with high regulatory impact provides insights into the potentially meaningful gene-gene interactions involved in the variation of phenotypes of bovine host resistance to ticks.
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Affiliation(s)
- Emily F Mantilla Valdivieso
- Queensland Alliance for Agriculture and Food Innovation, Centre for Animal Science, The University of Queensland, St Lucia, QLD, 4072, Australia
| | - Elizabeth M Ross
- Queensland Alliance for Agriculture and Food Innovation, Centre for Animal Science, The University of Queensland, St Lucia, QLD, 4072, Australia.
| | - Ali Raza
- Queensland Alliance for Agriculture and Food Innovation, Centre for Animal Science, The University of Queensland, St Lucia, QLD, 4072, Australia
| | - Loan Nguyen
- Queensland Alliance for Agriculture and Food Innovation, Centre for Animal Science, The University of Queensland, St Lucia, QLD, 4072, Australia
| | - Ben J Hayes
- Queensland Alliance for Agriculture and Food Innovation, Centre for Animal Science, The University of Queensland, St Lucia, QLD, 4072, Australia
| | - Nicholas N Jonsson
- Institute of Biodiversity One Health and Veterinary Medicine, University of Glasgow, Glasgow, G61 1QH, UK.
| | - Peter James
- Queensland Alliance for Agriculture and Food Innovation, Centre for Animal Science, The University of Queensland, St Lucia, QLD, 4072, Australia
| | - Ala E Tabor
- Queensland Alliance for Agriculture and Food Innovation, Centre for Animal Science, The University of Queensland, St Lucia, QLD, 4072, Australia.
- School of Chemistry and Molecular Biosciences, The University of Queensland, St Lucia, QLD, 4072, Australia.
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11
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Shibl AA, Ochsenkühn MA, Mohamed AR, Isaac A, Coe LSY, Yun Y, Skrzypek G, Raina JB, Seymour JR, Afzal AJ, Amin SA. Molecular mechanisms of microbiome modulation by the eukaryotic secondary metabolite azelaic acid. eLife 2024; 12:RP88525. [PMID: 38189382 PMCID: PMC10945470 DOI: 10.7554/elife.88525] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/09/2024] Open
Abstract
Photosynthetic eukaryotes, such as microalgae and plants, foster fundamentally important relationships with their microbiome based on the reciprocal exchange of chemical currencies. Among these, the dicarboxylate metabolite azelaic acid (Aze) appears to play an important, but heterogeneous, role in modulating these microbiomes, as it is used as a carbon source for some heterotrophs but is toxic to others. However, the ability of Aze to promote or inhibit growth, as well as its uptake and assimilation mechanisms into bacterial cells are mostly unknown. Here, we use transcriptomics, transcriptional factor coexpression networks, uptake experiments, and metabolomics to unravel the uptake, catabolism, and toxicity of Aze on two microalgal-associated bacteria, Phycobacter and Alteromonas, whose growth is promoted or inhibited by Aze, respectively. We identify the first putative Aze transporter in bacteria, a 'C4-TRAP transporter', and show that Aze is assimilated through fatty acid degradation, with further catabolism occurring through the glyoxylate and butanoate metabolism pathways when used as a carbon source. Phycobacter took up Aze at an initial uptake rate of 3.8×10-9 nmol/cell/hr and utilized it as a carbon source in concentrations ranging from 10 μM to 1 mM, suggesting a broad range of acclimation to Aze availability. For growth-impeded bacteria, we infer that Aze inhibits the ribosome and/or protein synthesis and that a suite of efflux pumps is utilized to shuttle Aze outside the cytoplasm. We demonstrate that seawater amended with Aze becomes enriched in bacterial families that can catabolize Aze, which appears to be a different mechanism from that in soil, where modulation by the host plant is required. This study enhances our understanding of carbon cycling in the oceans and how microscale chemical interactions can structure marine microbial populations. In addition, our findings unravel the role of a key chemical currency in the modulation of eukaryote-microbiome interactions across diverse ecosystems.
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Affiliation(s)
- Ahmed A Shibl
- Biology Program, New York University Abu DhabiAbu DhabiUnited Arab Emirates
| | | | - Amin R Mohamed
- Biology Program, New York University Abu DhabiAbu DhabiUnited Arab Emirates
| | - Ashley Isaac
- Biology Program, New York University Abu DhabiAbu DhabiUnited Arab Emirates
- Max Planck Institute for Marine MicrobiologyBremenGermany
| | - Lisa SY Coe
- Biology Program, New York University Abu DhabiAbu DhabiUnited Arab Emirates
| | - Yejie Yun
- Biology Program, New York University Abu DhabiAbu DhabiUnited Arab Emirates
| | - Grzegorz Skrzypek
- West Australian Biogeochemistry Centre, School of Biological Sciences, The University of Western AustraliaPerthAustralia
| | - Jean-Baptiste Raina
- Climate Change Cluster, Faculty of Science, University of Technology SydneyUltimoAustralia
| | - Justin R Seymour
- Climate Change Cluster, Faculty of Science, University of Technology SydneyUltimoAustralia
| | - Ahmed J Afzal
- Biology Program, New York University Abu DhabiAbu DhabiUnited Arab Emirates
| | - Shady A Amin
- Biology Program, New York University Abu DhabiAbu DhabiUnited Arab Emirates
- Center for Genomics and Systems Biology (CGSB), New York University Abu DhabiAbu DhabiUnited Arab Emirates
- Arabian Center for Climate and Environmental Sciences (ACCESS), New York University Abu DhabiAbu DhabiUnited Arab Emirates
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12
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Pereira-Junior SAG, Costa RV, Rodrigues JL, Torrecilhas JA, Chiaratti MR, Lanna DPD, das Chagas JC, Nociti RP, Meirelles FV, Ferraz JBS, Fernandes MHMR, Almeida MTC, Ezequiel JMB. Soybean molasses increases subcutaneous fat deposition while reducing lipid oxidation in the meat of castrated lambs. J Anim Sci 2024; 102:skae130. [PMID: 38719973 PMCID: PMC11208934 DOI: 10.1093/jas/skae130] [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: 02/10/2024] [Accepted: 05/07/2024] [Indexed: 06/29/2024] Open
Abstract
This study aimed to evaluate the effect of including soybean molasses (SM) on performance, blood parameters, carcass traits, meat quality, fatty acid, and muscle (longissimus thoracis) transcriptomic profiles of castrated lambs. Twenty Dorper × Santa Inês lambs (20.06 ± 0.76 kg body weight [BW]) were assigned to a randomized block design, stratified by BW, with the following treatments: CON: 0 g/kg of SM and SM20: 200 g/kg of SM on dry matter basis, allocated in individual pens. The diet consisted of 840 g/kg concentrate and 160 g/kg corn silage for 76 d, with the first 12 d as an adaptation period and the remaining 64 d on the finishing diet. The SM20 diet increased blood urea concentration (P = 0.03) while reduced glucose concentration (P = 0.04). Lambs fed SM showed higher subcutaneous fat deposition (P = 0.04) and higher subcutaneous adipocyte diameter (P < 0.01), in addition to reduced meat lipid oxidation (P < 0.01). SM reduced the quantity of branched-chain fatty acids in longissimus thoracis (P = 0.05) and increased the quantity of saturated fatty acids (P = 0.01). In the transcriptomic analysis, 294 genes were identified as differentially expressed, which belong to pathways such as oxidative phosphorylation, citric acid cycle, and monosaccharide metabolic process. In conclusion, diet with SM increased carcass fat deposition, reduced lipid oxidation, and changed the energy metabolism, supporting its use in ruminant nutrition.
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Affiliation(s)
- Sérgio A G Pereira-Junior
- Department of Animal Science, Agrarian Science and Veterinary College, São Paulo State University “Unesp”, Jaboticabal, SP, Brazil
| | - Rayanne V Costa
- Department of Animal Science, Agrarian Science and Veterinary College, São Paulo State University “Unesp”, Jaboticabal, SP, Brazil
| | - Julia L Rodrigues
- Department of Animal Science, Agrarian Science and Veterinary College, São Paulo State University “Unesp”, Jaboticabal, SP, Brazil
| | - Juliana A Torrecilhas
- Department of Animal Production, Veterinary Medicine and Animal Science College, São Paulo State University “Unesp”, Botucatu, SP, Brazil
| | - Marcos R Chiaratti
- Departamento de Genética e Evolução, Universidade Federal de São Carlos, São Carlos, SP, Brazil
| | - Dante P D Lanna
- Department of Animal Science, “Luiz de Queiroz” College of Agriculture, University of São Paulo, Piracicaba, SP, Brazil
| | - Julia C das Chagas
- Department of Animal Science, Agrarian Science and Veterinary College, São Paulo State University “Unesp”, Jaboticabal, SP, Brazil
| | - Ricardo P Nociti
- Department of Veterinary Medicine, College of Animal Science and Food Engineering, University of São Paulo, Pirassununga, SPBrazil
| | - Flavio V Meirelles
- Department of Veterinary Medicine, College of Animal Science and Food Engineering, University of São Paulo, Pirassununga, SPBrazil
| | - José Bento S Ferraz
- Department of Veterinary Medicine, College of Animal Science and Food Engineering, University of São Paulo, Pirassununga, SPBrazil
| | - Márcia H M R Fernandes
- Department of Animal Science, Agrarian Science and Veterinary College, São Paulo State University “Unesp”, Jaboticabal, SP, Brazil
| | - Marco Túlio C Almeida
- Department of Animal Science, Federal University of Espírito Santo, Vitória, ES, Brazil
| | - Jane M B Ezequiel
- Department of Animal Science, Agrarian Science and Veterinary College, São Paulo State University “Unesp”, Jaboticabal, SP, Brazil
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13
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Martins FB, Aono AH, Moraes ADCL, Ferreira RCU, Vilela MDM, Pessoa-Filho M, Rodrigues-Motta M, Simeão RM, de Souza AP. Genome-wide family prediction unveils molecular mechanisms underlying the regulation of agronomic traits in Urochloa ruziziensis. FRONTIERS IN PLANT SCIENCE 2023; 14:1303417. [PMID: 38148869 PMCID: PMC10749977 DOI: 10.3389/fpls.2023.1303417] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Figures] [Subscribe] [Scholar Register] [Received: 09/28/2023] [Accepted: 11/15/2023] [Indexed: 12/28/2023]
Abstract
Tropical forage grasses, particularly those belonging to the Urochloa genus, play a crucial role in cattle production and serve as the main food source for animals in tropical and subtropical regions. The majority of these species are apomictic and tetraploid, highlighting the significance of U. ruziziensis, a sexual diploid species that can be tetraploidized for use in interspecific crosses with apomictic species. As a means to support breeding programs, our study investigates the feasibility of genome-wide family prediction in U. ruziziensis families to predict agronomic traits. Fifty half-sibling families were assessed for green matter yield, dry matter yield, regrowth capacity, leaf dry matter, and stem dry matter across different clippings established in contrasting seasons with varying available water capacity. Genotyping was performed using a genotyping-by-sequencing approach based on DNA samples from family pools. In addition to conventional genomic prediction methods, machine learning and feature selection algorithms were employed to reduce the necessary number of markers for prediction and enhance predictive accuracy across phenotypes. To explore the regulation of agronomic traits, our study evaluated the significance of selected markers for prediction using a tree-based approach, potentially linking these regions to quantitative trait loci (QTLs). In a multiomic approach, genes from the species transcriptome were mapped and correlated to those markers. A gene coexpression network was modeled with gene expression estimates from a diverse set of U. ruziziensis genotypes, enabling a comprehensive investigation of molecular mechanisms associated with these regions. The heritabilities of the evaluated traits ranged from 0.44 to 0.92. A total of 28,106 filtered SNPs were used to predict phenotypic measurements, achieving a mean predictive ability of 0.762. By employing feature selection techniques, we could reduce the dimensionality of SNP datasets, revealing potential genotype-phenotype associations. The functional annotation of genes near these markers revealed associations with auxin transport and biosynthesis of lignin, flavonol, and folic acid. Further exploration with the gene coexpression network uncovered associations with DNA metabolism, stress response, and circadian rhythm. These genes and regions represent important targets for expanding our understanding of the metabolic regulation of agronomic traits and offer valuable insights applicable to species breeding. Our work represents an innovative contribution to molecular breeding techniques for tropical forages, presenting a viable marker-assisted breeding approach and identifying target regions for future molecular studies on these agronomic traits.
