WO2020253894A1 - Method of preparing genetically modified poultry resistent to subgroup j avian leukosis virus - Google Patents

Method of preparing genetically modified poultry resistent to subgroup j avian leukosis virus Download PDF

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WO2020253894A1
WO2020253894A1 PCT/CZ2020/000030 CZ2020000030W WO2020253894A1 WO 2020253894 A1 WO2020253894 A1 WO 2020253894A1 CZ 2020000030 W CZ2020000030 W CZ 2020000030W WO 2020253894 A1 WO2020253894 A1 WO 2020253894A1
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alv
poultry
avian leukosis
virus
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PCT/CZ2020/000030
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French (fr)
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Jiří Hejnar
Pavel Trefil
Anna Koslová
Jitka Mucksová
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Ústav molekulární genetiky AV ČR, v.v.i.
Biopharm, A.S.
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Priority to CN202080044789.4A priority Critical patent/CN115003155A/en
Priority to EP20743052.1A priority patent/EP4075964A1/en
Priority to AU2020297483A priority patent/AU2020297483A1/en
Priority to KR1020227000427A priority patent/KR20220018016A/en
Publication of WO2020253894A1 publication Critical patent/WO2020253894A1/en

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    • AHUMAN NECESSITIES
    • A01AGRICULTURE; FORESTRY; ANIMAL HUSBANDRY; HUNTING; TRAPPING; FISHING
    • A01KANIMAL HUSBANDRY; AVICULTURE; APICULTURE; PISCICULTURE; FISHING; REARING OR BREEDING ANIMALS, NOT OTHERWISE PROVIDED FOR; NEW BREEDS OF ANIMALS
    • A01K67/00Rearing or breeding animals, not otherwise provided for; New or modified breeds of animals
    • A01K67/027New or modified breeds of vertebrates
    • A01K67/0275Genetically modified vertebrates, e.g. transgenic
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    • C07ORGANIC CHEMISTRY
    • C07KPEPTIDES
    • C07K14/00Peptides having more than 20 amino acids; Gastrins; Somatostatins; Melanotropins; Derivatives thereof
    • C07K14/435Peptides having more than 20 amino acids; Gastrins; Somatostatins; Melanotropins; Derivatives thereof from animals; from humans
    • C07K14/46Peptides having more than 20 amino acids; Gastrins; Somatostatins; Melanotropins; Derivatives thereof from animals; from humans from vertebrates
    • C07K14/465Peptides having more than 20 amino acids; Gastrins; Somatostatins; Melanotropins; Derivatives thereof from animals; from humans from vertebrates from birds
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    • C12N15/00Mutation or genetic engineering; DNA or RNA concerning genetic engineering, vectors, e.g. plasmids, or their isolation, preparation or purification; Use of hosts therefor
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    • C12N15/00Mutation or genetic engineering; DNA or RNA concerning genetic engineering, vectors, e.g. plasmids, or their isolation, preparation or purification; Use of hosts therefor
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    • C12N15/00Mutation or genetic engineering; DNA or RNA concerning genetic engineering, vectors, e.g. plasmids, or their isolation, preparation or purification; Use of hosts therefor
    • C12N15/09Recombinant DNA-technology
    • C12N15/87Introduction of foreign genetic material using processes not otherwise provided for, e.g. co-transformation
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    • C12N15/902Stable introduction of foreign DNA into chromosome using homologous recombination
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    • C12N15/00Mutation or genetic engineering; DNA or RNA concerning genetic engineering, vectors, e.g. plasmids, or their isolation, preparation or purification; Use of hosts therefor
    • C12N15/09Recombinant DNA-technology
    • C12N15/87Introduction of foreign genetic material using processes not otherwise provided for, e.g. co-transformation
    • C12N15/90Stable introduction of foreign DNA into chromosome
    • C12N15/902Stable introduction of foreign DNA into chromosome using homologous recombination
