Next Gen Porcine Genetics and Genomics: Implications for Health

A special issue of Genes (ISSN 2073-4425). This special issue belongs to the section "Animal Genetics and Genomics".

Deadline for manuscript submissions: closed (31 January 2020) | Viewed by 12111

Special Issue Editors


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Guest Editor
Department of Animal Sciences, University of Illinois at Urbana-Champaign, Champaign, IL, USA
Interests: pancreatic ductal adenocarcinoma; pig genetics; pig as a biomedical cancer model

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Guest Editor
Department of Radiology, University of Illinois at Chicago, Chicago, IL 60607, USA
Interests: methylation; epigenetic; animal model; pig; genetic; porcine

Special Issue Information

Dear Colleagues,

This Genes proposal provides futuristic perspectives with respect to emerging tools and techniques related to porcine genetics and genomics, with an emphasis on biomedical applications and implications for health. The pig (Sus scrofa) was domesticated ∼10,000 years ago in multiple locations across Eurasia and since then has become an invaluable agricultural species. In addition, its use in biomedical research and medical training is well established and anticipated to increase with the emergence of gene-editing technologies for development of new human disease models. The recent completion of an improved porcine reference genome (Sscrofa11.1) provides an opportunity for the porcine genetics and genomics community to improve its understanding of the genetic and epigenetic mechanisms underlying agriculturally and biomedically relevant phenotypes. This high-quality annotated reference genome sequence has already proven to be a critical framework for comparing individual genomes. Furthermore, the genome sequence also provides a valuable resource enabling effective uses of pigs, both in agricultural production and biomedical research. This Special Issue will focus on the continued development of tools, methodologies, and databases required to advance our knowledge of porcine genetics and genomics. Contributions to this call will expand our knowledge of the genomic and epigenomic mechanisms underlying agricultural and biomedically relevant phenotypes. The scope of topics includes development of novel porcine genomic tools, integration of multi-omics analyses, utilization of machine learning approaches, elucidation of molecular mechanisms underlying relevant phenotypes, and improving health for both pigs and humans. Comparative genomic analysis with humans and other relevant agricultural and biomedical species will also be covered, as will the development of genetically edited pigs for agricultural and biomedical purposes.

Dr. Lawrence Schook
Dr. Kyle Schachtschneider
Guest Editors

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Keywords

Pigs; Health; Biomedical Models; Genomics; Epigenomics; Gene editing

Published Papers (4 papers)