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Affiliation(s)
- Felipe Bitencourt Martins
- Center for Molecular Biology and Genetic Engineering (CBMEG), University of Campinas (UNICAMP), Campinas, São Paulo, Brazil
| | - Alexandre Hild Aono
- Center for Molecular Biology and Genetic Engineering (CBMEG), University of Campinas (UNICAMP), Campinas, São Paulo, Brazil
| | - Aline da Costa Lima Moraes
- Department of Plant Biology, Biology Institute, University of Campinas (UNICAMP), Campinas, São Paulo, Brazil
| | | | | | - Marco Pessoa-Filho
- Embrapa Cerrados, Brazilian Agricultural Research Corporation, Brasília, Brazil
| | | | - Rosangela Maria Simeão
- Embrapa Gado de Corte, Brazilian Agricultural Research Corporation, Campo Grande, Mato Grosso, Brazil
| | - Anete Pereira de Souza
- Center for Molecular Biology and Genetic Engineering (CBMEG), University of Campinas (UNICAMP), Campinas, São Paulo, Brazil
- Department of Plant Biology, Biology Institute, University of Campinas (UNICAMP), Campinas, São Paulo, Brazil
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14
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Aguila L, Nociti RP, Sampaio RV, Therrien J, Meirelles FV, Felmer RN, Smith LC. Haploid androgenetic development of bovine embryos reveals imbalanced WNT signaling and impaired cell fate differentiation†. Biol Reprod 2023; 109:821-838. [PMID: 37788061 DOI: 10.1093/biolre/ioad124] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/09/2023] [Revised: 08/09/2023] [Accepted: 09/11/2023] [Indexed: 10/04/2023] Open
Abstract
Haploid embryos have contributed significantly to our understanding of the role of parental genomes in development and can be applied to important biotechnology for human and animal species. However, development to the blastocyst stage is severely hindered in bovine haploid androgenetic embryos (hAE). To further our understanding of such developmental arrest, we performed a comprehensive comparison of the transcriptomic profile of morula-stage embryos, which were validated by quantitative reverse transcription-polymerase chain reaction (qRT-PCR) of transcripts associated with differentiation in haploid and biparental embryos. Among numerous disturbances, results showed that pluripotency pathways, especially the wingless-related integration site (WNT) signaling, were particularly unbalanced in hAE. Moreover, transcript levels of KLF4, NANOG, POU5F1, SOX2, CDX2, CTNNBL1, AXIN2, and GSK3B were noticeably altered in hAE, suggesting disturbance of pluripotency and canonical WNT pathways. To evaluate the role of WNT on hAE competence, we exposed early Day-5 morula stage embryos to the GSK3B inhibitor CHIR99021. Although no alterations were observed in pluripotency and WNT-related transcripts, exposure to CHIR99021 improved their ability to reach the blastocysts stage, confirming the importance of the WNT pathway in the developmental outcome of bovine hAE.
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Affiliation(s)
- Luis Aguila
- Centre de Recherche en Reproduction et Fértilité (CRRF), Département de biomédecine vétérinaire, Université de Montréal, St-Hyacinthe, QC, Canada
- Laboratory of Reproduction, Centre of Reproductive Biotechnology (CEBIOR-BIOREN), Faculty of Agriculture and Forestry, Universidad de La Frontera, Temuco, Chile
| | - Ricardo P Nociti
- Centre de Recherche en Reproduction et Fértilité (CRRF), Département de biomédecine vétérinaire, Université de Montréal, St-Hyacinthe, QC, Canada
- Department of Veterinary Medicine, Faculty of Animal Sciences and Food Engineering, University of Sao Paulo, São Paulo, Brazil
| | - Rafael V Sampaio
- Centre de Recherche en Reproduction et Fértilité (CRRF), Département de biomédecine vétérinaire, Université de Montréal, St-Hyacinthe, QC, Canada
| | - Jacinthe Therrien
- Centre de Recherche en Reproduction et Fértilité (CRRF), Département de biomédecine vétérinaire, Université de Montréal, St-Hyacinthe, QC, Canada
| | - Flavio V Meirelles
- Department of Veterinary Medicine, Faculty of Animal Sciences and Food Engineering, University of Sao Paulo, São Paulo, Brazil
| | - Ricardo N Felmer
- Laboratory of Reproduction, Centre of Reproductive Biotechnology (CEBIOR-BIOREN), Faculty of Agriculture and Forestry, Universidad de La Frontera, Temuco, Chile
| | - Lawrence C Smith
- Centre de Recherche en Reproduction et Fértilité (CRRF), Département de biomédecine vétérinaire, Université de Montréal, St-Hyacinthe, QC, Canada
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15
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Bar H, Wells MT. On Graphical Models and Convex Geometry. Comput Stat Data Anal 2023; 187:107800. [PMID: 37396752 PMCID: PMC10310290 DOI: 10.1016/j.csda.2023.107800] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 07/04/2023]
Abstract
A mixture-model of beta distributions framework is introduced to identify significant correlations among P features when P is large. The method relies on theorems in convex geometry, which are used to show how to control the error rate of edge detection in graphical models. The proposed 'betaMix' method does not require any assumptions about the network structure, nor does it assume that the network is sparse. The results hold for a wide class of data-generating distributions that include light-tailed and heavy-tailed spherically symmetric distributions. The results are robust for sufficiently large sample sizes and hold for non-elliptically-symmetric distributions.
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Affiliation(s)
- Haim Bar
- Department of Statistics, University of Connecticut, Room 315, Philip E. Austin Building, Storrs, 06269-4120, CT, USA
| | - Martin T. Wells
- Department of Statistics and Data Science, Cornell University, 1190 Comstock Hall, Ithaca, 14853, NY, USA
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16
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Yang S, Yang Y, Long X, Li H, Zhang F, Wang Z. Integrated Analysis of the Effects of Cecal Microbiota and Serum Metabolome on Market Weights of Chinese Native Chickens. Animals (Basel) 2023; 13:3034. [PMID: 37835639 PMCID: PMC10571757 DOI: 10.3390/ani13193034] [Citation(s) in RCA: 1] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/07/2023] [Revised: 09/20/2023] [Accepted: 09/21/2023] [Indexed: 10/15/2023] Open
Abstract
The gut microbiota plays an important role in the physiological activities of the host and affects the formation of important economic traits in livestock farming. The effects of cecal microbiota on chicken weights were investigated using the Guizhou yellow chicken as a model. Experimental cohorts from chickens with high- (HC, n = 16) and low-market-weights (LC, n = 16) were collected. Microbial 16S rRNA gene sequencing and non-targeted serum metabolome data were integrated to explore the effect and metabolic mechanism of cecal microbiota on market weight. The genera Lachnoclostridium, Alistipes, Negativibacillus, Sellimonas, and Ruminococcus torques were enriched in the HC group, while Phascolarctobacterium was enriched in the LC group (p < 0.05). Metabolomic analysis determined that pantothenic acid (vitamin B5), luvangetin (2H-1-benzopyran-6-acrylic acid), and menadione (vitamin K3) were significantly higher in HC serum, while beclomethasone dipropionate (a glucocorticoid) and chlorophene (2-benzyl-4-chlorophenol) were present at higher levels in the LC group. The microbes enriched in HC were significantly positively correlated with metabolites, including pantothenic acid and menadione, and negatively correlated with beclomethasone dipropionate and chlorophene. These results indicated that specific cecal bacteria in Guizhou yellow chickens alter the host metabolism and growth performance. This study provides a reference for revealing the mechanism of cecal microbe actions that affect chicken body weight.
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Affiliation(s)
| | | | | | | | | | - Zhong Wang
- Key Laboratory of Animal Genetics, Breeding and Reproduction in the Plateau Mountainous Region, Ministry of Education, College of Animal Science, Guizhou University, Guiyang 550025, China; (S.Y.); (Y.Y.); (X.L.); (H.L.); (F.Z.)
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17
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Motta GA, Neto PSM, Nociti RP, Santana ÁE. Hematological Normality, Serum Biochemistry, and Acute Phase Proteins in Healthy Beef Calves in the Brazilian Savannah. Animals (Basel) 2023; 13:2398. [PMID: 37570207 PMCID: PMC10473239 DOI: 10.3390/ani13152398] [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: 04/18/2023] [Revised: 06/20/2023] [Accepted: 06/26/2023] [Indexed: 08/13/2023] Open
Abstract
The Brazilian savannah region, characterized by high average temperatures, well-defined rainy and dry seasons, soil with low productive potential, and high pressure for parasitic diseases, is home to the highest percentage of the beef herd, which is the world's largest commercial beef producer. Therefore, breeds that present rusticity combined with productivity are the focus of research in cattle breeding in the region. Considering their geographic particularities and their effects on the animals' blood parameters, the objective was to study the behavior of hematological variables, serum biochemistry, and acute phase proteins in beef calves at weaning age. Jugular blood samples were collected in a single day from 30 weaning calves (about eight months old and 200 kg of body weight) from the following breeds: Nellore, Senepol, Nellore × Aberdeen Angus cross, Nellore × Senepol cross, and Nellore × Aberdeen Angus × Senepol cross. Hematological data were obtained using an automatic cell counter, serum biochemical measurements were obtained using commercial kits, and the electrophoretogram was obtained using the SDS-page technique. In general, the results were consistent with data already published in similar situations regarding health status, age, and level of metabolic activity. However, differences observed between groups can be explained by differences observed in other concurrent variables like temperament. The pure zebu breed was more reactive than pure taurine. While crossbreds showed intermediate values, and parasitic infestation, the pure taurine breed with higher parasite infestation, while the zebu breed had lower values, which produced effects in some laboratory tests, and generated differences between breeds. In conclusion, the reference intervals available for healthy animals can be routinely used without interference from the geographic region for animals produced without nutritional failures as long as changes are recorded in pathological, infectious, metabolic, or nutritional deficiency situations. However, it is suggested that a study covering a larger number of herds may demonstrate a greater geographic effect on the studied variables.
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Affiliation(s)
- Guilherme Augusto Motta
- Department of Veterinary Clinic and Surgery, School of Agricultural and Veterinary Sciences, São Paulo State University, Jaboticabal 14884-900, São Paulo, Brazil;
- Department of Veterinary Medicine, Araraquara University—UNIARA, Araraquara 14801-340, São Paulo, Brazil
| | - Paulo Sabino Milhomen Neto
- Department of Veterinary Medicine, Federal University of Tocantins, Araguaína 77824-838, Tocantins, Brazil;
| | - Ricardo Perecin Nociti
- Department of Biomedicine Veterinary, Faculty of Veterinary Medicine, Montreal University/Saint Hyacinthe, Saint-Hyacinthe, QC J2S 2M2, Canada;
- Laboratory of Molecular Morphophysiology and DevelopmentSchool of Veterinary Medicine and Animal Science, Department of Veterinary Medicine, Faculty of Animal Science and Food Engineering, University of São Paulo, Pirassununga 13635-900, São Paulo, Brazil
| | - Áureo Evangelista Santana
- Department of Veterinary Clinic and Surgery, School of Agricultural and Veterinary Sciences, São Paulo State University, Jaboticabal 14884-900, São Paulo, Brazil;
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18
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Barone M, Ramayo-Caldas Y, Estellé J, Tambosco K, Chadi S, Maillard F, Gallopin M, Planchais J, Chain F, Kropp C, Rios-Covian D, Sokol H, Brigidi P, Langella P, Martín R. Gut barrier-microbiota imbalances in early life lead to higher sensitivity to inflammation in a murine model of C-section delivery. MICROBIOME 2023; 11:140. [PMID: 37394428 PMCID: PMC10316582 DOI: 10.1186/s40168-023-01584-0] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 10/06/2022] [Accepted: 05/25/2023] [Indexed: 07/04/2023]
Abstract
BACKGROUND Most interactions between the host and its microbiota occur at the gut barrier, and primary colonizers are essential in the gut barrier maturation in the early life. The mother-offspring transmission of microorganisms is the most important factor influencing microbial colonization in mammals, and C-section delivery (CSD) is an important disruptive factor of this transfer. Recently, the deregulation of symbiotic host-microbe interactions in early life has been shown to alter the maturation of the immune system, predisposing the host to gut barrier dysfunction and inflammation. The main goal of this study is to decipher the role of the early-life gut microbiota-barrier alterations and its links with later-life risks of intestinal inflammation in a murine model of CSD. RESULTS The higher sensitivity to chemically induced inflammation in CSD mice is related to excessive exposure to a too diverse microbiota too early in life. This early microbial stimulus has short-term consequences on the host homeostasis. It switches the pup's immune response to an inflammatory context and alters the epithelium structure and the mucus-producing cells, disrupting gut homeostasis. This presence of a too diverse microbiota in the very early life involves a disproportionate short-chain fatty acids ratio and an excessive antigen exposure across the vulnerable gut barrier in the first days of life, before the gut closure. Besides, as shown by microbiota transfer experiments, the microbiota is causal in the high sensitivity of CSD mice to chemical-induced colitis and in most of the phenotypical parameters found altered in early life. Finally, supplementation with lactobacilli, the main bacterial group impacted by CSD in mice, reverts the higher sensitivity to inflammation in ex-germ-free mice colonized by CSD pups' microbiota. CONCLUSIONS Early-life gut microbiota-host crosstalk alterations related to CSD could be the linchpin behind the phenotypic effects that lead to increased susceptibility to an induced inflammation later in life in mice. Video Abstract.
