Germline engineering of the chicken genome using CRISPR/Cas9 by in vivo transfection of PGCs

Development of simple and readily adoptable methods to mediate germline engineering of the chicken genome will have many applications in research, agriculture and industrial biotechnology. We report germline targeting of the endogenous chicken Interferon Alpha and Beta Receptor Subunit 1 (IFNAR1) gene by in vivo transgenic expression of the high-fidelity Cas9 (Cas9-HF1) and guide RNAs (gRNAs) in chickens. First, we developed a Tol2 transposon vector carrying Cas9-HF1, IFNAR1-gRNAs (IF-gRNAs) and green fluorescent protein (GFP) transgenes (pTgRCG) and validated in chicken fibroblast DF1 cells. Next, the pTgRCG plasmid was directly injected into the dorsal aorta of embryonic day (ED) 2.5 chicken embryos targeting the circulating primordial germ cells (PGCs). The resulting chimera roosters generated a fully transgenic generation 1 (G1) hen with constitutive expression of Cas9-HF1 and IF-gRNAs (G1_Tol2-Cas9/IF-gRNA). We detected a spectrum of indels at gRNA-targeted loci in the G1_Tol2-Cas9/IF-gRNA hen and the indels were stably inherited by the G2 progeny. Breeding of the G1_Tol2-Cas9/IF-gRNA hen resulted in up to 10% transgene-free heterozygote IFNAR1 mutants, following null-segregation of the Tol2 insert. The method described here will provide new opportunities for genome editing in chicken and other avian species that lack PGC culture.

Marker counter-selection via CRISPR/Cas9 co-targeting for efficient generation of genome edited avian cell lines and germ cells

Efficient isolation of genetically modified cells that are phenotypically indistinguishable from the unmodified cells remains a major technical barrier for the broader utilization of CRISPR/Cas9. Here, we report a novel enrichment approach to select the genome engineered cells by co-targeting a genomically integrated GFP gene along with the endogenous gene of interest (GOI). Using this co-targeting approach, multiple genomic loci were successfully targeted in chicken (DF1) and quail (CEC-32) fibroblast cell lines by transient transfection of Cas9 and guide RNAs (gRNAs). Clonal isolation of co-targeted DF1 cells showed 75% of cell clones had deletion of GFP and biallelic deletion of the GOI. To assess the utility of this approach to generate genome modified animals, we tested it on chicken primordial germ cells (PGCs) expressing GFP by co-targeting with gRNAs against GFP and endogenous ovomucoid (OVM) gene. PGCs enriched for loss of GFP and confirmed for OVM deletion, derived by co-targeting, were injected into Hamburger and Hamilton stage 14-15 chicken embryos, and their ability to migrate to the genital ridge was confirmed. This simple, efficient enrichment approach could easily be applied to the creation of knock-out or edited cell lines or animals.

Innovative approaches to genome editing in avian species

The tools available for genome engineering have significantly improved over the last 5 years, allowing scientist to make precise edits to the genome. Along with the development of these new genome editing tools has come advancements in technologies used to deliver them. In mammals genome engineering tools are typically delivered into in vitro fertilized single cell embryos which are subsequently cultured and then implanted into a recipient animal. In avian species this is not possible, so other methods have been developed for genome engineering in birds. The most common involves in vitro culturing of primordial germ cells (PGCs), which are cells that migrate through the embryonic circulatory system to the developing gonad and colonize the gonad, eventually differentiating into the gonadocytes which produce either sperm or ova. While in culture the PGCs can be modified to carry novel transgenes or gene edits, the population can be screened and enriched, and then transferred into a recipient embryo. The largest drawback of PGC culture is that culture methods do not transfer well across avian species, thus there are reliable culture methods for only a few species including the chicken. Two newer technologies that appear to be more easily adapted in a wider range of avian species are direct injection and sperm transfection assisted gene editing (STAGE). The direct injection method involves injecting genome engineering tools into the circulatory system of the developing embryo just prior to the developmental time point when the PGCs are migrating to the gonads. The genome engineering tools are complexed with transfection reagents, allowing for in vivo transfection of the PGCs. STAGE utilizes sperm transfection to deliver genome engineering tools directly to the newly fertilized embryo. Preliminary evidence indicates that both methodologies have the potential to be adapted for use in birds species other than the chicken, however further work is needed in this area.

Generation of gene edited birds in one generation using sperm transfection assisted gene editing (STAGE)

Generating transgenic and gene edited mammals involves in vitro manipulation of oocytes or single cell embryos. Due to the comparative inaccessibility of avian oocytes and single cell embryos, novel protocols have been developed to produce transgenic and gene edited birds. While these protocols are relatively efficient, they involve two generation intervals before reaching complete somatic and germline expressing transgenic or gene edited birds. Most of this work has been done with chickens, and many protocols require in vitro culturing of primordial germ cells (PGCs). However, for many other bird species no methodology for long term culture of PGCs exists. Developing methodologies to produce germline transgenic or gene edited birds in the first generation would save significant amounts of time and resource. Furthermore, developing protocols that can be readily adapted to a wide variety of avian species would open up new research opportunities. Here we report a method using sperm as a delivery mechanism for gene editing vectors which we call sperm transfection assisted gene editing (STAGE). We have successfully used this method to generate GFP knockout embryos and chickens, as well as generate embryos with mutations in the doublesex and mab-3 related transcription factor 1 (DMRT1) gene using the CRISPR/Cas9 system. The efficiency of the method varies from as low as 0% to as high as 26% with multiple factors such as CRISPR guide efficiency and mRNA stability likely impacting the outcome. This straightforward methodology could simplify gene editing in many bird species including those for which no methodology currently exists.

