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Vijayakumar V, Gaba RC, Huang YH, Davis I, Roman R, Guzman G, Lokken RP, Schachtschneider KM. Hepatocellular Carcinoma Epigenetic Patterns Correspond to Differences in Ethnoracial Status and Treatment Response in a Single-Center Retrospective Study. J Vasc Interv Radiol 2024; 35:731-743.e36. [PMID: 38320622 DOI: 10.1016/j.jvir.2024.01.029] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/07/2023] [Revised: 01/16/2024] [Accepted: 01/30/2024] [Indexed: 02/08/2024] Open
Abstract
PURPOSE To correlate epigenetic patterns with ethnoracial status and locoregional therapy (LRT) response in patients with hepatocellular carcinoma (HCC). MATERIALS AND METHODS DNA and RNA were extracted from 47 distinct formalin-fixed paraffin-embedded tumor samples from 42 patients with HCC (n = 14 Black, n = 19 White, n = 9 Hispanic). LRT response was determined using computed tomography (CT) or magnetic resonance (MR) imaging 3 months posttreatment of 35 tumors (n = 22 complete response, n = 13 retreatment candidates). RNA expression and DNA methylation were used to stratify patients by ethnoracial status and treatment response using partial least-squares discriminant analysis (PLS-DA). Results were validated using hierarchical clustering. Ingenuity pathway analysis was performed to identify upstream regulators and pathways. RESULTS PLS-DA identified 100 genes and 12 methylated regions that differentiated tumors from Black from White/Hispanic patients. Hierarchical clustering clustered samples with the top 16 genes or the top 5 methylation regions. Dysregulated pathways included adrenomedullin pathway (P = .030), EIF2 signaling (P = .007), and several metabolic pathways. AGTR1 (log2fold = 1.59) and GSTM3 (log2fold = 2.53) represented potential differentially expressed therapeutic targets. PLS-DA identified 100 genes and 150 methylation regions that differentiated between complete responders and retreatment candidates. Hierarchical clustering clustered samples with the top 30 genes or the top 13 methylation regions. Dysregulated pathways included metabolic and DNA repair-related pathways. ASAP2 (log2fold = 0.29) and RAD50 (log2fold = 0.22) represented potential differentially expressed therapeutic targets. CONCLUSIONS Variation in gene expression and DNA methylation patterns in patients with HCC corresponded to ethnoracial status and LRT response. These initial results suggest tumor profiling has the potential to close ethnoracial disparities and improve treatment stratification.
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Affiliation(s)
- Vishwaarth Vijayakumar
- Carle Illinois College of Medicine, University of Illinois at Urbana-Champaign, Urbana, Illinois
| | - Ron C Gaba
- Department of Radiology, University of Illinois at Chicago, Chicago, Illinois
| | - Yu-Hui Huang
- Department of Radiology, University of Illinois at Chicago, Chicago, Illinois
| | - Isaiah Davis
- Department of Radiology, University of Illinois at Chicago, Chicago, Illinois
| | - Ricardo Roman
- Department of Radiology, University of Illinois at Chicago, Chicago, Illinois
| | - Grace Guzman
- Department of Pathology, University of Illinois at Chicago, Chicago, Illinois
| | - R Peter Lokken
- Department of Radiology, University of Illinois at Chicago, Chicago, Illinois
| | - Kyle M Schachtschneider
- Department of Radiology, University of Illinois at Chicago, Chicago, Illinois; Department of Biochemistry and Molecular Genetics, University of Illinois at Chicago, Chicago, Illinois; National Center for Supercomputing Applications, University of Illinois at Urbana-Champaign, Urbana, Illinois.
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Remzső G, Kovács V, Tóth-Szűki V, Domoki F. The effects of CO 2 levels and body temperature on brain interstitial pH alterations during the induction of hypoxic-ischemic encephalopathy in newborn pigs. Heliyon 2024; 10:e28607. [PMID: 38571587 PMCID: PMC10988055 DOI: 10.1016/j.heliyon.2024.e28607] [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: 09/06/2023] [Revised: 03/21/2024] [Accepted: 03/21/2024] [Indexed: 04/05/2024] Open
Abstract
Brain interstitial pH (pHbrain) alterations play a crucial role in the development of hypoxic-ischemic (HI) encephalopathy (HIE) caused by asphyxia in neonates. The newborn pig is one of the most suitable large animal models for studying HIE, however, compared to rats, experimental data on pHbrain alterations during HIE induction are limited. The major objective of the present study was thus to compare pHbrain changes during HIE development induced by experimental normocapnic hypoxia (H) or asphyxia (A), elicited with ventilation of a gas mixture containing 6%O2 or 6%O2/20%CO2, respectively for 20 min, under either normothermia (NT) or hypothermia (HT) (38.5 ± 0.5 °C or 33.5 ± 0.5 °C core temperature, respectively) in anesthetized piglets yielding four groups: H-NT, A-NT, H-HT, and A-HT. pHbrain changes during HI stress and the 60 min reoxygenation period were measured using a pH-selective microelectrode inserted into the parietal cortex through an open cranial window. In all groups, the pHbrain response to HI stress was acidosis, at the nadir pHbrain values dropped from the baseline of 7.27 ± 0.02 to H-NT:5.93 ± 0.30, A-NT:5.90 ± 0.52, H-HT:6.81 ± 0.27, and A-HT:6.27 ± 0.24 indicating that (1) H and A elicited similar, severe brain acidosis under NT greatly exceeding pH changes in arterial blood (pHa dropped to 7.24 ± 0.07 and 6.78 ± 0.03 from 7.52 ± 0.06 and 7.50 ± 0.05, respectively), and (2) HT ameliorated more the brain acidosis induced by H than by A. In all four groups, pHbrain was restored to baseline values without an alkalotic overshoot during the observed reoxygenation, Our findings suggest that under NT either H or A - both commonly employed HI stresses to elicit HIE in piglet models - would result in a similar acidotic pHbrain response without an alkalotic component either during the HI stress or the early reoxygenation period.
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Affiliation(s)
- Gábor Remzső
- Department of Physiology, Albert Szent-Györgyi Medical School, University of Szeged, Szeged, Hungary
| | - Viktória Kovács
- Department of Physiology, Albert Szent-Györgyi Medical School, University of Szeged, Szeged, Hungary
| | - Valéria Tóth-Szűki
- Department of Physiology, Albert Szent-Györgyi Medical School, University of Szeged, Szeged, Hungary
| | - Ferenc Domoki
- Department of Physiology, Albert Szent-Györgyi Medical School, University of Szeged, Szeged, Hungary
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3
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Segatto NV, Simões LD, Bender CB, Sousa FS, Oliveira TL, Paschoal JDF, Pacheco BS, Lopes I, Seixas FK, Qazi A, Thomas FM, Chaki S, Robertson N, Newsom J, Patel S, Rund LA, Jordan LR, Bolt C, Schachtschneider KM, Schook LB, Collares TV. Oncopig bladder cancer cells recapitulate human bladder cancer treatment responses in vitro. Front Oncol 2024; 14:1323422. [PMID: 38469237 PMCID: PMC10926022 DOI: 10.3389/fonc.2024.1323422] [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: 10/19/2023] [Accepted: 01/05/2024] [Indexed: 03/13/2024] Open
Abstract
Introduction Bladder cancer is a common neoplasia of the urinary tract that holds the highest cost of lifelong treatment per patient, highlighting the need for a continuous search for new therapies for the disease. Current bladder cancer models are either imperfect in their ability to translate results to clinical practice (mouse models), or rare and not inducible (canine models). Swine models are an attractive alternative to model the disease due to their similarities with humans on several levels. The Oncopig Cancer Model has been shown to develop tumors that closely resemble human tumors. However, urothelial carcinoma has not yet been studied in this platform. Methods We aimed to develop novel Oncopig bladder cancer cell line (BCCL) and investigate whether these urothelial swine cells mimic human bladder cancer cell line (5637 and T24) treatment-responses to cisplatin, doxorubicin, and gemcitabine in vitro. Results Results demonstrated consistent treatment responses between Oncopig and human cells in most concentrations tested (p>0.05). Overall, Oncopig cells were more predictive of T24 than 5637 cell therapeutic responses. Microarray analysis also demonstrated similar alterations in expression of apoptotic (GADD45B and TP53INP1) and cytoskeleton-related genes (ZMYM6 and RND1) following gemcitabine exposure between 5637 (human) and Oncopig BCCL cells, indicating apoptosis may be triggered through similar signaling pathways. Molecular docking results indicated that swine and humans had similar Dg values between the chemotherapeutics and their target proteins. Discussion Taken together, these results suggest the Oncopig could be an attractive animal to model urothelial carcinoma due to similarities in in vitro therapeutic responses compared to human cells.
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Affiliation(s)
- Natália V. Segatto
- Technology Development Center, Laboratory of Cancer Biotechnology, Federal University of Pelotas, Pelotas, Rio Grande do Sul, Brazil
| | - Lucas D. Simões
- Technology Development Center, Laboratory of Cancer Biotechnology, Federal University of Pelotas, Pelotas, Rio Grande do Sul, Brazil
| | - Camila B. Bender
- Technology Development Center, Laboratory of Cancer Biotechnology, Federal University of Pelotas, Pelotas, Rio Grande do Sul, Brazil
| | - Fernanda S. Sousa
- Technology Development Center, Laboratory of Cancer Biotechnology, Federal University of Pelotas, Pelotas, Rio Grande do Sul, Brazil
| | - Thais L. Oliveira
- Technology Development Center, Laboratory of Cancer Biotechnology, Federal University of Pelotas, Pelotas, Rio Grande do Sul, Brazil
| | - Júlia D. F. Paschoal
- Technology Development Center, Laboratory of Cancer Biotechnology, Federal University of Pelotas, Pelotas, Rio Grande do Sul, Brazil
| | - Bruna S. Pacheco
- Technology Development Center, Laboratory of Cancer Biotechnology, Federal University of Pelotas, Pelotas, Rio Grande do Sul, Brazil
| | - Isadora Lopes
- Technology Development Center, Laboratory of Cancer Biotechnology, Federal University of Pelotas, Pelotas, Rio Grande do Sul, Brazil
| | - Fabiana K. Seixas
- Technology Development Center, Laboratory of Cancer Biotechnology, Federal University of Pelotas, Pelotas, Rio Grande do Sul, Brazil
| | - Aisha Qazi
- Department of Animal Sciences, University of Illinois, Urbana, IL, United States
| | - Faith M. Thomas
- Department of Animal Sciences, University of Illinois, Urbana, IL, United States
| | - Sulalita Chaki
- Department of Animal Sciences, University of Illinois, Urbana, IL, United States
| | | | | | - Shovik Patel
- Department of Animal Sciences, University of Illinois, Urbana, IL, United States
| | - Laurie A. Rund
- Department of Animal Sciences, University of Illinois, Urbana, IL, United States
| | - Luke R. Jordan
- Department of Animal Sciences, University of Illinois, Urbana, IL, United States
- Sus Clinicals Inc., Chicago, IL, United States
| | - Courtni Bolt
- Department of Animal Sciences, University of Illinois, Urbana, IL, United States
- Sus Clinicals Inc., Chicago, IL, United States
| | | | - Lawrence B. Schook
- Department of Animal Sciences, University of Illinois, Urbana, IL, United States
- Sus Clinicals Inc., Chicago, IL, United States
| | - Tiago V. Collares
- Technology Development Center, Laboratory of Cancer Biotechnology, Federal University of Pelotas, Pelotas, Rio Grande do Sul, Brazil
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Amrein Almira A, Chen MW, El Demerdash N, Javdan C, Park D, Lee JK, Martin LJ. Proteasome localization and activity in pig brain and in vivo small molecule screening for activators. Front Cell Neurosci 2024; 18:1353542. [PMID: 38469354 PMCID: PMC10925635 DOI: 10.3389/fncel.2024.1353542] [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: 12/10/2023] [Accepted: 02/06/2024] [Indexed: 03/13/2024] Open
Abstract
Introduction Loss of proteasome function, proteinopathy, and proteotoxicity may cause neurodegeneration across the human lifespan in several forms of brain injury and disease. Drugs that activate brain proteasomes in vivo could thus have a broad therapeutic impact in neurology. Methods Using pigs, a clinically relevant large animal with a functionally compartmental gyrencephalic cerebral cortex, we evaluated the localization and biochemical activity of brain proteasomes and tested the ability of small molecules to activate brain proteasomes. Results By Western blotting, proteasome protein subunit PSMB5 and PSMA3 levels were similar in different pig brain regions. Immunohistochemistry for PSMB5 showed localization in the cytoplasm (diffuse and particulate) and nucleus (cytoplasm < nucleus). Some PSMB5 immunoreactivity was colocalized with mitochondrial (voltage-gated anion channel and cyclophilin D) and cell death (Aven) proteins in the neuronal soma and neuropil in the neocortex of pig and human brains. In the nucleus, PSMB5 immunoreactivity was diffuse, particulate, and clustered, including perinucleolar decorations. By fluorogenic assay, proteasome chymotrypsin-like activities (CTL) in crude tissue soluble fractions were generally similar within eight different pig brain regions. Proteasome CTL activity in the hippocampus was correlated with activity in nasal mucosa biopsies. In pilot analyses of subcellular fractions of pig cerebral cortex, proteasome CTL activity was highest in the cytosol and then ~50% lower in nuclear fractions; ~15-20% of total CTL activity was in pure mitochondrial fractions. With in-gel activity assay, 26S-singly and -doubly capped proteasomes were the dominant forms in the pig cerebral cortex. With a novel in situ histochemical activity assay, MG132-inhibitable proteasome CTL activity was localized to the neuropil, as a mosaic, and to cell bodies, nuclei, and centrosome-like perinuclear satellites. In piglets treated intravenously with pyrazolone derivative and chlorpromazine over 24 h, brain proteasome CTL activity was modestly increased. Discussion This study shows that the proteasome in the pig brain has relative regional uniformity, prominent nuclear and perinuclear presence with catalytic activity, a mitochondrial association with activity, 26S-single cap dominance, and indications from small molecule systemic administration of pyrazolone derivative and chlorpromazine that brain proteasome function appears safely activable.
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Affiliation(s)
- Adriana Amrein Almira
- Department of Anesthesiology and Critical Care Medicine, Johns Hopkins University School of Medicine, Baltimore, MD, United States
| | - May W. Chen
- Departments of Pediatrics, Johns Hopkins University School of Medicine, Baltimore, MD, United States
| | - Nagat El Demerdash
- Department of Anesthesiology and Critical Care Medicine, Johns Hopkins University School of Medicine, Baltimore, MD, United States
| | - Cameron Javdan
- Department of Anesthesiology and Critical Care Medicine, Johns Hopkins University School of Medicine, Baltimore, MD, United States
| | - Dongseok Park
- Department of Pathology, Johns Hopkins University School of Medicine, Baltimore, MD, United States
| | - Jennifer K. Lee
- Department of Anesthesiology and Critical Care Medicine, Johns Hopkins University School of Medicine, Baltimore, MD, United States
| | - Lee J. Martin
- Department of Anesthesiology and Critical Care Medicine, Johns Hopkins University School of Medicine, Baltimore, MD, United States
- Department of Pathology, Johns Hopkins University School of Medicine, Baltimore, MD, United States
- Department of Neuroscience, Johns Hopkins University School of Medicine, Baltimore, MD, United States
- Pathobiology Graduate Training Program, Johns Hopkins University School of Medicine, Baltimore, MD, United States
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5
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Benjamin NR, Crooijmans RPMA, Jordan LR, Bolt CR, Schook LB, Schachtschneider KM, Groenen MAM, Roca AL. Swine global genomic resources: insights into wild and domesticated populations. Mamm Genome 2023; 34:520-530. [PMID: 37805667 DOI: 10.1007/s00335-023-10012-5] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/02/2023] [Accepted: 07/25/2023] [Indexed: 10/09/2023]
Abstract
Suids, both domesticated and wild, are found on all continents except for Antarctica and provide valuable food resources for humans in addition to serving as important models for biomedical research. Continuing advances in genome sequencing have allowed researchers to compare the genomes from diverse populations of suids helping to clarify their evolution and dispersal. Further analysis of these samples may provide clues to improve disease resistance/resilience and productivity in domestic suids as well as better ways of classifying and conserving genetic diversity within wild and captive suids. Collecting samples from diverse populations of suids is resource intensive and may negatively impact endangered populations. Here we catalog extensive tissue and DNA samples from suids in collections in both Europe and North America. We include samples that have previously been used for whole genome sequencing, targeted DNA sequencing, RNA sequencing, and reduced representation bisulfite sequencing (RRBS). This work provides an important centralized resource for researchers who wish to access published databases.
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Affiliation(s)
- Neal R Benjamin
- The Program in Ecology, Evolution and Conservation Biology, University of Illinois Urbana-Champaign, Urbana, IL, USA
| | | | - Luke R Jordan
- Department of Radiology, University of Illinois at Chicago, Chicago, IL, USA
| | - Courtni R Bolt
- Department of Animal Sciences, University of Illinois Urbana-Champaign, Urbana, IL, USA
| | - Lawrence B Schook
- Department of Animal Sciences, University of Illinois Urbana-Champaign, Urbana, IL, USA
- National Center for Supercomputing Applications, University of Illinois at Chicago, Chicago, IL, USA
| | - Kyle M Schachtschneider
- National Center for Supercomputing Applications, University of Illinois at Chicago, Chicago, IL, USA.
- Department of Biochemistry and Molecular Genetics, University of Illinois at Chicago, Chicago, IL, USA.
- Department of Radiology, University of Illinois at Chicago, Chicago, IL, USA.
| | - Martien A M Groenen
- Animal Breeding and Genomics, Wageningen University and Research, Wageningen, The Netherlands
| | - Alfred L Roca
- The Program in Ecology, Evolution and Conservation Biology, University of Illinois Urbana-Champaign, Urbana, IL, USA.
- Department of Animal Sciences, University of Illinois Urbana-Champaign, Urbana, IL, USA.
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de Vos J, Crooijmans RP, Derks MF, Kloet SL, Dibbits B, Groenen MA, Madsen O. Detailed molecular and epigenetic characterization of the pig IPEC-J2 and chicken SL-29 cell lines. iScience 2023; 26:106252. [PMID: 36936794 PMCID: PMC10018572 DOI: 10.1016/j.isci.2023.106252] [Citation(s) in RCA: 1] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/27/2022] [Revised: 12/05/2022] [Accepted: 02/16/2023] [Indexed: 02/22/2023] Open
Abstract
The pig IPEC-J2 and chicken SL-29 cell lines are of interest because of their untransformed nature and wide use in functional studies. Molecular characterization of these cell lines is important to gain insight into possible molecular aberrations. The aim of this paper is to provide a molecular and epigenetic characterization of the IPEC-J2 and SL-29 cell lines, a cell-line reference for the FAANG community, and future biomedical research. Whole genome sequencing, gene expression, DNA methylation, chromatin accessibility, and ChIP-seq of four histone marks (H3K4me1, H3K4me3, H3K27ac, H3K27me3) and an insulator (CTCF) are used to achieve these aims. Heteroploidy (aneuploidy) of various chromosomes was observed from whole genome sequencing analysis in both cell lines. Furthermore, higher gene expression for genes located on chromosomes with aneuploidy in comparison to diploid chromosomes was observed. Regulatory complexity of gene expression, DNA methylation, and chromatin accessibility was investigated through an integrative approach.