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Affiliation(s)
- M. Barone
- Microbiomics Unit, Department of Medical and Surgical Sciences, University of Bologna, 40138 Bologna, Italy
| | - Y. Ramayo-Caldas
- INRAE, AgroParisTech, GABI, Paris-Saclay University, 78350 Jouy-en-Josas, France
- Animal Breeding and Genetics Program, Institute for Research and Technology in Food and Agriculture (IRTA), Torre Marimon, 08140 Caldes de Montbui, Spain
| | - J. Estellé
- INRAE, AgroParisTech, GABI, Paris-Saclay University, 78350 Jouy-en-Josas, France
| | - K. Tambosco
- INRAE, AgroParisTech, Micalis Institut,, Paris-Saclay University, 78350 Jouy-en-Josas, France
| | - S. Chadi
- INRAE, AgroParisTech, Micalis Institut,, Paris-Saclay University, 78350 Jouy-en-Josas, France
| | - F. Maillard
- INRAE, AgroParisTech, Micalis Institut,, Paris-Saclay University, 78350 Jouy-en-Josas, France
| | - M. Gallopin
- CNRS, CEA, l’Institut de Biologie Intégrative de La Cellule (I2BC), Paris-Saclay University, 91405 Orsay, France
| | - J. Planchais
- INRAE, AgroParisTech, Micalis Institut,, Paris-Saclay University, 78350 Jouy-en-Josas, France
| | - F. Chain
- INRAE, AgroParisTech, Micalis Institut,, Paris-Saclay University, 78350 Jouy-en-Josas, France
| | - C. Kropp
- INRAE, AgroParisTech, Micalis Institut,, Paris-Saclay University, 78350 Jouy-en-Josas, France
| | - D. Rios-Covian
- INRAE, AgroParisTech, Micalis Institut,, Paris-Saclay University, 78350 Jouy-en-Josas, France
| | - H. Sokol
- INRAE, AgroParisTech, Micalis Institut,, Paris-Saclay University, 78350 Jouy-en-Josas, France
- Gastroenterology Department, Centre de Recherche Saint-Antoine, Centre de Recherche Saint-Antoine, CRSA, AP-HP, INSERM, Saint Antoine Hospital, Sorbonne Université, 75012 Paris, France
- Paris Centre for Microbiome Medicine (PaCeMM) FHU, Paris, France
| | - P. Brigidi
- Microbiomics Unit, Department of Medical and Surgical Sciences, University of Bologna, 40138 Bologna, Italy
| | - P. Langella
- INRAE, AgroParisTech, Micalis Institut,, Paris-Saclay University, 78350 Jouy-en-Josas, France
- Paris Centre for Microbiome Medicine (PaCeMM) FHU, Paris, France
| | - R. Martín
- INRAE, AgroParisTech, Micalis Institut,, Paris-Saclay University, 78350 Jouy-en-Josas, France
- Paris Centre for Microbiome Medicine (PaCeMM) FHU, Paris, France
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19
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Herrera-Uribe J, Lim KS, Byrne KA, Daharsh L, Liu H, Corbett RJ, Marco G, Schroyen M, Koltes JE, Loving CL, Tuggle CK. Integrative profiling of gene expression and chromatin accessibility elucidates specific transcriptional networks in porcine neutrophils. Front Genet 2023; 14:1107462. [PMID: 37287538 PMCID: PMC10242145 DOI: 10.3389/fgene.2023.1107462] [Citation(s) in RCA: 1] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/24/2022] [Accepted: 04/27/2023] [Indexed: 06/09/2023] Open
Abstract
Neutrophils are vital components of the immune system for limiting the invasion and proliferation of pathogens in the body. Surprisingly, the functional annotation of porcine neutrophils is still limited. The transcriptomic and epigenetic assessment of porcine neutrophils from healthy pigs was performed by bulk RNA sequencing and transposase accessible chromatin sequencing (ATAC-seq). First, we sequenced and compared the transcriptome of porcine neutrophils with eight other immune cell transcriptomes to identify a neutrophil-enriched gene list within a detected neutrophil co-expression module. Second, we used ATAC-seq analysis to report for the first time the genome-wide chromatin accessible regions of porcine neutrophils. A combined analysis using both transcriptomic and chromatin accessibility data further defined the neutrophil co-expression network controlled by transcription factors likely important for neutrophil lineage commitment and function. We identified chromatin accessible regions around promoters of neutrophil-specific genes that were predicted to be bound by neutrophil-specific transcription factors. Additionally, published DNA methylation data from porcine immune cells including neutrophils were used to link low DNA methylation patterns to accessible chromatin regions and genes with highly enriched expression in porcine neutrophils. In summary, our data provides the first integrative analysis of the accessible chromatin regions and transcriptional status of porcine neutrophils, contributing to the Functional Annotation of Animal Genomes (FAANG) project, and demonstrates the utility of chromatin accessible regions to identify and enrich our understanding of transcriptional networks in a cell type such as neutrophils.
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Affiliation(s)
- Juber Herrera-Uribe
- Department of Animal Science, Iowa State University, Ames, IA, United States
| | - Kyu-Sang Lim
- Department of Animal Science, Iowa State University, Ames, IA, United States
- Department of Animal Resource Science, Kongju National University, Yesan, Republic of Korea
| | - Kristen A. Byrne
- USDA-Agriculture Research Service, National Animal Disease Center, Food Safety and Enteric Pathogens Research Unit, Ames, IA, United States
| | - Lance Daharsh
- Department of Animal Science, Iowa State University, Ames, IA, United States
| | - Haibo Liu
- Department of Animal Science, Iowa State University, Ames, IA, United States
| | - Ryan J. Corbett
- Department of Animal Science, Iowa State University, Ames, IA, United States
| | - Gianna Marco
- Department of Animal Science, Iowa State University, Ames, IA, United States
| | - Martine Schroyen
- Department of Animal Science, Iowa State University, Ames, IA, United States
| | - James E. Koltes
- Department of Animal Science, Iowa State University, Ames, IA, United States
| | - Crystal L. Loving
- USDA-Agriculture Research Service, National Animal Disease Center, Food Safety and Enteric Pathogens Research Unit, Ames, IA, United States
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20
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Banerjee P, Diniz WJS, Rodning SP, Dyce PW. miRNA expression profiles of peripheral white blood cells from beef heifers with varying reproductive potential. Front Genet 2023; 14:1174145. [PMID: 37234872 PMCID: PMC10206245 DOI: 10.3389/fgene.2023.1174145] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/25/2023] [Accepted: 05/02/2023] [Indexed: 05/28/2023] Open
Abstract
Reproductive performance is the most critical factor affecting production efficiency in the cow-calf industry. Heifers with low reproductive efficiency may fail to become pregnant during the breeding season or maintain a pregnancy. The cause of reproductive failure often remains unknown, and the non-pregnant heifers are not identified until several weeks after the breeding season. Therefore, improving heifer fertility utilizing genomic information has become increasingly important. One approach is using microRNAs (miRNA) in the maternal blood that play an important role in regulating the target genes underlying pregnancy success and thereby in selecting reproductively efficient heifers. Therefore, the current study hypothesized that miRNA expression profiles from peripheral white blood cells (PWBC) at weaning could predict the future reproductive outcome of beef heifers. To this end, we measured the miRNA profiles using small RNA-sequencing in Angus-Simmental crossbred heifers sampled at weaning and retrospectively classified as fertile (FH, n = 7) or subfertile (SFH, n = 7). In addition to differentially expressed miRNAs (DEMIs), their target genes were predicted from TargetScan. The PWBC gene expression from the same heifers were retrieved and co-expression networks were constructed between DEMIs and their target genes. We identified 16 differentially expressed miRNAs between the groups (p-value ≤0.05 and absolute (log2 fold change ≥0.05)). Interestingly, based on a strong negative correlation identified from miRNA-gene network analysis with PCIT (partial correlation and information theory), we identified miRNA-target genes in the SFH group. Additionally, TargetScan predictions and differential expression analysis identified bta-miR-1839 with ESR1 , bta-miR-92b with KLF4 and KAT2B, bta-miR-2419-5p with LILRA4, bta-miR-1260b with UBE2E1, SKAP2 and CLEC4D, and bta-let-7a-5p with GATM, MXD1 as miRNA-gene targets. The miRNA-target gene pairs in the FH group are over-represented for MAPK, ErbB, HIF-1, FoxO, p53, mTOR, T-cell receptor, insulin and GnRH signaling pathways, while those in the SFH group include cell cycle, p53 signaling pathway and apoptosis. Some miRNAs, miRNA-target genes and regulated pathways identified in this study have a potential role in fertility; other targets are identified as novel and need to be validated in a bigger cohort that could help to predict the future reproductive outcomes of beef heifers.
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21
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Mohamed AR, Ochsenkühn MA, Kazlak AM, Moustafa A, Amin SA. The coral microbiome: towards an understanding of the molecular mechanisms of coral-microbiota interactions. FEMS Microbiol Rev 2023; 47:fuad005. [PMID: 36882224 PMCID: PMC10045912 DOI: 10.1093/femsre/fuad005] [Citation(s) in RCA: 6] [Impact Index Per Article: 6.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/07/2022] [Revised: 02/10/2023] [Accepted: 02/15/2023] [Indexed: 03/09/2023] Open
Abstract
Corals live in a complex, multipartite symbiosis with diverse microbes across kingdoms, some of which are implicated in vital functions, such as those related to resilience against climate change. However, knowledge gaps and technical challenges limit our understanding of the nature and functional significance of complex symbiotic relationships within corals. Here, we provide an overview of the complexity of the coral microbiome focusing on taxonomic diversity and functions of well-studied and cryptic microbes. Mining the coral literature indicate that while corals collectively harbour a third of all marine bacterial phyla, known bacterial symbionts and antagonists of corals represent a minute fraction of this diversity and that these taxa cluster into select genera, suggesting selective evolutionary mechanisms enabled these bacteria to gain a niche within the holobiont. Recent advances in coral microbiome research aimed at leveraging microbiome manipulation to increase coral's fitness to help mitigate heat stress-related mortality are discussed. Then, insights into the potential mechanisms through which microbiota can communicate with and modify host responses are examined by describing known recognition patterns, potential microbially derived coral epigenome effector proteins and coral gene regulation. Finally, the power of omics tools used to study corals are highlighted with emphasis on an integrated host-microbiota multiomics framework to understand the underlying mechanisms during symbiosis and climate change-driven dysbiosis.
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Affiliation(s)
- Amin R Mohamed
- Biology Program, New York University Abu Dhabi, Abu Dhabi 129188, United Arab Emirates
| | - Michael A Ochsenkühn
- Biology Program, New York University Abu Dhabi, Abu Dhabi 129188, United Arab Emirates
| | - Ahmed M Kazlak
- Systems Genomics Laboratory, American University in Cairo, New Cairo 11835, Egypt
- Biotechnology Graduate Program, American University in Cairo, New Cairo 11835, Egypt
| | - Ahmed Moustafa
- Systems Genomics Laboratory, American University in Cairo, New Cairo 11835, Egypt
- Biotechnology Graduate Program, American University in Cairo, New Cairo 11835, Egypt
- Department of Biology, American University in Cairo, New Cairo 11835, Egypt
| | - Shady A Amin
- Biology Program, New York University Abu Dhabi, Abu Dhabi 129188, United Arab Emirates
- Center for Genomics and Systems Biology (CGSB), New York University Abu Dhabi, Abu Dhabi 129188, United Arab Emirates
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22
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Flores-Díaz A, Escoto-Sandoval C, Cervantes-Hernández F, Ordaz-Ortiz JJ, Hayano-Kanashiro C, Reyes-Valdés H, Garcés-Claver A, Ochoa-Alejo N, Martínez O. Gene Functional Networks from Time Expression Profiles: A Constructive Approach Demonstrated in Chili Pepper ( Capsicum annuum L.). PLANTS (BASEL, SWITZERLAND) 2023; 12:1148. [PMID: 36904008 PMCID: PMC10005043 DOI: 10.3390/plants12051148] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Figures] [Subscribe] [Scholar Register] [Received: 01/31/2023] [Revised: 02/20/2023] [Accepted: 02/27/2023] [Indexed: 06/18/2023]
Abstract
Gene co-expression networks are powerful tools to understand functional interactions between genes. However, large co-expression networks are difficult to interpret and do not guarantee that the relations found will be true for different genotypes. Statistically verified time expression profiles give information about significant changes in expressions through time, and genes with highly correlated time expression profiles, which are annotated in the same biological process, are likely to be functionally connected. A method to obtain robust networks of functionally related genes will be useful to understand the complexity of the transcriptome, leading to biologically relevant insights. We present an algorithm to construct gene functional networks for genes annotated in a given biological process or other aspects of interest. We assume that there are genome-wide time expression profiles for a set of representative genotypes of the species of interest. The method is based on the correlation of time expression profiles, bound by a set of thresholds that assure both, a given false discovery rate, and the discard of correlation outliers. The novelty of the method consists in that a gene expression relation must be repeatedly found in a given set of independent genotypes to be considered valid. This automatically discards relations particular to specific genotypes, assuring a network robustness, which can be set a priori. Additionally, we present an algorithm to find transcription factors candidates for regulating hub genes within a network. The algorithms are demonstrated with data from a large experiment studying gene expression during the development of the fruit in a diverse set of chili pepper genotypes. The algorithm is implemented and demonstrated in a new version of the publicly available R package "Salsa" (version 1.0).
