Papers by Scott FAHRENKRUG
Journal of Animal Science, Sep 1, 2016
Biology of Reproduction, Aug 1, 2001
The zinc finger transcription factor Gata4, is associated with gonadal development in many specie... more The zinc finger transcription factor Gata4, is associated with gonadal development in many species. The present study characterizes temporal and spatial localization of Gata4 throughout gonadogenesis in porcine embryos. Immunohistochemical studies illustrated that Gata4 protein is present in the coelomic epithelium prior to histological differentiation of the nascent bipotential gonad, marking the future site of both XX and XY porcine gonads. Many somatic cells of both XX and XY bipotential gonads continue to retain Gata4 immunoreactivity throughout sexual differentiation and subsequent gonadal development. Testicular cords were evident by 26 days postcoitum. Gata4 was present in Sertoli cells, identified by virtue of coexpression with Mü llerian inhibiting substance and also interstitial cells including Leydig cells throughout fetal and postnatal life. Many somatic cells of the differentiating ovary including follicular cells also contained Gata4 protein throughout fetal and postnatal life. Gata4 was not present in germ cells, endothelial cells, or other undifferentiated mesenchymal cells of both XX and XY gonads. A population of Gata4-positive cells in the dorsal mesentery was continuous with the coelomic epithelium of the gonad. This localization pattern led to the hypothesis that a subpopulation of somatic cells in the dorsal mesentery moves toward the gonad. An in vitro cell migration assay demonstrated that Gata4-positive cells preferentially migrate toward explanted gonadal tissue, and morphological features of the developing gonad supported this hypothesis. This study illustrates that Gata4 is a very early marker for gonad formation, highlights species differences in temporal and spatial localization patterns, and suggests a potential role for Gata4 in the development of both XX and XY porcine gonads. Further, we suggest that mesenchymal cells of the dorsal mesentery may provide a source of somatic cells that migrate and incorporate into the gonad and contribute to various somatic cell lineages. Overall, the spatial and temporal localization patterns of Gata4 during porcine gonadogenesis implies a much earlier and wider role for Gata4 than previously reported in other species.
Proceedings of the National Academy of Sciences of the United States of America, Sep 6, 2013
Proceedings of the National Academy of Sciences of the United States of America, Oct 1, 2012
The majority of causative variants in familial breast cancer remain unknown. Of the known risk va... more The majority of causative variants in familial breast cancer remain unknown. Of the known risk variants, most are tumor cell autonomous, and little attention has been paid yet to germline variants that may affect the tumor microenvironment. In this study, we developed a system called the Consomic Xenograft Model (CXM) to map germline variants that affect only the tumor microenvironment. In CXM, human breast cancer cells are orthotopically implanted into immunodeficient consomic strains and tumor metrics are quantified (e.g., growth, vasculogenesis, and metastasis). Because the strain backgrounds vary, whereas the malignant tumor cells do not, any observed changes in tumor progression are due to genetic differences in the nonmalignant microenvironment. Using CXM, we defined genetic variants on rat chromosome 3 that reduced relative tumor growth and hematogenous metastasis in the SS.BN3IL2Rγ consomic model compared with the SSIL2Rγ parental strain. Paradoxically, these effects occurred despite an increase in the density of tumor-associated blood vessels. In contrast, lymphatic vasculature and lymphogenous metastasis were unaffected by the SS.BN3IL2Rγ background. Through comparative mapping and whole-genome sequence analysis, we narrowed candidate variants on rat chromosome 3 to six genes with a priority for future analysis. Collectively, our results establish the utility of CXM to localize genetic variants affecting the tumor microenvironment that underlie differences in breast cancer risk. Cancer Res; 74(22); 6419–29. ©2014 AACR.