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Affiliation(s)
- Jani de Vos
- Animal Breeding and Genomics, Wageningen University & Research, Wageningen 6708PB, the Netherlands
- Corresponding author
| | | | - Martijn F.L. Derks
- Animal Breeding and Genomics, Wageningen University & Research, Wageningen 6708PB, the Netherlands
| | - Susan L. Kloet
- Human Genetics, Leids Universitair Medisch Centrum, Leiden 2333ZC, the Netherlands
| | - Bert Dibbits
- Animal Breeding and Genomics, Wageningen University & Research, Wageningen 6708PB, the Netherlands
| | - Martien A.M. Groenen
- Animal Breeding and Genomics, Wageningen University & Research, Wageningen 6708PB, the Netherlands
| | - Ole Madsen
- Animal Breeding and Genomics, Wageningen University & Research, Wageningen 6708PB, the Netherlands
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7
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Xu L, Shi Z, Li H, He J, Chen B, Tao Z, Tian Y, Chen L, Li G, Tao Z, Gu T, Xu W, Lu L. Genome-wide DNA methylation differences between conservation and breeding populations of Shaoxing ducks. Heliyon 2022; 8:e11644. [DOI: 10.1016/j.heliyon.2022.e11644] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/20/2022] [Revised: 07/28/2022] [Accepted: 11/10/2022] [Indexed: 11/18/2022] Open
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Epigenetic regulation of fetal brain development in pig. Gene 2022; 844:146823. [PMID: 35988784 DOI: 10.1016/j.gene.2022.146823] [Citation(s) in RCA: 3] [Impact Index Per Article: 1.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/22/2022] [Revised: 07/27/2022] [Accepted: 08/15/2022] [Indexed: 02/01/2023]
Abstract
How fetal brain development is regulated at the molecular level is not well understood. Due to ethical challenges associated with research on the human fetus, large animals particularly pigs are increasingly used to study development and disorders of fetal brain. The pig fetal brain grows rapidly during the last ∼ 50 days before birth which is around day 60 (d60) of pig gestation. But what regulates the onset of accelerated growth of the brain is unknown. The current study tests the hypothesis that epigenetic alteration around d60 is involved in the onset of rapid growth of fetal brain of pig. To test this hypothesis, DNA methylation changes of fetal brain was assessed in a genome-wide manner by Enzymatic Methyl-seq (EM-seq) during two gestational periods (GP): d45 vs. d60 (GP1) and d60 vs. d90 (GP2). The cytosine-guanine (CpG) methylation data was analyzed in an integrative manner with the RNA-seq data generated from the same brain samples from our earlier study. A neural network based modeling approach was implemented to learn changes in methylation patterns of the differentially expressed genes, and then predict methylations of the brain in a genome-wide manner during rapid growth. This approach identified specific methylations that changed in a mutually informative manner during rapid growth of the fetal brain. These methylations were significantly overrepresented in specific genic as well as intergenic features including CpG islands, introns, and untranslated regions. In addition, sex-bias methylations of known single nucleotide polymorphic sites were also identified in the fetal brain ide during rapid growth.
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Tian H, He Y, Xue Y, Gao YQ. Expression regulation of genes is linked to their CpG density distributions around transcription start sites. Life Sci Alliance 2022; 5:5/9/e202101302. [PMID: 35580989 PMCID: PMC9113945 DOI: 10.26508/lsa.202101302] [Citation(s) in RCA: 6] [Impact Index Per Article: 3.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/17/2021] [Revised: 05/07/2022] [Accepted: 05/09/2022] [Indexed: 11/24/2022] Open
Abstract
The CpG dinucleotide and its methylation behaviors play vital roles in gene regulation. Previous studies have divided genes into several categories based on the CpG intensity around transcription starting sites and found that housekeeping genes tend to possess high CpG density, whereas tissue-specific genes are generally characterized by low CpG density. In this study, we investigated how the CpG density distribution of a gene affects its transcription and regulation pattern. Based on the CpG density distribution around transcription starting site, by means of a semi-supervised neural network we designed, which took data augmentation into account, we divided the human genes into three categories, and genes within each cluster shared similar CpG density distribution. Not only sequence properties, these different clusters exhibited distinctly different structural features, regulatory mechanisms, correlation patterns between the expression level and CpG/TpG density, and expression and epigenetic mark variations during tumorigenesis. For instance, the activation of cluster 3 genes relies more on 3D genome reorganization, compared with cluster 1 and 2 genes, whereas cluster 2 genes showed the strongest correlation between gene expression and H3K27me3. Genes exhibiting uncoupled correlation between gene regulation and histone modifications are mainly in cluster 3. These results emphasized that the usage of epigenetic marks in gene regulation is partially rooted in the sequence property of genes such as their CpG density distribution and explained to some extent why the relation between epigenetic marks and gene expression is controversial.
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Affiliation(s)
- Hao Tian
- Beijing National Laboratory for Molecular Sciences, College of Chemistry and Molecular Engineering, Peking University, Beijing, China
| | - Yueying He
- Beijing National Laboratory for Molecular Sciences, College of Chemistry and Molecular Engineering, Peking University, Beijing, China
| | - Yue Xue
- Beijing National Laboratory for Molecular Sciences, College of Chemistry and Molecular Engineering, Peking University, Beijing, China
| | - Yi Qin Gao
- Beijing National Laboratory for Molecular Sciences, College of Chemistry and Molecular Engineering, Peking University, Beijing, China .,Biomedical Pioneering Innovation Center (BIOPIC), Peking University, Beijing, China.,Beijing Advanced Innovation Center for Genomics (ICG), Peking University, Beijing, China
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10
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Ma J, Zhang L, Huang Y, Shen F, Wu H, Yang Z, Hou R, Song Z, Yue B, Zhang X. Epigenomic profiling indicates a role for DNA methylation in the postnatal liver and pancreas development of giant pandas. Genomics 2022; 114:110342. [PMID: 35306168 DOI: 10.1016/j.ygeno.2022.110342] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/27/2021] [Revised: 02/14/2022] [Accepted: 03/13/2022] [Indexed: 01/14/2023]
Abstract
Giant pandas are unique within Carnivora with a strict bamboo diet. Here, the epigenomic profiles of giant panda liver and pancreas tissues collected from three important feeding stages were investigated using BS-seq. Few differences in DNA methylation profiles were exhibited between no feeding and suckling groups in both tissues. However, we observed a tendency toward a global loss of DNA methylation in the gene-body and promoter region of metabolism-related genes from newborn to adult. Correlation analysis revealed a significant negative correlation between the changes in methylation levels within gene promoters and gene expression. The majority of genes related to nutrition metabolism had lost DNA methylation with increased mRNA expression in adult giant pandas. The few galactose metabolism and unsaturated fatty acid metabolism related genes that were hypomethylated and highly-expressed at early stages of giant panda development may meet the nutritional requirement of this species' highly altricial neonates.
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Affiliation(s)
- Jinnan Ma
- Key Laboratory of Bio-resources and Eco-environment, Ministry of Education, College of Life Sciences, Sichuan University, No.24 South Section 1, Yihuan Road, Chengdu, Sichuan 610065, China
| | - Liang Zhang
- The Sichuan Key Laboratory for Conservation Biology of Endangered Wildlife, Chengdu Research Base of Giant Panda Breeding, 1375 Panda Road, Northern Suburb, Chengdu, Sichuan 610081, China
| | - Yan Huang
- China Conservation and Research Center for the Giant Panda, 98 Tongjiang Road, Dujiangyan, Chengdu, Sichuan 611800, China
| | - Fujun Shen
- The Sichuan Key Laboratory for Conservation Biology of Endangered Wildlife, Chengdu Research Base of Giant Panda Breeding, 1375 Panda Road, Northern Suburb, Chengdu, Sichuan 610081, China
| | - Honglin Wu
- China Conservation and Research Center for the Giant Panda, 98 Tongjiang Road, Dujiangyan, Chengdu, Sichuan 611800, China
| | - Zhisong Yang
- Sichuan Academy of Giant Panda, 1375 Panda Road, Northern Suburb, Chengdu, Sichuan 610081, China
| | - Rong Hou
- The Sichuan Key Laboratory for Conservation Biology of Endangered Wildlife, Chengdu Research Base of Giant Panda Breeding, 1375 Panda Road, Northern Suburb, Chengdu, Sichuan 610081, China
| | - Zhaobin Song
- Key Laboratory of Bio-resources and Eco-environment, Ministry of Education, College of Life Sciences, Sichuan University, No.24 South Section 1, Yihuan Road, Chengdu, Sichuan 610065, China
| | - Bisong Yue
- Key Laboratory of Bio-resources and Eco-environment, Ministry of Education, College of Life Sciences, Sichuan University, No.24 South Section 1, Yihuan Road, Chengdu, Sichuan 610065, China
| | - Xiuyue Zhang
- Key Laboratory of Bio-resources and Eco-environment, Ministry of Education, College of Life Sciences, Sichuan University, No.24 South Section 1, Yihuan Road, Chengdu, Sichuan 610065, China.
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Malgwi IH, Halas V, Grünvald P, Schiavon S, Jócsák I. Genes Related to Fat Metabolism in Pigs and Intramuscular Fat Content of Pork: A Focus on Nutrigenetics and Nutrigenomics. Animals (Basel) 2022; 12:ani12020150. [PMID: 35049772 PMCID: PMC8772548 DOI: 10.3390/ani12020150] [Citation(s) in RCA: 22] [Impact Index Per Article: 11.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/22/2021] [Revised: 12/29/2021] [Accepted: 01/05/2022] [Indexed: 02/04/2023] Open
Abstract
Simple Summary The intramuscular fat (IMF) or marbling is an essential pork sensory quality that influences the preference of the consumers and premiums for pork. IMF is the streak of visible fat intermixed with the lean within a muscle fibre and determines sensorial qualities of pork such as flavour, tenderness and juiciness. Fat metabolism and IMF development are controlled by dietary nutrients, genes, and their metabolic pathways in the pig. Nutrigenetics explains how the genetic make-up of an individual pig influences the pig’s response to dietary nutrient intake. Differently, nutrigenomics is the analysis of how the entire genome of an individual pig is affected by dietary nutrient intake. The knowledge of nutrigenetics and nutrigenomics, when harmonized, is a powerful tool in estimating nutrient requirements for swine and programming dietary nutrient supply according to an individual pig’s genetic make-up. The current paper aimed to highlight the roles of nutrigenetics and nutrigenomics in elucidating the underlying mechanisms of fat metabolism and IMF deposition in pigs. This knowledge is essential in redefining nutritional intervention for swine production and the improvement of some economically important traits such as growth performance, backfat thickness, IMF accretion, disease resistance etc., in animals. Abstract Fat metabolism and intramuscular fat (IMF) are qualitative traits in pigs whose development are influenced by several genes and metabolic pathways. Nutrigenetics and nutrigenomics offer prospects in estimating nutrients required by a pig. Application of these emerging fields in nutritional science provides an opportunity for matching nutrients based on the genetic make-up of the pig for trait improvements. Today, integration of high throughput “omics” technologies into nutritional genomic research has revealed many quantitative trait loci (QTLs) and single nucleotide polymorphisms (SNPs) for the mutation(s) of key genes directly or indirectly involved in fat metabolism and IMF deposition in pigs. Nutrient–gene interaction and the underlying molecular mechanisms involved in fatty acid synthesis and marbling in pigs is difficult to unravel. While existing knowledge on QTLs and SNPs of genes related to fat metabolism and IMF development is yet to be harmonized, the scientific explanations behind the nature of the existing correlation between the nutrients, the genes and the environment remain unclear, being inconclusive or lacking precision. This paper aimed to: (1) discuss nutrigenetics, nutrigenomics and epigenetic mechanisms controlling fat metabolism and IMF accretion in pigs; (2) highlight the potentials of these concepts in pig nutritional programming and research.
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Affiliation(s)
- Isaac Hyeladi Malgwi
- Department of Agronomy, Food, Natural Resources, Animals and Environment (DAFNAE), University of Padua, Viale dell’ Università 16, 35020 Padova, Italy;
- Correspondence: ; Tel.: +39-33-17566768
| | - Veronika Halas
- Department of Farm Animal Nutrition, Kaposvár Campus, Hungarian University of Agriculture and Life Sciences, Guba Sándor Utca 40, 7400 Kaposvár, Hungary; (V.H.); (P.G.)
| | - Petra Grünvald
- Department of Farm Animal Nutrition, Kaposvár Campus, Hungarian University of Agriculture and Life Sciences, Guba Sándor Utca 40, 7400 Kaposvár, Hungary; (V.H.); (P.G.)
| | - Stefano Schiavon
- Department of Agronomy, Food, Natural Resources, Animals and Environment (DAFNAE), University of Padua, Viale dell’ Università 16, 35020 Padova, Italy;
| | - Ildikó Jócsák
- Institute of Agronomy, Kaposvár Campus, Hungarian University of Agriculture and Life Sciences, Guba Sándor Utca 40, 7400 Kaposvár, Hungary;
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12
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Exposure of pigs to glyphosate affects gene-specific DNA methylation and gene expression. Toxicol Rep 2022; 9:298-310. [PMID: 35284244 PMCID: PMC8908043 DOI: 10.1016/j.toxrep.2022.02.007] [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: 09/19/2021] [Revised: 02/09/2022] [Accepted: 02/14/2022] [Indexed: 12/24/2022] Open
Abstract
Glyphosate (N-(phosphonomethyl)glycine) is a broad-spectrum systemic herbicide and crop desiccant. Glyphosate has long been suspected of leading to the development of cancer and of compromising fertility. Herbicides have been increasingly recognized as epigenetic modifiers, and the impact of glyphosate on human and animal health might be mediated by epigenetic modifications. This article presents the results from an animal study where pigs were exposed to glyphosate while feeding. The experimental setup included a control group with no glyphosate added to the feed and two groups of pigs with 20 ppm and 200 ppm of glyphosate added to the feed, respectively. After exposure, the pigs were dissected, and tissues of the small intestine, liver, and kidney were used for DNA methylation and gene expression analyses. No significant change in global DNA methylation was found in the small intestine, kidney, or liver. Methylation status was determined for selected genes involved in various functions such as DNA repair and immune defense. In a CpG island of the promoter for IL18, we observed significantly reduced DNA methylation for certain individual CpG positions. However, this change in DNA methylation had no influence on IL18 mRNA expression. The expression of the DNA methylation enzymes DNMT1, DNMT3A, and DNMT3B was measured in the small intestine, kidney, and liver of pigs exposed to glyphosate. No significant changes in relative gene expression were found for these enzymes following dietary exposure to 20 and 200 ppm glyphosate. In contrast, a significant increase in expression of the enzyme TET3, responsible for demethylation, was observed in kidneys exposed to 200 ppm glyphosate. A large animal study with exposure of pigs to glyphosate is presented here. Pigs were exposed to 20 ppm and 200 ppm in the diet. No significant changes in global DNA methylation was observed. A significantly reduced DNA methylation was found in the porcine IL18 promoter. A significant increase in TET3 expression was seen in porcine kidneys exposed to 200 ppm glyphosate.
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13
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Schachtschneider KM, Schook LB, Meudt JJ, Shanmuganayagam D, Zoller JA, Haghani A, Li CZ, Zhang J, Yang A, Raj K, Horvath S. Epigenetic clock and DNA methylation analysis of porcine models of aging and obesity. GeroScience 2021; 43:2467-2483. [PMID: 34523051 PMCID: PMC8599541 DOI: 10.1007/s11357-021-00439-6] [Citation(s) in RCA: 20] [Impact Index Per Article: 6.7] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/18/2021] [Accepted: 08/09/2021] [Indexed: 12/29/2022] Open
Abstract
DNA-methylation profiles have been used successfully to develop highly accurate biomarkers of age, epigenetic clocks, for many species. Using a custom methylation array, we generated DNA methylation data from n = 238 porcine tissues including blood, bladder, frontal cortex, kidney, liver, and lung, from domestic pigs (Sus scrofa domesticus) and minipigs (Wisconsin Miniature Swine™). Samples used in this study originated from Large White X Landrace crossbred pigs, Large White X Minnesota minipig crossbred pigs, and Wisconsin Miniature Swine™. We present 4 epigenetic clocks for pigs that are distinguished by their compatibility with tissue type (pan-tissue and blood clock) and species (pig and human). Two dual-species human-pig pan-tissue clocks accurately measure chronological age and relative age, respectively. We also characterized CpGs that differ between minipigs and domestic pigs. Strikingly, several genes implicated by our epigenetic studies of minipig status overlap with genes (ADCY3, TFAP2B, SKOR1, and GPR61) implicated by genetic studies of body mass index in humans. In addition, CpGs with different levels of methylation between the two pig breeds were identified proximal to genes involved in blood LDL levels and cholesterol synthesis, of particular interest given the minipig's increased susceptibility to cardiovascular disease compared to domestic pigs. Thus, breed-specific differences of domestic and minipigs may potentially help to identify biological mechanisms underlying weight gain and aging-associated diseases. Our porcine clocks are expected to be useful for elucidating the role of epigenetics in aging and obesity, and the testing of anti-aging interventions.
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Affiliation(s)
- Kyle M. Schachtschneider
- Department of Radiology, University of Illinois At Chicago, Chicago, IL USA
- Department of Biochemistry and Molecular Genetics, University of Illinois At Chicago, Chicago, IL USA
- National Center for Supercomputing Applications, University of Illinois At Urbana-Champaign, Urban, IL USA
| | - Lawrence B. Schook
- Department of Radiology, University of Illinois At Chicago, Chicago, IL USA
- Department of Animal Sciences, University of Illinois At Urbana-Champaign, Urbana, IL USA
| | - Jennifer J. Meudt
- Biomedical & Genomic Research Group, Department of Animal and Dairy Sciences, University of Wisconsin – Madison, Madison, WI USA
| | - Dhanansayan Shanmuganayagam
- Biomedical & Genomic Research Group, Department of Animal and Dairy Sciences, University of Wisconsin – Madison, Madison, WI USA
- Department of Surgery, University of Wisconsin School of Medicine and Public Health, Madison, WI USA
| | - Joseph A. Zoller
- Department of Biostatistics, Fielding School of Public Health, University of California, Los Angeles, Los Angeles, CA USA
| | - Amin Haghani
- Department of Biostatistics, Fielding School of Public Health, University of California, Los Angeles, Los Angeles, CA USA
| | - Caesar Z. Li
- Department of Biostatistics, Fielding School of Public Health, University of California, Los Angeles, Los Angeles, CA USA
| | - Joshua Zhang
- Department of Human Genetics, David Geffen School of Medicine, University of California, Los Angeles, Gonda Building, 695 Charles Young Drive South, Los Angeles, CA 90095 USA
| | - Andrew Yang
- Department of Biostatistics, Fielding School of Public Health, University of California, Los Angeles, Los Angeles, CA USA
| | - Ken Raj
- Radiation Effects Department, Centre for Radiation, Chemical and Environmental Hazards, Public Health England, Chilton, Didcot, UK
| | - Steve Horvath
- Department of Biostatistics, Fielding School of Public Health, University of California, Los Angeles, Los Angeles, CA USA
- Department of Human Genetics, David Geffen School of Medicine, University of California, Los Angeles, Gonda Building, 695 Charles Young Drive South, Los Angeles, CA 90095 USA
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14
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Porcine pancreatic ductal epithelial cells transformed with KRAS G12D and SV40T are tumorigenic. Sci Rep 2021; 11:13436. [PMID: 34183736 PMCID: PMC8238942 DOI: 10.1038/s41598-021-92852-2] [Citation(s) in RCA: 3] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/22/2021] [Accepted: 06/16/2021] [Indexed: 12/27/2022] Open
Abstract
We describe our initial studies in the development of an orthotopic, genetically defined, large animal model of pancreatic cancer. Primary pancreatic epithelial cells were isolated from pancreatic duct of domestic pigs. A transformed cell line was generated from these primary cells with oncogenic KRAS and SV40T. The transformed cell lines outperformed the primary and SV40T immortalized cells in terms of proliferation, population doubling time, soft agar growth, transwell migration and invasion. The transformed cell line grew tumors when injected subcutaneously in nude mice, forming glandular structures and staining for epithelial markers. Future work will include implantation studies of these tumorigenic porcine pancreatic cell lines into the pancreas of allogeneic and autologous pigs. The resultant large animal model of pancreatic cancer could be utilized for preclinical research on diagnostic, interventional, and therapeutic technologies.
