1
|
Swietlik EM, Prapa M, Martin JM, Pandya D, Auckland K, Morrell NW, Gräf S. 'There and Back Again'-Forward Genetics and Reverse Phenotyping in Pulmonary Arterial Hypertension. Genes (Basel) 2020; 11:E1408. [PMID: 33256119 PMCID: PMC7760524 DOI: 10.3390/genes11121408] [Citation(s) in RCA: 7] [Impact Index Per Article: 1.8] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/26/2020] [Revised: 11/17/2020] [Accepted: 11/23/2020] [Indexed: 02/07/2023] Open
Abstract
Although the invention of right heart catheterisation in the 1950s enabled accurate clinical diagnosis of pulmonary arterial hypertension (PAH), it was not until 2000 when the landmark discovery of the causative role of bone morphogenetic protein receptor type II (BMPR2) mutations shed new light on the pathogenesis of PAH. Since then several genes have been discovered, which now account for around 25% of cases with the clinical diagnosis of idiopathic PAH. Despite the ongoing efforts, in the majority of patients the cause of the disease remains elusive, a phenomenon often referred to as "missing heritability". In this review, we discuss research approaches to uncover the genetic architecture of PAH starting with forward phenotyping, which in a research setting should focus on stable intermediate phenotypes, forward and reverse genetics, and finally reverse phenotyping. We then discuss potential sources of "missing heritability" and how functional genomics and multi-omics methods are employed to tackle this problem.
Collapse
Affiliation(s)
- Emilia M. Swietlik
- Department of Medicine, University of Cambridge, Cambridge Biomedical Campus, Cambridge CB2 0QQ, UK; (E.M.S.); (M.P.); (J.M.M.); (D.P.); (K.A.); (N.W.M.)
- Royal Papworth Hospital NHS Foundation Trust, Cambridge CB2 0AY, UK
- Addenbrooke’s Hospital NHS Foundation Trust, Cambridge CB2 0QQ, UK
| | - Matina Prapa
- Department of Medicine, University of Cambridge, Cambridge Biomedical Campus, Cambridge CB2 0QQ, UK; (E.M.S.); (M.P.); (J.M.M.); (D.P.); (K.A.); (N.W.M.)
- Addenbrooke’s Hospital NHS Foundation Trust, Cambridge CB2 0QQ, UK
| | - Jennifer M. Martin
- Department of Medicine, University of Cambridge, Cambridge Biomedical Campus, Cambridge CB2 0QQ, UK; (E.M.S.); (M.P.); (J.M.M.); (D.P.); (K.A.); (N.W.M.)
| | - Divya Pandya
- Department of Medicine, University of Cambridge, Cambridge Biomedical Campus, Cambridge CB2 0QQ, UK; (E.M.S.); (M.P.); (J.M.M.); (D.P.); (K.A.); (N.W.M.)
| | - Kathryn Auckland
- Department of Medicine, University of Cambridge, Cambridge Biomedical Campus, Cambridge CB2 0QQ, UK; (E.M.S.); (M.P.); (J.M.M.); (D.P.); (K.A.); (N.W.M.)
| | - Nicholas W. Morrell
- Department of Medicine, University of Cambridge, Cambridge Biomedical Campus, Cambridge CB2 0QQ, UK; (E.M.S.); (M.P.); (J.M.M.); (D.P.); (K.A.); (N.W.M.)
- Royal Papworth Hospital NHS Foundation Trust, Cambridge CB2 0AY, UK
- Addenbrooke’s Hospital NHS Foundation Trust, Cambridge CB2 0QQ, UK
- NIHR BioResource for Translational Research, University of Cambridge, Cambridge Biomedical Campus, Cambridge CB2 0QQ, UK
| | - Stefan Gräf
- Department of Medicine, University of Cambridge, Cambridge Biomedical Campus, Cambridge CB2 0QQ, UK; (E.M.S.); (M.P.); (J.M.M.); (D.P.); (K.A.); (N.W.M.)