Overexpression of Anti-Müllerian Hormone Disrupts Gonadal Sex Differentiation, Blocks Sex Hormone Synthesis, and Supports Cell Autonomous Sex Development in the Chicken

The primary role of Anti-Müllerian hormone (AMH) during mammalian development is the regression of Müllerian ducts in males. This highly conserved function is retained in birds and is supported by the high levels of AMH expression in developing testes. Mammalian AMH expression is regulated by a combination of transcription factors, the most important being Sry-type high-mobility-group box transcription factor-9 (SOX9). In the chicken embryo, however, AMH mRNA expression precedes that of SOX9, leading to the view that AMH may play a more central role in avian testicular development. To define its role in chicken gonadal development, AMH was overexpressed using the RCASBP viral vector. AMH caused the gonads of both sexes to develop as small and undeveloped structures at both embryonic and adult stages. Molecular analysis revealed that although female gonads developed testis-like cords, gonads lacked Sertoli cells and were incapable of steroidogenesis. A similar gonadal phenotype was also observed in males, with a complete loss of both Sertoli cells, disrupted SOX9 expression and gonadal steroidogenesis. At sexual maturity both sexes showed a female external phenotype but retained sexually dimorphic body weights that matched their genetic sexes. These data suggest that AMH does not operate as an early testis activator in the chicken but can affect downstream events, such as sex steroid hormone production. In addition, this study provides a unique opportunity to assess chicken sexual development in an environment of sex hormone deficiency, demonstrating the importance of both hormonal signaling and direct cell autonomous factors for somatic sex identity in birds.

Advances in genetic engineering of the avian genome: "Realising the promise"

This review provides an historic perspective of the key steps from those reported at the 1st Transgenic Animal Research Conference in 1997 through to the very latest developments in avian transgenesis. Eighteen years later, on the occasion of the 10th conference in this series, we have seen breakthrough advances in the use of viral vectors and transposons to transform the germline via the direct manipulation of the chicken embryo, through to the establishment of PGC cultures allowing in vitro modification, expansion into populations to analyse the genetic modifications and then injection of these cells into embryos to create germline chimeras. We have now reached an unprecedented time in the history of chicken transgenic research where we have the technology to introduce precise, targeted modifications into the chicken genome, ranging from; new transgenes that provide improved phenotypes such as increased resilience to economically important diseases; the targeted disruption of immunoglobulin genes and replacement with human sequences to generate transgenic chickens that express "humanised" antibodies for biopharming; and the deletion of specific nucleotides to generate targeted gene knockout chickens for functional genomics. The impact of these advances is set to be realised through applications in chickens, and other bird species as models in scientific research, for novel biotechnology and to protect and improve agricultural productivity.

Transgenic Chickens Overexpressing Aromatase Have High Estrogen Levels but Maintain a Predominantly Male Phenotype

Estrogens play a key role in sexual differentiation of both the gonads and external traits in birds. The production of estrogen occurs via a well-characterized steroidogenic pathway, which is a multistep process involving several enzymes, including cytochrome P450 aromatase. In chicken embryos, the aromatase gene (CYP19A1) is expressed female-specifically from the time of gonadal sex differentiation. Ectopic overexpression of aromatase in male chicken embryos induces gonadal sex reversal, and male embryos treated with estradiol become feminized; however, this is not permanent. To test whether a continuous supply of estrogen in adult chickens could induce stable male to female sex reversal, 2 transgenic male chickens overexpressing aromatase were generated using the Tol2/transposase system. These birds had robust ectopic aromatase expression, which resulted in the production of high serum levels of estradiol. Transgenic males had female-like wattle and comb growth and feathering, but they retained male weights, displayed leg spurs, and developed testes. Despite the small sample size, this data strongly suggests that high levels of circulating estrogen are insufficient to maintain a female gonadal phenotype in adult birds. Previous observations of gynandromorph birds and embryos with mixed sex chimeric gonads have highlighted the role of cell autonomous sex identity in chickens. This might imply that in the study described here, direct genetic effects of the male chromosomes largely prevailed over the hormonal profile of the aromatase transgenic birds. This data therefore support the emerging view of at least partial cell autonomous sex development in birds. However, a larger study will confirm this intriguing observation.

Anti-Müllerian Hormone Is Required for Chicken Embryonic Urogenital System Growth but Not Sexual Differentiation

In mammals, the primary role of anti-Müllerian hormone (AMH) during development is the regression of Müllerian ducts in males. These structures otherwise develop into fallopian tubes, oviducts, and upper vagina, as in females. This highly conserved function is retained in birds and is supported by the high levels of AMH expression in developing testes. In mammals, AMH expression is controlled partly by the transcription factor, SOX9. However, in the chicken, AMH mRNA expression precedes that of SOX9 , leading to the view that AMH may lie upstream of SOX9 and play a more central role in avian testicular development. To help define the role of AMH in chicken gonad development, we suppressed AMH expression in chicken embryos using RNA interference. In males, AMH knockdown did not affect the expression of key testis pathway genes, and testis cords developed normally. However, a reduction in the size of the mesonephros and gonads was observed, a phenotype that was evident in both sexes. This growth defect occurred as a result of the reduced proliferative capacity of the cells of these tissues, and male gonads also had a significant reduction in germ cell numbers. These data suggest that although AMH does not directly contribute to testicular or ovarian differentiation, it is required in a sex-independent manner for proper cell proliferation and urogenital system growth.

Overexpression of aromatase alone is sufficient for ovarian development in genetically male chicken embryos

Estrogens play a key role in sexual differentiation of both the gonads and external traits in birds. The production of estrogen occurs via a well-characterised steroidogenic pathway, which is a multi-step process involving several enzymes, including cytochrome P450 aromatase. In chicken embryos, the aromatase gene (CYP19A1) is expressed female-specifically from the time of gonadal sex differentiation. To further explore the role of aromatase in sex determination, we ectopically delivered this enzyme using the retroviral vector RCASBP in ovo. Aromatase overexpression in male chicken embryos induced gonadal sex-reversal characterised by an enlargement of the left gonad and development of ovarian structures such as a thickened outer cortex and medulla with lacunae. In addition, the expression of key male gonad developmental genes (DMRT1, SOX9 and Anti-Müllerian hormone (AMH)) was suppressed, and the distribution of germ cells in sex-reversed males followed the female pattern. The detection of SCP3 protein in late stage sex-reversed male embryonic gonads indicated that these genetically male germ cells had entered meiosis, a process that normally only occurs in female embryonic germ cells. This work shows for the first time that the addition of aromatase into a developing male embryo is sufficient to direct ovarian development, suggesting that male gonads have the complete capacity to develop as ovaries if provided with aromatase.