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15
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Abstract
Pigs represent a potentially attractive model for medical research. Similar body size and physiological patterns of kidney injury that more closely mimic those described in humans make larger animals attractive for experimentation. Using larger animals, including pigs, to investigate the pathogenesis of acute kidney injury (AKI) also serves as an experimental bridge, narrowing the gap between clinical disease and preclinical discoveries. This article compares the advantages and disadvantages of large versus small AKI animal models and provides a comprehensive overview of the development and application of porcine models of AKI induced by clinically relevant insults, including ischemia-reperfusion, sepsis, and nephrotoxin exposure. The primary focus of this review is to evaluate the use of pigs for AKI studies by current investigators, including areas where more information is needed.
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Affiliation(s)
- Jianni Huang
- Department of Nephrology, Shanghai East Hospital, Tongji University School of Medicine, Shanghai, China
| | - George Bayliss
- Department of Medicine, Rhode Island Hospital and Alpert Medical School, Brown University, Providence, Rhode Island
| | - Shougang Zhuang
- Department of Nephrology, Shanghai East Hospital, Tongji University School of Medicine, Shanghai, China.,Department of Medicine, Rhode Island Hospital and Alpert Medical School, Brown University, Providence, Rhode Island
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16
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Li Z, Zheng W, Wang H, Cheng Y, Fang Y, Wu F, Sun G, Sun G, Lv C, Hui B. Application of Animal Models in Cancer Research: Recent Progress and Future Prospects. Cancer Manag Res 2021; 13:2455-2475. [PMID: 33758544 PMCID: PMC7979343 DOI: 10.2147/cmar.s302565] [Citation(s) in RCA: 39] [Impact Index Per Article: 13.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/20/2021] [Accepted: 02/25/2021] [Indexed: 12/18/2022] Open
Abstract
Animal models refers to the animal experimental objects and related materials that can simulate human body established in medical research. As the second-largest disease in terms of morbidity and mortality after cardiovascular disease, cancer has always been the focus of human attention all over the world, which makes it a research hotspot in the medical field. At the same time, more and more animal models have been constructed and used in cancer research. With the deepening of research, the construction methods of cancer animal models are becoming more and more diverse, including chemical induction, xenotransplantation, gene programming, and so on. In recent years, patient-derived xenotransplantation (PDX) model has become a research hotspot because it can retain the microenvironment of the primary tumor and the basic characteristics of cells. Animal models can be used not only to study the biochemical and physiological processes of the occurrence and development of cancer in objects but also for the screening of cancer drugs and the exploration of gene therapy. In this paper, several main tumor animal models and the application progress of animal models in tumor research are systematically reviewed. Finally, combined with the latest progress and development trend in this field, the future research of tumor animal model was prospected.
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Affiliation(s)
- Zhitao Li
- Department of General Surgery, Nanjing First Hospital, Nanjing Medical University, Nanjing, People's Republic of China
| | - Wubin Zheng
- Department of General Surgery, Nanjing First Hospital, Nanjing Medical University, Nanjing, People's Republic of China
| | - Hanjin Wang
- Department of General Surgery, Nanjing First Hospital, Nanjing Medical University, Nanjing, People's Republic of China
| | - Ye Cheng
- Department of General Surgery, Nanjing First Hospital, Nanjing Medical University, Nanjing, People's Republic of China
| | - Yijiao Fang
- Department of Anesthesiology, Fudan University Shanghai Cancer Center, Fudan University, Shanghai, 200032, People's Republic of China.,Department of Oncology, Shanghai Medical College, Fudan University, Shanghai, 200032, People's Republic of China
| | - Fan Wu
- Department of General Surgery, Nanjing First Hospital, Nanjing Medical University, Nanjing, People's Republic of China
| | - Guoqiang Sun
- Department of General Surgery, Nanjing First Hospital, Nanjing Medical University, Nanjing, People's Republic of China
| | - Guangshun Sun
- Department of General Surgery, Nanjing First Hospital, Nanjing Medical University, Nanjing, People's Republic of China
| | - Chengyu Lv
- Department of General Surgery, Nanjing First Hospital, Nanjing Medical University, Nanjing, People's Republic of China
| | - Bingqing Hui
- Department of Oncology, The First Affiliated Hospital of Nanjing Medical University, Nanjing, People's Republic of China
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17
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López-Albors O, Llamas-López PJ, Ortuño JÁ, Latorre R, García-Vázquez FA. In vivo measurement of pH and CO 2 levels in the uterus of sows through the estrous cycle and after insemination. Sci Rep 2021; 11:3194. [PMID: 33542361 PMCID: PMC7862298 DOI: 10.1038/s41598-021-82620-7] [Citation(s) in RCA: 5] [Impact Index Per Article: 1.7] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/04/2020] [Accepted: 01/19/2021] [Indexed: 02/07/2023] Open
Abstract
The pH-CO2-HCO3- system is a ubiquitous biological regulator with important functional implications for reproduction. Knowledge of the physiological values of its components is relevant for reproductive biology and the optimization of Assisted Reproductive Technologies (ARTs). However, in situ measurements of these parameters in the uterus are scarce or null. This study describes a non-invasive method for in situ time-lapse recording of pH and CO2 within the uterus of non-anesthetized sows. Animals were at three different reproductive conditions, estrous with no insemination and two hours after insemination, and diestrous. From pH and CO2 data, HCO3- concentration was estimated. The non-invasive approach to the porcine uterus with novel optical probes allowed the obtaining of in situ physiological values of pH, CO2, and HCO3-. Variable oscillatory patterns of pH, CO2 and HCO3- were found independently of the estrous condition. Insemination did not immediately change the levels of uterine pH, CO2 (%) and HCO3- concentration, but all the values were affected by the estrous cycle decreasing significantly at diestrous condition. This study contributes to a better understanding of the in vivo regulation of the pH-CO2-HCO3- system in the uterus and may help to optimize the protocols of sperm treatment for in vitro fertilization.
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Affiliation(s)
- Octavio López-Albors
- grid.10586.3a0000 0001 2287 8496Department of Anatomy and Comparative Pathology, University of Murcia, 30100 Murcia, Spain ,International Excellence Campus for Higher Education and Research (Campus Mare Nostrum), Murcia, Spain
| | - Pedro José Llamas-López
- grid.10586.3a0000 0001 2287 8496Department of Physiology, Faculty of Veterinary Science, University of Murcia, 30100 Murcia, Spain
| | - Joaquín Ángel Ortuño
- grid.10586.3a0000 0001 2287 8496Department of Analytical Chemistry, Faculty of Chemistry, University of Murcia, 30100 Murcia, Spain
| | - Rafael Latorre
- grid.10586.3a0000 0001 2287 8496Department of Anatomy and Comparative Pathology, University of Murcia, 30100 Murcia, Spain ,International Excellence Campus for Higher Education and Research (Campus Mare Nostrum), Murcia, Spain
| | - Francisco Alberto García-Vázquez
- International Excellence Campus for Higher Education and Research (Campus Mare Nostrum), Murcia, Spain ,grid.10586.3a0000 0001 2287 8496Department of Physiology, Faculty of Veterinary Science, University of Murcia, 30100 Murcia, Spain ,grid.452553.0Institute for Biomedical Research of Murcia, IMIB-Arrixaca, Murcia, Spain
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18
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Li XJ, Liu LQ, Dong H, Yang JJ, Wang WW, Zhang Q, Wang CL, Zhou J, Chen HQ. Comparative genome-wide methylation analysis of longissimus dorsi muscles in Yorkshire and Wannanhua pigs. Anim Genet 2020; 52:78-89. [PMID: 33301219 DOI: 10.1111/age.13029] [Citation(s) in RCA: 9] [Impact Index Per Article: 2.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Accepted: 11/12/2020] [Indexed: 12/11/2022]
Abstract
DNA methylation was one of the earliest discovered epigenetic modifications in vertebrates, and is an important epigenetic mechanism involved in the expression of genes in many biological processes, including muscle growth and development. Its effects on economically important traits are evidenced in reported differences in meat quality traits between Chinese indigenous pig breeds (Wannanhua pig) and Western commercial pig breeds (Yorkshire pig), and this presents a unique model for analyzing the effects of DNA methylation on these traits. In the present study, a whole genome DNA methylation analysis was performed on the two breeds using methylated DNA immunoprecipitation. GO functional enrichment and pathway enrichment analyses identified differentially methylated genes primarily associated with fatty acid metabolism, biological processes of muscle development and signaling pathways related to muscle development and pork quality. Differentially methylated genes were verified by sodium pyrosequencing, and the results were consistent with the sequencing results. The results of the integrative analysis between DNA methylation and gene expression revealed that the DNA methylation levels showed a significantly negative correlation with gene expression levels around the transcription start site of genes. In total, 41 genes were both differentially expressed and methylated; these genes were related to fat metabolism, lipid metabolism and skeletal muscle development. This study could help further explore the molecular mechanisms and phenotypic differences in pig growth and development among different breeds.
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Affiliation(s)
- X-J Li
- College of Animal Science and Technology, Anhui Agricultural University, Hefei, 230036, China.,Institute of Animal Husbandry and Veterinary Medicine, Anhui Academy of Agricultural Sciences, Hefei, 230031, China
| | - L-Q Liu
- Institute of Animal Husbandry and Veterinary Medicine, Anhui Academy of Agricultural Sciences, Hefei, 230031, China
| | - H Dong
- College of Animal Science and Technology, Anhui Agricultural University, Hefei, 230036, China.,Institute of Animal Husbandry and Veterinary Medicine, Anhui Academy of Agricultural Sciences, Hefei, 230031, China
| | - J-J Yang
- Institute of Animal Husbandry and Veterinary Medicine, Anhui Academy of Agricultural Sciences, Hefei, 230031, China
| | - W-W Wang
- Department of Animal Genetics and Breeding, College of Animal Science and Technology, Shandong Agricultural University, Tai'an, 271018, China
| | - Q Zhang
- Department of Animal Genetics and Breeding, College of Animal Science and Technology, Shandong Agricultural University, Tai'an, 271018, China
| | - C-L Wang
- Institute of Animal Husbandry and Veterinary Medicine, Anhui Academy of Agricultural Sciences, Hefei, 230031, China
| | - J Zhou
- College of Animal Science and Technology, Anhui Agricultural University, Hefei, 230036, China
| | - H-Q Chen
- College of Animal Science and Technology, Anhui Agricultural University, Hefei, 230036, China
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19
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Corbett RJ, Te Pas MFW, van den Brand H, Groenen MAM, Crooijmans RPMA, Ernst CW, Madsen O. Genome-Wide Assessment of DNA Methylation in Chicken Cardiac Tissue Exposed to Different Incubation Temperatures and CO 2 Levels. Front Genet 2020; 11:558189. [PMID: 33193638 PMCID: PMC7655987 DOI: 10.3389/fgene.2020.558189] [Citation(s) in RCA: 6] [Impact Index Per Article: 1.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/01/2020] [Accepted: 09/30/2020] [Indexed: 12/26/2022] Open
Abstract
Temperature and CO2 concentration during incubation have profound effects on broiler chick development, and numerous studies have identified significant effects on hatch heart weight (HW) as a result of differences in these parameters. Early life environment has also been shown to affect broiler performance later in life; it has thus been suggested that epigenetic mechanisms may mediate long-term physiological changes induced by environmental stimuli. DNA methylation is an epigenetic modification that can confer heritable changes in gene expression. Using reduced-representation bisulfite sequencing (RRBS), we assessed DNA methylation patterns in cardiac tissue of 84 broiler hatchlings incubated at two egg shell temperatures (EST; 37.8°C and 38.9°C) and three CO2 concentrations (0.1%, 0.4%, and 0.8%) from day 8 of incubation onward. We assessed differential methylation between EST treatments and identified 2,175 differentially methylated (DM) CpGs (1,121 hypermethylated, 1,054 hypomethylated at 38.9° vs. 37.8°) in 269 gene promoters and 949 intragenic regions. DM genes (DMGs) were associated with heart developmental processes, including cardiomyocyte proliferation and differentiation. We identified enriched binding motifs among DM loci, including those for transcription factors associated with cell proliferation and heart development among hypomethylated CpGs that suggest increased binding ability at higher EST. We identified 9,823 DM CpGs between at least two CO2 treatments, with the greatest difference observed between 0.8 and 0.1% CO2 that disproportionately impacted genes involved in cardiac muscle development and response to low oxygen levels. Using HW measurements from the same chicks, we performed an epigenome-wide association study (EWAS) for HW, and identified 23 significantly associated CpGs, nine of which were also DM between ESTs. We found corresponding differences in transcript abundance between ESTs in three DMGs (ABLIM2, PITX2, and THRSP). Hypomethylation of an exonic CpG in PITX2 at 38.9°C was associated with increased expression, and suggests increased cell proliferation in broiler hatchlings incubated at higher temperatures. Overall, these results identified numerous epigenetic associations between chick incubation factors and heart development that may manifest in long-term differences in animal performance.
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Affiliation(s)
- Ryan J Corbett
- Genetics and Genome Sciences Graduate Program, Michigan State University, East Lansing, MI, United States
| | - Marinus F W Te Pas
- Animal Breeding and Genomics, Wageningen University & Research, Wageningen, Netherlands
| | - Henry van den Brand
- Adaptation Physiology Group, Wageningen University & Research, Wageningen, Netherlands
| | - Martien A M Groenen
- Animal Breeding and Genomics, Wageningen University & Research, Wageningen, Netherlands
| | | | - Catherine W Ernst
- Department of Animal Science, Michigan State University, East Lansing, MI, United States
| | - Ole Madsen
- Animal Breeding and Genomics, Wageningen University & Research, Wageningen, Netherlands
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20
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Hu Y, Zhang Y, Liu C, Qin R, Gong D, Wang R, Zhang D, Che L, Chen D, Xin G, Gao F, Hu Q. Multi-omics profiling highlights lipid metabolism alterations in pigs fed low-dose antibiotics. BMC Genet 2020; 21:112. [PMID: 32957918 PMCID: PMC7507292 DOI: 10.1186/s12863-020-00918-3] [Citation(s) in RCA: 3] [Impact Index Per Article: 0.8] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/23/2019] [Accepted: 09/11/2020] [Indexed: 02/02/2023] Open
Abstract
Background In order to study the relations of hepatocellular functions, weight gain and metabolic imbalance caused by low-dose antibiotics (LDA) via epigenetic regulation of gene transcription, 32 weaned piglets were employed as animal models and randomly allocated into two groups with diets supplemented with 0 or LDA (chlorotetracycline and virginiamycin). Results During the 4 weeks of the experiment, LDA showed a clear growth-promoting effect, which was exemplified by the significantly elevated body weight and average daily gain. Promoter methylome profiling using liquid hybridization capture-based bisulfite sequencing (LHC-BS) indicated that most of the 745 differential methylation regions (DMRs) were hypermethylated in the LDA group. Several DMRs were significantly enriched in genes related with fatty acids metabolic pathways, such as FABP1 and PCK1. In addition, 71 differentially expressed genes (DEGs) were obtained by strand-specific transcriptome analysis of liver tissues, including ALOX15, CXCL10 and NNMT, which are three key DEGs that function in lipid metabolism and immunity and which had highly elevated expression in the LDA group. In accordance with these molecular changes, the lipidome analyses of serum by LC-MS identified 38 significantly differential lipids, most of which were downregulated in the LDA group. Conclusions Our results indicate that LDA could induce epigenetic and transcriptional changes of key genes and lead to enhanced efficiency of lipid metabolism in the liver.
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Affiliation(s)
- Yue Hu
- Genome Analysis Laboratory of the Ministry of Agriculture, Agricultural Genomics Institute at Shenzhen, Chinese Academy of Agricultural Sciences, Shenzhen, 518120, China
| | - Yihe Zhang
- Genome Analysis Laboratory of the Ministry of Agriculture, Agricultural Genomics Institute at Shenzhen, Chinese Academy of Agricultural Sciences, Shenzhen, 518120, China
| | - Cong Liu
- Genome Analysis Laboratory of the Ministry of Agriculture, Agricultural Genomics Institute at Shenzhen, Chinese Academy of Agricultural Sciences, Shenzhen, 518120, China
| | - Rui Qin
- Genome Analysis Laboratory of the Ministry of Agriculture, Agricultural Genomics Institute at Shenzhen, Chinese Academy of Agricultural Sciences, Shenzhen, 518120, China
| | - Desheng Gong
- Genome Analysis Laboratory of the Ministry of Agriculture, Agricultural Genomics Institute at Shenzhen, Chinese Academy of Agricultural Sciences, Shenzhen, 518120, China
| | - Ru Wang
- Institute of Animal Nutrition, Sichuan Agricultural University, Ya'an, 625014, Sichuan Province, China
| | - Du Zhang
- Genome Analysis Laboratory of the Ministry of Agriculture, Agricultural Genomics Institute at Shenzhen, Chinese Academy of Agricultural Sciences, Shenzhen, 518120, China
| | - Lianqiang Che
- Institute of Animal Nutrition, Sichuan Agricultural University, Ya'an, 625014, Sichuan Province, China
| | - Daiwen Chen
- Institute of Animal Nutrition, Sichuan Agricultural University, Ya'an, 625014, Sichuan Province, China
| | - Guizhong Xin
- State Key Laboratory of Natural Medicines, Department of Chinese Medicines Analysis, China Pharmaceutical University, Nanjing, China
| | - Fei Gao
- Genome Analysis Laboratory of the Ministry of Agriculture, Agricultural Genomics Institute at Shenzhen, Chinese Academy of Agricultural Sciences, Shenzhen, 518120, China.,Comparative Pediatrics and Nutrition, Department of Veterinary and Animal Sciences, Faculty of Health and Medical Sciences, University of Copenhagen, Frederiksberg, DK, Denmark
| | - Qi Hu
- Genome Analysis Laboratory of the Ministry of Agriculture, Agricultural Genomics Institute at Shenzhen, Chinese Academy of Agricultural Sciences, Shenzhen, 518120, China.