The FASEB Journal, Apr 1, 2015
Transgenic Research, Feb 1, 2014
Reproduction, Fertility and Development, 2011
Somatic cell nuclear transfer (SCNT) of genetically modified (GM) cells is currently the most wid... more Somatic cell nuclear transfer (SCNT) of genetically modified (GM) cells is currently the most widely applied method for the creation of transgenic swine. However, significant clone-to-clone variation in the efficiency of SCNT for a variety of genetically modified cell lines is commonly observed and contributes to the expense of transgenic animal production. A retrospective look at our own results based on the use of monoclonal GM cell lines as donors revealed a dismal efficiency of only 13% (15 embryo transfers resulting in only 2 full term pregnancies). Thus, while SCNT of individual GM clones offers the perceived advantage of prior characterisation of transgene expression or structure, the variability of clonability for any given cell line adds risk to SCNT. In contrast, rates of pregnancy when we used pools of GM cells as donors for SCNT were much better (9 full term pregnancies from 11 transfers, ∼82% efficiency). Four of these litters were derived from polyclonal but monogenic GM cell populations constitutively expressing either human APOBEC3G or YFP-Cre transgenes integrated using the Sleeping Beauty transposon system. Four litters relied on a novel approach, wherein different polyclonal and monogenic GM cell populations (containing different transgenes) were mixed before being used as donors for SCNT. For example, 2 litters were derived from the pooling of 2 GM cell populations carrying different tetracycline inducible or repressible shRNA transgenes, resulting in founders harboring each of the shRNA transgenes (4 in total). Two litters were also created from a pool of 3 distinct polyclonal cell populations, each harboring a different Cre-lox regulated transgene, resulting in the birth of 11 live piglets with founders corresponding to each of the transgenes. Thus, both mono- and polygenic pooling of GM cells significantly enhances the success of SCNT, largely avoiding variation in cell clonability. Furthermore, pooling results in a significant reduction in the time and number of surrogates required to generate a diversity of genetically modified pigs. Importantly, the use of Sleeping Beauty transgene integration resulted in a high rate of transgene-expressing founders. Where expected, the gene of interest transgenes were expressed in 23 of 29 founders (79%), whereas selectable marker transgene expression was observed in 35 of 40 founders (88%). The combination of efficient SCNT from polyclonal and polygenic cell populations and the high proportion of expressers delivered by Sleeping Beauty transgene integration offer a high-efficiency, low-risk solution to swine transgenesis.
Journal of Animal Science, Mar 1, 2017
Theriogenology, Nov 1, 2016
The recently developed engineered nucleases, such as zinc-finger nucleases, transcription activat... more The recently developed engineered nucleases, such as zinc-finger nucleases, transcription activator-like effector nucleases, and clustered regularly interspaced short palindromic repeat (CRISPR)/CRISPR-associated nuclease (Cas) 9, provide new opportunities for gene editing in a straightforward manner. However, few reports are available regarding CRISPR application and efficiency in cattle. Here, the CRISPR/Cas9 system was used with the aim of inducing knockout and knock-in alleles of the bovine PRNP gene, responsible for mad cow disease, both in bovine fetal fibroblasts and in IVF embryos. Five single-guide RNAs were designed to target 875 bp of PRNP exon 3, and all five were codelivered with Cas9. The feasibility of inducing homologous recombination (HR) was evaluated with a reporter vector carrying EGFP flanked by 1 kbp PRNP regions (pHRegfp). For somatic cells, plasmids coding for Cas9 and for each of the five single-guide RNAs (pCMVCas9 and pSPgRNAs) were transfected under two different conditions (1X and 2X). For IVF zygotes, cytoplasmic injection was conducted with either plasmids or mRNA. For plasmid injection groups, 1 pg pCMVCas9 + 0.1 pg of each pSPgRNA (DNA2X) was used per zygote. In the case of RNA, two amounts (RNA1X and RNA2X) were compared. To assess the occurrence of HR, a group additionally cotransfected or coinjected with pHRegfp plasmid was included. Somatic cell lysates were analyzed by polymerase chain reaction and surveyor assay. In the case of embryos, the in vitro development and the genotype of blastocysts were evaluated by polymerase chain reaction and sequencing. In somatic cells, 2X transfection resulted in indels and large deletions of the targeted PRNP region. Regarding embryo injection, higher blastocyst rates were obtained for RNA injected groups (46/103 [44.6%] and 55/116 [47.4%] for RNA1X and RNA2X) than for the DNA2X group (26/140 [18.6%], P < 0.05). In 46% (26/56) of the total sequenced blastocysts, specific gene editing was detected. The total number of genetic modifications (29) was higher than the total number of gene-edited embryos, as three blastocysts from the group RNA2X reported more than one type of modification. The modifications included indels (10/56; 17.9%) and large deletions (19/56; 33.9%). Moreover, it was possible to detect HR in 1/8 (12.5%) embryos treated with RNA2X. These results report that the CRISPR/Cas9 system can be applied for site-specific edition of the bovine genome, which could have a great impact on the development of large animals resistant to important zoonotic diseases.
Nucleic Acids Research, Feb 23, 2004
The proteins processed by the secretory pathway (secretome) are critical players in the developme... more The proteins processed by the secretory pathway (secretome) are critical players in the development of multi-cellular eukaryotic organisms but have yet to be comprehensively studied at the genomic level. In this study, we use the Target P algorithm to predict human (13±20% of proteins found in individual datasets) and Fugu (14%) secretomes based on analysis of their nearly complete proteomes. We combine internal processing with prediction software to automate secreted protein identi®cation and overcome one of the major challenges associated with EST data: identi®cation of the minority of clones that encode N-terminallycomplete proteins. We discuss the use of these methods to predict secreted proteins in EST-based consensus sequence sets, and we validate these predictions using an assay for cell-free cotranslational translocation. Analysis of TIGR Porcine Gene Index 4.0 as a test dataset resulted in the identi®cation of 352 N-terminally-complete, putative secreted proteins. In functional agreement with our predictions, 34 of 40 (85%) of these cDNAs were veri®ed to be cotranslationally translocated in an in vitro translation system. The methods developed here are speci®cally designed to accept partial open reading frames and improve secreted protein predictions in eukaryotic transcriptomes, and are valuable for the analysis and annotation of eukaryotic EST databases.