A new method for producing transgenic birds via direct in vivo transfection of primordial germ cells

Traditional methods of avian transgenesis involve complex manipulations involving either retroviral infection of blastoderms or the ex vivo manipulation of primordial germ cells (PGCs) followed by injection of the cells back into a recipient embryo. Unlike in mammalian systems, avian embryonic PGCs undergo a migration through the vasculature on their path to the gonad where they become the sperm or ova producing cells. In a development which simplifies the procedure of creating transgenic chickens we have shown that PGCs are directly transfectable in vivo using commonly available transfection reagents. We used Lipofectamine 2000 complexed with Tol2 transposon and transposase plasmids to stably transform PGCs in vivo generating transgenic offspring that express a reporter gene carried in the transposon. The process has been shown to be highly effective and as robust as the other methods used to create germ-line transgenic chickens while substantially reducing time, infrastructure and reagents required. The method described here defines a simple direct approach for transgenic chicken production, allowing researchers without extensive PGC culturing facilities or skills with retroviruses to produce transgenic chickens for wide-ranging applications in research, biotechnology and agriculture.

Manipulation of estrogen synthesis alters MIR202* expression in embryonic chicken gonads

Tissue-specific patterns of microRNA (miRNA) expression contribute to organogenesis during embryonic development. Using the embryonic chicken gonads as a model for vertebrate gonadogenesis, we previously reported that miRNAs are expressed in a sexually dimorphic manner during gonadal sex differentiation. Being male biased, we hypothesised that up-regulation of microRNA 202* (MIR202*) is characteristic of testicular differentiation. To address this hypothesis, we used estrogen modulation to induce gonadal sex reversal in embryonic chicken gonads and analyzed changes in MIR202* expression. In ovo injection of estradiol-17beta at Embryonic Day 4.5 (E4.5) caused feminization of male gonads at E9.5 and reduced MIR202* expression to female levels. Female gonads treated at E3.5 with an aromatase inhibitor, which blocks estrogen synthesis, were masculinized by E9.5, and MIR202* expression was increased. Reduced MIR202* expression correlated with reduced expression of the testis-associated genes DMRT1 and SOX9, and up-regulation of ovary-associated genes FOXL2 and CYP19A1 (aromatase). Increased MIR202* expression correlated with down-regulation of FOXL2 and aromatase and up-regulation of DMRT1 and SOX9. These results confirm that up-regulation of MIR202* coincides with testicular differentiation in embryonic chicken gonads.

Sexually dimorphic microRNA expression during chicken embryonic gonadal development

MicroRNAs are a highly conserved class of small RNAs that function in a sequence-specific manner to posttranscriptionally regulate gene expression. Tissue-specific miRNA expression studies have discovered numerous functions for miRNAs in various aspects of embryogenesis, but a role for miRNAs in gonadal development and sex differentiation has not yet been reported. Using the chicken embryo as a model, microarrays were used to profile the expression of chicken miRNAs prior to, during, and after the time of gonadal sex differentiation (Embryonic Day 5.5 [E5.5], E6.5, and E9.5). Sexually dimorphic miRNAs were identified, and the expression patterns of several were subjected to further validation by in situ hybridization and Northern blot analysis. Expression of one chicken miRNA, MIR202*, was observed to be sexually dimorphic, with upregulation in the developing testis from the onset of sexual differentiation. Additional data from deep sequencing of male and female embryonic gonad RNA samples also indicated upregulation of MIR202* in male gonads. These findings provide the first evidence of sexually dimorphic miRNA expression during vertebrate gonadal sex differentiation and suggest that MIR202* may function in regulating testicular development.

Octa-guanidine morpholino restores dystrophin expression in cardiac and skeletal muscles and ameliorates pathology in dystrophic mdx mice

Steric-block antisense oligonucleotides (AONs) are able to target RNAs for destruction and splicing alteration. Reading frame restoration of the dystrophin transcript can be achieved by AON-mediated exon skipping in the dystrophic mdx mouse model. However, simple, unmodified AONs exhibit inefficient delivery systemically, leading to dystrophin induction with high variability in skeletal muscles and barely detectable in cardiac muscle. Here, we examined a Morpholino oligomer conjugated with a dendrimeric octaguanidine (Vivo-Morpholino) and demonstrated that the delivery moiety significantly improved dystrophin production in both skeletal and cardiac muscles in mdx mice in vivo. Single intravenous (IV) injections of 6 mg/kg Vivo-MorpholinoE23 (Vivo-ME23) generated dystrophin expression in skeletal muscles at the levels higher than the injection of 300 mg/kg unmodified ME23. Repeated injections at biweekly intervals achieved near 100% of fibers expressing dystrophin in skeletal muscles bodywide without eliciting a detectable immune response. Dystrophin protein was restored to approximately 50 and 10% of normal levels in skeletal and cardiac muscles, respectively. Vivo-Morpholinos showed no signs of toxicity with the effective dosages and regime, thus offering realistic prospects for the treatment of a majority of Duchenne muscular dystrophy (DMD) patients and many other diseases by targeting RNAs.

Inhibition of chicken anaemia virus replication using multiple short-hairpin RNAs

RNA interference is becoming a powerful tool in gene-specific silencing. New generation vaccines against many pathogens will attempt to incorporate these molecules. Here we report the efficient silencing of chicken anaemia virus (CAV) genes in vitro using short-hairpin RNAs (shRNAs) targeting the region of the CAV transcript encoding either viral protein (VP) 1, or overlapping sections of VP2/3 and VP1/2. The shRNAs were first validated against a EGFP-CAV fusion transcript reporter system and then against CAV grown in MDCC-MSB1 cells. The decrease in CAV replication was shown with a flow cytometry assay specific for VP3. Overall the results showed efficient silencing of CAV replication in tissue culture using shRNAs. It was also shown that the combination of three shRNAs being expressed from a single plasmid is less effective at silencing CAV replication than the most active shRNA alone.