- NIHR BioResource for Translational Research, University of Cambridge, Cambridge Biomedical Campus, Cambridge CB2 0QQ, UK
- Department of Haematology, University of Cambridge, Cambridge Biomedical Campus, Cambridge CB2 0PT, UK
| |
Collapse
|
2
|
Abstract
The first and only published version of the rat reference genome sequence was RGSC3.1, accomplished by the Rat Genome Sequencing Project Consortium. Here we present the history of the community effort in the correction of sequence errors and filling missing gaps in the process of refining and providing researchers with a high-quality rat reference sequence. The genome assembly improvements, addition of different evidence resources over time, such as RNA-Seq data, and software development methodologies had a positive impact on the gene model annotations. Over the years we observed a great increase in the numbers of genes, protein coding sequences, predicted transcripts and transcript features. Before the sequencing of the rat genome was possible, first biochemical and next genomic markers like RAPD, AFLP, RFLP, and SSLP were fundamental in research studies involving cross-breeding between different rat strains, in finding the level of polymorphism, linkage mapping, and phylogeny. Linkage maps provide information on recombination rates, give insight into intra- and interspecies gene rearrangements, and help to identify Mendelian loci and Quantitative Trait Loci (QTL). In the 1990s many reports were published on the construction of rat linkage maps that incorporated increasing numbers of markers and facilitated the localization of disease loci. Current genetic monitoring and linkage mapping relies on single nucleotide polymorphisms (SNPs). The Rat Genome Database collects information on genetic variation from the worldwide community of rat researchers and provides tools for searching and retrieving these data. As of today we show details about almost 605 million variants coming from many studies in our Variant Visualizer tool.
Collapse
|
3
|
Ehret T, Torelli F, Klotz C, Pedersen AB, Seeber F. Translational Rodent Models for Research on Parasitic Protozoa-A Review of Confounders and Possibilities. Front Cell Infect Microbiol 2017. [PMID: 28638807 PMCID: PMC5461347 DOI: 10.3389/fcimb.2017.00238] [Citation(s) in RCA: 21] [Impact Index Per Article: 3.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/04/2023] Open
Abstract
Rodents, in particular Mus musculus, have a long and invaluable history as models for human diseases in biomedical research, although their translational value has been challenged in a number of cases. We provide some examples in which rodents have been suboptimal as models for human biology and discuss confounders which influence experiments and may explain some of the misleading results. Infections of rodents with protozoan parasites are no exception in requiring close consideration upon model choice. We focus on the significant differences between inbred, outbred and wild animals, and the importance of factors such as microbiota, which are gaining attention as crucial variables in infection experiments. Frequently, mouse or rat models are chosen for convenience, e.g., availability in the institution rather than on an unbiased evaluation of whether they provide the answer to a given question. Apart from a general discussion on translational success or failure, we provide examples where infections with single-celled parasites in a chosen lab rodent gave contradictory or misleading results, and when possible discuss the reason for this. We present emerging alternatives to traditional rodent models, such as humanized mice and organoid primary cell cultures. So-called recombinant inbred strains such as the Collaborative Cross collection are also a potential solution for certain challenges. In addition, we emphasize the advantages of using wild rodents for certain immunological, ecological, and/or behavioral questions. The experimental challenges (e.g., availability of species-specific reagents) that come with the use of such non-model systems are also discussed. Our intention is to foster critical judgment of both traditional and newly available translational rodent models for research on parasitic protozoa that can complement the existing mouse and rat models.