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Affiliation(s)
- Alan Flores-Díaz
- Unidad de Genómica Avanzada (Langebio), Centro de Investigación y de Estudios Avanzados del Instituto Politécnico Nacional (Cinvestav), Irapuato 36824, Mexico
| | - Christian Escoto-Sandoval
- Unidad de Genómica Avanzada (Langebio), Centro de Investigación y de Estudios Avanzados del Instituto Politécnico Nacional (Cinvestav), Irapuato 36824, Mexico
| | - Felipe Cervantes-Hernández
- Unidad de Genómica Avanzada (Langebio), Centro de Investigación y de Estudios Avanzados del Instituto Politécnico Nacional (Cinvestav), Irapuato 36824, Mexico
| | - José J. Ordaz-Ortiz
- Unidad de Genómica Avanzada (Langebio), Centro de Investigación y de Estudios Avanzados del Instituto Politécnico Nacional (Cinvestav), Irapuato 36824, Mexico
| | - Corina Hayano-Kanashiro
- Departamento de Investigaciones Científicas y Tecnológicas de la Universidad de Sonora, Hermosillo 83000, Mexico
| | - Humberto Reyes-Valdés
- Department of Plant Breeding, Universidad Autónoma Agraria Antonio Narro, Saltillo 25315, Mexico
| | - Ana Garcés-Claver
- Unidad de Hortofruticultura, Centro de Investigación y Tecnología Agroalimentaria de Aragón, Instituto Agroalimentario de Aragón-IA2 (CITA-Universidad de Zaragoza), 50059 Zaragoza, Spain
| | - Neftalí Ochoa-Alejo
- Departamento de Ingeniería Genética, Centro de Investigación y de Estudios Avanzados del Instituto Politécnico Nacional (Cinvestav), Irapuato 36824, Mexico
| | - Octavio Martínez
- Unidad de Genómica Avanzada (Langebio), Centro de Investigación y de Estudios Avanzados del Instituto Politécnico Nacional (Cinvestav), Irapuato 36824, Mexico
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23
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Banerjee P, Diniz WJS, Hollingsworth R, Rodning SP, Dyce PW. mRNA Signatures in Peripheral White Blood Cells Predict Reproductive Potential in Beef Heifers at Weaning. Genes (Basel) 2023; 14:498. [PMID: 36833425 PMCID: PMC9957530 DOI: 10.3390/genes14020498] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/19/2023] [Revised: 02/10/2023] [Accepted: 02/13/2023] [Indexed: 02/18/2023] Open
Abstract
Reproductive failure is a major contributor to inefficiency within the cow-calf industry. Particularly problematic is the inability to diagnose heifer reproductive issues prior to pregnancy diagnosis following their first breeding season. Therefore, we hypothesized that gene expression from the peripheral white blood cells at weaning could predict the future reproductive potential of beef heifers. To investigate this, the gene expression was measured using RNA-Seq in Angus-Simmental crossbred heifers sampled at weaning and retrospectively classified as fertile (FH, n = 8) or subfertile (SFH, n = 7) after pregnancy diagnosis. We identified 92 differentially expressed genes between the groups. Network co-expression analysis identified 14 and 52 hub targets. ENSBTAG00000052659, OLR1, TFF2, and NAIP were exclusive hubs to the FH group, while 42 hubs were exclusive to the SFH group. The differential connectivity between the networks of each group revealed a gain in connectivity due to the rewiring of major regulators in the SFH group. The exclusive hub targets from FH were over-represented for the CXCR chemokine receptor pathway and inflammasome complex, while for the SFH, they were over-represented for immune response and cytokine production pathways. These multiple interactions revealed novel targets and pathways predicting reproductive potential at an early stage of heifer development.
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Affiliation(s)
| | | | | | | | - Paul W. Dyce
- Department of Animal Sciences, Auburn University, Auburn, AL 36849, USA
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24
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Manaig YJY, Criado-Mesas L, Esteve-Codina A, Mármol-Sánchez E, Castelló A, Sánchez A, Folch JM. Identifying miRNA-mRNA regulatory networks on extreme n-6/n-3 polyunsaturated fatty acid ratio expression profiles in porcine skeletal muscle. PLoS One 2023; 18:e0283231. [PMID: 37141193 PMCID: PMC10159129 DOI: 10.1371/journal.pone.0283231] [Citation(s) in RCA: 2] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/13/2022] [Accepted: 03/06/2023] [Indexed: 05/05/2023] Open
Abstract
Omega-3 (n-3) and omega-6 (n-6) polyunsaturated fatty acids (PUFAs) are essential fatty acids with antagonistic inflammatory functions that play vital roles in metabolic health and immune response. Current commercial swine diets tend to over-supplement with n-6 PUFAs, which may increase the likelihood of developing inflammatory diseases and affect the overall well-being of the animals. However, it is still poorly understood how n-6/n-3 PUFA ratios affect the porcine transcriptome expression and how messenger RNAs (mRNAs) and microRNAs (miRNAs) might regulate biological processes related to PUFA metabolism. On account of this, we selected a total of 20 Iberian × Duroc crossbred pigs with extreme values for n-6/n-3 FA ratio (10 high vs 10 low), and longissimus dorsi muscle samples were used to identify differentially expressed mRNAs and miRNAs. The observed differentially expressed mRNAs were associated to biological pathways related to muscle growth and immunomodulation, while the differentially expressed microRNAs (ssc-miR-30a-3p, ssc-miR-30e-3p, ssc-miR-15b and ssc-miR-7142-3p) were correlated to adipogenesis and immunity. Relevant miRNA-to-mRNA regulatory networks were also predicted (i.e., mir15b to ARRDC3; mir-7142-3p to METTL21C), and linked to lipolysis, obesity, myogenesis, and protein degradation. The n-6/n-3 PUFA ratio differences in pig skeletal muscle revealed genes, miRNAs and enriched pathways involved in lipid metabolism, cell proliferation and inflammation.
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Affiliation(s)
- Yron Joseph Yabut Manaig
- Departament de Ciència Animal i dels Aliments, Universitat Autònoma de Barcelona, Bellaterra, Barcelona, Spain
- Plant and Animal Genomics, Centre for Research in Agricultural Genomics (CRAG), CSIC-IRTA-UAB-UB Consortium, Bellaterra, Barcelona, Spain
- Department of Veterinary Medicine and Animal Sciences, Università degli Studi di Milano, Lodi, Italy
| | - Lourdes Criado-Mesas
- Plant and Animal Genomics, Centre for Research in Agricultural Genomics (CRAG), CSIC-IRTA-UAB-UB Consortium, Bellaterra, Barcelona, Spain
| | - Anna Esteve-Codina
- CNAG-CRG, Centre for Genomic Regulation (CRG), Barcelona Institute of Science and Technology (BIST), Barcelona, Spain
| | - Emilio Mármol-Sánchez
- Department of Molecular Biosciences, Science for Life Laboratory, The Wenner-Gren Institute, Stockholm University, Stockholm, Sweden
- Centre for Palaeogenetics, Stockholm, Sweden
| | - Anna Castelló
- Departament de Ciència Animal i dels Aliments, Universitat Autònoma de Barcelona, Bellaterra, Barcelona, Spain
- Plant and Animal Genomics, Centre for Research in Agricultural Genomics (CRAG), CSIC-IRTA-UAB-UB Consortium, Bellaterra, Barcelona, Spain
| | - Armand Sánchez
- Departament de Ciència Animal i dels Aliments, Universitat Autònoma de Barcelona, Bellaterra, Barcelona, Spain
- Plant and Animal Genomics, Centre for Research in Agricultural Genomics (CRAG), CSIC-IRTA-UAB-UB Consortium, Bellaterra, Barcelona, Spain
| | - Josep M Folch
- Departament de Ciència Animal i dels Aliments, Universitat Autònoma de Barcelona, Bellaterra, Barcelona, Spain
- Plant and Animal Genomics, Centre for Research in Agricultural Genomics (CRAG), CSIC-IRTA-UAB-UB Consortium, Bellaterra, Barcelona, Spain
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25
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Porto-Neto LR, Alexandre PA, Hudson NJ, Bertram J, McWilliam SM, Tan AWL, Fortes MRS, McGowan MR, Hayes BJ, Reverter A. Multi-breed genomic predictions and functional variants for fertility of tropical bulls. PLoS One 2023; 18:e0279398. [PMID: 36701372 PMCID: PMC9879470 DOI: 10.1371/journal.pone.0279398] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/28/2022] [Accepted: 12/07/2022] [Indexed: 01/27/2023] Open
Abstract
Worldwide, most beef breeding herds are naturally mated. As such, the ability to identify and select fertile bulls is critically important for both productivity and genetic improvement. Here, we collected ten fertility-related phenotypes for 6,063 bulls from six tropically adapted breeds. Phenotypes were comprised of four bull conformation traits and six traits directly related to the quality of the bull's semen. We also generated high-density DNA genotypes for all the animals. In total, 680,758 single nucleotide polymorphism (SNP) genotypes were analyzed. The genomic correlation of the same trait observed in different breeds was positive for scrotal circumference and sheath score on most breed comparisons, but close to zero for the percentage of normal sperm, suggesting a divergent genetic background for this trait. We confirmed the importance of a breed being present in the reference population to the generation of accurate genomic estimated breeding values (GEBV) in an across-breed validation scenario. Average GEBV accuracies varied from 0.19 to 0.44 when the breed was not included in the reference population. The range improved to 0.28 to 0.59 when the breed was in the reference population. Variants associated with the gene HDAC4, six genes from the spermatogenesis-associated (SPATA) family of proteins, and 29 transcription factors were identified as candidate genes. Collectively these results enable very early in-life selection for bull fertility traits, supporting genetic improvement strategies currently taking place within tropical beef production systems. This study also improves our understanding of the molecular basis of male fertility in mammals.
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Affiliation(s)
| | | | - Nicholas J. Hudson
- School of Animal Studies, The University of Queensland, Gatton, QLD, Australia
| | - John Bertram
- Agriculture Consultant, Livestock Management and Breeding, Toowoomba, QLD, Australia
| | | | - Andre W. L. Tan
- School of Chemistry and Molecular Bioscience, The University of Queensland, St Lucia, QLD, Australia
| | - Marina R. S. Fortes
- School of Chemistry and Molecular Bioscience, The University of Queensland, St Lucia, QLD, Australia
| | - Michael R. McGowan
- School of Veterinary Sciences, The University of Queensland, Gatton, QLD, Australia
| | - Ben J. Hayes
- Queensland Alliance for Agriculture and Food Innovation, The University of Queensland, St Lucia, QLD, Australia
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26
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Falker-Gieske C, Bennewitz J, Tetens J. Structural variation and eQTL analysis in two experimental populations of chickens divergently selected for feather-pecking behavior. Neurogenetics 2023; 24:29-41. [PMID: 36449109 PMCID: PMC9823035 DOI: 10.1007/s10048-022-00705-5] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/05/2022] [Accepted: 11/19/2022] [Indexed: 12/02/2022]
Abstract
Feather pecking (FP) is a damaging nonaggressive behavior in laying hens with a heritable component. Its occurrence has been linked to the immune system, the circadian clock, and foraging behavior. Furthermore, dysregulation of miRNA biogenesis, disturbance of the gamma-aminobutyric acid (GABAergic) system, as well as neurodevelopmental deficiencies are currently under debate as factors influencing the propensity for FP behavior. Past studies, which focused on the dissection of the genetic factors involved in FP, relied on single nucleotide polymorphisms (SNPs) and short insertions and deletions < 50 bp (InDels). These variant classes only represent a certain fraction of the genetic variation of an organism. Hence, we reanalyzed whole-genome sequencing data from two experimental populations, which have been divergently selected for FP behavior for over more than 15 generations, performed variant calling for structural variants (SVs) as well as tandem repeats (TRs), and jointly analyzed the data with SNPs and InDels. Genotype imputation and subsequent genome-wide association studies, in combination with expression quantitative trait loci analysis, led to the discovery of multiple variants influencing the GABAergic system. These include a significantly associated TR downstream of the GABA receptor subunit beta-3 (GABRB3) gene, two microRNAs targeting several GABA receptor genes, and dystrophin (DMD), a direct regulator of GABA receptor clustering. Furthermore, we found the transcription factor ETV1 to be associated with the differential expression of 23 genes, which points toward a role of ETV1, together with SMAD4 and KLF14, in the disturbed neurodevelopment of high-feather pecking chickens.
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Affiliation(s)
- Clemens Falker-Gieske
- Department of Animal Sciences, Georg-August-University, Burckhardtweg 2, 37077, Göttingen, Germany.
| | - Jörn Bennewitz
- grid.9464.f0000 0001 2290 1502Institute of Animal Science, University of Hohenheim, Garbenstr. 17, 70599 Stuttgart, Germany
| | - Jens Tetens
- grid.7450.60000 0001 2364 4210Department of Animal Sciences, Georg-August-University, Burckhardtweg 2, 37077 Göttingen, Germany ,grid.7450.60000 0001 2364 4210Center for Integrated Breeding Research, Georg-August-University, Albrecht-Thaer-Weg 3, 37075 Göttingen, Germany
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27
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Crespo-Piazuelo D, Acloque H, González-Rodríguez O, Mongellaz M, Mercat MJ, Bink MCAM, Huisman AE, Ramayo-Caldas Y, Sánchez JP, Ballester M. Identification of transcriptional regulatory variants in pig duodenum, liver, and muscle tissues. Gigascience 2022; 12:giad042. [PMID: 37354463 PMCID: PMC10290502 DOI: 10.1093/gigascience/giad042] [Citation(s) in RCA: 2] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/03/2022] [Revised: 04/13/2023] [Accepted: 05/25/2023] [Indexed: 06/26/2023] Open
Abstract
BACKGROUND In humans and livestock species, genome-wide association studies (GWAS) have been applied to study the association between variants distributed across the genome and a phenotype of interest. To discover genetic polymorphisms affecting the duodenum, liver, and muscle transcriptomes of 300 pigs from 3 different breeds (Duroc, Landrace, and Large White), we performed expression GWAS between 25,315,878 polymorphisms and the expression of 13,891 genes in duodenum, 12,748 genes in liver, and 11,617 genes in muscle. RESULTS More than 9.68 × 1011 association tests were performed, yielding 14,096,080 significantly associated variants, which were grouped in 26,414 expression quantitative trait locus (eQTL) regions. Over 56% of the variants were within 1 Mb of their associated gene. In addition to the 100-kb region upstream of the transcription start site, we identified the importance of the 100-kb region downstream of the 3'UTR for gene regulation, as most of the cis-regulatory variants were located within these 2 regions. We also observed 39,874 hotspot regulatory polymorphisms associated with the expression of 10 or more genes that could modify the protein structure or the expression of a regulator gene. In addition, 2 motifs (5'-GATCCNGYGTTGCYG-3' and a poly(A) sequence) were enriched across the 3 tissues within the neighboring sequences of the most significant single-nucleotide polymorphisms in each cis-eQTL region. CONCLUSIONS The 14 million significant associations obtained in this study are publicly available and have enabled the identification of expression-associated cis-, trans-, and hotspot regulatory variants within and across tissues, thus shedding light on the molecular mechanisms of regulatory variations that shape end-trait phenotypes.