Identification and characterisation of the porcine 7SK RNA polymerase III promoter for short hairpin RNA expression

The RNA polymerase III (pol III) type III promoters U6 and 7SK are routinely used to express short hairpin RNA (shRNA) molecules from a DNA construct. In this study, we identified, characterised and compared the porcine 7SK promoter in porcine (homologous) and non-porcine (heterologous) derived cell lines. The porcine 7SK small nuclear RNA (snRNA) was identified by alignment with known sequences and further characterisation of the upstream regions determined the presence of typical RNA pol III sequence motifs. The porcine 7SK (po7SK) promoter was cloned and a one-step PCR strategy used to construct shRNA expression cassettes. The 7SK promoter activity was quantified by knockdown of the exogenous reporter gene encoding the enhanced green fluorescent protein (EGFP). Results indicated the po7SK promoter was functional in both homologous and heterologous cells lines. The identification and characterisation of the porcine RNA pol III promoter will contribute to the area of RNAi delivery and further develop our understanding of RNA promoter structure and function.

Native microRNA loop sequences can improve short hairpin RNA processing for virus gene silencing in animal cells

Introduction of small interfering RNAs (siRNAs) into cells results in transitory silencing of target genes with complementary sequence. Incorporating siRNAs into short-hairpin RNAs (shRNAs) or microRNA-adapted shRNAs (shRNAmir) is a popular tool for targeted gene silencing. shRNAmirs mimicking endogenous pre-microRNAs (unprocessed hairpin microRNAs) are more difficult to design and result in longer RNA molecules. The use of microRNA (miRNA) loop sequences in shRNAs as an alternative to an entire pre-microRNA structure on silencing efficiency has not been studied extensively. This report shows that loop sequences derived from native miRNAs improves the efficiency of silencing due to the processing of the shRNAs into mature siRNAs.

Comparison of chicken 7SK and U6 RNA polymerase III promoters for short hairpin RNA expression

BACKGROUND

RNA polymerase III (pol III) type 3 promoters such as U6 or 7SK are commonly used to express short-hairpin RNA (shRNA) effectors for RNA interference (RNAi). To extend the use of RNAi for studies of development using the chicken as a model system, we have developed a system for expressing shRNAs using the chicken 7SK (ch7SK) promoter.

RESULTS

We identified and characterised the ch7SK promoter sequence upstream of the full-length 7SK small nuclear RNA (snRNA) sequence in the chicken genome and used this to construct vectors to express shRNAs targeting enhanced green fluorescent protein (EGFP). We transfected chicken DF-1 cells with these constructs and found that anti-EGFP-shRNAs (shEGFP) expressed from the ch7SK promoter could induce efficient knockdown of EGFP expression. We further compared the efficiency of ch7SK-directed knockdown to that of chicken U6 (cU6) promoters and found that the efficiency of the ch7SK promoter was not greater than, but comparable to the efficiency of cU6 promoters.

CONCLUSION

In this study we have demonstrated that the ch7SK promoter can express shRNAs capable of mediating efficient RNAi in a chicken cell line. However, our finding that RNAi driven by the ch7SK promoter is not more efficient than cU6 promoters contrasts previous comparisons of mammalian U6 and 7SK promoters. Since the ch7SK promoter is the first non-mammalian vertebrate 7SK promoter to be characterised, this finding may be helpful in understanding the divergence of pol III promoter activities between mammalian and non-mammalian vertebrates. This aside, our results clearly indicate that the ch7SK promoter is an efficient alternative to U6-based shRNA expression systems for inducing efficient RNAi activity in chicken cells.

Manipulation of small RNAs to modify the chicken transcriptome and enhance productivity traits

In recent years there has been a revolution in our understanding of genes and how they come to control the physical outcomes of development. Central to this has been the understanding of the cellular processes of RNA interference (RNAi), for which the Nobel Prize for Physiology or Medicine was awarded in 2006. Coupled with this has been the recognition that microRNAs are key mediators of this process within cells. RNAi whether mediated exogenously by synthetic oligonucleotides or vector-delivered double stranded RNA or endogenously by microRNAs can have a profound and specific effect on gene expression. Elucidating and understanding these processes in the chicken will provide critical information to enable more precise control over breeding strategies for improvement of traits in production poultry, either by direct or indirect means. It will also provide alternative strategies for the control and prevention of important avian diseases.

Suppression of bovine viral diarrhea virus replication by small interfering RNA and short hairpin RNA-mediated RNA interference

Bovine viral diarrhea virus (BVDV) is a ubiquitous viral pathogen that affects cattle herds' worldwide causing significant economic loss. The current strategies to control BVDV infection include vaccination (modified-live or killed) and control of virus spread by enhanced biosecurity management, however, the disease remains prevalent. With the discovery of the sequence-specific method of gene silencing known as RNA interference (RNAi), a new era in antiviral therapies has begun. Here we report the efficient inhibition of BVDV replication by small interfering (siRNA) and short hairpin RNA (shRNA)-mediated gene silencing. siRNAs were generated to target the 5' non-translated (NTR) region and the regions encoding the C, NS4B and NS5A proteins of the BVDV genome. The siRNAs were first validated using an EGFP/BVDV reporter system and were then shown to suppress BVDV-induced cytopathic effects and viral titers in cell culture with surprisingly different activities compared to the reporter system. Efficient viral suppression was then achieved by bovine 7SK-expressed BVDV-specific shRNAs. Overall, our results demonstrated the use of siRNA and shRNA-mediated gene silencing to achieve efficient inhibition of the replication of this virus in cell culture.