Collapse
Affiliation(s)
- Totta Ehret
- FG16 - Mycotic and Parasitic Agents and Mycobacteria, Robert Koch InstituteBerlin, Germany.,Department of Molecular Parasitology, Humboldt-Universität zu BerlinBerlin, Germany
| | - Francesca Torelli
- FG16 - Mycotic and Parasitic Agents and Mycobacteria, Robert Koch InstituteBerlin, Germany
| | - Christian Klotz
- FG16 - Mycotic and Parasitic Agents and Mycobacteria, Robert Koch InstituteBerlin, Germany
| | - Amy B Pedersen
- School of Biological Sciences, University of EdinburghEdinburgh, United Kingdom
| | - Frank Seeber
- FG16 - Mycotic and Parasitic Agents and Mycobacteria, Robert Koch InstituteBerlin, Germany
| |
Collapse
|
4
|
Li T, Shuai L, Mao J, Wang X, Wang M, Zhang X, Wang L, Li Y, Li W, Zhou Q. Efficient Production of Fluorescent Transgenic Rats using the piggyBac Transposon. Sci Rep 2016; 6:33225. [PMID: 27624004 PMCID: PMC5021943 DOI: 10.1038/srep33225] [Citation(s) in RCA: 15] [Impact Index Per Article: 1.9] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/10/2016] [Accepted: 08/23/2016] [Indexed: 01/24/2023] Open
Abstract
Rats with fluorescent markers are of great value for studies that trace lineage-specific development, particularly those assessing the differentiation potential of embryonic stem cells (ESCs). The piggyBac (PB) transposon is widely used for the efficient introduction of genetic modifications into genomes, and has already been successfully used to produce transgenic mice and rats. Here, we generated transgenic rats carrying either the desRed fluorescent protein (RFP) gene or the enhanced green fluorescent protein (eGFP) gene by injecting pronuclei with PB plasmids. We showed that the transgenic rats expressed the RFP or eGFP gene in many organs and had the capability to transmit the marker gene to the next generation through germline integration. In addition, rat embryonic stem cells (ESCs) carrying an RFP reporter gene can be derived from the blastocysts of the transgenic rats. Moreover, the RFP gene can be detected in chimeras derived from RFP ESCs via blastocyst injection. This work suggests that PB-mediated transgenesis is a powerful tool to generate transgenic rats expressing fluorescent proteins with high efficiency, and this technique can be used to derive rat ESCs expressing a reporter protein.
Collapse
Affiliation(s)
- Tianda Li
- State Key Laboratory of Reproductive Biology, Institute of Zoology, Chinese Academy of Sciences, Beijing 100101, China
| | - Ling Shuai
- State Key Laboratory of Reproductive Biology, Institute of Zoology, Chinese Academy of Sciences, Beijing 100101, China
- State Key Laboratory of Medicinal Chemical Biology, Nankai University, Tianjin 300350, China
| | - Junjie Mao
- State Key Laboratory of Reproductive Biology, Institute of Zoology, Chinese Academy of Sciences, Beijing 100101, China
- Graduate School of Chinese Academy of Sciences, Beijing 100049, China
| | - Xuepeng Wang
- State Key Laboratory of Reproductive Biology, Institute of Zoology, Chinese Academy of Sciences, Beijing 100101, China
| | - Mei Wang
- State Key Laboratory of Reproductive Biology, Institute of Zoology, Chinese Academy of Sciences, Beijing 100101, China
| | - Xinxin Zhang
- State Key Laboratory of Reproductive Biology, Institute of Zoology, Chinese Academy of Sciences, Beijing 100101, China
- College of Life Science, Northeast Agricultural University of China, Harbin 150030, China
| | - Leyun Wang
- State Key Laboratory of Reproductive Biology, Institute of Zoology, Chinese Academy of Sciences, Beijing 100101, China
- College of Life Science, Northeast Agricultural University of China, Harbin 150030, China
| | - Yanni Li
- State Key Laboratory of Medicinal Chemical Biology, Nankai University, Tianjin 300350, China
| | - Wei Li
- State Key Laboratory of Reproductive Biology, Institute of Zoology, Chinese Academy of Sciences, Beijing 100101, China
| | - Qi Zhou
- State Key Laboratory of Reproductive Biology, Institute of Zoology, Chinese Academy of Sciences, Beijing 100101, China
| |
Collapse
|
5
|
Vasilenko T, Slezák M, Novotný M, Kováč I, Durkáč J, Tomková I, Torma N, Vrzgula A, Lenhardt L, Levkut M, Gál P. Pre- and/or postsurgical administration of estradiol benzoate increases skin flap viability in female rats. Aesthetic Plast Surg 2013; 37:1003-9. [PMID: 23722351 DOI: 10.1007/s00266-013-0151-z] [Citation(s) in RCA: 5] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/30/2012] [Accepted: 05/08/2013] [Indexed: 01/10/2023]
Abstract
BACKGROUND It has been shown that estrogens have a protective effect with regard to tissue ischemia. Therefore, in this macroscopic and histological investigation, the effect of estradiol benzoate on skin flap viability was studied in sham-operated and ovariectomized Sprague-Dawley rats. METHODS Three months prior to flap surgery a group of rats underwent ovariectomy, while the remaining animals underwent a sham operation. Subsequently, all rats had a 2 × 8-cm skin flap created on the dorsum. Rats were randomly divided into estradiol- or saline-treated groups. Treatment started either on the day of flap excision or 3 days prior to the surgery. RESULTS Our results showed that administration of estradiol benzoate prior to and after flap surgery significantly decreases skin flap necrosis in both sham-operated and ovariectomized rats, with the highest survival rate in animals where treatment started 3 days prior to flap surgery. CONCLUSION In conclusion, the observed protective effect of estradiol on skin flap viability could potentially be applied to plastic and reconstructive surgery in postmenopausal women. Nevertheless, further research is needed to explain the exact underlying mechanism and to find the optimal treatment protocol for human clinical practice.