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Affiliation(s)
- Daniel Crespo-Piazuelo
- Animal Breeding and Genetics Program, IRTA, Torre Marimon, Caldes de Montbui (08140), Spain
| | - Hervé Acloque
- GABI, Université Paris-Saclay, INRAE, AgroParisTech, Jouy-en-Josas (78350), France
| | | | - Mayrone Mongellaz
- GABI, Université Paris-Saclay, INRAE, AgroParisTech, Jouy-en-Josas (78350), France
| | | | - Marco C A M Bink
- Hendrix Genetics Research Technology & Services B.V., Boxmeer (5830 AC), The Netherlands
| | | | - Yuliaxis Ramayo-Caldas
- Animal Breeding and Genetics Program, IRTA, Torre Marimon, Caldes de Montbui (08140), Spain
| | - Juan Pablo Sánchez
- Animal Breeding and Genetics Program, IRTA, Torre Marimon, Caldes de Montbui (08140), Spain
| | - Maria Ballester
- Animal Breeding and Genetics Program, IRTA, Torre Marimon, Caldes de Montbui (08140), Spain
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28
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Kuang J, Scoglio C, Michel K. Feature learning and network structure from noisy node activity data. Phys Rev E 2022; 106:064301. [PMID: 36671154 PMCID: PMC9869472 DOI: 10.1103/physreve.106.064301] [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: 10/26/2021] [Accepted: 11/17/2022] [Indexed: 06/17/2023]
Abstract
In the studies of network structures, much attention has been devoted to developing approaches to reconstruct networks and predict missing links when edge-related information is given. However, such approaches are not applicable when we are only given noisy node activity data with missing values. This work presents an unsupervised learning framework to learn node vectors and construct networks from such node activity data. First, we design a scheme to generate random node sequences from node context sets, which are generated from node activity data. Then, a three-layer neural network is adopted training the node sequences to obtain node vectors, which allow us to construct networks and capture nodes with synergistic roles. Furthermore, we present an entropy-based approach to select the most meaningful neighbors for each node in the resulting network. Finally, the effectiveness of the method is validated through both synthetic and real data.
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Affiliation(s)
- Junyao Kuang
- Department of Electrical and Computer Engineering
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29
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Das T, Kaur H, Gour P, Prasad K, Lynn AM, Prakash A, Kumar V. Intersection of network medicine and machine learning towards investigating the key biomarkers and pathways underlying amyotrophic lateral sclerosis: a systematic review. Brief Bioinform 2022; 23:6780269. [PMID: 36411673 DOI: 10.1093/bib/bbac442] [Citation(s) in RCA: 6] [Impact Index Per Article: 3.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/24/2022] [Revised: 08/12/2022] [Accepted: 09/13/2022] [Indexed: 11/22/2022] Open
Abstract
BACKGROUND Network medicine is an emerging area of research that focuses on delving into the molecular complexity of the disease, leading to the discovery of network biomarkers and therapeutic target discovery. Amyotrophic lateral sclerosis (ALS) is a complicated rare disease with unknown pathogenesis and no available treatment. In ALS, network properties appear to be potential biomarkers that can be beneficial in disease-related applications when explored independently or in tandem with machine learning (ML) techniques. OBJECTIVE This systematic literature review explores recent trends in network medicine and implementations of network-based ML algorithms in ALS. We aim to provide an overview of the identified primary studies and gather details on identifying the potential biomarkers and delineated pathways. METHODS The current study consists of searching for and investigating primary studies from PubMed and Dimensions.ai, published between 2018 and 2022 that reported network medicine perspectives and the coupling of ML techniques. Each abstract and full-text study was individually evaluated, and the relevant studies were finally included in the review for discussion once they met the inclusion and exclusion criteria. RESULTS We identified 109 eligible publications from primary studies representing this systematic review. The data coalesced into two themes: application of network science to identify disease modules and promising biomarkers in ALS, along with network-based ML approaches. Conclusion This systematic review gives an overview of the network medicine approaches and implementations of network-based ML algorithms in ALS to determine new disease genes, and identify critical pathways and therapeutic target discovery for personalized treatment.
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Affiliation(s)
- Trishala Das
- School of Computational & Integrative Sciences, Jawaharlal Nehru University, New Delhi-110067, India
| | - Harbinder Kaur
- School of Computational & Integrative Sciences, Jawaharlal Nehru University, New Delhi-110067, India
| | - Pratibha Gour
- Dept. of Plant Molecular Biology, University of Delhi, South Campus, New Delhi-110021, India
| | - Kartikay Prasad
- Amity Institute of Neuropsychology & Neurosciences (AINN), Amity University, Noida, UP-201303, India
| | - Andrew M Lynn
- School of Computational & Integrative Sciences, Jawaharlal Nehru University, New Delhi-110067, India
| | - Amresh Prakash
- Amity Institute of Integrative Sciences and Health, Amity University Haryana, Gurgaon-122413, India
| | - Vijay Kumar
- Amity Institute of Neuropsychology & Neurosciences (AINN), Amity University, Noida, UP-201303, India
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Evaluation of Fusarium Head Blight Resistance Effects by Haplotype-Based Genome-Wide Association Study in Winter Wheat Lines Derived by Marker Backcrossing Approach. Int J Mol Sci 2022; 23:ijms232214233. [PMID: 36430711 PMCID: PMC9695032 DOI: 10.3390/ijms232214233] [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: 10/11/2022] [Revised: 11/09/2022] [Accepted: 11/15/2022] [Indexed: 11/19/2022] Open
Abstract
Fusarium head blight (FHB) of wheat caused by Fusarium species is a destructive disease, causing grain yield and quality losses. Developing FHB-resistant cultivars is crucial to minimize the extent of the disease. The first objective of this study was incorporation of Fhb1 from a resistant donor into five Polish wheat breeding lines with good agronomical traits and different origins. We also performed a haplotype-based GWAS to identify chromosome regions in derived wheat families associated with Fusarium head blight resistance. As a result of marker-assisted backcrossing (MABC), five wheat combinations were obtained. Fungal inoculation and disease assessment were conducted for two years, 2019 and 2020. In 2019 the average phenotypic response of type II resistance was 2.2, whereas in 2020 it was 2.1. A haploblock-based GWAS performed on 10 phenotypic traits (related to type of resistance, year of experiment and FHB index) revealed nine marker-trait associations (MTA), among which six belong to chromosome 2D, two to 3B and one to 7D. Phenotypic variation (R2) explained by the identified haplotypes in haploblocks ranged from 6% to 49%. Additionally, an association weight matrix (AWM) was created, giving the partial correlation-information theory (PCIT) pipeline of 171 edges and 19 nodes. The resultant data and high level of explained phenotypic variance of MTA create the opportunity for data utilization in MAS.
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Liang H, Zhao Y, Liu K, Xiao Y, Chen K, Li D, Zhong S, Zhao Z, Wu D, Peng Y. The mechanism of lncRNAs in the crosstalk between epithelial-mesenchymal transition and tumor microenvironment for early colon adenocarcinoma based on molecular subtyping. Front Genet 2022; 13:997739. [PMID: 36467998 PMCID: PMC9708740 DOI: 10.3389/fgene.2022.997739] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/19/2022] [Accepted: 10/17/2022] [Indexed: 09/10/2024] Open
Abstract
A large number of colon adenocarcinoma (COAD) patients are already advanced when diagnosed. In this study, we aimed to further understand the mechanism of tumor development in early COAD by focusing on epithelial-mesenchymal transition (EMT) and long non-coding RNAs (lncRNAs). Expression profiles of early COAD patients were obtained from public databases. EMT-related lncRNAs were used as a basis for constructing molecular subtypes through unsupervised consensus clustering. Genomic features, pathways and tumor microenvironment (TME) were compared between two subtypes. LncATLAS database was applied to analyze the relation between lncRNAs and transcription factors (TFs). First order partial correlation analysis was conducted to identify key EMT-related lncRNAs.C1 and C2 subtypes with distinct prognosis were constructed. Oncogenic pathways such as EMT, KRAS signaling, JAK-STAT signaling, and TGF-β signaling were significantly enriched in C2 subtype. Higher immune infiltration and expression of immune checkpoints were also observed in C2 subtype, suggesting the key EMT-related lncRNAs may play a critical role in the modulation of TME. In addition, JAK-STAT signaling pathway was obviously enriched in upregulated TFs in C2 subtype, which indicated a link between key lncRNAs and JAK-STAT signaling that may regulate TME. The study further expanded the research on the role of EMT-related lncRNAs in the early COAD. The six identified EMT-related lncRNAs could serve as biomarkers for early screening COAD.
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Affiliation(s)
- Hanlin Liang
- Chemotherapy Department, Zhongshan City People’s Hospital, Zhongshan, China
| | - Yi Zhao
- GI Medicine, The Third Hospital Affiliated to Naval Medical University, Shanghai, China
| | - Kai Liu
- Department of Colorectal Oncology, National Clinical Research Center for Cancer, Key Laboratory of Cancer Prevention and Therapy of Tianjin, Tianjin’s Clinical Research Center for Cancer, Tianjin Medical University Cancer Institute and Hospital, Tianjin, China
| | - Yajie Xiao
- Department of Medicine, YuceBio Technology Co., Ltd., Shenzhen, China
| | - Kexu Chen
- Chemotherapy Department, Zhongshan City People’s Hospital, Zhongshan, China
| | - Delan Li
- Chemotherapy Department, Zhongshan City People’s Hospital, Zhongshan, China
| | - Shupeng Zhong
- Chemotherapy Department, Zhongshan City People’s Hospital, Zhongshan, China
| | - Zhikun Zhao
- Department of Medicine, YuceBio Technology Co., Ltd., Shenzhen, China
| | - Dongfang Wu
- Department of Medicine, YuceBio Technology Co., Ltd., Shenzhen, China
| | - Yu Peng
- Oncology Department, Jiangmen Central Hospital, Jiangmen, China
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Perdomo-González DI, Laseca N, Demyda-Peyrás S, Valera M, Cervantes I, Molina A. Fine-tuning genomic and pedigree inbreeding rates in equine population with a deep and reliable stud book: the case of the Pura Raza Española horse. J Anim Sci Biotechnol 2022; 13:127. [PMID: 36336696 PMCID: PMC9639299 DOI: 10.1186/s40104-022-00781-5] [Citation(s) in RCA: 4] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/08/2022] [Accepted: 09/13/2022] [Indexed: 11/09/2022] Open
Abstract
BACKGROUND Estimating inbreeding, which is omnipresent and inevitable in livestock populations, is a primary goal for management and animal breeding especially for those interested in mitigating the negative consequences of inbreeding. Inbreeding coefficients have been historically estimated by using pedigree information; however, over the last decade, genome-base inbreeding coefficients have come to the forefront in this field. The Pura Raza Española (PRE) horse is an autochthonous Spanish horse breed which has been recognised since 1912. The total PRE population (344,718 horses) was used to estimate Classical (F), Ballou's ancestral, Kalinowski's ancestral, Kalinowski's new and the ancestral history coefficient values. In addition, genotypic data from a selected population of 805 PRE individuals was used to determine the individual inbreeding coefficient using SNP-by-SNP-based techniques (methods of moments -FHOM-, the diagonal elements of the genomic -FG-, and hybrid matrixes -FH-) and ROH measures (FRZ). The analyse of both pedigree and genomic based inbreeding coefficients in a large and robust population such as the PRE horse, with proven parenteral information for the last 40 years and a high degree of completeness (over 90% for the last 70 years) will allow us to understand PRE genetic variability better and the correlations between the estimations will give the data greater reliability. RESULTS The mean values of the pedigree-based inbreeding coefficients ranged from 0.01 (F for the last 3 generations -F3-) to 0.44 (ancestral history coefficient) and the mean values of genomic-based inbreeding coefficients varied from 0.05 (FRZ for three generations, FH and FHOM) to 0.11 (FRZ for nine generations). Significant correlations were also found between pedigree and genomic inbreeding values, which ranged between 0.58 (F3 with FHOM) and 0.79 (F with FRZ). In addition, the correlations between FRZ estimated for the last 20 generations and the pedigree-based inbreeding highlight the fact that fewer generations of genomic data are required when comparing total inbreeding values, and the opposite when ancient values are calculated. CONCLUSIONS Ultimately, our results show that it is still useful to work with a deep and reliable pedigree in pedigree-based genetic studies with very large effective population sizes. Obtaining a satisfactory parameter will always be desirable, but the approximation obtained with a robust pedigree will allow us to work more efficiently and economically than with massive genotyping.