Comparison of bovine RNA polymerase III promoters for short hairpin RNA expression

RNA interference (RNAi) mediated by DNA-based expression of short hairpin RNA (shRNA) is a powerful method of sequence-specific gene knockdown. A number of vectors for expression of shRNA have been developed that feature promoters from RNA polymerase III (pol III)-transcribed genes of mouse or human origin. To advance the use of RNAi as a tool for functional genomic research and for future development of specific therapeutics in the bovine species, we have developed shRNA expression vectors that feature novel bovine RNA pol III promoters. We characterized two bovine U6 small nuclear RNA (snRNA) promoters (bU6-2 and bU6-3) and a bovine 7SK snRNA promoter (b7SK). We compared the efficiency of each of these promoters to express shRNA molecules. Promoter activity was measured in the context of RNAi by targeting and suppressing the reporter gene encoding enhanced green fluorescent protein. Results show that the b7SK promoter induced the greatest level of suppression in a range of cell lines. The comparison of these bovine promoters in shRNA expression is an important component for the future development of bovine-specific RNAi-based research.

Characterisation and application of a bovine U6 promoter for expression of short hairpin RNAs

BACKGROUND

The use of small interfering RNA (siRNA) molecules in animals to achieve double-stranded RNA-mediated interference (RNAi) has recently emerged as a powerful method of sequence-specific gene knockdown. As DNA-based expression of short hairpin RNA (shRNA) for RNAi may offer some advantages over chemical and in vitro synthesised siRNA, a number of vectors for expression of shRNA have been developed. These often feature polymerase III (pol. III) promoters of either mouse or human origin.

RESULTS

To develop a shRNA expression vector specifically for bovine RNAi applications, we identified and characterised a novel bovine U6 small nuclear RNA (snRNA) promoter from bovine sequence data. This promoter is the putative bovine homologue of the human U6-8 snRNA promoter, and features a number of functional sequence elements that are characteristic of these types of pol. III promoters. A PCR based cloning strategy was used to incorporate this promoter sequence into plasmid vectors along with shRNA sequences for RNAi. The promoter was then used to express shRNAs, which resulted in the efficient knockdown of an exogenous reporter gene and an endogenous bovine gene.

CONCLUSION

We have mined data from the bovine genome sequencing project to identify a functional bovine U6 promoter and used the promoter sequence to construct a shRNA expression vector. The use of this native bovine promoter in shRNA expression is an important component of our future development of RNAi therapeutic and transgenic applications in bovine species.

Improved vectors for expression library immunization--application to Mycoplasma hyopneumoniae infection in pigs

Expression library immunization (ELI) has previously been used in a number of disease models in mice. Here, we describe the first example of the application of ELI to a large animal model with the immunization of pigs against enzootic pneumonia, a disease caused by Mycoplasma hyopneumoniae. The development of new plasmid vectors and library screening methods facilitated the application of ELI to this disease by allowing random libraries to be screened for clones expressing recombinant proteins. In this way the vast majority of clones in random libraries that are unproductive can be eliminated, meaning that libraries are more likely to give protection and are subsequently easier to further screen and analyze. By using this approach we have used one library screen and two animal trials to progress from an original library of 20,000 clones to a group of just 96 clones.

A large, single center investigation of the immunogenetic factors affecting liver transplantation

BACKGROUND

Reports on the relevance of immunogenetic factors in liver transplantation are often conflicting or inconclusive. We have, therefore, investigated a range of factors that may underlie liver graft survival.

METHODS

The influences of HLA, flow cytometric, and enhanced cytotoxic crossmatching and immunoglobulin (Ig)A levels on graft survival, and acute and chronic rejection were investigated for a single center involving 446 patients over 13 years.

RESULTS

The effect of HLA mismatching on graft survival was significant (P<10(-2)) and was reversed in recipients with autoimmune diseases (P<0.5x10(-2)), whereas the effect of HLA mismatches on the level of acute rejection was detrimental in all recipients. There was a significant effect of a positive cytotoxic crossmatch on 3-month (P<10(-5)) and 1-year (P<10(-4)) graft survival, and an additional effect of the flow cytometric crossmatch was seen for chronic rejection (P<10(-2)) and acute rejection (P<10(-2)). Recipients with HLA-A1,B8,DRB1*0301 had higher levels of acute rejection (P<0.5x10(-2)), and recipients who received an ABO compatible-nonidentical transplant have a significantly higher risk (P<10(-2)) of developing chronic rejection. Finally, the beneficial effect of high serum IgA and, specifically, IgA anti Fab, seen in renal transplants was not evident in liver transplants, and in fact the opposite may be true, at least for acute rejection (P<0.5x10(-2)).

CONCLUSIONS

By separating the recipients with autoimmune disease from other patients and by including acute and chronic rejection as outcome parameters, we have used the power of a large single-centre study to delineate the significance of some of the important immunogenetic factors involved in liver transplantation.

IgA class antibodies and flow cytometric cross-matching in renal transplantation

BACKGROUND

The established method of pretransplant cross-matching does not detect IgA antibodies, and IgA antibodies have thus been ignored when assessing patients for transplantation. The aim of this study was to detect IgA allo- and autoreactive antibodies using flow cytometry and to correlate the results with transplant outcome.

METHODS

Pretransplant sera from 231 sequential renal recipients were tested for serum IgA levels and antibodies directed against the Fab portion of the human IgG molecule. Fifty-nine recipients with sufficient stored donor lymphocytes were also tested by flow cytometry for donor-specific alloantibodies of the IgA isotype.

RESULTS

Graft survival was improved in recipients with higher IgA levels. High IgA anti-Fab levels led to a significantly higher 1-year graft survival (P<0.05). Graft survival was further enhanced where both serum IgA and IgA anti-Fab were raised (P<0.01). Although the mean IgA level tended to be higher for recipients with a positive IgA flow cytometric cross-match (FCXM), the IgA FCXM was not associated with increased IgA anti-Fab, suggesting that the IgA FCXM is detecting a different subset of IgA reactivity. Additionally, for primary grafts, a positive IgA FCXM was not associated with enhanced graft survival.