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21
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Zhou Y, Liu S, Hu Y, Fang L, Gao Y, Xia H, Schroeder SG, Rosen BD, Connor EE, Li CJ, Baldwin RL, Cole JB, Van Tassell CP, Yang L, Ma L, Liu GE. Comparative whole genome DNA methylation profiling across cattle tissues reveals global and tissue-specific methylation patterns. BMC Biol 2020; 18:85. [PMID: 32631327 PMCID: PMC7339546 DOI: 10.1186/s12915-020-00793-5] [Citation(s) in RCA: 30] [Impact Index Per Article: 7.5] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/04/2020] [Accepted: 05/12/2020] [Indexed: 12/21/2022] Open
Abstract
BACKGROUND Efforts to improve animal health, and understand genetic bases for production, may benefit from a comprehensive analysis of animal genomes and epigenomes. Although DNA methylation has been well studied in humans and other model species, its distribution patterns and regulatory impacts in cattle are still largely unknown. Here, we present the largest collection of cattle DNA methylation epigenomic data to date. RESULTS Using Holstein cattle, we generated 29 whole genome bisulfite sequencing (WGBS) datasets for 16 tissues, 47 corresponding RNA-seq datasets, and 2 whole genome sequencing datasets. We did read mapping and DNA methylation calling based on two different cattle assemblies, demonstrating the high quality of the long-read-based assembly markedly improved DNA methylation results. We observed large differences across cattle tissues in the methylation patterns of global CpG sites, partially methylated domains (PMDs), hypomethylated regions (HMRs), CG islands (CGIs), and common repeats. We detected that each tissue had a distinct set of PMDs, which showed tissue-specific patterns. Similar to human PMD, cattle PMDs were often linked to a general decrease of gene expression and a decrease in active histone marks and related to long-range chromatin organizations, like topologically associated domains (TADs). We tested a classification of the HMRs based on their distributions relative to transcription start sites (TSSs) and detected tissue-specific TSS-HMRs and genes that showed strong tissue effects. When performing cross-species comparisons of paired genes (two opposite strand genes with their TSS located in the same HMR), we found out they were more consistently co-expressed among human, mouse, sheep, goat, yak, pig, and chicken, but showed lower consistent ratios in more divergent species. We further used these WGBS data to detect 50,023 experimentally supported CGIs across bovine tissues and found that they might function as a guard against C-to-T mutations for TSS-HMRs. Although common repeats were often heavily methylated, some young Bov-A2 repeats were hypomethylated in sperm and could affect the promoter structures by exposing potential transcription factor binding sites. CONCLUSIONS This study provides a comprehensive resource for bovine epigenomic research and enables new discoveries about DNA methylation and its role in complex traits.
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Affiliation(s)
- Yang Zhou
- Key Laboratory of Agricultural Animal Genetics, Breeding and Reproduction of Ministry of Education & College of Animal Science and Technology, Huazhong Agricultural University, Wuhan, 430070 China
| | - Shuli Liu
- Animal Genomics and Improvement Laboratory, Agricultural Research Service, USDA, Beltsville, MD 20705 USA
- National Engineering Laboratory for Animal Breeding, Key Laboratory of Animal Genetics, Breeding and Reproduction of Ministry of Agriculture and Rural Affairs, College of Animal Science and Technology, China Agricultural University, Beijing, 100193 China
| | - Yan Hu
- Key Laboratory of Agricultural Animal Genetics, Breeding and Reproduction of Ministry of Education & College of Animal Science and Technology, Huazhong Agricultural University, Wuhan, 430070 China
| | - Lingzhao Fang
- MRC Human Genetics Unit, Institute of Genetics and Molecular Medicine, University of Edinburgh, Edinburgh, EH4 2XU UK
| | - Yahui Gao
- Animal Genomics and Improvement Laboratory, Agricultural Research Service, USDA, Beltsville, MD 20705 USA
| | - Han Xia
- Key Laboratory of Agricultural Animal Genetics, Breeding and Reproduction of Ministry of Education & College of Animal Science and Technology, Huazhong Agricultural University, Wuhan, 430070 China
| | - Steven G. Schroeder
- Animal Genomics and Improvement Laboratory, Agricultural Research Service, USDA, Beltsville, MD 20705 USA
| | - Benjamin D. Rosen
- Animal Genomics and Improvement Laboratory, Agricultural Research Service, USDA, Beltsville, MD 20705 USA
| | - Erin E. Connor
- Department of Animal and Food Sciences, University of Delaware, Newark, DE 19716 USA
| | - Cong-jun Li
- Animal Genomics and Improvement Laboratory, Agricultural Research Service, USDA, Beltsville, MD 20705 USA
| | - Ransom L. Baldwin
- Animal Genomics and Improvement Laboratory, Agricultural Research Service, USDA, Beltsville, MD 20705 USA
| | - John B. Cole
- Animal Genomics and Improvement Laboratory, Agricultural Research Service, USDA, Beltsville, MD 20705 USA
| | - Curtis P. Van Tassell
- Animal Genomics and Improvement Laboratory, Agricultural Research Service, USDA, Beltsville, MD 20705 USA
| | - Liguo Yang
- Key Laboratory of Agricultural Animal Genetics, Breeding and Reproduction of Ministry of Education & College of Animal Science and Technology, Huazhong Agricultural University, Wuhan, 430070 China
| | - Li Ma
- Department of Animal and Avian Sciences, University of Maryland, College Park, MD 20742 USA
| | - George E. Liu
- Animal Genomics and Improvement Laboratory, Agricultural Research Service, USDA, Beltsville, MD 20705 USA
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22
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Schachtschneider KM, Welge ME, Auvil LS, Chaki S, Rund LA, Madsen O, Elmore MR, Johnson RW, Groenen MA, Schook LB. Altered Hippocampal Epigenetic Regulation Underlying Reduced Cognitive Development in Response to Early Life Environmental Insults. Genes (Basel) 2020; 11:genes11020162. [PMID: 32033187 PMCID: PMC7074491 DOI: 10.3390/genes11020162] [Citation(s) in RCA: 5] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/13/2019] [Revised: 01/30/2020] [Accepted: 02/01/2020] [Indexed: 12/13/2022] Open
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 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.
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Affiliation(s)
- Kyle M. Schachtschneider
- Department of Radiology, University of Illinois at Chicago, Chicago, IL 60607, USA;
- Department of Biochemistry and Molecular Genetics, University of Illinois at Chicago, Chicago, IL 60607, USA
- National Center for Supercomputing Applications, University of Illinois at Urbana-Champaign, Urbana, IL 61820, USA; (M.E.W.); (L.S.A.)
| | - Michael E. Welge
- National Center for Supercomputing Applications, University of Illinois at Urbana-Champaign, Urbana, IL 61820, USA; (M.E.W.); (L.S.A.)
| | - Loretta S. Auvil
- National Center for Supercomputing Applications, University of Illinois at Urbana-Champaign, Urbana, IL 61820, USA; (M.E.W.); (L.S.A.)
| | - Sulalita Chaki
- Department of Animal Sciences, University of Illinois at Urbana-Champaign, Urbana, IL 616280, USA; (S.C.); (L.A.R.); (M.R.P.E.); (R.W.J.)
| | - Laurie A. Rund
- Department of Animal Sciences, University of Illinois at Urbana-Champaign, Urbana, IL 616280, USA; (S.C.); (L.A.R.); (M.R.P.E.); (R.W.J.)
| | - Ole Madsen
- Animal Breeding and Genomics, Wageningen University, 6708 Wageningen, The Netherlands; (O.M.); (M.A.M.G.)
| | - Monica R.P. Elmore
- Department of Animal Sciences, University of Illinois at Urbana-Champaign, Urbana, IL 616280, USA; (S.C.); (L.A.R.); (M.R.P.E.); (R.W.J.)
| | - Rodney W. Johnson
- Department of Animal Sciences, University of Illinois at Urbana-Champaign, Urbana, IL 616280, USA; (S.C.); (L.A.R.); (M.R.P.E.); (R.W.J.)
| | - Martien A.M. Groenen
- Animal Breeding and Genomics, Wageningen University, 6708 Wageningen, The Netherlands; (O.M.); (M.A.M.G.)
| | - Lawrence B. Schook
- Department of Radiology, University of Illinois at Chicago, Chicago, IL 60607, USA;
- National Center for Supercomputing Applications, University of Illinois at Urbana-Champaign, Urbana, IL 61820, USA; (M.E.W.); (L.S.A.)
- Department of Animal Sciences, University of Illinois at Urbana-Champaign, Urbana, IL 616280, USA; (S.C.); (L.A.R.); (M.R.P.E.); (R.W.J.)
- Correspondence:
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23
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Khezri A, Narud B, Stenseth EB, Johannisson A, Myromslien FD, Gaustad AH, Wilson RC, Lyle R, Morrell JM, Kommisrud E, Ahmad R. DNA methylation patterns vary in boar sperm cells with different levels of DNA fragmentation. BMC Genomics 2019; 20:897. [PMID: 31775629 PMCID: PMC6880426 DOI: 10.1186/s12864-019-6307-8] [Citation(s) in RCA: 23] [Impact Index Per Article: 4.6] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/13/2019] [Accepted: 11/18/2019] [Indexed: 12/12/2022] Open
Abstract
BACKGROUND Sperm DNA integrity is considered essential for successful transmission of the paternal genome, fertilization and normal embryo development. DNA fragmentation index (DFI, %) has become a key parameter in the swine artificial insemination industry to assess sperm DNA integrity. Recently, in some elite Norwegian Landrace boars (boars with excellent field fertility records), a higher level of sperm DFI has been observed. In order to obtain a better understanding of this, and to study the complexity of sperm DNA integrity, liquid preserved semen samples from elite boars with contrasting DFI levels were examined for protamine deficiency, thiol profile and disulphide bonds. Additionally, the DNA methylation profiles of the samples were determined by reduced representation bisulphite sequencing (RRBS). RESULTS In this study, different traits related to sperm DNA integrity were investigated (n = 18 ejaculates). Upon liquid storage, the levels of total thiols and disulphide bonds decreased significantly, while the DFI and protamine deficiency level increased significantly. The RRBS results revealed similar global patterns of low methylation from semen samples with different levels of DFI (low, medium and high). Differential methylation analyses indicated that the number of differentially methylated cytosines (DMCs) increased in the low-high compared to the low-medium and the medium-high DFI groups. Annotating the DMCs with gene and CpG features revealed clear differences between DFI groups. In addition, the number of annotated transcription starting sites (TSS) and associated pathways in the low-high comparison was greater than the other two groups. Pathway analysis showed that genes (based on the closest TSS to DMCs) corresponding to low-high DFI comparison were associated with important processes such as membrane function, metabolic cascade and antioxidant defence system. CONCLUSION To our knowledge, this is the first study evaluating DNA methylation in boar sperm cells with different levels of DFI. The present study shows that sperm cells with varying levels of DNA fragmentation exhibit similar global methylation, but different site-specific DNA methylation signatures. Moreover, with increasing DNA fragmentation in spermatozoa, there is an increase in the number of potentially affected downstream genes and their respective regulatory pathways.
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Affiliation(s)
- Abdolrahman Khezri
- Department of Biotechnology, Inland Norway University of Applied Sciences, Hamar, Norway
| | - Birgitte Narud
- Department of Biotechnology, Inland Norway University of Applied Sciences, Hamar, Norway
| | - Else-Berit Stenseth
- Department of Biotechnology, Inland Norway University of Applied Sciences, Hamar, Norway
| | - Anders Johannisson
- Department of Clinical Sciences, Swedish University of Agricultural Sciences, Uppsala, Sweden
| | | | - Ann Helen Gaustad
- Department of Biotechnology, Inland Norway University of Applied Sciences, Hamar, Norway
- Topigs Norsvin, Hamar, Norway
| | - Robert C Wilson
- Department of Biotechnology, Inland Norway University of Applied Sciences, Hamar, Norway
| | - Robert Lyle
- Department of Medical Genetics and Norwegian Sequencing Centre, Oslo University Hospital and the University of Oslo, Oslo, Norway
| | - Jane M Morrell
- Department of Clinical Sciences, Swedish University of Agricultural Sciences, Uppsala, Sweden
| | - Elisabeth Kommisrud
- Department of Biotechnology, Inland Norway University of Applied Sciences, Hamar, Norway
| | - Rafi Ahmad
- Department of Biotechnology, Inland Norway University of Applied Sciences, Hamar, Norway.
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24
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Overgaard NH, Fan TM, Schachtschneider KM, Principe DR, Schook LB, Jungersen G. Of Mice, Dogs, Pigs, and Men: Choosing the Appropriate Model for Immuno-Oncology Research. ILAR J 2019; 59:247-262. [PMID: 30476148 DOI: 10.1093/ilar/ily014] [Citation(s) in RCA: 30] [Impact Index Per Article: 6.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/10/2017] [Revised: 07/30/2018] [Indexed: 02/06/2023] Open
Abstract
The immune system plays dual roles in response to cancer. The host immune system protects against tumor formation via immunosurveillance; however, recognition of the tumor by immune cells also induces sculpting mechanisms leading to a Darwinian selection of tumor cell variants with reduced immunogenicity. Cancer immunoediting is the concept used to describe the complex interplay between tumor cells and the immune system. This concept, commonly referred to as the three E's, is encompassed by 3 distinct phases of elimination, equilibrium, and escape. Despite impressive results in the clinic, cancer immunotherapy still has room for improvement as many patients remain unresponsive to therapy. Moreover, many of the preclinical results obtained in the widely used mouse models of cancer are lost in translation to human patients. To improve the success rate of immuno-oncology research and preclinical testing of immune-based anticancer therapies, using alternative animal models more closely related to humans is a promising approach. Here, we describe 2 of the major alternative model systems: canine (spontaneous) and porcine (experimental) cancer models. Although dogs display a high rate of spontaneous tumor formation, an increased number of genetically modified porcine models exist. We suggest that the optimal immuno-oncology model may depend on the stage of cancer immunoediting in question. In particular, the spontaneous canine tumor models provide a unique platform for evaluating therapies aimed at the escape phase of cancer, while genetically engineered swine allow for elucidation of tumor-immune cell interactions especially during the phases of elimination and equilibrium.
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Affiliation(s)
- Nana H Overgaard
- Department of Micro- and Nanotechnology, Technical University of Denmark, Kgs Lyngby, Denmark
| | - Timothy M Fan
- Department of Veterinary Clinical Medicine, University of Illinois, Urbana-Champaign, Illinois
| | | | - Daniel R Principe
- Medical Scientist Training Program, University of Illinois College of Medicine, Chicago, Illinois
| | - Lawrence B Schook
- Department of Radiology, University of Illinois, Chicago, Illinois.,Department of Animal Sciences, University of Illinois, Urbana-Champaign, Illinois
| | - Gregers Jungersen
- Department of Biotechnology and Biomedicine, Technical University of Denmark, Kgs. Lyngby, Denmark
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25
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Sajjanar B, Trakooljul N, Wimmers K, Ponsuksili S. DNA methylation analysis of porcine mammary epithelial cells reveals differentially methylated loci associated with immune response against Escherichia coli challenge. BMC Genomics 2019; 20:623. [PMID: 31366318 PMCID: PMC6670134 DOI: 10.1186/s12864-019-5976-7] [Citation(s) in RCA: 14] [Impact Index Per Article: 2.8] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/08/2019] [Accepted: 07/16/2019] [Indexed: 12/15/2022] Open
Abstract
Background Epigenetic changes such as cytosine (CpG) DNA methylations regulate gene expression patterns in response to environmental cues including infections. Microbial infections induce DNA methylations that play a potential role in modulating host-immune response. In the present study, we sought to determine DNA methylation changes induced by the mastitis causing Escherichia coli (E. coli) in porcine mammary epithelial cells (PMEC). Two time points (3 h and 24 h) were selected based on specific transcriptomic changes during the early and late immune responses, respectively. Results DNA methylation analysis revealed 561 and 898 significant (P < 0.01) differentially methylated CpG sites at 3 h and 24 h after E. coli challenge in PMEC respectively. These CpG sites mapped to genes that have functional roles in innate and adaptive immune responses. Significantly, hypomethylated CpG sites were found in the promoter regions of immune response genes such as SDF4, SRXN1, CSF1 and CXCL14. The quantitative transcript estimation indicated higher expression associated with the DNA CpG methylation observed in these immune response genes. Further, E. coli challenge significantly reduced the expression levels of DNMT3a, a subtype of de novo DNA methylation enzyme, in PMEC indicating the probable reason for the hypomethylation observed in the immune response genes. Conclusions Our study revealed E. coli infection induced DNA methylation loci in the porcine genome. The differentially methylated CpGs were identified in the regulatory regions of genes that play important role in immune response. These results will help to understand epigenetic mechanisms for immune regulation during coliform mastitis in pigs. Electronic supplementary material The online version of this article (10.1186/s12864-019-5976-7) contains supplementary material, which is available to authorized users.
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Affiliation(s)
- Basavaraj Sajjanar
- Leibniz Institute for Farm Animal Biology (FBN), Institute for Genome Biology, Functional Genome Analysis Research Unit, Wilhelm-Stahl-Allee 2, D-18196, Dummerstorf, Germany
| | - Nares Trakooljul
- Leibniz Institute for Farm Animal Biology (FBN), Institute for Genome Biology, Genomics Research Unit, Wilhelm-Stahl-Allee 2, D-18196, Dummerstorf, Germany
| | - Klaus Wimmers
- Leibniz Institute for Farm Animal Biology (FBN), Institute for Genome Biology, Genomics Research Unit, Wilhelm-Stahl-Allee 2, D-18196, Dummerstorf, Germany
| | - Siriluck Ponsuksili
- Leibniz Institute for Farm Animal Biology (FBN), Institute for Genome Biology, Functional Genome Analysis Research Unit, Wilhelm-Stahl-Allee 2, D-18196, Dummerstorf, Germany.