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Affiliation(s)
- Davinia Isabel Perdomo-González
- Departamento Agronomía, Escuela Técnica Superior de Ingeniería Agromómica, Universidad de Sevilla, Ctra Utrera Km 1, 41013, Sevilla, Spain.
| | - Nora Laseca
- Departamento de Genética, Universidad de Córdoba, Córdoba, Spain
| | - Sebastián Demyda-Peyrás
- Facultad de Ciencias Veterinarias, Universidad Nacional de La Plata, La Plata, Argentina.,Consejo Nacional de Investigaciones Científicas y Técnicas (CONICET), La Plata, Argentina
| | - Mercedes Valera
- Departamento Agronomía, Escuela Técnica Superior de Ingeniería Agromómica, Universidad de Sevilla, Ctra Utrera Km 1, 41013, Sevilla, Spain
| | - Isabel Cervantes
- Departamento de Producción Animal, Facultad de Veterinaria, Universidad Complutense de Madrid, Madrid, Spain
| | - Antonio Molina
- Departamento de Genética, Universidad de Córdoba, Córdoba, Spain
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Causal Network Inference and Functional Decomposition for Decentralized Statistical Process Monitoring: Detection and Diagnosis. Chem Eng Sci 2022. [DOI: 10.1016/j.ces.2022.118338] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/26/2022]
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Buzzatto-Leite I, Afonso J, Silva-Vignato B, Coutinho L, Alvares L. Differential gene co-expression network analyses reveal novel molecules associated with transcriptional dysregulation of key biological processes in osteoarthritis knee cartilage. OSTEOARTHRITIS AND CARTILAGE OPEN 2022; 4:100316. [PMID: 36474801 PMCID: PMC9718204 DOI: 10.1016/j.ocarto.2022.100316] [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: 03/09/2022] [Revised: 09/09/2022] [Accepted: 10/17/2022] [Indexed: 12/24/2022] Open
Abstract
OBJECTIVES To compare co-expression networks of normal and osteoarthritis knee cartilage to uncover molecules associated with the transcriptional misregulation compromising biological processes (BPs) critical for cartilage homeostasis. DESIGN Normal and osteoarthritis human knee cartilage RNA-seq GSE114007 dataset was obtained from the Gene Expression Omnibus database. Partial Correlation and Information Theory (PCIT) algorithm was used to build co-expression networks containing all nodes connecting to at least one differentially expressed gene (DEG) in normal and osteoarthritis networks. Hub and hub centrality genes were used to perform functional enrichment analysis. Enriched BPs known to be associated with both healthy and diseased cartilage were compared in depth. RESULTS Differential co-expression network analyses allowed the identification of DDX43 and USP42 as exclusively co-expressed with DEGs in normal and osteoarthritis networks, respectively. The top hub and hub centrality genes of these networks were HIST1H3A and SNHG12 (normal) and TAF9B and OTUD1 (osteoarthritis). Enrichment analysis revealed several shared BPs between the contrasting groups, which are well-known in osteoarthritis pathogenesis. Protein-protein interaction network analysis for these BPs showed a global down-regulation of transcription factors in osteoarthritis. Specific transcription factors were identified as pleiotropic mediators in articular cartilage maintenance since they take part in several BPs. In addition, chromatin organisation and modification proteins were found relevant for osteoarthritis development. CONCLUSION Differential gene co-expression analysis allowed the identification of novel and high priority therapeutic candidate genes that may drive modifications in the transcriptional "status" of cartilage in osteoarthritis.
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Affiliation(s)
- I. Buzzatto-Leite
- Department of Biochemistry and Tissue Biology, Institute of Biology, University of Campinas (UNICAMP), Campinas, Brazil
| | - J. Afonso
- Department of Animal Science, College of Agriculture “Luiz de Queiroz”, University of São Paulo (ESALQ/USP), Piracicaba, Brazil
| | - B. Silva-Vignato
- Department of Animal Science, College of Agriculture “Luiz de Queiroz”, University of São Paulo (ESALQ/USP), Piracicaba, Brazil
| | - L.L. Coutinho
- Department of Animal Science, College of Agriculture “Luiz de Queiroz”, University of São Paulo (ESALQ/USP), Piracicaba, Brazil
| | - L.E. Alvares
- Department of Biochemistry and Tissue Biology, Institute of Biology, University of Campinas (UNICAMP), Campinas, Brazil,Corresponding author. Department of Biochemistry and Tissue Biology, University of Campinas – UNICAMP, Rua Monteiro Lobato 255, Cx. Postal 6109, CEP 13083-862, Campinas, SP, Brazil.
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Diniz WJS, Banerjee P, Rodning SP, Dyce PW. Machine Learning-Based Co-Expression Network Analysis Unravels Potential Fertility-Related Genes in Beef Cows. Animals (Basel) 2022; 12:2715. [PMID: 36230456 PMCID: PMC9559512 DOI: 10.3390/ani12192715] [Citation(s) in RCA: 5] [Impact Index Per Article: 2.5] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/19/2022] [Revised: 09/22/2022] [Accepted: 10/07/2022] [Indexed: 11/06/2022] Open
Abstract
Reproductive failure is still a challenge for beef producers and a significant cause of economic loss. The increased availability of transcriptomic data has shed light on the mechanisms modulating pregnancy success. Furthermore, new analytical tools, such as machine learning (ML), provide opportunities for data mining and uncovering new biological events that explain or predict reproductive outcomes. Herein, we identified potential biomarkers underlying pregnancy status and fertility-related networks by integrating gene expression profiles through ML and gene network modeling. We used public transcriptomic data from uterine luminal epithelial cells of cows retrospectively classified as pregnant (P, n = 25) and non-pregnant (NP, n = 18). First, we used a feature selection function from BioDiscML and identified SERPINE3, PDCD1, FNDC1, MRTFA, ARHGEF7, MEF2B, NAA16, ENSBTAG00000019474, and ENSBTAG00000054585 as candidate biomarker predictors of pregnancy status. Then, based on co-expression networks, we identified seven genes significantly rewired (gaining or losing connections) between the P and NP networks. These biomarkers were co-expressed with genes critical for uterine receptivity, including endometrial tissue remodeling, focal adhesion, and embryo development. We provided insights into the regulatory networks of fertility-related processes and demonstrated the potential of combining different analytical tools to prioritize candidate genes.
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Fomins A, Sych Y, Helmchen F. Conservative significance testing of tripartite statistical relations in multivariate neural data. Netw Neurosci 2022; 6:1243-1274. [PMID: 38800452 PMCID: PMC11117094 DOI: 10.1162/netn_a_00259] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/22/2022] [Accepted: 06/14/2022] [Indexed: 05/29/2024] Open
Abstract
An important goal in systems neuroscience is to understand the structure of neuronal interactions, frequently approached by studying functional relations between recorded neuronal signals. Commonly used pairwise measures (e.g., correlation coefficient) offer limited insight, neither addressing the specificity of estimated neuronal interactions nor potential synergistic coupling between neuronal signals. Tripartite measures, such as partial correlation, variance partitioning, and partial information decomposition, address these questions by disentangling functional relations into interpretable information atoms (unique, redundant, and synergistic). Here, we apply these tripartite measures to simulated neuronal recordings to investigate their sensitivity to noise. We find that the considered measures are mostly accurate and specific for signals with noiseless sources but experience significant bias for noisy sources.We show that permutation testing of such measures results in high false positive rates even for small noise fractions and large data sizes. We present a conservative null hypothesis for significance testing of tripartite measures, which significantly decreases false positive rate at a tolerable expense of increasing false negative rate. We hope our study raises awareness about the potential pitfalls of significance testing and of interpretation of functional relations, offering both conceptual and practical advice.
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Affiliation(s)
- Aleksejs Fomins
- Brain Research Institute, University of Zurich, Zurich, Switzerland
- Neuroscience Center Zurich, University of Zurich, Switzerland
| | - Yaroslav Sych
- Brain Research Institute, University of Zurich, Zurich, Switzerland
- Experimental Neurology Center, Department of Neurology, Inselspital University Hospital Bern, Bern, Switzerland
- Present address: Institute of Cellular and Integrative Neurosciences, University of Strasbourg and CNRS, Strasbourg, France
| | - Fritjof Helmchen
- Brain Research Institute, University of Zurich, Zurich, Switzerland
- Neuroscience Center Zurich, University of Zurich, Switzerland
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Mott AC, Mott A, Preuß S, Bennewitz J, Tetens J, Falker-Gieske C. eQTL analysis of laying hens divergently selected for feather pecking identifies KLF14 as a potential key regulator for this behavioral disorder. Front Genet 2022; 13:969752. [PMID: 36061196 PMCID: PMC9428588 DOI: 10.3389/fgene.2022.969752] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Abstract] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/15/2022] [Accepted: 07/25/2022] [Indexed: 02/03/2023] Open
Abstract
Feather pecking in chickens is a damaging behavior, seriously impacting animal welfare and leading to economic losses. Feather pecking is a complex trait, which is partly under genetic control. Different hypotheses have been proposed to explain the etiology of feather pecking and notably, several studies have identified similarities between feather pecking and human mental disorders such as obsessive-compulsive disorder and schizophrenia. This study uses transcriptomic and phenotypic data from 167 chickens to map expression quantitative trait loci and to identify regulatory genes with a significant effect on this behavioral disorder using an association weight matrix approach. From 70 of the analyzed differentially expressed genes, 11,790 genome wide significantly associated variants were detected, of which 23 showed multiple associations (≥15). These were located in proximity to a number of genes, which are transcription regulators involved in chromatin binding, nucleic acid metabolism, protein translation and putative regulatory RNAs. The association weight matrix identified 36 genes and the two transcription factors: SP6 (synonym: KLF14) and ENSGALG00000042129 (synonym: CHTOP) as the most significant, with an enrichment of KLF14 binding sites being detectable in 40 differentially expressed genes. This indicates that differential expression between animals showing high and low levels of feather pecking was significantly associated with a genetic variant in proximity to KLF14. This multiallelic variant was located 652 bp downstream of KLF14 and is a deletion of 1-3 bp. We propose that a deletion downstream of the transcription factor KLF14 has a negative impact on the level of T cells in the developing brain of high feather pecking chickens, which leads to developmental and behavioral abnormalities. The lack of CD4 T cells and gamma-Aminobutyric acid (GABA) receptors are important factors for the increased propensity of laying hens to perform feather pecking. As such, KLF14 is a clear candidate regulator for the expression of genes involved in the pathogenic development. By further elucidating the regulatory pathways involved in feather pecking we hope to take significant steps forward in explaining and understanding other mental disorders, not just in chickens.
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Affiliation(s)
| | - Andrea Mott
- Department of Animal Sciences, Georg-August-University, Göttingen, Germany
| | - Siegfried Preuß
- Institute of Animal Science, University of Hohenheim, Stuttgart, Germany
| | - Jörn Bennewitz
- Institute of Animal Science, University of Hohenheim, Stuttgart, Germany
| | - Jens Tetens
- Department of Animal Sciences, Georg-August-University, Göttingen, Germany
- Center for Integrated Breeding Research, Georg-August-University, Göttingen, Germany
| | - Clemens Falker-Gieske
- Department of Animal Sciences, Georg-August-University, Göttingen, Germany
- *Correspondence: Clemens Falker-Gieske,
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Algabri YA, Li L, Liu ZP. scGENA: A Single-Cell Gene Coexpression Network Analysis Framework for Clustering Cell Types and Revealing Biological Mechanisms. Bioengineering (Basel) 2022; 9:bioengineering9080353. [PMID: 36004879 PMCID: PMC9405199 DOI: 10.3390/bioengineering9080353] [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: 06/10/2022] [Revised: 07/27/2022] [Accepted: 07/27/2022] [Indexed: 11/16/2022] Open
Abstract
Single-cell RNA-sequencing (scRNA-seq) is a recent high-throughput technique that can measure gene expression, reveal cell heterogeneity, rare and complex cell populations, and discover cell types and their relationships. The analysis of scRNA-seq data is challenging because of transcripts sparsity, replication noise, and outlier cell populations. A gene coexpression network (GCN) analysis effectively deciphers phenotypic differences in specific states by describing gene–gene pairwise relationships. The underlying gene modules with different coexpression patterns partially bridge the gap between genotype and phenotype. This study presents a new framework called scGENA (single-cell gene coexpression network analysis) for GCN analysis based on scRNA-seq data. Although there are several methods for scRNA-seq data analysis, we aim to build an integrative pipeline for several purposes that cover primary data preprocessing, including data exploration, quality control, normalization, imputation, and dimensionality reduction of clustering as downstream of GCN analysis. To demonstrate this integrated workflow, an scRNA-seq dataset of the human diabetic pancreas with 1600 cells and 39,851 genes was implemented to perform all these processes in practice. As a result, scGENA is demonstrated to uncover interesting gene modules behind complex diseases, which reveal biological mechanisms. scGENA provides a state-of-the-art method for gene coexpression analysis for scRNA-seq data.
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Banerjee P, Rodning SP, Diniz WJS, Dyce PW. Co-Expression Network and Integrative Analysis of Metabolome and Transcriptome Uncovers Biological Pathways for Fertility in Beef Heifers. Metabolites 2022; 12:metabo12080708. [PMID: 36005579 PMCID: PMC9413342 DOI: 10.3390/metabo12080708] [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: 07/04/2022] [Revised: 07/27/2022] [Accepted: 07/28/2022] [Indexed: 12/13/2022] Open
Abstract
Reproductive failure remains a significant challenge to the beef industry. The omics technologies have provided opportunities to improve reproductive efficiency. We used a multistaged analysis from blood profiles to integrate metabolome (plasma) and transcriptome (peripheral white blood cells) in beef heifers. We used untargeted metabolomics and RNA-Seq paired data from six AI-pregnant (AI-P) and six nonpregnant (NP) Angus-Simmental crossbred heifers at artificial insemination (AI). Based on network co-expression analysis, we identified 17 and 37 hub genes in the AI-P and NP groups, respectively. Further, we identified TGM2, TMEM51, TAC3, NDRG4, and PDGFB as more connected in the NP heifers’ network. The NP gene network showed a connectivity gain due to the rewiring of major regulators. The metabolomic analysis identified 18 and 15 hub metabolites in the AI-P and NP networks. Tryptophan and allantoic acid exhibited a connectivity gain in the NP and AI-P networks, respectively. The gene–metabolite integration identified tocopherol-a as positively correlated with ENSBTAG00000009943 in the AI-P group. Conversely, tocopherol-a was negatively correlated in the NP group with EXOSC2, TRNAUIAP, and SNX12. In the NP group, α-ketoglutarate-SMG8 and putrescine-HSD17B13 were positively correlated, whereas a-ketoglutarate-ALAS2 and tryptophan-MTMR1 were negatively correlated. These multiple interactions identified novel targets and pathways underlying fertility in bovines.