CONCLUSIONS

Within the repertoire of IgA activity, there are two recognizable groups, the IgA anti-Fab specificity, which is significantly associated with enhanced graft survival, and that detected by the IgA FCXM, which surprisingly is more likely to be positive in less sensitized first grafts and is not associated with enhanced graft survival.

Putative functional domain within ORF2 on the Mycobacterium insertion sequences IS900 and IS902

Repeated DNA sequences have been identified in a range of mycobacterial species and have been implicated in the increased virulence of some of these species, namely, Mycobacterium paratuberculosis and M. avium subsp. silvaticum. Here we present a case to suggest that the insertion sequences IS900 and IS902 encode a protein from a putative gene positioned on the complementary strand to their transposase genes. Based on amino acid homology analyses, this open reading frame (ORF2) could encode a transport protein. The ORF2 protein thus IS900 and IS902, may have a role in the increased pathogenicity of M. paratuberculosis and M. avium subsp. silvaticum from an M. avium background.

Molecular analysis of the F plasmid traVR region: traV encodes a lipoprotein

The nucleotide sequences of the conjugative F plasmid transfer region genes, traV and traR, have been determined. The deduced amino acid sequence of TraV indicated that it may be a lipoprotein; this was confirmed by examining the effect of globomycin on traV-encoded polypeptides synthesized in minicells. An open reading frame that may represent a previously undetected transfer gene, now designated trbG, was identified immediately upstream of traV. The deduced product of traR was found to share amino acid similarity with proteins from the bacteriophages 186 and P2 and with the dosage-dependent dnaK suppressor DksA.

Characterisation of a highly repeated DNA sequence from Mycobacterium bovis

We report characterisation of a novel repeat sequence from a Mycobacterium bovis genomic library. The highly repeated sequence belongs to a family consisting of a 24 base pair (bp) direct repeat (DR), that appears to be organized into clusters on the chromosome. We classify the 24-bp DR into the group of prokaryotic DNA repeats known as the interspersed repetitive sequence elements. The 24-bp DR will be of potential use as a DNA fingerprinting tool in epidemiological studies of M. bovis.

Restriction fragment length polymorphism analysis of Fusobacterium necrophorum using a novel repeat DNA sequence and a 16S rRNA gene probe

A repeated DNA sequence was isolated from Fusobacterium necrophorum biotype AB, strain FnS1. The repeated sequence shared considerable homology with the transposase gene from the Pseudomonas syringiae insertion sequence IS801. The repeat sequence was used together with a 16S ribosomal RNA gene probe to type F. necrophorum isolates using restriction fragment length polymorphisms. The probes revealed differences between several clinical isolates and will be useful tools to study the epidemiology of ovine foot abscess and other diseases caused by F. necrophorum.

Treatment of recurrent spontaneous abortion by immunization with paternal lymphocytes: results of a controlled trial

PROBLEM

It remains unclear whether maternal immunization with paternal lymphocytes prior to conception improves the reproductive outcome in women with recurrent abortion in whom all secondary causes have been excluded.

METHOD

A double-blind placebo controlled trial was instituted in women with unexplained recurrent spontaneous abortion, comparing immunization with 400 million paternal to 400 million maternal (autologous) lymphocytes. The groups were compared in a paired sequential trials chart, by logistic regression, and, in addition, a meta-analysis of this and other published trials was carried out.

RESULTS

The live birth rate among pregnancies in paired couples with paternal lymphocyte immunization was 68% compared to 47% in the women who received their own cells. The results bordered on, but did not achieve, statistical significance. The women in each group were thoroughly investigated to exclude known causes of recurrent pregnancy loss and appeared to have been well matched in all variables. Women with lymphocytotoxic antibodies against paternal lymphocytes were excluded. Unlike our previous study there was not association between the time to conception and the chance of a successful outcome. Indeed, the time to conception was relatively short, 12 wk in all groups. The meta-analysis supported an overall modest favorable experience with paternal cells.

CONCLUSION

The study is consistent with a general trend favoring paternal over maternal lymphocyte immunization but reinforces the need for larger multicenter controlled trials as well as more detailed biological study in humans to understand the nature of the maternal-fetal interface and its breakdown.

Characterisation of a novel repetitive DNA sequence from Mycobacterium bovis

We report characterisation of three copies of a novel repeat sequence isolated from a Mycobacterium bovis genomic library. The repeat occurs within open reading frames, potentially encoding a conserved tandem array of a pentapeptide sequence with the consensus X-Gly-Asn-X-Gly. The tandem array is present up to five times in M. bovis and it is proposed that they may occur in a family of genes expressing functionally related proteins. We postulate that these proteins may play a role in binding of M. bovis to host cell receptors.

Patients with thick melanomas surviving at least 10 years: histological, cytometric and HLA analyses

Survival for melanoma patients with thick primary tumours is notoriously short. A small number of patients with tumours greater than 5.5 mm thick do, however, have protracted survival intervals. Attempts were made to account for this phenomenon by means of histological, cytometric and HLA serotyping analyses. Patients with thick lesions surviving more than 10 years were matched--by sex, age, anatomical site of primary lesion, stage of disease and, whenever possible, by initial surgical therapy--to patients dying of their disease within 5 years. This case-control study on 13 long-term survivors and 13 short-term survivors did not show that any of the following attributes of the primary lesion were useful in predicting survival: Clark's level of invasion, ulceration, mitotic rate, host inflammatory response, tumour regression, tumour necrosis, vascular invasion, satellitosis, radial or vertical growth phase, predominant cell type, histogenetic type, borders, DNA quantification and cytomorphometry. HLA serotyping of long-term survivors showed an excess of antigen DQw1 compared with the general population, although this excess was not statistically significant.