American Journal of Physiology-cell Physiology, Jul 1, 2003
Functional properties of a brain-specific NH 2-terminally spliced modulator of Kv4 channels.
Nature Biotechnology, May 1, 2016
This letter provides comments to Docket No. FDA-2008-D-0394. FDA Must Revise Current Regulatory P... more This letter provides comments to Docket No. FDA-2008-D-0394. FDA Must Revise Current Regulatory Proposal for Gene-Edited Animals On January 19, 2017, FDA published and invited comment on a document titled "Guidance for Industry, Regulation of Intentionally Altered Genomic DNA in Animals, Draft Guidance." FDA described it as "a revision of Guidance #187, 'Regulation of Genetically Engineered Animals,' … revised to update information concerning the products of different technologies used to produce such animals." 1 FDA states it "is intended to clarify our requirements and recommendations for producers and developers ('sponsors,' 'you') of animals with intentionally altered genomic DNA" and that it: "… addresses animals whose genomes have been intentionally altered using modern molecular technologies, which may include random or targeted DNA sequence changes including nucleotide insertions, substitutions, or deletions, or other technologies that introduce specific changes to the genome of the animal. This guidance applies to the intentionally altered genomic DNA in both the founder animal in which the initial alteration event occurred and the entire subsequent lineage of animals that contains the genomic alteration." 2
Transgenic Research, Oct 1, 2014
Reproduction, Fertility and Development, 2014
Transcription activator-like effector nuclease (TALEN) and zinc finger nuclease (ZFN) DNA editing... more Transcription activator-like effector nuclease (TALEN) and zinc finger nuclease (ZFN) DNA editing technology enables site-directed engineering of the genome. To date, all gene-edited large animals have been produced by treatment of somatic cells and cloning to produce gene-edited offspring. Although effective, it does not take advantage of the ‘leave-no-trace&amp;#39; aspect of site-specific nucleases, and the derivation of food animals by cloning is negatively perceived by the public. Thus, we have investigated production of gene-edited pigs, cattle and sheep by direct injection of TALEN or ZFN mRNAs to develop loss-of-function alleles for disease resistance (RELA) or enhanced meat production (GDF8). In vitro studies demonstrated activity of TALENs by cytoplasmic injection of mRNAs from dosages of 2 to 20 ng mL–1 with an apparent increase in both editing frequency and toxicity at high dosage. Our first pregnancies were produced by transfer of pig embryos (in vivo produced) injected with 2 ng mL–1 RELA TALEN mRNA. Pregnancy was confirmed in 5 of 7 recipients 4 of which went full term giving rise to 39 piglets, 8 of which carried editing events (21%). In parallel, we injected ZFN mRNA (2 ng mL–1) targeted to a similar site of the RELA gene and 2 of 2 recipients became pregnant, resulting in the birth of 9 piglets, one of which was edited (11%). For cattle injections, we derived zygotes by ovum pickup from selected Nelore dams followed by in vitro maturation and fertilization with Nelore semen. Low (2 ng mL–1) and medium (5 ng mL–1) dosages of GDF8-targeted TALENs resulted in Day 7 development to morula/blastocyst stage in 40% (n = 18) and 10% (n = 66) of cultured embryos, respectively. A total of 20 morula/blastocysts were chosen for transfer to 11 recipients, resulting in two full-term pregnancies. One pregnancy produced two calves, both of which carried edited GDF8 alleles. Complications with parturition of the second pregnancy resulted in 2 stillborn calves, the genotypes of which are under investigation. Finally, 2 ng mL–1 of TALEN mRNA targeted to ovine GDF8 was injected into in vivo-produced sheep zygotes and transferred into nine recipients, 3 blastocysts each. The pregnancy rate, number of live-born animals, and gene editing frequency is under investigation and will be reported.
American Journal of Respiratory Cell and Molecular Biology, Oct 1, 2013
Cystic fibrosis (CF) is caused by mutations in the tightly regulated anion channel cystic fibrosi... more Cystic fibrosis (CF) is caused by mutations in the tightly regulated anion channel cystic fibrosis transmembrane conductance regulator (CFTR), yet much of the pathology in this disease results from mucus obstruction of the small airways and other organs. Mucus stasis has been attributed to the abnormal luminal environment of CF airways, which results from dehydration of the mucus gel or low bicarbonate concentration. We show here that CFTR and MUC5AC are present in single mucin-containing granules isolated from a human airway epithelial cell line and from highly differentiated airway primary cell cultures. CFTR was not detected in MUC5AC granules from CFTR knockdown cells or CF primary cells. The results suggest a direct link between CFTR and the mucus defect.