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Identification of fatty acid metabolism-related lncRNAs in the prognosis and immune microenvironment of colon adenocarcinoma. Biol Direct 2022; 17:19. [PMID: 35902970 PMCID: PMC9331591 DOI: 10.1186/s13062-022-00332-y] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/23/2022] [Accepted: 07/23/2022] [Indexed: 02/08/2023] Open
Abstract
BACKGROUND Cancer metabolism is largely altered compared to normal cells. This study aims to explore critical metabolism pathways in colon adenocarcinoma (COAD), and reveal the possible mechanism of their role in cancer progression. METHODS Expression data and sequencing data of COAD samples were obtained from The Cancer Genome Atlas and Gene Expression Omnibus databases. The expression profiles between tumor and normal samples were compared to identify differential metabolism pathways through single sample gene set enrichment analysis. RESULTS Fatty acid synthesis was identified as a key metabolism pathway in COAD. Based on fatty acid-related lncRNAs, two molecular subtypes (C1 and C2) were defined. C2 subtype with worse prognosis had higher immune infiltration and higher expression of immune checkpoints. Five transcription factors (TFs) including FOS, JUN, HIF1A, STAT3 and STAT2 were highly expressed in C2 subtype. Five fatty acid-related lncRNAs were identified to be biomarkers for predicting COAD prognosis. Finally, further experients showed that knockdown of lncRNA PAXIP1-AS1 decreased the triglyceride content and the fatty acid synthase and acetyl-CoA carboxylase 1 expressions, which suggested that lncRNA PAXIP1-AS1 plays an important role in fatty acid metabolism of COAD. CONCLUSIONS This study demonstrated that fatty acid synthesis was greatly altered in COAD. Fatty acid-related lncRNAs were speculated to be involved in cancer progression through associating with TFs. The five screened TFs may serve as new drug targets for treating COAD.
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Liu D, Wan Y, Qu N, Fu Q, Liang C, Zeng L, Yang Y. LncRNA-FAM66C Was Identified as a Key Regulator for Modulating Tumor Microenvironment and Hypoxia-Related Pathways in Glioblastoma. Front Public Health 2022; 10:898270. [PMID: 35874989 PMCID: PMC9299378 DOI: 10.3389/fpubh.2022.898270] [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: 03/17/2022] [Accepted: 06/08/2022] [Indexed: 11/13/2022] Open
Abstract
Although the role of hypoxia has been greatly explored and unveiled in glioblastoma (GBM), the mechanism of hypoxia-related long non-coding (lnc) RNAs has not been clearly understood. This study aims to reveal the crosstalk among hypoxia-related lncRNAs, tumor microenvironment (TME), and tumorigenesis for GBM. Gene expression profiles of GBM patients were used as a basis for identifying hypoxia-related lncRNAs. Unsupervised consensus clustering was conducted for classifying samples into different molecular subtypes. Gene set enrichment analysis (GSEA) was performed to analyze the enrichment of a series of genes or gene signatures. Three molecular subtypes were constructed based on eight identified hypoxia-related lncRNAs. Oncogenic pathways, such as epithelial mesenchymal transition (EMT), tumor necrosis factor-α (TNF-α) signaling, angiogenesis, hypoxia, P53 signaling, and glycolysis pathways, were significantly enriched in C1 subtype with poor overall survival. C1 subtype showed high immune infiltration and high expression of immune checkpoints. Furthermore, we identified 10 transcription factors (TFs) that were highly correlated with lncRNA-FAM66C. Three key lncRNAs (ADAMTS9-AS2, LINC00968, and LUCAT1) were screened as prognostic biomarkers for GBM. This study shed light on the important role of hypoxia-related lncRNAs for TME modulation and tumorigenesis in GBM. The eight identified hypoxia-related lncRNAs, especially FAM66C may serve as key regulators involving in hypoxia-related pathways.
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Affiliation(s)
- Dan Liu
- Oncology Department, Jinzhou Central Hospital, Jinzhou, China
| | - Yue Wan
- Oncology Department, Jinzhou Central Hospital, Jinzhou, China
| | - Ning Qu
- Department of Pediatrics, Jinzhou Central Hospital, Jinzhou, China
| | - Qiang Fu
- Department of Neurosurgery, Shengjing Hospital Affiliated to China Medical University, Shenyang, China
| | - Chao Liang
- Department of General Surgery, The First Affiliated Hospital of Jinzhou Medical University, Jinzhou, China
| | - Lingda Zeng
- Department of Otorhinolaryngology Surgery, Jinzhou Central Hospital, Jinzhou, China
| | - Yang Yang
- Department of Neurosurgery, Jinzhou Central Hospital, Jinzhou, China
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Cardoso TF, Bruscadin JJ, Afonso J, Petrini J, Andrade BGN, de Oliveira PSN, Malheiros JM, Rocha MIP, Zerlotini A, Ferraz JBS, Mourão GB, Coutinho LL, Regitano LCA. EEF1A1 transcription cofactor gene polymorphism is associated with muscle gene expression and residual feed intake in Nelore cattle. Mamm Genome 2022; 33:619-628. [PMID: 35816191 DOI: 10.1007/s00335-022-09959-8] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/22/2021] [Accepted: 06/22/2022] [Indexed: 12/01/2022]
Abstract
Cis-acting effects of noncoding variants on gene expression and regulatory molecules constitute a significant factor for phenotypic variation in complex traits. To provide new insights into the impacts of single-nucleotide polymorphisms (SNPs) on transcription factors (TFs) and transcription cofactors (TcoF) coding genes, we carried out a multi-omic analysis to identify cis-regulatory effects of SNPs on these genes' expression in muscle and describe their association with feed efficiency-related traits in Nelore cattle. As a result, we identified one SNP, the rs137256008C > T, predicted to impact the EEF1A1 gene expression (β = 3.02; P-value = 3.51E-03) and the residual feed intake trait (β = - 3.47; P-value = 0.02). This SNP was predicted to modify transcription factor sites and overlaps with several QTL for feed efficiency traits. In addition, co-expression network analyses showed that animals containing the T allele of the rs137256008 SNP may be triggering changes in the gene network. Therefore, our analyses reinforce and contribute to a better understanding of the biological mechanisms underlying gene expression control of feed efficiency traits in bovines. The cis-regulatory SNP can be used as biomarker for feed efficiency in Nelore cattle.
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Affiliation(s)
- T F Cardoso
- Embrapa Southeast Livestock, São Carlos, SP, Brazil
| | - J J Bruscadin
- Program on Evolutionary Genetics and Molecular Biology, Federal University of São Carlos, São Carlos, SP, Brazil
| | - J Afonso
- Embrapa Southeast Livestock, São Carlos, SP, Brazil
| | - J Petrini
- Department of Animal Science, "Luiz de Queiroz" College of Agriculture, University of São Paulo/ESALQ, Piracicaba, SP, Brazil
| | - B G N Andrade
- Computer Science Department, Munster Technological University, MTU/ADAPT, Cork, Ireland
| | - P S N de Oliveira
- Program on Evolutionary Genetics and Molecular Biology, Federal University of São Carlos, São Carlos, SP, Brazil
| | - J M Malheiros
- Federal University of Latin American Integration, Foz do Iguaçu, Paraná, Brazil
| | - M I P Rocha
- Program on Evolutionary Genetics and Molecular Biology, Federal University of São Carlos, São Carlos, SP, Brazil
| | - A Zerlotini
- Embrapa Agricultural Informatics, Campinas, SP, Brazil
| | - J B S Ferraz
- Department of Veterinary Medicine, University of São Paulo/FZEA, Pirassununga, Brazil
| | - G B Mourão
- Department of Animal Science, "Luiz de Queiroz" College of Agriculture, University of São Paulo/ESALQ, Piracicaba, SP, Brazil
| | - L L Coutinho
- Department of Animal Science, "Luiz de Queiroz" College of Agriculture, University of São Paulo/ESALQ, Piracicaba, SP, Brazil
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Mármol-Sánchez E, Cirera S, Zingaretti LM, Jacobsen MJ, Ramayo-Caldas Y, Jørgensen CB, Fredholm M, Cardoso TF, Quintanilla R, Amills M. Modeling microRNA-driven post-transcriptional regulation using exon-intron split analysis in pigs. Anim Genet 2022; 53:613-626. [PMID: 35811409 DOI: 10.1111/age.13238] [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: 10/22/2021] [Revised: 04/23/2022] [Accepted: 06/16/2022] [Indexed: 11/27/2022]
Abstract
The contribution of microRNAs (miRNAs) to mRNA post-transcriptional regulation has often been explored by the post hoc selection of downregulated genes and determining whether they harbor binding sites for miRNAs of interest. This approach, however, does not discriminate whether these mRNAs are also downregulated at the transcriptional level. Here, we have characterized the transcriptional and post-transcriptional changes in mRNA expression in two porcine tissues: gluteus medius muscle of fasted and fed Duroc gilts and adipose tissue of lean and obese Duroc-Göttingen minipigs. Exon-intron split analysis of RNA-seq data allowed us to identify downregulated mRNAs with high post-transcriptional signals in fed or obese states, and we assessed whether they harbor binding sites for upregulated miRNAs in any of these two physiological states. We found 26 downregulated mRNAs with high post-transcriptional signals in the muscle of fed gilts and 21 of these were predicted targets of miRNAs upregulated in fed pigs. For adipose tissue, 44 downregulated mRNAs in obese minipigs displayed high post-transcriptional signals, and 25 of these were predicted targets of miRNAs upregulated in the obese state. These results suggest that the contribution of miRNAs to mRNA repression is more prominent in the skeletal muscle system. Finally, we identified several genes that may play relevant roles in the energy homeostasis of the pig skeletal muscle (DKK2 and PDK4) and adipose (SESN3 and ESRRG) tissues. By differentiating transcriptional from post-transcriptional changes in mRNA expression, exon-intron split analysis provides a valuable view of the regulation of gene expression, complementary to canonical differential expression analyses.
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Affiliation(s)
- Emilio Mármol-Sánchez
- Centre for Research in Agricultural Genomics (CRAG), CSIC-IRTA-UAB-UB, Universitat Autònoma de Barcelona, Bellaterra, Spain
| | - Susanna Cirera
- Department of Veterinary and Animal Sciences, Faculty of Health and Medical Sciences, University of Copenhagen, Frederiksberg C, Denmark
| | | | - Mette Juul Jacobsen
- Department of Veterinary and Animal Sciences, Faculty of Health and Medical Sciences, University of Copenhagen, Frederiksberg C, Denmark
| | - Yuliaxis Ramayo-Caldas
- Animal Breeding and Genetics Program, Institute for Research and Technology in Food and Agriculture, Barcelona, Spain
| | - Claus B Jørgensen
- Department of Veterinary and Animal Sciences, Faculty of Health and Medical Sciences, University of Copenhagen, Frederiksberg C, Denmark
| | - Merete Fredholm
- Department of Veterinary and Animal Sciences, Faculty of Health and Medical Sciences, University of Copenhagen, Frederiksberg C, Denmark
| | - Tainã Figueiredo Cardoso
- Centre for Research in Agricultural Genomics (CRAG), CSIC-IRTA-UAB-UB, Universitat Autònoma de Barcelona, Bellaterra, Spain.,Empresa Brasileira de Pesquisa Agropecuária, Embrapa Pecuária Sudeste, São Carlos, Brazil
| | - Raquel Quintanilla
- Animal Breeding and Genetics Program, Institute for Research and Technology in Food and Agriculture, Barcelona, Spain
| | - Marcel Amills
- Centre for Research in Agricultural Genomics (CRAG), CSIC-IRTA-UAB-UB, Universitat Autònoma de Barcelona, Bellaterra, Spain.,Departament de Ciència Animal i dels Aliments, Universitat Autònoma de Barcelona, Barcelona, Spain
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44
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Samsing F, Wynne JW, Valenzuela-Muñoz V, Valenzuela-Miranda D, Gallardo-Escárate C, Alexandre PA. Competing endogenous RNA-networks reveal key regulatory microRNAs involved in the response of Atlantic salmon to a novel orthomyxovirus. DEVELOPMENTAL AND COMPARATIVE IMMUNOLOGY 2022; 132:104396. [PMID: 35304180 DOI: 10.1016/j.dci.2022.104396] [Citation(s) in RCA: 2] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 01/31/2022] [Revised: 03/10/2022] [Accepted: 03/10/2022] [Indexed: 06/14/2023]
Abstract
One of the most intriguing discoveries of the genomic era is that only a small fraction of the genome is dedicated to protein coding. The remaining fraction of the genome contains, amongst other elements, a number of non-coding transcripts that regulate the transcription of protein coding genes. Here we used transcriptome sequencing data to explore these gene regulatory networks using RNA derived from gill tissue of Atlantic salmon (Salmo salar) infected with Pilchard orthomyxovirus (POMV), but showing no clinical signs of disease. We examined fish sampled early during the challenge trial (8-12 days after infection) to uncover potential biomarkers of early infection and innate immunity, and fish sampled late during the challenge trial (19 dpi) to elucidate potential markers of resistance to POMV. We analysed total RNA-sequencing data to find differentially expressed messenger RNAs (mRNA) and identify new long-noncoding RNAs (lncRNAs). We also evaluated small RNA sequencing data to find differentially transcribed microRNAs (miRNAs) and explore their role in gene regulatory networks. Whole-genome expression data (both coding and non-coding transcripts) were used to explore the crosstalk between RNA molecules by constructing competing endogenous RNA networks (ceRNA). The teleost specific miR-462/miR-731 cluster was strongly induced in POMV infected fish and deemed a potential biomarker of early infection. Gene networks also identified a selenoprotein (selja), downregulated in fish sampled late during the challenge, which may be associated to viral clearance and the return to homeostasis after infection. This study provides the basis for further investigations using molecular tools to overexpress or inhibit miRNAs to confirm the functional impact of the interactions presented here on gene expression and their potential application at commercial level.