Amino acid sequences recognized by T cells: studies on a merozoite surface antigen from the FCQ-27/PNG isolate of Plasmodium falciparum

Twenty-six overlapping peptides, spanning the entire FCQ-27/PNG sequence of the Plasmodium falciparum antigen known as merozoite surface antigen 2 were screened for their ability to induce the proliferation of peripheral blood lymphocytes (PBL) obtained from 12 donors living in Honiara, Solomon Islands where P. falciparum is endemic. A recombinant (r) form of MSA2, known as Ag 1609 was also screened in these assays and tetanus toxoid (TT) antigen was included as a control. The location of the predicted T cell determinants within MSA2 was examined using the algorithm, AMPHI and by scanning MSA2 for amino acid sequences showing the Rothbard motif. There were 13 predicted amphipathic helical sites and five examples of Rothbard sequences in the antigen. The location of these with regard to the peptides tested is shown. Nine of the 12 individuals responded to TT with high stimulation indices (greater than 4) being obtained in the majority of donors. Only three individuals responded to r-MSA2 with the stimulation indices (SI) in the range of 2.4-4.1. Peptides from both the constant and variable regions of MSA2 were recognized in the proliferative assays. However, the majority of the positive proliferative responses were to peptides which spanned the central variable region which included the two copies of the 32-amino-acid repeat occurring in the antigen. High SI comparable to those obtained to TT were seen in some individuals with some peptides. There was considerable variation between donors in number and nature of the peptides recognised and two donors did not respond to any of the antigens tested. The significance of these findings to vaccine development is discussed.

Identification of two promiscuous T cell epitopes from tetanus toxin

Tetanus toxoid-specific T cell clones were isolated from a human donor. To determine the T cell epitopes recognized by the clones, 30 peptides representing amphipathic alpha helical regions of the tetanus toxin were screened for ability to induce proliferation of the clones. Two T epitopes were identified. These occurred within peptides 12 and 21, and had the amino acid sequences NSVDDALINSTKIYSYFPSV and PGINGKAIHLVNNESSE, respectively. An unusual feature was that both peptides could be presented to their respective T cell clones by antigen-presenting cells of many HLA specificities. Further investigation of peptide 12 showed that the epitope was only seven amino acids in length and had a very hydrophobic sequence, namely YSYFPSV. The ability of the T cell epitope-containing peptides 12 and 21 to interact with many different HLA alleles means they may potentially be very useful as "universal carrier molecules" in synthetic vaccines.

HLA antigens in chronic inflammatory demyelinating polyneuropathy

HLA typing of 71 patients with chronic inflammatory demyelinating polyneuropathy (CIDP) showed an overall increase in frequencies of HLA-A3, -B7, -DR2 as well as concomitantly decreased frequencies of HLA-44 and DR7. The strongest associations were seen with HLA-DR2, -DR7 and -B44 in CIDP overall, although they did not reach statistical significance.

Analysis of human T cell response to two Plasmodium falciparum merozoite surface antigens

Eight novel human T cell epitopes were identified within the two major merozoite surface antigens (MSA1 and MSA2) of Plasmodium falciparum using synthetic peptides. All except one of the peptides conformed structurally to an amphipathic alpha helix and three out of the four MSA1 peptides also contained sequences containing the Rothbard motif. Peptide MSA2/2, which fitted none of these criteria, was recognized by our donors to a similar degree as the other peptides. This peptide also contains a B cell epitope. Proliferative responses were obtained in both immune and nonimmune donors, however, the number of responses in the immune donor group was significantly higher. There was no correlation between the level of proliferation and antibody titers to these antigens. No peptides were preferentially recognized in association with specific HLA class II antigens.

Treatment of recurrent spontaneous abortion by immunization with paternal lymphocytes: correlates with outcome

Previous observations have suggested that defective recognition of fetal alloantigens by the maternal immune system is associated with recurrent pregnancy failure and that this may be prevented by boosting the maternal immune system with paternal or pooled third-party leukocytes. The mechanism whereby this process achieves success is not clear, and accordingly to explore this we immunized 28 couples with recurrent fetal loss with 80 x 10(6) paternal peripheral blood mononuclear leukocytes (PBML) and followed various immunological parameters. The couples studied, in whom 55% achieved a successful pregnancy, showed no increase in sharing of human lymphocyte antigen (HLA)-A, -B, or -DR antigens and no consistent evidence of a decreased mixed leukocyte reaction (MLR) or MLR plasma-blocking factors compared with control couples. Immunization did not alter these parameters but did induce antipaternal lymphocytotoxins, although the presence of the latter did not correlate with pregnancy outcome. There was a correlation between rapid conception after immunization and a subsequent successful pregnancy. A successful pregnancy also correlated with sustained postimmunization, postconception maternal antipaternal allospecific CD-8+ suppressor T cells. Although these findings provide overall evidence that immunization produces changes in the way in which the maternal immune system interacts with the fetus, larger numbers of couples and a higher dose of paternal lymphocytes will be needed to establish clearly whether this therapy works and its mechanism of action.

Definition of the HLA-Aw43 antigen

The HLA antigen Aw43 has been observed only in Southern African populations. In order to confirm its identity and clarify its definition, ten cells with this specificity were shipped to laboratories in England, the United States of America and Australia to be tested with the sera from the 10th International Histocompatibility Workshop. The results of tests on nine of these cells which were sufficiently viable indicated that HLA-Aw43 is a distinct serological specificity which could be distinguished from both the A10 cross-reacting group (A25, A26 and Aw34) and A29. The Aw43 specificity segregated in two South African Negro families, and occurred commonly in association with Bw70. The occurrence of HLA-Aw43 in South African Caucasoids, in contrast to its absence in other Caucasoid groups, is probably due to genetic admixture with indigenous South African populations.