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26
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García-Martínez S, Sánchez Hurtado MA, Gutiérrez H, Sánchez Margallo FM, Romar R, Latorre R, Coy P, López Albors O. Mimicking physiological O2 tension in the female reproductive tract improves assisted reproduction outcomes in pig. Mol Hum Reprod 2019; 24:260-270. [PMID: 29490063 DOI: 10.1093/molehr/gay008] [Citation(s) in RCA: 27] [Impact Index Per Article: 5.4] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/20/2017] [Accepted: 02/26/2018] [Indexed: 01/20/2023] Open
Abstract
STUDY QUESTION Is O2 tension in the pig oviduct and uterus affected by the estrous cycle stage and the animal's age, and can the outcome of in vitro embryo development be improved by mimicking these physiological values? SUMMARY ANSWER O2 tension within the pig reproductive organs is affected by the animal's age, and values close to those measured in vivo have a positive impact on embryo development and quality when used during IVF and embryo culture (EC). WHAT IS KNOWN ALREADY To obtain a healthy embryo in vitro, it is necessary to adopt a culture microenvironment that approximates physiological conditions. Despite advances in surgical procedures and sensitive probes that allow accurate assessment of in vivo O2 tension, few such studies have been conducted recently in mammals. In addition, no reference values of physiological O2 tension in the reproductive tract exist for large animal models such as pig, and the effect of O2 tension on ART outcomes is unknown. STUDY DESIGN, SIZE, DURATION This study was conducted in pigs. We measured oviductal and uterine O2 tension (n = 29 and 13, respectively) and then examined how the use of the physiological values in pig IVF and EC affected pig ART output (n = 1447 oocytes). PARTICIPANTS/MATERIALS, SETTING, METHODS The oviductal and uterine O2 tension at the different stages of the estrous cycle was monitored using a laparo-endoscopic single-site surgery (LESS) assisted approach along with a flexible and thin miniaturized luminescent probe. Two groups of pigs, Large-white × Landrace breed, were used: for the first group, 16 pre-pubertal gilts (5 months old and 95 kg) were induced to ovulate with equine chorionic gonadotropin (eCG) and human chorionic gonadotropin (hCG); in the second group 13 mature sows (24-48 months and 185 kg) were used. IVF and EC were performed at two different O2 tensions: Atmospheric O2 (20%) and the mean in vivo value measured (7%). At 18-20 h post-insemination (hpi), a small sample of presumptive zygotes were fixed, stained and examined under epifluorescence microscopy to assess the fertilization rates. At 48 hpi, cleavage was evaluated under the stereomicroscope. Finally, at 180 hpi, development to the blastocyst stage was quantified, blastocyst morphology was assessed, and embryos were fixed and stained to count the mean cell number per blastocyst. MAIN RESULTS AND THE ROLE OF CHANCE The mean O2 content within the pig oviduct and uterus was always lower than in ambient air. The average O2 percentage was higher in gilts (10.0%) than in sows (7.6%) (P < 0.0001). The cleavage rate of porcine in vitro fertilized embryos maintained under 7% O2 during IVF and EC was significantly higher (60.0 ± 2.3) compared with those cultured under 20% O2 (32.0 ± 2.2) (P < 0.05). An increase in the number of cells in embryos cultured under the low O2 concentration (88.9 ± 5.9) was observed compared to those cultured under 20% O2 (59.0 ± 5.0) (P < 0.05). LARGE SCALE DATA None. LIMITATIONS, REASONS FOR CAUTION Although minimally invasive surgery was used the effect of anesthesia and manipulations on O2 tension within the organs are unknown. WIDER IMPLICATIONS OF THE FINDINGS Using physiological oxygen concentrations in IVF/EC could improve ART outcomes. STUDY FUNDING AND COMPETING INTEREST(S) This study was funded by Spanish Ministry of Economy and Competitiveness (MINECO) and European Regional Development Fund (FEDER). Grants AGL2012-40180-C03-01 and AGL2015-66341-R. The authors declare no conflict of interest.
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Affiliation(s)
- S García-Martínez
- Dept. Physiology, Facultad de Veterinaria, Campus Internacional de Excelencia de Educación Superior (Campus Mare Nostrum), Universidad de Murcia, Murcia 30100, España.,Instituto Murciano de Investigación Biosanitaria Virgen de la Arrixaca (IMIB-Arrixaca), Murcia, España
| | - M A Sánchez Hurtado
- Laparoscopy Unit, Minimally Invasive Surgery Center Jesús Usón, Cáceres 10071, España
| | - H Gutiérrez
- Dept. Animal Health, Faculty of Veterinary Medicine and Zootechnics, University Nacional of Colombia, Carrera 30 45-03, Bogotá, Colombia.,Dept. Anatomy & Comparative Physiology, Facultad de Veterinaria, Campus Internacional de Excelencia de Educación Superior (Campus Mare Nostrum), Universidad de Murcia, Murcia 30100, España
| | - F M Sánchez Margallo
- Laparoscopy Unit, Minimally Invasive Surgery Center Jesús Usón, Cáceres 10071, España
| | - R Romar
- Dept. Physiology, Facultad de Veterinaria, Campus Internacional de Excelencia de Educación Superior (Campus Mare Nostrum), Universidad de Murcia, Murcia 30100, España.,Instituto Murciano de Investigación Biosanitaria Virgen de la Arrixaca (IMIB-Arrixaca), Murcia, España
| | - R Latorre
- Dept. Anatomy & Comparative Physiology, Facultad de Veterinaria, Campus Internacional de Excelencia de Educación Superior (Campus Mare Nostrum), Universidad de Murcia, Murcia 30100, España
| | - P Coy
- Dept. Physiology, Facultad de Veterinaria, Campus Internacional de Excelencia de Educación Superior (Campus Mare Nostrum), Universidad de Murcia, Murcia 30100, España.,Instituto Murciano de Investigación Biosanitaria Virgen de la Arrixaca (IMIB-Arrixaca), Murcia, España
| | - O López Albors
- Dept. Anatomy & Comparative Physiology, Facultad de Veterinaria, Campus Internacional de Excelencia de Educación Superior (Campus Mare Nostrum), Universidad de Murcia, Murcia 30100, España
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27
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Wang X, Kadarmideen HN. An Epigenome-Wide DNA Methylation Map of Testis in Pigs for Study of Complex Traits. Front Genet 2019; 10:405. [PMID: 31114612 PMCID: PMC6502962 DOI: 10.3389/fgene.2019.00405] [Citation(s) in RCA: 20] [Impact Index Per Article: 4.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/24/2018] [Accepted: 04/12/2019] [Indexed: 12/17/2022] Open
Abstract
Epigenetic changes are important for understanding complex trait variation and inheritance in pigs that are also a valuable biomedical model for human health research. Testis is the main organ for reproduction and boar taint in pigs; however, there have been no studies to-date on adult pig testis epigenome. The main objective of this study was to establish a genome-wide DNA methylation map of pig testis that would help identify candidate epigenetic biomarkers and methylated genes for complex traits such as male reproduction, fertility or boar taint. Reduced Representation Bisulfite Sequencing (RRBS) was used to study methylation levels of cytosine in nine pig testis samples. The results showed that genome-wide methylation status of nine samples overlapped greatly and their variation among pigs were low. The methylation levels of promoter, exon, intron, cytosine and guanine dinucleotide (CpG) islands and CpG island shores regions were 0.15, 0.47, 0.55, 0.39, and 0.53, respectively. Cytosines binding to CpG islands showed different methylation levels between exon and intron regions. All methylation levels of CpG islands were lower than CpG island shores in different genic features. The distribution of 12,738 differentially methylated cytosines (DMCs) within CpG islands, CpG island shores and other regions was 36.86, 21.65, and 41.49%, respectively, and was 0.33, 1.71, 5.95, and 92.01% in promoter, exon, intron and intergenic regions, respectively. Methylation levels of DMCs in promoter, exon and intron regions were significantly different between CpG islands and CpG island shores (P < 0.05). A total of 898 genes with 2089 DMCs were enriched in 112 Gene Ontology (GO) terms. Fifteen methylated genes from our study were associated with fertility or boar taint traits. Our analysis revealed the methylation patterns in different genic features and CpG island regions of testis in pigs, and summarized several candidate genes associated with DMCs and the involved GO terms. These findings are helpful to understand the relationship between DNA methylation and genic CpG islands, to provide candidate epigenetic regions or biomarkers for pig production and welfare and for translational epigenomic studies that use pigs as an animal model for human research.
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Affiliation(s)
- Xiao Wang
- Quantitative Genomics, Bioinformatics and Computational Biology Group, Department of Applied Mathematics and Computer Science, Technical University of Denmark, Kongens Lyngby, Denmark
| | - Haja N Kadarmideen
- Quantitative Genomics, Bioinformatics and Computational Biology Group, Department of Applied Mathematics and Computer Science, Technical University of Denmark, Kongens Lyngby, Denmark
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28
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Xu C, Wu S, Schook LB, Schachtschneider KM. Translating Human Cancer Sequences Into Personalized Porcine Cancer Models. Front Oncol 2019; 9:105. [PMID: 30873383 PMCID: PMC6401626 DOI: 10.3389/fonc.2019.00105] [Citation(s) in RCA: 7] [Impact Index Per Article: 1.4] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/17/2018] [Accepted: 02/04/2019] [Indexed: 12/31/2022] Open
Abstract
The global incidence of cancer is rapidly rising, and despite an improved understanding of cancer molecular biology, immune landscapes, and advancements in cytotoxic, biologic, and immunologic anti-cancer therapeutics, cancer remains a leading cause of death worldwide. Cancer is caused by the accumulation of a series of gene mutations called driver mutations that confer selective growth advantages to tumor cells. As cancer therapies move toward personalized medicine, predictive modeling of the role driver mutations play in tumorigenesis and therapeutic susceptibility will become essential. The development of next-generation sequencing technology has made the evaluation of mutated genes possible in clinical practice, allowing for identification of driver mutations underlying cancer development in individual patients. This, combined with recent advances in gene editing technologies such as CRISPR-Cas9 enables development of personalized tumor models for prediction of treatment responses for mutational profiles observed clinically. Pigs represent an ideal animal model for development of personalized tumor models due to their similar size, anatomy, physiology, metabolism, immunity, and genetics compared to humans. Such models would support new initiatives in precision medicine, provide approaches to create disease site tumor models with designated spatial and temporal clinical outcomes, and create standardized tumor models analogous to human tumors to enable therapeutic studies. In this review, we discuss the process of utilizing genomic sequencing approaches, gene editing technologies, and transgenic porcine cancer models to develop clinically relevant, personalized large animal cancer models for use in co-clinical trials, ultimately improving treatment stratification and translation of novel therapeutic approaches to clinical practice.
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Affiliation(s)
- Chunlong Xu
- State Key Laboratory of Agrobiotechnology, College of Biological Sciences, China Agricultural University, Beijing, China
| | - Sen Wu
- State Key Laboratory of Agrobiotechnology, College of Biological Sciences, China Agricultural University, Beijing, China
| | - Lawrence B Schook
- Department of Radiology, University of Illinois at Chicago, Chicago, IL, United States.,Department of Animal Sciences, University of Illinois at Urbana-Champaign, Urbana, IL, United States.,National Center for Supercomputing Applications, University of Illinois at Urbana-Champaign, Urbana, IL, United States
| | - Kyle M Schachtschneider
- Department of Radiology, University of Illinois at Chicago, Chicago, IL, United States.,National Center for Supercomputing Applications, University of Illinois at Urbana-Champaign, Urbana, IL, United States.,Department of Biochemistry and Molecular Genetics, University of Illinois at Chicago, Chicago, IL, United States
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Analysis of allele-specific expression of seven candidate genes involved in lipid metabolism in pig skeletal muscle and fat tissues reveals allelic imbalance of ACACA, LEP, SCD, and TNF. J Appl Genet 2019; 60:97-101. [PMID: 30684136 PMCID: PMC6373405 DOI: 10.1007/s13353-019-00485-z] [Citation(s) in RCA: 5] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/17/2018] [Revised: 01/14/2019] [Accepted: 01/15/2019] [Indexed: 12/13/2022]
Abstract
Analysis of allele-specific expression may help to elucidate the genetic architecture of complex traits including fat deposition in pigs. Here, we used pyrosequencing to investigate the allele proportions of candidate genes (ACACA, ADIPOR1, FASN, LEP, ME1, SCD, and TNF) involved in regulation of lipid metabolism in two fat deposits (subcutaneous and visceral fat) and longissimus dorsi muscle of pigs representing Polish Large White, Polish Landrace, Duroc, and Pietrain breeds. We detected differential allelic expression of ACACA, LEP, SCD, and TNF in all tissues analyzed. To search for putative cis-regulatory elements involved in allele-specific expression, we quantified the methylation level within CpG islands located in 5′-flanking regions of ACACA and SCD. Comparison between samples showing markedly disproportionate allelic expression and control groups with similar levels of both alleles did not reveal significant differences. We also assessed the association of rs321308225 (c.*195C>A) an SNP located in the 3′UTR of ACACA with its allelic expression in Polish Landrace pigs, but it was not significant. We conclude that allelic imbalance occurs frequently in regard to genes involved in regulation of lipid deposition in pigs, and further studies are necessary to identify cis-regulatory elements affecting ACACA, LEP, SCD, and TNF expression in porcine fat tissues and skeletal muscle.
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30
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Koehler RC, Yang ZJ, Lee JK, Martin LJ. Perinatal hypoxic-ischemic brain injury in large animal models: Relevance to human neonatal encephalopathy. J Cereb Blood Flow Metab 2018; 38:2092-2111. [PMID: 30149778 PMCID: PMC6282216 DOI: 10.1177/0271678x18797328] [Citation(s) in RCA: 47] [Impact Index Per Article: 7.8] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Indexed: 12/18/2022]
Abstract
Perinatal hypoxia-ischemia resulting in death or lifelong disabilities remains a major clinical disorder. Neonatal models of hypoxia-ischemia in rodents have enhanced our understanding of cellular mechanisms of neural injury in developing brain, but have limitations in simulating the range, accuracy, and physiology of clinical hypoxia-ischemia and the relevant systems neuropathology that contribute to the human brain injury pattern. Large animal models of perinatal hypoxia-ischemia, such as partial or complete asphyxia at the time of delivery of fetal monkeys, umbilical cord occlusion and cerebral hypoperfusion at different stages of gestation in fetal sheep, and severe hypoxia and hypoperfusion in newborn piglets, have largely overcome these limitations. In monkey, complete asphyxia produces preferential injury to cerebellum and primary sensory nuclei in brainstem and thalamus, whereas partial asphyxia produces preferential injury to somatosensory and motor cortex, basal ganglia, and thalamus. Mid-gestational fetal sheep provide a valuable model for studying vulnerability of progenitor oligodendrocytes. Hypoxia followed by asphyxia in newborn piglets replicates the systems injury seen in term newborns. Efficacy of post-insult hypothermia in animal models led to the success of clinical trials in term human neonates. Large animal models are now being used to explore adjunct therapy to augment hypothermic neuroprotection.
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Affiliation(s)
- Raymond C Koehler
- 1 Department of Anesthesiology and Critical Care Medicine, Johns Hopkins University, Baltimore, MD, USA
| | - Zeng-Jin Yang
- 1 Department of Anesthesiology and Critical Care Medicine, Johns Hopkins University, Baltimore, MD, USA
| | - Jennifer K Lee
- 1 Department of Anesthesiology and Critical Care Medicine, Johns Hopkins University, Baltimore, MD, USA.,2 The Pathobiology Graduate Training Program, Johns Hopkins University, Baltimore, MD, USA
| | - Lee J Martin
- 2 The Pathobiology Graduate Training Program, Johns Hopkins University, Baltimore, MD, USA.,3 Department of Pathology, Division of Neuropathology, Johns Hopkins University, Baltimore, MD, USA
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31
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Boettcher AN, Loving CL, Cunnick JE, Tuggle CK. Development of Severe Combined Immunodeficient (SCID) Pig Models for Translational Cancer Modeling: Future Insights on How Humanized SCID Pigs Can Improve Preclinical Cancer Research. Front Oncol 2018; 8:559. [PMID: 30560086 PMCID: PMC6284365 DOI: 10.3389/fonc.2018.00559] [Citation(s) in RCA: 26] [Impact Index Per Article: 4.3] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/27/2018] [Accepted: 11/09/2018] [Indexed: 12/13/2022] Open
Abstract
Within the last decade there have been several severe combined immunodeficient (SCID) pig models discovered or genetically engineered. The animals have mutations in ARTEMIS, IL2RG, or RAG1/2 genes, or combinations thereof, providing SCID pigs with NK cells, but deficient in T and B cells, or deficient in NK, T, and B cells for research studies. Biocontainment facilities and positive pressure isolators are developed to limit pathogen exposure and prolong the life of SCID pigs. Raising SCID pigs in such facilities allows for completion of long-term studies such as xenotransplantation of human cells. Ectopically injected human cancer cell lines develop into tumors in SCID pigs, thus providing a human-sized in vivo model for evaluating imaging methods to improve cancer detection and therapeutic research and development. Immunocompromised pigs have the potential to be immunologically humanized by xenotransplantation with human hematopoietic stem cells, peripheral blood leukocytes, or fetal tissue. These cells can be introduced through various routes including injection into fetal liver or the intraperitoneal (IP) space, or into piglets by intravenous, IP, and intraosseous administration. The development and maintenance of transplanted human immune cells would be initially (at least) dependent on immune signaling from swine cells. Compared to mice, swine share higher homology in immune related genes with humans. We hypothesize that the SCID pig may be able to support improved engraftment and differentiation of a wide range of human immune cells as compared to equivalent mouse models. Humanization of SCID pigs would thus provide a valuable model system for researchers to study interactions between human tumor and human immune cells. Additionally, as the SCID pig model is further developed, it may be possible to develop patient-derived xenograft models for individualized therapy and drug testing. We thus theorize that the individualized therapeutic approach would be significantly improved with a humanized SCID pig due to similarities in size, metabolism, and physiology. In all, porcine SCID models have significant potential as an excellent preclinical animal model for therapeutic testing.
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Affiliation(s)
| | - Crystal L. Loving
- Food Safety and Enteric Pathogens Unit, National Animal Disease Center, Agricultural Research Service, United States Department of Agriculture, Ames, IA, United States
| | - Joan E. Cunnick
- Department of Animal Science, Iowa State University, Ames, IA, United States
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32
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Stachowiak M, Szczerbal I, Flisikowski K. Investigation of allele-specific expression of genes involved in adipogenesis and lipid metabolism suggests complex regulatory mechanisms of PPARGC1A expression in porcine fat tissues. BMC Genet 2018; 19:107. [PMID: 30497374 PMCID: PMC6267897 DOI: 10.1186/s12863-018-0696-6] [Citation(s) in RCA: 7] [Impact Index Per Article: 1.2] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/05/2018] [Accepted: 11/19/2018] [Indexed: 02/06/2023] Open
Abstract
Background The expression of genes involved in regulating adipogenesis and lipid metabolism may affect economically important fatness traits in pigs. Allele-specific expression (ASE) reflects imbalance between allelic transcript levels and can be used to identify underlying cis-regulatory elements. ASE has not yet been intensively studied in pigs. The aim of this investigation was to analyze the differential allelic expression of four genes, PPARA, PPARG, SREBF1, and PPARGC1A, which are involved in the regulation of fat deposition in porcine subcutaneous and visceral fat and longissimus dorsi muscle. Results Quantification of allelic proportions by pyrosequencing revealed that both alleles of PPARG and SREBF1 are expressed at similar levels. PPARGC1A showed the greatest ASE imbalance in fat deposits in Polish Large White (PLW), Polish Landrace and Pietrain pigs; and PPARA in PLW pigs. Significant deviations of mean PPARGC1A allelic transcript ratio between cDNA and genomic DNA were detected in all tissues, with the most pronounced difference (p < 0.001) in visceral fat of PLW pigs. To search for potential cis-regulatory elements affecting ASE in the PPARGC1A gene we analyzed the effects of four SNPs (rs337351686, rs340650517, rs336405906 and rs345224049) in the promoter region, but none were associated with ASE in the breeds studied. DNA methylation analysis revealed significant CpG methylation differences between samples showing balanced (allelic transcript ratio ≈1) and imbalanced allelic expression for CpG site at the genomic position in chromosome 8 (SSC8): 18527678 in visceral fat (p = 0.017) and two CpG sites (SSC8:18525215, p = 0.030; SSC8:18525237, p = 0.031) in subcutaneous fat. Conclusions Our analysis of differential allelic expression suggests that PPARGC1A is subjected to cis-regulation in porcine fat tissues. Further studies are necessary to identify other regulatory elements localized outside the PPARGC1A proximal promoter region. Electronic supplementary material The online version of this article (10.1186/s12863-018-0696-6) contains supplementary material, which is available to authorized users.