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Affiliation(s)
- Francisca Samsing
- CSIRO Agriculture and Food, Livestock and Aquaculture, Hobart, TAS, Australia
| | - James W Wynne
- CSIRO Agriculture and Food, Livestock and Aquaculture, Hobart, TAS, Australia.
| | | | - Diego Valenzuela-Miranda
- Interdisciplinary Center for Aquaculture Research (INCAR), University of Concepción, Concepción, Chile
| | | | - Pâmela A Alexandre
- CSIRO Agriculture and Food, Livestock and Aquaculture, Brisbane, QLD, Australia
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Mohamed AR, Naval-Sanchez M, Menzies M, Evans B, King H, Reverter A, Kijas JW. Leveraging transcriptome and epigenome landscapes to infer regulatory networks during the onset of sexual maturation. BMC Genomics 2022; 23:413. [PMID: 35650521 PMCID: PMC9158274 DOI: 10.1186/s12864-022-08514-8] [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: 11/28/2021] [Accepted: 03/29/2022] [Indexed: 12/03/2022] Open
Abstract
Background Despite sexual development being ubiquitous to vertebrates, the molecular mechanisms underpinning this fundamental transition remain largely undocumented in many organisms. We designed a time course experiment that successfully sampled the period when Atlantic salmon commence their trajectory towards sexual maturation. Results Through deep RNA sequencing, we discovered key genes and pathways associated with maturation in the pituitary-ovarian axis. Analyzing DNA methylomes revealed a bias towards hypermethylation in ovary that implicated maturation-related genes. Co-analysis of DNA methylome and gene expression changes revealed chromatin remodeling genes and key transcription factors were both significantly hypermethylated and upregulated in the ovary during the onset of maturation. We also observed changes in chromatin state landscapes that were strongly correlated with fundamental remodeling of gene expression in liver. Finally, a multiomic integrated analysis revealed regulatory networks and identified hub genes including TRIM25 gene (encoding the estrogen-responsive finger protein) as a putative key regulator in the pituitary that underwent a 60-fold change in connectivity during the transition to maturation. Conclusion The study successfully documented transcriptome and epigenome changes that involved key genes and pathways acting in the pituitary – ovarian axis. Using a Systems Biology approach, we identified hub genes and their associated networks deemed crucial for onset of maturation. The results provide a comprehensive view of the spatiotemporal changes involved in a complex trait and opens the door to future efforts aiming to manipulate puberty in an economically important aquaculture species. Supplementary Information The online version contains supplementary material available at 10.1186/s12864-022-08514-8.
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Aviña-Padilla K, Zambada-Moreno O, Herrera-Oropeza GE, Jimenez-Limas MA, Abrahamian P, Hammond RW, Hernández-Rosales M. Insights into the Transcriptional Reprogramming in Tomato Response to PSTVd Variants Using Network Approaches. Int J Mol Sci 2022; 23:5983. [PMID: 35682662 PMCID: PMC9181013 DOI: 10.3390/ijms23115983] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/30/2022] [Revised: 05/18/2022] [Accepted: 05/21/2022] [Indexed: 01/25/2023] Open
Abstract
Viroids are the smallest pathogens of angiosperms, consisting of non-coding RNAs that cause severe diseases in agronomic crops. Symptoms associated with viroid infection are linked to developmental alterations due to genetic regulation. To understand the global mechanisms of host viroid response, we implemented network approaches to identify master transcription regulators and their differentially expressed targets in tomato infected with mild and severe variants of PSTVd. Our approach integrates root and leaf transcriptomic data, gene regulatory network analysis, and identification of affected biological processes. Our results reveal that specific bHLH, MYB, and ERF transcription factors regulate genes involved in molecular mechanisms underlying critical signaling pathways. Functional enrichment of regulons shows that bHLH-MTRs are linked to metabolism and plant defense, while MYB-MTRs are involved in signaling and hormone-related processes. Strikingly, a member of the bHLH-TF family has a specific potential role as a microprotein involved in the post-translational regulation of hormone signaling events. We found that ERF-MTRs are characteristic of severe symptoms, while ZNF-TF, tf3a-TF, BZIP-TFs, and NAC-TF act as unique MTRs. Altogether, our results lay a foundation for further research on the PSTVd and host genome interaction, providing evidence for identifying potential key genes that influence symptom development in tomato plants.
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Affiliation(s)
- Katia Aviña-Padilla
- Centro de Investigación y de Estudios Avanzados del I.P.N Unidad Irapuato, Irapuato 36821, Mexico;
- Department of Crop Sciences, University of Illinois at Urbana-Champaign, Urbana, IL 61801, USA
| | - Octavio Zambada-Moreno
- Centro de Investigación y de Estudios Avanzados del I.P.N Unidad Irapuato, Irapuato 36821, Mexico;
| | - Gabriel Emilio Herrera-Oropeza
- Center for Developmental Neurobiology, Institute of Psychiatry, Psychology, and Neuroscience, King’s College London, London WC2R 2LS, UK;
| | - Marco A. Jimenez-Limas
- Centro de Investigación en Computación, Instituto Politécnico Nacional, Mexico City 07738, Mexico;
| | - Peter Abrahamian
- USDA, Agricultural Research Service, Beltsville Agricultural Research Center, Beltsville, MD 20705, USA;
| | - Rosemarie W. Hammond
- USDA, Agricultural Research Service, Beltsville Agricultural Research Center, Beltsville, MD 20705, USA;
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Schettini GP, Peripolli E, Alexandre PA, dos Santos WB, Pereira ASC, de Albuquerque LG, Baldi F, Curi RA. Transcriptome Profile Reveals Genetic and Metabolic Mechanisms Related to Essential Fatty Acid Content of Intramuscular Longissimus thoracis in Nellore Cattle. Metabolites 2022; 12:metabo12050471. [PMID: 35629975 PMCID: PMC9144777 DOI: 10.3390/metabo12050471] [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: 03/26/2022] [Revised: 05/05/2022] [Accepted: 05/16/2022] [Indexed: 02/05/2023] Open
Abstract
Beef is a source of essential fatty acids (EFA), linoleic (LA) and alpha-linolenic (ALA) acids, which protect against inflammatory and cardiovascular diseases in humans. However, the intramuscular EFA profile in cattle is a complex and polygenic trait. Thus, this study aimed to identify potential regulatory genes of the essential fatty acid profile in Longissimus thoracis of Nellore cattle finished in feedlot. Forty-four young bulls clustered in four groups of fifteen animals with extreme values for each FA were evaluated through differentially expressed genes (DEG) analysis and two co-expression methodologies (WGCNA and PCIT). We highlight the ECHS1, IVD, ASB5, and ERLIN1 genes and the TF NFIA, indicated in both FA. Moreover, we associate the NFYA, NFYB, PPARG, FASN, and FADS2 genes with LA, and the RORA and ELOVL5 genes with ALA. Furthermore, the functional enrichment analysis points out several terms related to FA metabolism. These findings contribute to our understanding of the genetic mechanisms underlying the beef EFA profile in Nellore cattle finished in feedlot.
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Affiliation(s)
- Gustavo Pimenta Schettini
- School of Agricultural and Veterinary Sciences, São Paulo State University, Jaboticabal 14884-900, SP, Brazil; (W.B.d.S.); (L.G.d.A.); (F.B.)
- Correspondence:
| | - Elisa Peripolli
- School of Veterinary Medicine and Animal Science, University of São Paulo, Pirassununga 13635-900, SP, Brazil; (E.P.); (A.S.C.P.)
| | - Pâmela Almeida Alexandre
- Commonwealth Scientific and Industrial Research Organization, Agriculture & Food, St Lucia, QLD 4067, Australia;
| | - Wellington Bizarria dos Santos
- School of Agricultural and Veterinary Sciences, São Paulo State University, Jaboticabal 14884-900, SP, Brazil; (W.B.d.S.); (L.G.d.A.); (F.B.)
| | - Angélica Simone Cravo Pereira
- School of Veterinary Medicine and Animal Science, University of São Paulo, Pirassununga 13635-900, SP, Brazil; (E.P.); (A.S.C.P.)
| | - Lúcia Galvão de Albuquerque
- School of Agricultural and Veterinary Sciences, São Paulo State University, Jaboticabal 14884-900, SP, Brazil; (W.B.d.S.); (L.G.d.A.); (F.B.)
| | - Fernando Baldi
- School of Agricultural and Veterinary Sciences, São Paulo State University, Jaboticabal 14884-900, SP, Brazil; (W.B.d.S.); (L.G.d.A.); (F.B.)
| | - Rogério Abdallah Curi
- School of Veterinary Medicine and Animal Science, São Paulo State University, Botucatu 18618-681, SP, Brazil;
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Kuang J, Buchon N, Michel K, Scoglio C. A global [Formula: see text] gene co-expression network constructed from hundreds of experimental conditions with missing values. BMC Bioinformatics 2022; 23:170. [PMID: 35534830 PMCID: PMC9082846 DOI: 10.1186/s12859-022-04697-9] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/09/2022] [Accepted: 04/25/2022] [Indexed: 11/21/2022] Open
Abstract
BACKGROUND Gene co-expression networks (GCNs) can be used to determine gene regulation and attribute gene function to biological processes. Different high throughput technologies, including one and two-channel microarrays and RNA-sequencing, allow evaluating thousands of gene expression data simultaneously, but these methodologies provide results that cannot be directly compared. Thus, it is complex to analyze co-expression relations between genes, especially when there are missing values arising for experimental reasons. Networks are a helpful tool for studying gene co-expression, where nodes represent genes and edges represent co-expression of pairs of genes. RESULTS In this paper, we establish a method for constructing a gene co-expression network for the Anopheles gambiae transcriptome from 257 unique studies obtained with different methodologies and experimental designs. We introduce the sliding threshold approach to select node pairs with high Pearson correlation coefficients. The resulting network, which we name AgGCN1.0, is robust to random removal of conditions and has similar characteristics to small-world and scale-free networks. Analysis of network sub-graphs revealed that the core is largely comprised of genes that encode components of the mitochondrial respiratory chain and the ribosome, while different communities are enriched for genes involved in distinct biological processes. CONCLUSION Analysis of the network reveals that both the architecture of the core sub-network and the network communities are based on gene function, supporting the power of the proposed method for GCN construction. Application of network science methodology reveals that the overall network structure is driven to maximize the integration of essential cellular functions, possibly allowing the flexibility to add novel functions.
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Affiliation(s)
- Junyao Kuang
- Department of Electrical and Computer Engineering, Kansas State University, Manhattan, KS 66506 USA
| | - Nicolas Buchon
- Department of Entomology, Cornell Institute of Host-Microbe Interactions and Disease, Cornell University, Ithaca, NY 14853 USA
| | - Kristin Michel
- Division of Biology, Kansas State University, Manhattan, KS 66506 USA
| | - Caterina Scoglio
- Department of Electrical and Computer Engineering, Kansas State University, Manhattan, KS 66506 USA
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Prediction of Metabolic Profiles from Transcriptomics Data in Human Cancer Cell Lines. Int J Mol Sci 2022; 23:ijms23073867. [PMID: 35409231 PMCID: PMC8998886 DOI: 10.3390/ijms23073867] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/28/2022] [Revised: 03/24/2022] [Accepted: 03/29/2022] [Indexed: 02/01/2023] Open
Abstract
The Metabolome and Transcriptome are mutually communicating within cancer cells, and this interplay is translated into the existence of quantifiable correlation structures between gene expression and metabolite abundance levels. Studying these correlations could provide a novel venue of understanding cancer and the discovery of novel biomarkers and pharmacological strategies, as well as laying the foundation for the prediction of metabolite quantities by leveraging information from the more widespread transcriptomics data. In the current paper, we investigate the correlation between gene expression and metabolite levels in the Cancer Cell Line Encyclopedia dataset, building a direct correlation network between the two molecular ensembles. We show that a metabolite/transcript correlation network can be used to predict metabolite levels in different samples and datasets, such as the NCI-60 cancer cell line dataset, both on a sample-by-sample basis and in differential contrasts. We also show that metabolite levels can be predicted in principle on any sample and dataset for which transcriptomics data are available, such as the Cancer Genome Atlas (TCGA).
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50
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Diniz WJ, Reynolds LP, Ward AK, Borowicz PP, Sedivec KK, McCarthy KL, Kassetas CJ, Baumgaertner F, Kirsch JD, Dorsam ST, Neville TL, Forcherio JC, Scott RR, Caton JS, Dahlen CR. Untangling the placentome gene network of beef heifers in early gestation. Genomics 2022; 114:110274. [DOI: 10.1016/j.ygeno.2022.110274] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/24/2021] [Revised: 01/10/2022] [Accepted: 01/21/2022] [Indexed: 11/04/2022]
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