Collapse
Affiliation(s)
- Tomáš Vasilenko
- Department of Pathological Anatomy, University of Veterinary Medicine and Pharmacy, Košice, Slovak Republic
| | | | | | | | | | | | | | | | | | | | | |
Collapse
|
6
|
Fahey JR, Katoh H, Malcolm R, Perez AV. The case for genetic monitoring of mice and rats used in biomedical research. Mamm Genome 2013; 24:89-94. [PMID: 23314661 PMCID: PMC3627018 DOI: 10.1007/s00335-012-9444-9] [Citation(s) in RCA: 23] [Impact Index Per Article: 2.1] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/24/2012] [Accepted: 12/07/2012] [Indexed: 11/24/2022]
Abstract
Currently, there is the potential to generate over 200,000 mutant mouse strains between existing mouse strains (over 24,000) and genetically modified mouse embryonic stem cells (over 209,000) that have been entered into the International Mouse Strain Resource Center (IMSR) from laboratories and repositories all over the world. The number of rat strains is also increasing exponentially. These mouse and rat mutants are a tremendous genetic resource; however, the awareness of their genetic integrity such as genetic background and genotyping of these models is not always carefully monitored. In this review, we make a case for the International Council for Laboratory Animal Science (ICLAS), which is interested in promoting and helping academic institutions develop a genetic monitoring program to bring a level of genetic quality assurance into the scientific interchange and use of mouse and rat genetically mutant models.
Collapse
Affiliation(s)
- James R Fahey
- Laboratory Animal Health Services Department, The Jackson Laboratory, Bar Harbor, ME 04609, USA.
| | | | | | | |
Collapse
|
7
|
|
8
|
Ahlemeyer B, Kehr K, Richter E, Hirz M, Baumgart-Vogt E, Herden C. Phenotype, differentiation, and function differ in rat and mouse neocortical astrocytes cultured under the same conditions. J Neurosci Methods 2012; 212:156-64. [PMID: 23026192 DOI: 10.1016/j.jneumeth.2012.09.016] [Citation(s) in RCA: 15] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/04/2012] [Revised: 07/06/2012] [Accepted: 09/14/2012] [Indexed: 01/08/2023]
Abstract
The study of slowly progressing brain diseases in which glial cells play a pathogenic role requires astrocytes that have been cultured for several weeks. We characterized neocortical astrocytes, grown for up to 42 days in vitro (DIV), from newborn rats and mice by indirect immunofluorescence technique, Western blot, and real-time RT-PCR analyses. We obtained highly enriched rat and mouse astrocyte cultures, where most cells were positively stained for the astrocyte markers GFAP, vimentin, and S100β, whereas neuronal and oligodendrocyte markers were undetectable. The protein and mRNA levels of GFAP, vimentin, and nestin were higher in rat than in mouse astrocytes. From 28 to 42 DIV, the levels of vimentin and nestin, but not of GFAP, decreased in both species, with an increase in the vimentin-GFAP ratio of 1.7 for rat, and of 0.9 for mouse astrocytes suggesting that the rat cultures were more differentiated than the mouse cultures, although both remained partially immature. The protoplasmic appearance of the cells, the negative A2B5 immunoreactivity, and the expression of the glutamate transporters GLAST and GLT-1 indicate that the rat and mouse cultures contained mainly type I astrocytes. The protein levels of GLAST and GLT-1 decreased from 28 to 42 DIV in the mouse, but not in the rat astrocytes, suggesting that the rat cultures are suitable for functional studies. Thus, under the same culture conditions, astrocyte cultures from rats and mice differ in phenotype, differentiation, and functionality. This finding should be taken into account when long-lasting glial reaction patterns are being studied.