Molecular therapy. Nucleic acids, 2012
Journal of Animal Science, Oct 1, 2010
Ruminants consuming diets with increased concentrations of nitrate (NO(3)(-)) can accumulate nitr... more Ruminants consuming diets with increased concentrations of nitrate (NO(3)(-)) can accumulate nitrite (NO(2)(-)) in the blood, resulting in toxicity. In a previous experiment, ewes identified as highly tolerant to subacute dietary NO(3)(-) were able to consume greater amounts of NO(3)(-) than lowly tolerant ewes without exhibiting signs of toxicity. We hypothesized that highly tolerant and lowly tolerant ewes differ in their ability to metabolize NO(3)(-) and thereby differ in the expression of hepatic genes involved in NO(3)(-) metabolism. Therefore, our objective was to identify hepatic genes differentially expressed between ewes classified as lowly tolerant and highly tolerant after administration of a subacute quantity of dietary NO(3)(-). Analysis of the Bovine Oligonucleotide Microarray data identified 100 oligonucleotides as differentially expressed (P &lt; 0.05) between lowly tolerant and highly tolerant ewes. Functional analysis of the genes associated with these oligonucleotides revealed 2 response clusters of interest: metabolic and stress. Genes of interest within these 2 clusters (n = 17) and nonclustered genes with the greatest fold changes (FC; n = 5) were selected for validation by real-time reverse-transcription PCR. Relative expression, genomic regulation, and FC agreed between microarray and real-time reverse-transcription-PCR analyses, and FC differences (P &lt; 0.05) between lowly tolerant and highly tolerant ewes were confirmed for 12 genes. Metabolic genes that were downregulated (P ≤ 0.032) in lowly tolerant ewes vs. highly tolerant ewes included aldehyde oxidase 1, argininosuccinate lyase, putative steroid dehydrogenase, 6-phosphofructo-2-kinase/fructose-2,6-biphosphatase1, and sterol carrier protein 2. In contrast, the metabolic gene homeobox was upregulated (P = 0.037) in lowly tolerant ewes. The glutathione peroxidase 3 and inter-α (globulin) inhibitor H4 genes in the stress response cluster were upregulated (P ≤ 0.045) in lowly tolerant ewes. Genes with the greatest FC, but did not cluster within the functional analysis included haptoglobin, which was upregulated (P = 0.024) in lowly tolerant ewes, and fatty acid desaturase 2 and thyroid hormone responsive, both of which were downregulated (P ≤ 0.019) in lowly tolerant ewes. Results from this study indicate that hepatic gene expression differs in ewes identified as lowly tolerant and highly tolerant to increased dietary NO(3)(-).
Differentiation, Dec 1, 1999
The regulation of protein synthesis is critical to diverse cellular processes and plays a pivotal... more The regulation of protein synthesis is critical to diverse cellular processes and plays a pivotal role in regulating gene expression during embryogenesis. The cap-binding protein eIF4E is a translational factor whose activity appears to be both ubiquitous and central to the regulation of protein synthesis in all cell-types. As a cellcycle regulator, mesoderm inducer and proto-oncogene, the amount and activity of the translational factor eIF4E must be under strict control, but the range of its expression and its concentration as a function of position and time in the developing embryo are unknown. Consequently, we have initiated studies to elucidate the expression of the eIF4E gene and its role in the regulating embryonic development. We have cloned a zebrafish gene encoding eIF4E, zeIF4E, and measured its developmental expression. Unexpectedly, we found that the zeIF4E gene produces two alternatively spliced transcripts that potentially encode different forms of the initiation factor. Molecular analyses and in situ hybridization reveal a potential role for eIF4E in regulating protein synthesis during vertebrate oogenesis, gastrulation, and erythropoiesis. The dynamic and asymmetric expression of eIF4E during zebrafish embryogenesis reveals that this ostensibly general translation factor may act as a tissue-specific translational enhancer.
Briefings in Functional Genomics and Proteomics, Oct 31, 2008
In the past decade, tools derived from DNA transposons have made major contributions to vertebrat... more In the past decade, tools derived from DNA transposons have made major contributions to vertebrate genetic studies from gene delivery to gene discovery. Multiple, highly complementary systems have been developed, and many more are in the pipeline. Judging which DNA transposon element will work the best in diverse uses from zebrafish genetic manipulation to human gene therapy is currently a complex task. We have summarized the major transposon vector systems active in vertebrates, comparing and contrasting known critical biochemical and in vivo properties, for future tool design and new genetic applications.
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Papers by Scott FAHRENKRUG