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Affiliation(s)
- Monika Stachowiak
- Department of Genetics and Animal Breeding, Poznan University of Life Sciences, Wolynska 33, 60-637, Poznan, Poland.
| | - Izabela Szczerbal
- Department of Genetics and Animal Breeding, Poznan University of Life Sciences, Wolynska 33, 60-637, Poznan, Poland
| | - Krzysztof Flisikowski
- Chair of Livestock Biotechnology, Technical University of Munich, Liesel-Beckmannstr. 1, 85354, Freising, Germany
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33
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Zhou Y, Connor EE, Bickhart DM, Li C, Baldwin RL, Schroeder SG, Rosen BD, Yang L, Van Tassell CP, Liu GE. Comparative whole genome DNA methylation profiling of cattle sperm and somatic tissues reveals striking hypomethylated patterns in sperm. Gigascience 2018; 7:4965117. [PMID: 29635292 PMCID: PMC5928411 DOI: 10.1093/gigascience/giy039] [Citation(s) in RCA: 42] [Impact Index Per Article: 7.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/07/2017] [Accepted: 03/28/2018] [Indexed: 12/21/2022] Open
Abstract
Background Although sperm DNA methylation has been studied in humans and other species, its status in cattle is largely unknown. Results Using whole-genome bisulfite sequencing (WGBS), we profiled the DNA methylome of cattle sperm through comparison with three somatic tissues (mammary gland, brain, and blood). Large differences between cattle sperm and somatic cells were observed in the methylation patterns of global CpGs, pericentromeric satellites, partially methylated domains (PMDs), hypomethylated regions (HMRs), and common repeats. As expected, we observed low methylation in the promoter regions and high methylation in the bodies of active genes. We detected selective hypomethylation of megabase domains of centromeric satellite clusters, which may be related to chromosome segregation during meiosis and their rapid transcriptional activation upon fertilization. We found more PMDs in sperm cells than in somatic cells and identified meiosis-related genes such asKIF2B and REPIN1, which are hypomethylated in sperm but hypermethylated in somatic cells. In addition to the common HMRs around gene promoters, which showed substantial differences between sperm and somatic cells, the sperm-specific HMRs also targeted to distinct spermatogenesis-related genes, including BOLL, MAEL, ASZ1, SYCP3, CTCFL, MND1, SPATA22, PLD6, DDX4, RBBP8, FKBP6, and SYCE1. Although common repeats were heavily methylated in both sperm and somatic cells, some young Bov-A2 repeats, which belong to the SINE family, were hypomethylated in sperm and could affect the promoter structures by introducing new regulatory elements. Conclusions Our study provides a comprehensive resource for bovine sperm epigenomic research and enables new discoveries about DNA methylation and its role in male fertility.
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Affiliation(s)
- Yang Zhou
- Key Laboratory of Agricultural Animal Genetics, Breeding and Reproduction, Education Ministry of China, Huazhong Agricultural University, Wuhan, Hubei, 430070, China.,Animal Genomics and Improvement Laboratory, BARC, US Department of Agriculture, Agriculture Research Service, Beltsville, MD 20705, USA
| | - Erin E Connor
- Animal Genomics and Improvement Laboratory, BARC, US Department of Agriculture, Agriculture Research Service, Beltsville, MD 20705, USA
| | - Derek M Bickhart
- The Cell Wall Utilization and Biology Laboratory, US Department of Agriculture, Agriculture Research Service, Madison, WI, 53706, USA
| | - Congjun Li
- Animal Genomics and Improvement Laboratory, BARC, US Department of Agriculture, Agriculture Research Service, Beltsville, MD 20705, USA
| | - Ransom L Baldwin
- Animal Genomics and Improvement Laboratory, BARC, US Department of Agriculture, Agriculture Research Service, Beltsville, MD 20705, USA
| | - Steven G Schroeder
- Animal Genomics and Improvement Laboratory, BARC, US Department of Agriculture, Agriculture Research Service, Beltsville, MD 20705, USA
| | - Benjamin D Rosen
- Animal Genomics and Improvement Laboratory, BARC, US Department of Agriculture, Agriculture Research Service, Beltsville, MD 20705, USA
| | - Liguo Yang
- Key Laboratory of Agricultural Animal Genetics, Breeding and Reproduction, Education Ministry of China, Huazhong Agricultural University, Wuhan, Hubei, 430070, China
| | - Curtis P Van Tassell
- Animal Genomics and Improvement Laboratory, BARC, US Department of Agriculture, Agriculture Research Service, Beltsville, MD 20705, USA
| | - George E Liu
- Animal Genomics and Improvement Laboratory, BARC, US Department of Agriculture, Agriculture Research Service, Beltsville, MD 20705, USA
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34
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Ye M, Misra SK, De AK, Ostadhossein F, Singh K, Rund L, Schook L, Pan D. Design, Synthesis, and Characterization of Globular Orphan Nuclear Receptor Regulator with Biological Activity in Soft Tissue Sarcoma. J Med Chem 2018; 61:10739-10752. [PMID: 30375864 DOI: 10.1021/acs.jmedchem.8b01387] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.2] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 02/04/2023]
Abstract
Sarcomas are rare and heterogeneous cancer variants of mesenchymal origin. Their genetic heterogeneity coupled with uncertain histogenesis makes them difficult to treat and results in poor prognosis. In this work, we show that structure-based drug discovery involving computational modeling can be used to identify a new retinoid X receptor (RXR) agonist ligand with a bis(indolyl)methane scaffold. This agent co-self-assembles with an amphiphilic diblock copolymer resulting in nanoparticles (Nano-RXR) with excellent kinetic stability, which were evaluated for efficacy and safety in transformed sarcoma cells, 63-3 Cre and 141-10 Cre of pig origin, and in rodent xenograft models. Responses at gene and protein levels established the treatment approach as a highly effective RXR agonist across cell, rodent, and "Oncopig" models. Interestingly, Nano-RXR was not only able to modulate metabolic and transporter genes related to orphan nuclear receptors but also played a major role in modulating programmed cell death in sarcomas developed in Oncopigs.
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Affiliation(s)
- Mao Ye
- Department of Bioengineering , University of Illinois at Urbana-Champaign , Urbana , Illinois 61801 , United States
| | - Santosh K Misra
- Department of Bioengineering , University of Illinois at Urbana-Champaign , Urbana , Illinois 61801 , United States
| | - Arun K De
- Department of Animal Sciences , University of Illinois at Urbana-Champaign , Urbana , Illinois 61801 , United States.,Agricultural Animal Care and Use Program , University of Illinois at Urbana-Champaign , Urbana , Illinois 61801 , United States
| | - Fatemeh Ostadhossein
- Department of Bioengineering , University of Illinois at Urbana-Champaign , Urbana , Illinois 61801 , United States
| | - Kuldeep Singh
- Veterinary Diagnostic Laboratory , University of Illinois at Urbana-Champaign , Urbana , Illinois 61801 , United States
| | - Laurie Rund
- Department of Animal Sciences , University of Illinois at Urbana-Champaign , Urbana , Illinois 61801 , United States.,Agricultural Animal Care and Use Program , University of Illinois at Urbana-Champaign , Urbana , Illinois 61801 , United States.,Veterinary Diagnostic Laboratory , University of Illinois at Urbana-Champaign , Urbana , Illinois 61801 , United States
| | - Lawrence Schook
- Department of Animal Sciences , University of Illinois at Urbana-Champaign , Urbana , Illinois 61801 , United States.,Agricultural Animal Care and Use Program , University of Illinois at Urbana-Champaign , Urbana , Illinois 61801 , United States.,Veterinary Diagnostic Laboratory , University of Illinois at Urbana-Champaign , Urbana , Illinois 61801 , United States
| | - Dipanjan Pan
- Department of Bioengineering , University of Illinois at Urbana-Champaign , Urbana , Illinois 61801 , United States.,Beckman Institute of Advanced Science and Technology , University of Illinois at Urbana-Champaign , Urbana , Illinois 61801 , United States.,Mills Breast Cancer Institute , Carle Foundation Hospital , 502 N. Busey , Urbana , Illinois 61801 , United States.,Department of Materials Science and Engineering , University of Illinois at Urbana-Champaign , Urbana , Illinois 61801 , United States.,Carle-Illinois College of Medicine , Urbana , Illinois 61801 , United States
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35
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Giuffra E, Tuggle CK. Functional Annotation of Animal Genomes (FAANG): Current Achievements and Roadmap. Annu Rev Anim Biosci 2018; 7:65-88. [PMID: 30427726 DOI: 10.1146/annurev-animal-020518-114913] [Citation(s) in RCA: 99] [Impact Index Per Article: 16.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/09/2022]
Abstract
Functional annotation of genomes is a prerequisite for contemporary basic and applied genomic research, yet farmed animal genomics is deficient in such annotation. To address this, the FAANG (Functional Annotation of Animal Genomes) Consortium is producing genome-wide data sets on RNA expression, DNA methylation, and chromatin modification, as well as chromatin accessibility and interactions. In addition to informing our understanding of genome function, including comparative approaches to elucidate constrained sequence or epigenetic elements, these annotation maps will improve the precision and sensitivity of genomic selection for animal improvement. A scientific community-driven effort has already created a coordinated data collection and analysis enterprise crucial for the success of this global effort. Although it is early in this continuing process, functional data have already been produced and application to genetic improvement reported. The functional annotation delivered by the FAANG initiative will add value and utility to the greatly improved genome sequences being established for domesticated animal species.
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Affiliation(s)
- Elisabetta Giuffra
- Génétique Animale et Biologie Intégrative (GABI), Institut National de la Recherche Agronomique (INRA), AgroParisTech, Université Paris Saclay, 78350 Jouy-en-Josas, France;
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36
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Zhao F, Wu W, Wei Q, Shen M, Li B, Jiang Y, Liu K, Liu H. Exogenous adrenocorticotropic hormone affects genome‐wide DNA methylation and transcriptome of corpus luteum in sows. FASEB J 2018; 33:3264-3278. [DOI: 10.1096/fj.201801081rrr] [Citation(s) in RCA: 3] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/29/2022]
Affiliation(s)
- Fang Zhao
- Laboratory of Animal Genetics and BreedingCollege of Animal Science and TechnologyNanjing Agricultural University Nanjing China
| | - Wangjun Wu
- Laboratory of Animal Genetics and BreedingCollege of Animal Science and TechnologyNanjing Agricultural University Nanjing China
| | - Quanwei Wei
- Laboratory of Animal ReproductionCollege of Animal Science and TechnologyNanjing Agricultural University Nanjing China
| | - Ming Shen
- Laboratory of Animal Genetics and BreedingCollege of Animal Science and TechnologyNanjing Agricultural University Nanjing China
| | - Bojiang Li
- Laboratory of Animal Genetics and BreedingCollege of Animal Science and TechnologyNanjing Agricultural University Nanjing China
| | - Yi Jiang
- Laboratory of Animal Genetics and BreedingCollege of Animal Science and TechnologyNanjing Agricultural University Nanjing China
| | - Kaiqing Liu
- Laboratory of Animal Genetics and BreedingCollege of Animal Science and TechnologyNanjing Agricultural University Nanjing China
| | - Honglin Liu
- Laboratory of Animal Genetics and BreedingCollege of Animal Science and TechnologyNanjing Agricultural University Nanjing China
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37
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Li C, Zou C, Cui Y, Fu Y, Fang C, Li Y, Li J, Wang W, Xiang H, Li C. Genome-wide epigenetic landscape of pig lincRNAs and their evolution during porcine domestication. Epigenomics 2018; 10:1603-1618. [PMID: 30371096 DOI: 10.2217/epi-2017-0117] [Citation(s) in RCA: 3] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 02/06/2023] Open
Abstract
AIM We aimed to identify previously unreported long intergenic noncoding RNAs (lincRNAs) in the porcine liver, an important metabolic tissue, and further illustrate the epigenomic landscapes and the evolution of lincRNAs. MATERIALS & METHODS We used porcine omics data and comprehensively analyzed and identified lincRNAs and their methylation, expression and evolutionary patterns during pig domestication. RESULTS LincRNAs exhibit highly methylated promoter and downstream regions, as well as lower expression levels and higher tissue specificity than protein-coding genes. We identified a batch of lincRNAs with selection signals that are associated with pig domestication, which are more highly expressed in the liver than in other tissues (19:10/8/6/3/2/1/1). Interestingly, the lincRNA linc-sscg1779 and its target gene C6, which is crucial in liver metabolism, are differentially expressed during pig domestication. CONCLUSION Although they may originate from noisy transcripts, lincRNAs may be subjected to artificial selection. This phenomenon implies the functional importance of lincRNAs in pig domestication.
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Affiliation(s)
- Cencen Li
- Key Lab of Agriculture Animal Genetics, Breeding, & Reproduction of Ministry of Education, College of Animal Science & Technology, Huazhong Agricultural University, Wuhan 430070, PR China
| | - Cheng Zou
- Key Lab of Agriculture Animal Genetics, Breeding, & Reproduction of Ministry of Education, College of Animal Science & Technology, Huazhong Agricultural University, Wuhan 430070, PR China
| | - Yong Cui
- Guangzhou Key Laboratory of Insect Development Regulation & Application Research, Institute of Insect Science & Technology & School of Life Sciences, South China Normal University, Guangzhou, 510631, PR China
| | - Yuhua Fu
- Key Lab of Agriculture Animal Genetics, Breeding, & Reproduction of Ministry of Education, College of Animal Science & Technology, Huazhong Agricultural University, Wuhan 430070, PR China
| | - Chengchi Fang
- Key Lab of Agriculture Animal Genetics, Breeding, & Reproduction of Ministry of Education, College of Animal Science & Technology, Huazhong Agricultural University, Wuhan 430070, PR China
| | - Yao Li
- Key Lab of Agriculture Animal Genetics, Breeding, & Reproduction of Ministry of Education, College of Animal Science & Technology, Huazhong Agricultural University, Wuhan 430070, PR China
| | - Jingxuan Li
- Key Lab of Agriculture Animal Genetics, Breeding, & Reproduction of Ministry of Education, College of Animal Science & Technology, Huazhong Agricultural University, Wuhan 430070, PR China
| | - Wen Wang
- Center for Ecological and Environmental Sciences, Key Laboratory for Space Bioscience & Biotechnology, Northwestern Poly-technical University, Xi'an, 710072, PR China
| | - Hui Xiang
- Guangzhou Key Laboratory of Insect Development Regulation & Application Research, Institute of Insect Science & Technology & School of Life Sciences, South China Normal University, Guangzhou, 510631, PR China
| | - Changchun Li
- Key Lab of Agriculture Animal Genetics, Breeding, & Reproduction of Ministry of Education, College of Animal Science & Technology, Huazhong Agricultural University, Wuhan 430070, PR China
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38
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Chen X, Shen LH, Gui LX, Yang F, Li J, Cao SZ, Zuo ZC, Ma XP, Deng JL, Ren ZH, Chen ZX, Yu SM. Genome-wide DNA methylation profile of prepubertal porcine testis. Reprod Fertil Dev 2018; 30:349-358. [PMID: 28727982 DOI: 10.1071/rd17067] [Citation(s) in RCA: 10] [Impact Index Per Article: 1.7] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/21/2017] [Accepted: 06/17/2017] [Indexed: 12/11/2022] Open
Abstract
The biological structure and function of the mammalian testis undergo important developmental changes during prepuberty and DNA methylation is dynamically regulated during testis development. In this study, we generated the first genome-wide DNA methylation profile of prepubertal porcine testis using methyl-DNA immunoprecipitation (MeDIP) combined with high-throughput sequencing (MeDIP-seq). Over 190 million high-quality reads were generated, containing 43642 CpG islands. There was an overall downtrend of methylation during development, which was clear in promoter regions but less so in gene-body regions. We also identified thousands of differentially methylated regions (DMRs) among the three prepubertal time points (1 month, T1; 2 months, T2; 3 months, T3), the majority of which showed decreasing methylation levels over time. Gene Ontology (GO) and Kyoto Encyclopedia of Genes and Genomes (KEGG) pathway analyses revealed that many genes in the DMRs were linked with cell proliferation and some important pathways in porcine testis development. Our data suggest that DNA methylation plays an important role in prepubertal development of porcine testis, with an obvious downtrend of methylation levels from T1 to T3. Overall, our study provides a foundation for future studies and gives new insights into mammalian testis development.
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Affiliation(s)
- Xi Chen
- College of Veterinary Medicine, Sichuan Agricultural University, No. 211 Huimin Road, Wenjiang District, Chengdu, 611130, China
| | - Liu-Hong Shen
- College of Veterinary Medicine, Sichuan Agricultural University, No. 211 Huimin Road, Wenjiang District, Chengdu, 611130, China
| | - Li-Xuan Gui
- OnMath Science and Technology Limited Company, No. 500 Tianfu Road, Chengdu, Sichuan, 611130, China
| | - Fang Yang
- College of Veterinary Medicine, Sichuan Agricultural University, No. 211 Huimin Road, Wenjiang District, Chengdu, 611130, China
| | - Jie Li
- College of Veterinary Medicine, Sichuan Agricultural University, No. 211 Huimin Road, Wenjiang District, Chengdu, 611130, China
| | - Sui-Zhong Cao
- College of Veterinary Medicine, Sichuan Agricultural University, No. 211 Huimin Road, Wenjiang District, Chengdu, 611130, China
| | - Zhi-Cai Zuo
- College of Veterinary Medicine, Sichuan Agricultural University, No. 211 Huimin Road, Wenjiang District, Chengdu, 611130, China
| | - Xiao-Ping Ma
- College of Veterinary Medicine, Sichuan Agricultural University, No. 211 Huimin Road, Wenjiang District, Chengdu, 611130, China
| | - Jun-Liang Deng
- College of Veterinary Medicine, Sichuan Agricultural University, No. 211 Huimin Road, Wenjiang District, Chengdu, 611130, China
| | - Zhi-Hua Ren
- College of Veterinary Medicine, Sichuan Agricultural University, No. 211 Huimin Road, Wenjiang District, Chengdu, 611130, China
| | - Zhong-Xu Chen
- OnMath Science and Technology Limited Company, No. 500 Tianfu Road, Chengdu, Sichuan, 611130, China
| | - Shu-Min Yu
- College of Veterinary Medicine, Sichuan Agricultural University, No. 211 Huimin Road, Wenjiang District, Chengdu, 611130, China
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Zou C, Li L, Cheng X, Li C, Fu Y, Fang C, Li C. Identification and Functional Analysis of Long Intergenic Non-coding RNAs Underlying Intramuscular Fat Content in Pigs. Front Genet 2018; 9:102. [PMID: 29662503 PMCID: PMC5890112 DOI: 10.3389/fgene.2018.00102] [Citation(s) in RCA: 22] [Impact Index Per Article: 3.7] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/29/2018] [Accepted: 03/13/2018] [Indexed: 12/12/2022] Open
Abstract
Intramuscular fat (IMF) content is an important trait that can affect pork quality. Previous studies have identified many genes that can regulate IMF. Long intergenic non-coding RNAs (lincRNAs) are emerging as key regulators in various biological processes. However, lincRNAs related to IMF in pig are largely unknown, and the mechanisms by which they regulate IMF are yet to be elucidated. Here we reconstructed 105,687 transcripts and identified 1,032 lincRNAs in pig longissimus dorsi muscle (LDM) of four stages with different IMF contents based on published RNA-seq. These lincRNAs show typical characteristics such as shorter length and lower expression compared with protein-coding genes. Combined with methylation data, we found that both the promoter and genebody methylation of lincRNAs can negatively regulate lincRNA expression. We found that lincRNAs exhibit high correlation with their protein-coding neighbors in expression. Co-expression network analysis resulted in eight stage-specific modules, gene ontology and pathway analysis of them suggested that some lincRNAs were involved in IMF-related processes, such as fatty acid metabolism and peroxisome proliferator-activated receptor signaling pathway. Furthermore, we identified hub lincRNAs and found six of them may play important roles in IMF development. This work detailed some lincRNAs which may affect of IMF development in pig, and facilitated future research on these lincRNAs and molecular assisted breeding for pig.