Identification of T epitopes within a potential Plasmodium falciparum vaccine antigen. A study of human lymphocyte responses to repeat and nonrepeat regions of Pf155/RESA

PBMC from Melanesians who had high antibody reactivities to fusion proteins encompassing the 3' and the 5' repeat regions of the ring infected E surface antigen (Pf155/RESA), were tested for their ability to respond to synthetic and recombinant peptides representing regions of Pf155/RESA. The aim was to identify T cell epitopes within the Ag. Most of the synthetic peptides from the nonrepeat regions of Pf155/RESA were selected for study on the basis of their tendency to form amphipathic alpha-helices. Peptides representing immunodominant B cell epitopes were also tested. Three-quarters of the Melanesian donors responded to the recombinant peptides (Ag 1505 and Ag 632-100) and to the 8 x 4 mer, a synthetic peptide representative of the 3' repeat region. Whereas all the remaining eight peptides tested elicited a response in at least one donor, three peptides (M40, M42, and BTA3) representing sequences in the nonrepeat regions showed greatest promise as potentially useful T epitopes. Responses in control donors were also observed to most of the peptides but the percentage of responders was lower. T cell bulk lines specific to Ag 1505 and Ag 632-100 were established. All donors were HLA tissue typed, but no obvious correlations between responsiveness and HLA type were observed. Our results suggest that there are T cell epitopes within and outside the repeat regions of Pf155/RESA.

Identification of T epitopes within a potential Plasmodium falciparum vaccine antigen. A study of human lymphocyte responses to repeat and nonrepeat regions of Pf155/RESA

PBMC from Melanesians who had high antibody reactivities to fusion proteins encompassing the 3' and the 5' repeat regions of the ring infected E surface antigen (Pf155/RESA), were tested for their ability to respond to synthetic and recombinant peptides representing regions of Pf155/RESA. The aim was to identify T cell epitopes within the Ag. Most of the synthetic peptides from the nonrepeat regions of Pf155/RESA were selected for study on the basis of their tendency to form amphipathic alpha-helices. Peptides representing immunodominant B cell epitopes were also tested. Three-quarters of the Melanesian donors responded to the recombinant peptides (Ag 1505 and Ag 632-100) and to the 8 x 4 mer, a synthetic peptide representative of the 3' repeat region. Whereas all the remaining eight peptides tested elicited a response in at least one donor, three peptides (M40, M42, and BTA3) representing sequences in the nonrepeat regions showed greatest promise as potentially useful T epitopes. Responses in control donors were also observed to most of the peptides but the percentage of responders was lower. T cell bulk lines specific to Ag 1505 and Ag 632-100 were established. All donors were HLA tissue typed, but no obvious correlations between responsiveness and HLA type were observed. Our results suggest that there are T cell epitopes within and outside the repeat regions of Pf155/RESA.

Acute optic neuritis: a prospective study of risk factors for multiple sclerosis

Eighty two patients with isolated optic neuritis were studied prospectively to determine the frequency with which multiple sclerosis developed and the factors which increased its risk. Patients were followed for 6 to 264 months (mean, 57 months). Twenty six patients (32%) developed clinically definite or probable multiple sclerosis during the period of follow-up. Actuarial analysis predicted that 42% would develop multiple sclerosis by 7 years. Of those patients who developed multiple sclerosis, 92% had symptoms within 4 years of the first attack of optic neuritis. The highest incidence of multiple sclerosis occurred in the 21-40 year age group. There was an increased risk of MS in patients with HLA-DR2 and HLA-B7 tissue types. The frequency of HLA-DR4 was increased in patients with optic neuritis alone compared to controls and to patients with multiple sclerosis, but further studies are required to confirm this finding.

Typing of human fetal organs for the histocompatibility antigens A, B and DR

In the transplantation of human fetal pancreatic explants into diabetic man, the importance of matching the histocompatibility antigens of donor and recipient to decrease the chances of rejection is unknown. Before this question can be answered human fetuses must be tissue typed. We have shown that lymphocytes harvested from fetal liver, thymus, bone marrow and spleen can be successfully HLA DR typed in 64% and A and B typed in 57% of 58 fetuses aged 15 wk or more. Typing should ideally be carried out on unseparated T and B cells. Best results were achieved if all four of the above organs were available and more than one million viable cells were able to be harvested for typing. Whilst the DR antigens could be typed from all tissues, the A and B antigens could be typed, with few exceptions only from thymus, spleen and bone marrow. The efficacy of matching the histocompatibility antigens of recipient and donor fetuses, especially the DR antigens can now be tested in the human diabetic being transplanted with pancreatic explants.

Idiopathic hemochromatosis: demonstration of homozygous-heterozygous mating by HLA typing of families

In five families with idiopathic (hereditary) hemochromatosis, clinical and biochemical expression of the disease occurred in offspring of probands, suggesting an autosomal dominant mode of inheritance. However, HLA typing of subjects indicated that a homozygous-heterozygous mating almost certainly had occurred in four of the five families, resulting in homozygous offspring. Thus, in these families inheritance of the hemochromatosis trait was best explained in terms of an autosomal recessive or intermediate mode of inheritance. This study demonstrates the value of HLA typing in identifying homozygous-heterozygous matings in hemochromatosis families.

Idiopathic haemochromatosis in the Australian population: HLA linkage and recessivity

Studies of 78 unrelated patients and 19 families with idiopathic haemochromatosis are reported. The unrelated patients showed a highly significant association between the disease and HLA-A3. There was a less strong association with HLA-B7 and HLA-DRw2 attributed to the linkage disequilibrium between HLA-A3, B7, and DRw2. Lod scores and haplotype analysis of the families indicated a recessive mode of inheritance for an idiopathic haemochromatosis susceptibility factor in close linkage with the HLA region. These results, for Australian caucasoid patients, are not in total agreement with those reported in studies of other populations.

A linkage study of manic-depressive disorder with HLA antigens, blood groups, serum proteins and red cell enzymes

Families with a two-generational history of affective disorder and well and ill sibs were selected from a population of bipolar manic-depressive patients and typed for HLA antigens, blood groups, serum proteins and red cell enzymes. Segregation of specific HLA alleles was not associated with affective illness across family pedigrees. Further, no significant associations were found between affective disorder and ABO, Rh, MNSs blood groups or Hp, EsD, C3, Gc or PGM. Using the lod score method of Morton (1955) for determining linkage, these data indicated that close linkage is unlikely for affective disorder and HLA alleles, haptoglobin, Rh factor, or ABO blood groups.