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Research

19 pages, 3307 KiB  
Article
Altered Hippocampal Epigenetic Regulation Underlying Reduced Cognitive Development in Response to Early Life Environmental Insults
by Kyle M. Schachtschneider, Michael E. Welge, Loretta S. Auvil, Sulalita Chaki, Laurie A. Rund, Ole Madsen, Monica R.P. Elmore, Rodney W. Johnson, Martien A.M. Groenen and Lawrence B. Schook
Genes 2020, 11(2), 162; https://doi.org/10.3390/genes11020162 - 4 Feb 2020
Cited by 8 | Viewed by 3008
Abstract
The hippocampus is involved in learning and memory and undergoes significant growth and maturation during the neonatal period. Environmental insults during this developmental timeframe can have lasting effects on brain structure and function. This study assessed hippocampal DNA methylation and gene transcription from [...] Read more.
The hippocampus is involved in learning and memory and undergoes significant growth and maturation during the neonatal period. Environmental insults during this developmental timeframe can have lasting effects on brain structure and function. This study assessed hippocampal DNA methylation and gene transcription from two independent studies reporting reduced cognitive development stemming from early life environmental insults (iron deficiency and porcine reproductive and respiratory syndrome virus (PRRSv) infection) using porcine biomedical models. In total, 420 differentially expressed genes (DEGs) were identified between the reduced cognition and control groups, including genes involved in neurodevelopment and function. Gene ontology (GO) terms enriched for DEGs were associated with immune responses, angiogenesis, and cellular development. In addition, 116 differentially methylated regions (DMRs) were identified, which overlapped 125 genes. While no GO terms were enriched for genes overlapping DMRs, many of these genes are known to be involved in neurodevelopment and function, angiogenesis, and immunity. The observed altered methylation and expression of genes involved in neurological function suggest reduced cognition in response to early life environmental insults is due to altered cholinergic signaling and calcium regulation. Finally, two DMRs overlapped with two DEGs, VWF and LRRC32, which are associated with blood brain barrier permeability and regulatory T-cell activation, respectively. These results support the role of altered hippocampal DNA methylation and gene expression in early life environmentally-induced reductions in cognitive development across independent studies. Full article
(This article belongs to the Special Issue Next Gen Porcine Genetics and Genomics: Implications for Health)
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11 pages, 1845 KiB  
Article
Identification of ADPKD-Related Genes and Pathways in Cells Overexpressing PKD2
by Zhe Zhang, Yanna Dang, Zizengceng Wang, Huanan Wang, Yuchun Pan and Jin He
Genes 2020, 11(2), 122; https://doi.org/10.3390/genes11020122 - 22 Jan 2020
Cited by 6 | Viewed by 2986
Abstract
Consistent with the gene dosage effect hypothesis, renal cysts can arise in transgenic murine models overexpressing either PKD1 or PKD2, which are causal genes for autosomal dominant polycystic kidney disease (ADPKD). To determine whether PKD gene overexpression is a universal mechanism driving [...] Read more.
Consistent with the gene dosage effect hypothesis, renal cysts can arise in transgenic murine models overexpressing either PKD1 or PKD2, which are causal genes for autosomal dominant polycystic kidney disease (ADPKD). To determine whether PKD gene overexpression is a universal mechanism driving cystogenesis or is merely restricted to rodents, other animal models are required. Previously, we failed to observe any renal cysts in a transgenic porcine model of PKD2 overexpression partially due to epigenetic silencing of the transgene. Thus, to explore the feasibility of porcine models and identify potential genes/pathways affected in ADPKD, LLC-PK1 cells with high PKD2 expression were generated. mRNA sequencing (RNA-seq) was performed, and MYC, IER3, and ADM were found to be upregulated genes common to the different PKD2 overexpression cell models. MYC is a well-characterized factor contributing to cystogenesis, and ADM is a biomarker for chronic kidney disease. Thus, these genes might be indicators of disease progression. Additionally, some ADPKD-associated pathways, e.g., the mitogen-activated protein kinase (MAPK) pathway, were enriched in the cells. Moreover, gene ontology (GO) analysis demonstrated that proliferation, apoptosis, and cell cycle regulation, which are hallmarks of ADPKD, were altered. Therefore, our experiment identified some biomarkers or indicators of ADPKD, indicating that high PKD2 expression would likely drive cystogenesis in future porcine models. Full article
(This article belongs to the Special Issue Next Gen Porcine Genetics and Genomics: Implications for Health)
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12 pages, 2149 KiB  
Article
Suppression of Notch Signaling Stimulates Progesterone Synthesis by Enhancing the Expression of NR5A2 and NR2F2 in Porcine Granulosa Cells
by Rihong Guo, Fang Chen and Zhendan Shi
Genes 2020, 11(2), 120; https://doi.org/10.3390/genes11020120 - 22 Jan 2020
Cited by 8 | Viewed by 2675
Abstract
The conserved Notch pathway is reported to be involved in progesterone synthesis and secretion; however, the exact effects remain controversial. To determine the role and potential mechanisms of the Notch signaling pathway in progesterone biosynthesis in porcine granulosa cells (pGCs), we first used [...] Read more.
The conserved Notch pathway is reported to be involved in progesterone synthesis and secretion; however, the exact effects remain controversial. To determine the role and potential mechanisms of the Notch signaling pathway in progesterone biosynthesis in porcine granulosa cells (pGCs), we first used a pharmacological γ-secretase inhibitor, N-(N-(3,5-difluorophenacetyl-l-alanyl))-S-phenylglycine t-butyl ester (DAPT), to block the Notch pathway in cultured pGCs and then evaluated the expression of genes in the progesterone biosynthesis pathway and key transcription factors (TFs) regulating steroidogenesis. We found that DAPT dose- and time-dependently increased progesterone secretion. The expression of steroidogenic proteins NPC1 and StAR and two TFs, NR5A2 and NR2F2, was significantly upregulated, while the expression of HSD3B was significantly downregulated. Furthermore, knockdown of both NR5A2 and NR2F2 with specific siRNAs blocked the upregulatory effects of DAPT on progesterone secretion and reversed the effects of DAPT on the expression of NPC1, StAR, and HSD3B. Moreover, knockdown of NR5A2 and NR2F2 stimulated the expression of Notch3. In conclusion, the inhibition of Notch signaling stimulated progesterone secretion by enhancing the expression of NPC1 and StAR, and the two TFs NR5A2 and NR2F2 acted as downstream TFs of Notch signaling in regulating progesterone synthesis. Full article
(This article belongs to the Special Issue Next Gen Porcine Genetics and Genomics: Implications for Health)
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18 pages, 3711 KiB  
Article
Source of Dietary Fat in Pig Diet Affects Adipose Expression of Genes Related to Cancer, Cardiovascular, and Neurodegenerative Diseases
by Maria Oczkowicz, Tomasz Szmatoła and Małgorzata Świątkiewicz
Genes 2019, 10(12), 948; https://doi.org/10.3390/genes10120948 - 20 Nov 2019
Cited by 6 | Viewed by 3114
Abstract
It has been known for many years that excessive consumption of saturated fats has proatherogenic properties, contrary to unsaturated fats. However, the molecular mechanism covering these effects is not fully understood. In this paper, we aimed to identify differentially expressed genes (DEGs) using [...] Read more.
It has been known for many years that excessive consumption of saturated fats has proatherogenic properties, contrary to unsaturated fats. However, the molecular mechanism covering these effects is not fully understood. In this paper, we aimed to identify differentially expressed genes (DEGs) using RNA-sequencing, following feeding pigs with different sources of fat. After comparison of adipose samples from three dietary groups (rapeseed oil (n = 6), beef tallow (n = 5), coconut oil (n = 5)), we identified 29 DEGs (adjusted p-value < 0.05, fold change > 1.3) between beef tallow and rapeseed oil and 2 genes between coconut oil and rapeseed oil groups. No differentially expressed genes were observed between coconut oil and beef tallow groups. Almost all 29 DEGs between rapeseed oil and beef tallow groups are connected to neurodegenerative, cardiovascular diseases, or cancer (e.g., PLAU, CYBB, NCF2, ZNF217, CHAC1, CTCFL). Functional analysis of these genes revealed that they are associated with fluid shear stress response, complement and coagulation cascade, ROS signaling, neurogenesis, and regulation of protein binding and protein catabolic processes. Furthermore, gene set enrichment analysis (GSEA) of the whole datasets from all three comparisons suggests that both beef tallow and coconut oil may trigger changes in the expression level of genes crucial in the pathogenesis of civilization diseases. Full article
(This article belongs to the Special Issue Next Gen Porcine Genetics and Genomics: Implications for Health)
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