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Affiliation(s)
- Cheng Zou
- Key Laboratory of Agricultural Animal Genetics, Breeding and Reproduction of the Ministry of Education and Key Laboratory of Swine Genetics and Breeding of the Ministry of Agriculture, Huazhong Agricultural University, Wuhan, China
| | - Long Li
- Key Laboratory of Agricultural Animal Genetics, Breeding and Reproduction of the Ministry of Education and Key Laboratory of Swine Genetics and Breeding of the Ministry of Agriculture, Huazhong Agricultural University, Wuhan, China
| | - Xiaofang Cheng
- Key Laboratory of Agricultural Animal Genetics, Breeding and Reproduction of the Ministry of Education and Key Laboratory of Swine Genetics and Breeding of the Ministry of Agriculture, Huazhong Agricultural University, Wuhan, China
| | - Cencen Li
- Key Laboratory of Agricultural Animal Genetics, Breeding and Reproduction of the Ministry of Education and Key Laboratory of Swine Genetics and Breeding of the Ministry of Agriculture, Huazhong Agricultural University, Wuhan, China
| | - Yuhua Fu
- Key Laboratory of Agricultural Animal Genetics, Breeding and Reproduction of the Ministry of Education and Key Laboratory of Swine Genetics and Breeding of the Ministry of Agriculture, Huazhong Agricultural University, Wuhan, China
| | - Chengchi Fang
- Key Laboratory of Agricultural Animal Genetics, Breeding and Reproduction of the Ministry of Education and Key Laboratory of Swine Genetics and Breeding of the Ministry of Agriculture, Huazhong Agricultural University, Wuhan, China
| | - Changchun Li
- Key Laboratory of Agricultural Animal Genetics, Breeding and Reproduction of the Ministry of Education and Key Laboratory of Swine Genetics and Breeding of the Ministry of Agriculture, Huazhong Agricultural University, Wuhan, China.,The Cooperative Innovation Center for Sustainable Pig Production, Wuhan, China
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Pan X, Gong D, Nguyen DN, Zhang X, Hu Q, Lu H, Fredholm M, Sangild PT, Gao F. Early microbial colonization affects DNA methylation of genes related to intestinal immunity and metabolism in preterm pigs. DNA Res 2018; 25:4818260. [PMID: 29365082 PMCID: PMC6014285 DOI: 10.1093/dnares/dsy001] [Citation(s) in RCA: 31] [Impact Index Per Article: 5.2] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/13/2017] [Accepted: 01/08/2018] [Indexed: 01/08/2023] Open
Abstract
Epigenetic regulation may play an important role in mediating microbe-host interactions and adaptation of intestinal gene expression to bacterial colonization just after birth. This is particularly important after preterm birth because the immature intestine is hypersensitive to invading bacteria. We compared the intestinal DNA methylome and microbiome between conventional (CON) and antibiotics-treated (AB) preterm pigs, used as a model for preterm infants. Oral AB treatment reduced bacterial density (∼100-fold), diversity and fermentation, improved the resistance to necrotizing enterocolitis (NEC) and changed the genome-wide DNA methylation in the distal small intestine. Integration of epigenome data with previously obtained proteome data showed that intestinal immune-metabolic pathways were affected by the AB-induced delay in bacterial colonization. DNA methylation and expression of intestinal genes, related to innate immune response, phagocytosis, endothelial homeostasis and tissue metabolism (e.g. CPN1, C3, LBP, HIF1A, MicroRNA-126, PTPRE), differed between AB and CON pigs even before any evidence of NEC lesions. Our findings document that the newborn immature intestine is influenced by bacterial colonization via DNA methylation changes. Microbiota-dependent epigenetic programming of genes related to gut immunity, vascular integrity and metabolism may be critical for short- and long-term intestinal health in preterm neonates.
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Affiliation(s)
- Xiaoyu Pan
- Comparative Pediatrics and Nutrition, Department of Veterinary and Animal Sciences, Faculty of Health and Medical Sciences, University of Copenhagen, Frederiksberg DK 1870 C, Denmark
| | - Desheng Gong
- Genome Analysis Laboratory of the Ministry of Agriculture, Agricultural Genomics Institute at Shenzhen, Chinese Academy of Agricultural Sciences, Shenzhen 518120, China
| | - Duc Ninh Nguyen
- Comparative Pediatrics and Nutrition, Department of Veterinary and Animal Sciences, Faculty of Health and Medical Sciences, University of Copenhagen, Frederiksberg DK 1870 C, Denmark
| | - Xinxin Zhang
- Genome Analysis Laboratory of the Ministry of Agriculture, Agricultural Genomics Institute at Shenzhen, Chinese Academy of Agricultural Sciences, Shenzhen 518120, China
| | - Qi Hu
- Genome Analysis Laboratory of the Ministry of Agriculture, Agricultural Genomics Institute at Shenzhen, Chinese Academy of Agricultural Sciences, Shenzhen 518120, China
| | - Hanlin Lu
- Genome Analysis Laboratory of the Ministry of Agriculture, Agricultural Genomics Institute at Shenzhen, Chinese Academy of Agricultural Sciences, Shenzhen 518120, China
| | - Merete Fredholm
- Animal Genetics, Bioinformatics and Breeding, Department of Veterinary and Animal Sciences, Faculty of Health and Medical Sciences, University of Copenhagen, Frederiksberg DK 1870 C, Denmark
| | - Per T Sangild
- Comparative Pediatrics and Nutrition, Department of Veterinary and Animal Sciences, Faculty of Health and Medical Sciences, University of Copenhagen, Frederiksberg DK 1870 C, Denmark
| | - Fei Gao
- Genome Analysis Laboratory of the Ministry of Agriculture, Agricultural Genomics Institute at Shenzhen, Chinese Academy of Agricultural Sciences, Shenzhen 518120, China
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Fang C, Zou C, Fu Y, Li J, Li Y, Ma Y, Zhao S, Li C. DNA methylation changes and evolution of RNA-based duplication in Sus scrofa: based on a two-step strategy. Epigenomics 2018; 10:199-218. [PMID: 29334230 DOI: 10.2217/epi-2017-0071] [Citation(s) in RCA: 5] [Impact Index Per Article: 0.8] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/21/2022] Open
Abstract
AIM This study aims to couple DNA methylation changes and evolution of retrogenes. MATERIALS & METHODS A new two-step strategy was developed to screen retrogenes. Further, reduced representation bisulfite sequencing and RNA-seq data of eight tissues were used to analyze retrogenes. RESULTS A total of 964 retrocopies were identified and new retrocopies were available for the synthesis of glycans and lipids corresponding to pig phenotypic traits. Retrogenes were consistently hypermethylated. Hypomethylation of parental genes presented more susceptibility to retroposition. Promoter DNA methylation of retrogenes was negatively correlated with evolutionary time and played important roles in regulating retrogene tissue-specific expression pattern. CONCLUSION A two-step procedure is effective and necessary for identifying retrogenes. DNA methylation drives origination, survival, evolution and expression of retrogenes.
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Affiliation(s)
- Chengchi Fang
- Key Lab of Agriculture Animal Genetics, Breeding, & Reproduction of Ministry of Education, College of Animal Sciences & Technology, Huazhong Agricultural University, Wuhan 430070, PR China
| | - Cheng Zou
- Key Lab of Agriculture Animal Genetics, Breeding, & Reproduction of Ministry of Education, College of Animal Sciences & Technology, Huazhong Agricultural University, Wuhan 430070, PR China
| | - Yuhua Fu
- Key Lab of Agriculture Animal Genetics, Breeding, & Reproduction of Ministry of Education, College of Animal Sciences & Technology, Huazhong Agricultural University, Wuhan 430070, PR China
| | - Jingxuan Li
- Key Lab of Agriculture Animal Genetics, Breeding, & Reproduction of Ministry of Education, College of Animal Sciences & Technology, Huazhong Agricultural University, Wuhan 430070, PR China
| | - Yao Li
- Key Lab of Agriculture Animal Genetics, Breeding, & Reproduction of Ministry of Education, College of Animal Sciences & Technology, Huazhong Agricultural University, Wuhan 430070, PR China
| | - Yunlong Ma
- Key Lab of Agriculture Animal Genetics, Breeding, & Reproduction of Ministry of Education, College of Animal Sciences & Technology, Huazhong Agricultural University, Wuhan 430070, PR China
| | - Shuhong Zhao
- Key Lab of Agriculture Animal Genetics, Breeding, & Reproduction of Ministry of Education, College of Animal Sciences & Technology, Huazhong Agricultural University, Wuhan 430070, PR China
| | - Changchun Li
- Key Lab of Agriculture Animal Genetics, Breeding, & Reproduction of Ministry of Education, College of Animal Sciences & Technology, Huazhong Agricultural University, Wuhan 430070, PR China
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Su F, Guo X, Wang Y, Wang Y, Cao G, Jiang Y. Genome-Wide Analysis on the Landscape of Transcriptomes and Their Relationship With DNA Methylomes in the Hypothalamus Reveals Genes Related to Sexual Precocity in Jining Gray Goats. Front Endocrinol (Lausanne) 2018; 9:501. [PMID: 30214427 PMCID: PMC6125331 DOI: 10.3389/fendo.2018.00501] [Citation(s) in RCA: 19] [Impact Index Per Article: 3.2] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Received: 03/28/2018] [Accepted: 08/09/2018] [Indexed: 01/03/2023] Open
Abstract
The Jining Gray goat is famous for its sexual precocity; however, the exact regulatory mechanism is still unknown. The hypothalamus is the key centrum in the process of animal reproduction, especially in signal transduction, and the initiation of puberty. The identification of potential genes and pathways in the hypothalamus of Jining Gray goat is critical to understanding the regulatory mechanism of sexual precocity in these goats. In this study, mRNA transcriptome analysis of the hypothalamus of juvenile and pubertal goats revealed eight genes (NTS, ADORA1, CRH, UCN3, E2F2, PDGFRB, GNRH1, and CACNA1C) and three pathways [neuroactive ligand-receptor interaction; gonadotropin-releasing hormone (GnRH) signal; melanoma] that are involved in this regulation. Subsequent methylation analysis on differentially methylated region (DMR) genes revealed the potential regulation network that influences pubertal onset. Correlation analysis verified the methylation level of some DMR genes correlates negatively with expression level. Integrated analysis between transcriptomes and methylomes identified 80 candidate genes involved in GnRH and neuroactive ligand signal pathways, of which CACNA1C and CRH were differentially expressed genes (DEGs) influenced by methylation level. The GnRH gene was the only DEG not affected by its methylation level. In summary, in this study, we identified eight genes and three pathways that are related to pubertal onset in Jining Gray goats, and the expression of CACNA1C and CRH genes of the GnRH and neuroactive ligand signal pathways were influenced by DNA methylation, while that of the GnRH gene was not affected.
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Affiliation(s)
- Feng Su
- Shandong Provincial Key Laboratory of Animal Biotechnology and Disease Control and Prevention, College of Animal Science and Veterinary Medicine, Shandong Agricultural University, Taian, China
| | - Xiaoli Guo
- Shandong Provincial Key Laboratory of Animal Biotechnology and Disease Control and Prevention, College of Animal Science and Veterinary Medicine, Shandong Agricultural University, Taian, China
| | - Yanchao Wang
- Shandong Provincial Key Laboratory of Animal Biotechnology and Disease Control and Prevention, College of Animal Science and Veterinary Medicine, Shandong Agricultural University, Taian, China
| | - Yuding Wang
- Shandong Provincial Key Laboratory of Animal Biotechnology and Disease Control and Prevention, College of Animal Science and Veterinary Medicine, Shandong Agricultural University, Taian, China
| | - Guiling Cao
- College of Agronomy, Liaocheng University, Liaocheng, China
- *Correspondence: Guiling Cao
| | - Yunliang Jiang
- Shandong Provincial Key Laboratory of Animal Biotechnology and Disease Control and Prevention, College of Animal Science and Veterinary Medicine, Shandong Agricultural University, Taian, China
- Yunliang Jiang
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43
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Villadsen J, Hansen HD, Jørgensen LM, Keller SH, Andersen FL, Petersen IN, Knudsen GM, Svarer C. Automatic delineation of brain regions on MRI and PET images from the pig. J Neurosci Methods 2018; 294:51-58. [DOI: 10.1016/j.jneumeth.2017.11.008] [Citation(s) in RCA: 21] [Impact Index Per Article: 3.5] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/21/2017] [Revised: 10/09/2017] [Accepted: 11/12/2017] [Indexed: 12/20/2022]
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Segatto NV, Remião MH, Schachtschneider KM, Seixas FK, Schook LB, Collares T. The Oncopig Cancer Model as a Complementary Tool for Phenotypic Drug Discovery. Front Pharmacol 2017; 8:894. [PMID: 29259556 PMCID: PMC5723300 DOI: 10.3389/fphar.2017.00894] [Citation(s) in RCA: 10] [Impact Index Per Article: 1.4] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/28/2017] [Accepted: 11/22/2017] [Indexed: 12/14/2022] Open
Abstract
The screening of potential therapeutic compounds using phenotypic drug discovery (PDD) is being embraced once again by researchers and pharmaceutical companies as an approach to enhance the development of new effective therapeutics. Before the genomics and molecular biology era and the consecutive emergence of targeted-drug discovery approaches, PDD was the most common platform used for drug discovery. PDD, also known as phenotypic screening, consists of screening potential compounds in either in vitro cellular or in vivo animal models to identify compounds resulting in a desirable phenotypic change. Using this approach, the biological targets of the compounds are not taken into consideration. Suitable animal models are crucial for the continued validation and discovery of new drugs, as compounds displaying promising results in phenotypic in vitro cell-based and in vivo small animal model screenings often fail in clinical trials. Indeed, this is mainly a result of differential anatomy, physiology, metabolism, immunology, and genetics between humans and currently used pre-clinical small animal models. In contrast, pigs are more predictive of therapeutic treatment outcomes in humans than rodents. In addition, pigs provide an ideal platform to study cancer due to their similarities with humans at the anatomical, physiological, metabolic, and genetic levels. Here we provide a mini-review on the reemergence of PDD in drug development, highlighting the potential of porcine cancer models for improving pre-clinical drug discovery and testing. We also present precision medicine based genetically defined swine cancer models developed to date and their potential as biomedical models.
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Affiliation(s)
- Natalia V. Segatto
- Biotechnology Graduate Program, Molecular and Cellular Oncology Research Group, Laboratory of Cancer Biotechnology, Technology Development Center, Federal University of Pelotas, Pelotas, Brazil
| | - Mariana H. Remião
- Biotechnology Graduate Program, Molecular and Cellular Oncology Research Group, Laboratory of Cancer Biotechnology, Technology Development Center, Federal University of Pelotas, Pelotas, Brazil
| | | | - Fabiana K. Seixas
- Biotechnology Graduate Program, Molecular and Cellular Oncology Research Group, Laboratory of Cancer Biotechnology, Technology Development Center, Federal University of Pelotas, Pelotas, Brazil
| | - Lawrence B. Schook
- Department of Radiology, University of Illinois at Chicago, Chicago, IL, United States
- Department of Animal Sciences, University of Illinois at Urbana–Champaign, Champaign, IL, United States
| | - Tiago Collares
- Biotechnology Graduate Program, Molecular and Cellular Oncology Research Group, Laboratory of Cancer Biotechnology, Technology Development Center, Federal University of Pelotas, Pelotas, Brazil
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45
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Wang Y, Ma C, Sun Y, Li Y, Kang L, Jiang Y. Dynamic transcriptome and DNA methylome analyses on longissimus dorsi to identify genes underlying intramuscular fat content in pigs. BMC Genomics 2017; 18:780. [PMID: 29025412 PMCID: PMC5639760 DOI: 10.1186/s12864-017-4201-9] [Citation(s) in RCA: 33] [Impact Index Per Article: 4.7] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/17/2017] [Accepted: 10/08/2017] [Indexed: 01/12/2023] Open
Abstract
Background The intramuscular fat content (IMF) refers to the amount of fat within muscles, including the sum of phospholipids mainly found in cell membranes, triglycerides and cholesterol, and is determined both by hyperplasia and hypertrophy of adipocyte during the development of pigs. The IMF content is an important economic trait that is genetically controlled by multiple genes. The Laiwu pig is an indigenous fatty pig breed distributed in North China, characterized by excessively higher level of IMF content (9%~12%), therefore, is suitable for the identification of genes controlling IMF variations. To identify genes underlying IMF deposition, we performed genome-wide transcriptome and methylome analyses on longissimus dorsi (LD) muscle in Laiwu pigs across four developmental stages. Results A total of 22,524 expressed genes were detected and 1158 differentially expressed genes (DEGs) were hierarchically clustered in the LD muscle over four developmental stages from 60 d to 400 d. These genes were significantly clustered into four temporal expression profiles, and genes participating in fat cell differentiation and lipid biosynthesis processes were identified. From 120 d to 240 d, the period with the maximum IMF deposition rate, the lipid biosynthesis related genes (FOSL1, FAM213B and G0S2), transcription factors (TFs) (EGR1, KLF5, SREBF2, TP53 and TWIST1) and enriched pathways (steroid biosynthesis and fatty acid biosynthesis) were revealed; and fat biosynthesis relevant genes showing differences in DNA methylation in gene body or intergenic region were detected, such as FASN, PVALB, ID2, SH3PXD2B and EGR1. Conclusions This study provides a comprehensive landscape of transcriptome of the LD muscle in Laiwu pigs ranging from 60 to 400 days old, and methylome of the LD muscle in 120 d and 240 d Laiwu pigs. A set of candidate genes and TFs involved in fat biosynthesis process were identified, which were probably responsible for IMF deposition. The results from this study would provide a reference for the identification of genes controlling IMF variation, and for exploring molecular mechanisms underlying IMF deposition in pigs. Electronic supplementary material The online version of this article (10.1186/s12864-017-4201-9) contains supplementary material, which is available to authorized users.