Collapse
Affiliation(s)
- Barbara Ahlemeyer
- Institute for Anatomy and Cell Biology II, Division of Medical Cell Biology, Justus-Liebig University, Aulweg 123, 35385 Giessen, Germany.
| | | | | | | | | | | |
Collapse
|
9
|
Schönig K, Weber T, Frömmig A, Wendler L, Pesold B, Djandji D, Bujard H, Bartsch D. Conditional gene expression systems in the transgenic rat brain. BMC Biol 2012; 10:77. [PMID: 22943311 PMCID: PMC3520851 DOI: 10.1186/1741-7007-10-77] [Citation(s) in RCA: 34] [Impact Index Per Article: 2.8] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/19/2012] [Accepted: 09/03/2012] [Indexed: 12/18/2022] Open
Abstract
BACKGROUND Turning gene expression on and off at will is one of the most powerful tools for the study of gene function in vivo. While several conditional systems were successful in invertebrates, in mice the Cre/loxP recombination system and the tet-controlled transcription activation system are predominant. Both expression systems allow for spatial and temporal control of gene activities, and, in the case of tet regulation, even for the reversible activation/inactivation of gene expression. Although the rat is the principal experimental model in biomedical research, in particular in studies of neuroscience, conditional rat transgenic systems are exceptionally rare in this species. RESULTS We addressed this lack of technology, and established and thoroughly characterized CreERT2 and tTA transgenic rats with forebrain-specific transgene expression, controlled by the CaMKII alpha promoter. In addition, we developed new universal rat reporter lines for both transcription control systems and established inducible and efficient reporter gene expression in forebrain neurons. CONCLUSIONS We demonstrate that conditional genetic manipulations in the rat brain are both feasible and practicable and outline advantages and limitations of the Tet and Cre/loxP system in the rat brain.
Collapse
Affiliation(s)
- Kai Schönig
- Department of Molecular Biology, Central Institute of Mental Health and Heidelberg University, Medical Faculty Mannheim, J5, 68159 Mannheim, Germany
| | | | | | | | | | | | | | | |
Collapse
|
10
|
van Boxtel R, Kuiper RV, Toonen PW, van Heesch S, Hermsen R, de Bruin A, Cuppen E. Homozygous and heterozygous p53 knockout rats develop metastasizing sarcomas with high frequency. THE AMERICAN JOURNAL OF PATHOLOGY 2011; 179:1616-22. [PMID: 21854749 DOI: 10.1016/j.ajpath.2011.06.036] [Citation(s) in RCA: 30] [Impact Index Per Article: 2.3] [Reference Citation Analysis] [Abstract] [Track Full Text] [Subscribe] [Scholar Register] [Received: 05/09/2011] [Revised: 06/07/2011] [Accepted: 06/14/2011] [Indexed: 11/17/2022]
Abstract
The TP53 tumor suppressor gene is mutated in the majority of human cancers. Inactivation of p53 in a variety of animal models results in early-onset tumorigenesis, reflecting the importance of p53 as a gatekeeper tumor suppressor. We generated a mutant Tp53 allele in the rat using a target-selected mutagenesis approach. Here, we report that homozygosity for this allele results in complete loss of p53 function. Homozygous mutant rats predominantly develop sarcomas with an onset of 4 months of age with a high occurrence of pulmonary metastases. Heterozygous rats develop sarcomas starting at 8 months of age. Molecular analysis revealed that these tumors exhibit a loss-of-heterozygosity of the wild-type Tp53 allele. These unique features make this rat highly complementary to other rodent p53 knockout models and a versatile tool for investigating tumorigenesis processes as well as genotoxic studies.
Collapse
Affiliation(s)
- Ruben van Boxtel
- Hubrecht Institute for Developmental Biology and Stem Cell Research, Cancer Genomics Center, KNAW and University Medical Center Utrecht, Utrecht, The Netherlands
| | | | | | | | | | | | | |
Collapse
|