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Affiliation(s)
- Yuding Wang
- Shandong Provincial Key Laboratory of Animal Biotechnology and Disease Control and Prevention, College of Animal Science and Veterinary Medicine, Shandong Agricultural University, No. 61 Daizong Street, Taian, 271018, People's Republic of China.,Shandong Provincial Key Laboratory of Animal Disease Control and Breeding, Institute of Animal Science and Veterinary Medicine, Shandong Academy of Agricultural Sciences, Jinan, 250100, People's Republic of China
| | - Cai Ma
- Shandong Provincial Key Laboratory of Animal Biotechnology and Disease Control and Prevention, College of Animal Science and Veterinary Medicine, Shandong Agricultural University, No. 61 Daizong Street, Taian, 271018, People's Republic of China
| | - Yi Sun
- Shandong Provincial Key Laboratory of Animal Biotechnology and Disease Control and Prevention, College of Animal Science and Veterinary Medicine, Shandong Agricultural University, No. 61 Daizong Street, Taian, 271018, People's Republic of China
| | - Yi Li
- Central Hospital of Taian, Taian, 271018, People's Republic of China
| | - Li Kang
- Shandong Provincial Key Laboratory of Animal Biotechnology and Disease Control and Prevention, College of Animal Science and Veterinary Medicine, Shandong Agricultural University, No. 61 Daizong Street, Taian, 271018, People's Republic of China
| | - Yunliang Jiang
- Shandong Provincial Key Laboratory of Animal Biotechnology and Disease Control and Prevention, College of Animal Science and Veterinary Medicine, Shandong Agricultural University, No. 61 Daizong Street, Taian, 271018, People's Republic of China.
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Schachtschneider KM, Schwind RM, Darfour-Oduro KA, De AK, Rund LA, Singh K, Principe DR, Guzman G, Ray CE, Ozer H, Gaba RC, Schook LB. A validated, transitional and translational porcine model of hepatocellular carcinoma. Oncotarget 2017; 8:63620-63634. [PMID: 28969016 PMCID: PMC5609948 DOI: 10.18632/oncotarget.18872] [Citation(s) in RCA: 44] [Impact Index Per Article: 6.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/21/2016] [Accepted: 06/05/2017] [Indexed: 12/29/2022] Open
Abstract
Difficult questions are confronting clinicians attempting to improve hepatocellular carcinoma (HCC) outcomes. A large animal model with genetic, anatomical, and physiological similarities to humans is required to transition from mouse models to human clinical trials to address unmet clinical needs. To validate our previously reported inducible porcine cancer model (Oncopig) as a transitional HCC model, Oncopig hepatocyte cultures were transformed using Cre recombinase. The resulting porcine HCC cells (pHCC) expressed oncogenic TP53R167H and KRASG12D, and displayed nuclear pleomorphisms with pale to granular cytoplasm arranged in expanded plates similar to human HCC histopathology. Human HCC transcriptional hallmarks were detected in pHCC cells using RNA-seq, including TERT reactivation, apoptosis evasion, angiogenesis activation, and Wnt signaling activation. Master regulators of gene expression were conserved across Oncopig and 18 human HCC cell lines. pHCC injection into SCID mice resulted in tumors recapitulating human HCC characteristics, including thick trabeculae formation, pseudoacini patterning, and sheets of well-vascularized stroma. Finally, autologous injection of pHCC cells subcutaneously yielded a tumor histologically characterized as Edmondson Steiner (HCC nuclear grade assessment system) grade 2 HCC with trabecular patterning and T-lymphocyte infiltration. These data demonstrate the Oncopig HCC model's utility for improving detection, treatment, and biomarker discovery relevant to human HCC.
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Affiliation(s)
- Kyle M. Schachtschneider
- Department of Animal Sciences, University of Illinois, Urbana, IL, USA
- Animal Breeding and Genomics Centre, Wageningen University, Wageningen, The Netherlands
- Department of Radiology, University of Illinois at Chicago, Chicago, IL, USA
| | - Regina M. Schwind
- Department of Radiology, University of Illinois at Chicago, Chicago, IL, USA
| | | | - Arun K. De
- Department of Animal Sciences, University of Illinois, Urbana, IL, USA
| | - Lauretta A. Rund
- Department of Animal Sciences, University of Illinois, Urbana, IL, USA
| | - Kuldeep Singh
- Veterinary Diagnostic Laboratory, University of Illinois, Urbana, IL, USA
| | - Daniel R. Principe
- College of Medicine, University of Illinois at Chicago, Chicago, IL, USA
| | - Grace Guzman
- Department of Pathology, University of Illinois at Chicago, Chicago, IL, USA
| | - Charles E. Ray
- Department of Radiology, University of Illinois at Chicago, Chicago, IL, USA
- Department of Medicine, Division of Hematology/Oncology, University of Illinois at Chicago, Chicago, IL, USA
| | - Howard Ozer
- Department of Medicine, Division of Hematology/Oncology, University of Illinois at Chicago, Chicago, IL, USA
| | - Ron C. Gaba
- Department of Radiology, University of Illinois at Chicago, Chicago, IL, USA
| | - Lawrence B. Schook
- Department of Animal Sciences, University of Illinois, Urbana, IL, USA
- Department of Radiology, University of Illinois at Chicago, Chicago, IL, USA
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47
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Schachtschneider KM, Schwind RM, Newson J, Kinachtchouk N, Rizko M, Mendoza-Elias N, Grippo P, Principe DR, Park A, Overgaard NH, Jungersen G, Garcia KD, Maker AV, Rund LA, Ozer H, Gaba RC, Schook LB. The Oncopig Cancer Model: An Innovative Large Animal Translational Oncology Platform. Front Oncol 2017; 7:190. [PMID: 28879168 PMCID: PMC5572387 DOI: 10.3389/fonc.2017.00190] [Citation(s) in RCA: 63] [Impact Index Per Article: 9.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/17/2017] [Accepted: 08/10/2017] [Indexed: 12/20/2022] Open
Abstract
Despite an improved understanding of cancer molecular biology, immune landscapes, and advancements in cytotoxic, biologic, and immunologic anti-cancer therapeutics, cancer remains a leading cause of death worldwide. More than 8.2 million deaths were attributed to cancer in 2012, and it is anticipated that cancer incidence will continue to rise, with 19.3 million cases expected by 2025. The development and investigation of new diagnostic modalities and innovative therapeutic tools is critical for reducing the global cancer burden. Toward this end, transitional animal models serve a crucial role in bridging the gap between fundamental diagnostic and therapeutic discoveries and human clinical trials. Such animal models offer insights into all aspects of the basic science-clinical translational cancer research continuum (screening, detection, oncogenesis, tumor biology, immunogenicity, therapeutics, and outcomes). To date, however, cancer research progress has been markedly hampered by lack of a genotypically, anatomically, and physiologically relevant large animal model. Without progressive cancer models, discoveries are hindered and cures are improbable. Herein, we describe a transgenic porcine model—the Oncopig Cancer Model (OCM)—as a next-generation large animal platform for the study of hematologic and solid tumor oncology. With mutations in key tumor suppressor and oncogenes, TP53R167H and KRASG12D, the OCM recapitulates transcriptional hallmarks of human disease while also exhibiting clinically relevant histologic and genotypic tumor phenotypes. Moreover, as obesity rates increase across the global population, cancer patients commonly present clinically with multiple comorbid conditions. Due to the effects of these comorbidities on patient management, therapeutic strategies, and clinical outcomes, an ideal animal model should develop cancer on the background of representative comorbid conditions (tumor macro- and microenvironments). As observed in clinical practice, liver cirrhosis frequently precedes development of primary liver cancer or hepatocellular carcinoma. The OCM has the capacity to develop tumors in combination with such relevant comorbidities. Furthermore, studies on the tumor microenvironment demonstrate similarities between OCM and human cancer genomic landscapes. This review highlights the potential of this and other large animal platforms as transitional models to bridge the gap between basic research and clinical practice.
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Affiliation(s)
| | - Regina M Schwind
- Department of Radiology, University of Illinois at Chicago, Chicago, IL, United States
| | | | | | - Mark Rizko
- College of Medicine, University of Illinois at Chicago, Chicago, IL, United States
| | - Nasya Mendoza-Elias
- College of Medicine, University of Illinois at Chicago, Chicago, IL, United States
| | - Paul Grippo
- Department of Medicine, University of Illinois at Chicago, Chicago, IL, United States
| | - Daniel R Principe
- Department of Medicine, University of Illinois at Chicago, Chicago, IL, United States
| | - Alex Park
- College of Medicine, University of Illinois at Chicago, Chicago, IL, United States
| | - Nana H Overgaard
- Division of Immunology and Vaccinology, National Veterinary Institute, Technical University of Denmark, Kongens Lyngby, Denmark
| | - Gregers Jungersen
- Division of Immunology and Vaccinology, National Veterinary Institute, Technical University of Denmark, Kongens Lyngby, Denmark
| | - Kelly D Garcia
- Biologic Resources Laboratory, University of Illinois at Chicago, Chicago, IL, United States
| | - Ajay V Maker
- Department of Surgical Oncology, University of Illinois at Chicago, Chicago, IL, United States
| | - Laurie A Rund
- Department of Animal Sciences, University of Illinois, Urbana, IL, United States
| | - Howard Ozer
- Department of Medicine, University of Illinois at Chicago, Chicago, IL, United States
| | - Ron C Gaba
- Department of Radiology, University of Illinois at Chicago, Chicago, IL, United States
| | - Lawrence B Schook
- Department of Radiology, University of Illinois at Chicago, Chicago, IL, United States.,Department of Animal Sciences, University of Illinois, Urbana, IL, United States
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Transcriptome analysis reveals long intergenic non-coding RNAs involved in skeletal muscle growth and development in pig. Sci Rep 2017; 7:8704. [PMID: 28821716 PMCID: PMC5562803 DOI: 10.1038/s41598-017-07998-9] [Citation(s) in RCA: 18] [Impact Index Per Article: 2.6] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/23/2016] [Accepted: 07/06/2017] [Indexed: 02/06/2023] Open
Abstract
Long intergenic non-coding RNAs (lincRNAs) play essential roles in numerous biological processes and are widely studied. The skeletal muscle is an important tissue that plays an essential role in individual movement ability. However, lincRNAs in pig skeletal muscles are largely undiscovered and their biological functions remain elusive. In this study, we assembled transcriptomes using RNA-seq data published in previous studies of our laboratory group and identified 323 lincRNAs in porcine leg muscle. We found that these lincRNAs have shorter transcript length, fewer exons and lower expression level than protein-coding genes. Gene ontology and pathway analyses indicated that many potential target genes (PTGs) of lincRNAs were involved in skeletal-muscle-related processes, such as muscle contraction and muscle system process. Combined our previous studies, we found a potential regulatory mechanism in which the promoter methylation of lincRNAs can negatively regulate lincRNA expression and then positively regulate PTG expression, which can finally result in abnormal phenotypes of cloned piglets through a certain unknown pathway. This work detailed a number of lincRNAs and their target genes involved in skeletal muscle growth and development and can facilitate future studies on their roles in skeletal muscle growth and development.
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49
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Yuan XL, Zhang Z, Li B, Gao N, Zhang H, Sangild PT, Li JQ. Genome-wide DNA methylation analysis of the porcine hypothalamus-pituitary-ovary axis. Sci Rep 2017; 7:4277. [PMID: 28655931 PMCID: PMC5487323 DOI: 10.1038/s41598-017-04603-x] [Citation(s) in RCA: 10] [Impact Index Per Article: 1.4] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/03/2016] [Accepted: 04/03/2017] [Indexed: 12/21/2022] Open
Abstract
Previous studies have suggested that DNA methylation in both CpG and CpH (where H = C, T or A) contexts plays a critical role in biological functions of different tissues. However, the genome-wide DNA methylation patterns of porcine hypothalamus-pituitary-ovary (HPO) tissues remain virtually unexplored. In this study, methylomes of HPO tissues were profiled to investigate their differences and similarities. We found that HPO methylomes displayed tissue-specific methylation patterns in both CpG and CpH contexts. At gene locations, the methylation and density of CpGs was negatively linked at transcription start sites but positively linked at transcription end sites. The densities of CpGs and CpHs at CpG island (CGI) locations were negatively correlated with their methylation. Moreover, the methylation interactions between CGIs and genes showed similar pattern in the CpG context but tissue-specific pattern in the CpH context. CpGs located in CGIs, upstream regions and exons were protected from methylation dynamics, whereas CGI shores, CGI shelves and intergenic regions were more likely to be targets of methylation changes. The methylation dynamics enriching in a tissue-specific manner appeared to maintain and establish the biological functions of HPO tissues. Our analyses provided valuable insights into the tissue-specific methylomes of porcine HPO tissues.
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Affiliation(s)
- Xiao-Long Yuan
- Guangdong Provincial Key Lab of Agro-Animal Genomics and Molecular Breeding, National Engineering Research Centre for Breeding Swine Industry, College of Animal Science, South China Agricultural University, Guangzhou, Guangdong, China
- Section of Comparative Pediatrics and Nutrition, Department of Veterinary Clinical and Animal Sciences, University of Copenhagen, Frederiksberg, Denmark
| | - Zhe Zhang
- Guangdong Provincial Key Lab of Agro-Animal Genomics and Molecular Breeding, National Engineering Research Centre for Breeding Swine Industry, College of Animal Science, South China Agricultural University, Guangzhou, Guangdong, China
| | - Bin Li
- Guangdong Provincial Key Lab of Agro-Animal Genomics and Molecular Breeding, National Engineering Research Centre for Breeding Swine Industry, College of Animal Science, South China Agricultural University, Guangzhou, Guangdong, China
| | - Ning Gao
- Guangdong Provincial Key Lab of Agro-Animal Genomics and Molecular Breeding, National Engineering Research Centre for Breeding Swine Industry, College of Animal Science, South China Agricultural University, Guangzhou, Guangdong, China
- Department of Animal Sciences, Georg-August University, Albrecht Thaer-Weg 3, Göttingen, Germany
| | - Hao Zhang
- Guangdong Provincial Key Lab of Agro-Animal Genomics and Molecular Breeding, National Engineering Research Centre for Breeding Swine Industry, College of Animal Science, South China Agricultural University, Guangzhou, Guangdong, China
| | - Per Torp Sangild
- Section of Comparative Pediatrics and Nutrition, Department of Veterinary Clinical and Animal Sciences, University of Copenhagen, Frederiksberg, Denmark
| | - Jia-Qi Li
- Guangdong Provincial Key Lab of Agro-Animal Genomics and Molecular Breeding, National Engineering Research Centre for Breeding Swine Industry, College of Animal Science, South China Agricultural University, Guangzhou, Guangdong, China.
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Yuan XL, Zhang Z, Pan RY, Gao N, Deng X, Li B, Zhang H, Sangild PT, Li JQ. Performances of Different Fragment Sizes for Reduced Representation Bisulfite Sequencing in Pigs. Biol Proced Online 2017; 19:5. [PMID: 28596713 PMCID: PMC5463379 DOI: 10.1186/s12575-017-0054-5] [Citation(s) in RCA: 5] [Impact Index Per Article: 0.7] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/06/2017] [Accepted: 05/09/2017] [Indexed: 12/23/2022] Open
Abstract
Background Reduced representation bisulfite sequencing (RRBS) has been widely used to profile genome-scale DNA methylation in mammalian genomes. However, the applications and technical performances of RRBS with different fragment sizes have not been systematically reported in pigs, which serve as one of the important biomedical models for humans. The aims of this study were to evaluate capacities of RRBS libraries with different fragment sizes to characterize the porcine genome. Results We found that the MspI-digested segments between 40 and 220 bp harbored a high distribution peak at 74 bp, which were highly overlapped with the repetitive elements and might reduce the unique mapping alignment. The RRBS library of 110–220 bp fragment size had the highest unique mapping alignment and the lowest multiple alignment. The cost-effectiveness of the 40–110 bp, 110–220 bp and 40–220 bp fragment sizes might decrease when the dataset size was more than 70, 50 and 110 million reads for these three fragment sizes, respectively. Given a 50-million dataset size, the average sequencing depth of the detected CpG sites in the 110–220 bp fragment size appeared to be deeper than in the 40–110 bp and 40–220 bp fragment sizes, and these detected CpG sties differently located in gene- and CpG island-related regions. Conclusions In this study, our results demonstrated that selections of fragment sizes could affect the numbers and sequencing depth of detected CpG sites as well as the cost-efficiency. No single solution of RRBS is optimal in all circumstances for investigating genome-scale DNA methylation. This work provides the useful knowledge on designing and executing RRBS for investigating the genome-wide DNA methylation in tissues from pigs.
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Affiliation(s)
- Xiao-Long Yuan
- Guangdong Provincial Key Lab of Agro-Animal Genomics and Molecular Breeding, National Engineering Research Centre for Breeding Swine Industry, College of Animal Science, South China Agricultural University, Guangzhou, Guangdong China.,Section of Comparative Pediatrics and Nutrition, Department of Veterinary Clinical and Animal Sciences, University of Copenhagen, Frederiksberg, Denmark
| | - Zhe Zhang
- Guangdong Provincial Key Lab of Agro-Animal Genomics and Molecular Breeding, National Engineering Research Centre for Breeding Swine Industry, College of Animal Science, South China Agricultural University, Guangzhou, Guangdong China
| | - Rong-Yang Pan
- Guangdong Provincial Key Lab of Agro-Animal Genomics and Molecular Breeding, National Engineering Research Centre for Breeding Swine Industry, College of Animal Science, South China Agricultural University, Guangzhou, Guangdong China
| | - Ning Gao
- Guangdong Provincial Key Lab of Agro-Animal Genomics and Molecular Breeding, National Engineering Research Centre for Breeding Swine Industry, College of Animal Science, South China Agricultural University, Guangzhou, Guangdong China.,Department of Animal Sciences, Georg-August University, Albrecht Thaer-Weg 3, Göttingen, Germany
| | - Xi Deng
- Guangdong Provincial Key Lab of Agro-Animal Genomics and Molecular Breeding, National Engineering Research Centre for Breeding Swine Industry, College of Animal Science, South China Agricultural University, Guangzhou, Guangdong China
| | - Bin Li
- Guangdong Provincial Key Lab of Agro-Animal Genomics and Molecular Breeding, National Engineering Research Centre for Breeding Swine Industry, College of Animal Science, South China Agricultural University, Guangzhou, Guangdong China
| | - Hao Zhang
- Guangdong Provincial Key Lab of Agro-Animal Genomics and Molecular Breeding, National Engineering Research Centre for Breeding Swine Industry, College of Animal Science, South China Agricultural University, Guangzhou, Guangdong China
| | - Per Torp Sangild
- Section of Comparative Pediatrics and Nutrition, Department of Veterinary Clinical and Animal Sciences, University of Copenhagen, Frederiksberg, Denmark
| | - Jia-Qi Li
- Guangdong Provincial Key Lab of Agro-Animal Genomics and Molecular Breeding, National Engineering Research Centre for Breeding Swine Industry, College of Animal Science, South China Agricultural University, Guangzhou, Guangdong China
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