    • C12N15/907Stable introduction of foreign DNA into chromosome using homologous recombination in mammalian cells
    • AHUMAN NECESSITIES
    • A01AGRICULTURE; FORESTRY; ANIMAL HUSBANDRY; HUNTING; TRAPPING; FISHING
    • A01KANIMAL HUSBANDRY; AVICULTURE; APICULTURE; PISCICULTURE; FISHING; REARING OR BREEDING ANIMALS, NOT OTHERWISE PROVIDED FOR; NEW BREEDS OF ANIMALS
    • A01K2217/00Genetically modified animals
    • A01K2217/07Animals genetically altered by homologous recombination
    • A01K2217/072Animals genetically altered by homologous recombination maintaining or altering function, i.e. knock in
    • AHUMAN NECESSITIES
    • A01AGRICULTURE; FORESTRY; ANIMAL HUSBANDRY; HUNTING; TRAPPING; FISHING
    • A01KANIMAL HUSBANDRY; AVICULTURE; APICULTURE; PISCICULTURE; FISHING; REARING OR BREEDING ANIMALS, NOT OTHERWISE PROVIDED FOR; NEW BREEDS OF ANIMALS
    • A01K2217/00Genetically modified animals
    • A01K2217/07Animals genetically altered by homologous recombination
    • A01K2217/075Animals genetically altered by homologous recombination inducing loss of function, i.e. knock out
    • AHUMAN NECESSITIES
    • A01AGRICULTURE; FORESTRY; ANIMAL HUSBANDRY; HUNTING; TRAPPING; FISHING
    • A01KANIMAL HUSBANDRY; AVICULTURE; APICULTURE; PISCICULTURE; FISHING; REARING OR BREEDING ANIMALS, NOT OTHERWISE PROVIDED FOR; NEW BREEDS OF ANIMALS
    • A01K2227/00Animals characterised by species
    • A01K2227/30Bird
    • AHUMAN NECESSITIES
    • A01AGRICULTURE; FORESTRY; ANIMAL HUSBANDRY; HUNTING; TRAPPING; FISHING
    • A01KANIMAL HUSBANDRY; AVICULTURE; APICULTURE; PISCICULTURE; FISHING; REARING OR BREEDING ANIMALS, NOT OTHERWISE PROVIDED FOR; NEW BREEDS OF ANIMALS
    • A01K2267/00Animals characterised by purpose
    • A01K2267/02Animal zootechnically ameliorated
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    • C12N15/00Mutation or genetic engineering; DNA or RNA concerning genetic engineering, vectors, e.g. plasmids, or their isolation, preparation or purification; Use of hosts therefor
    • C12N15/09Recombinant DNA-technology
    • C12N15/63Introduction of foreign genetic material using vectors; Vectors; Use of hosts therefor; Regulation of expression
    • C12N15/79Vectors or expression systems specially adapted for eukaryotic hosts
    • C12N15/85Vectors or expression systems specially adapted for eukaryotic hosts for animal cells
    • C12N15/8509Vectors or expression systems specially adapted for eukaryotic hosts for animal cells for producing genetically modified animals, e.g. transgenic
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    • C12N2310/00Structure or type of the nucleic acid
    • C12N2310/10Type of nucleic acid
    • C12N2310/20Type of nucleic acid involving clustered regularly interspaced short palindromic repeats [CRISPRs]

Definitions

  • the present invention relates to engineered, permanent, and genetically determined resistance of poultry to a severe poultry disease - avian leukosis, induced by subgroup J ALV virus.
  • Avian leukosis is a neoplastic disease of the haematopoietic system of poultry caused by avian leukosis viruses.
  • avian leukosis viruses ABV of family Retroviridae, most often of subgroups A and B, more recently of subgroup J, and most recently of subgroup K.
  • ALV avian leukosis viruses
  • Infections with exogenous ALV are encountered in the poultry population very frequently (Jurajda,V., 2002), but the incidence of clinical disease is, in general, markedly lower (1 to 5 % of infected animals) than, e.g., in the case of Mark disease.
  • LL lymphoid leukosis
  • other pathological manifestations of ALV including osteopetrosis, sarcomas and related tumours are found in the field sporadically, or even rarely.
  • myelocytomatosis induced by subgroup J ALV, which in the 1990 started to occur in the meat-type breeds and broilers in many countries worldwide, including the Czech Republic.
  • the economic impact of type J ALV is not only reflected in direct loss by death, but mostly in the negative effect on breeding yields (lower weight gain and laying).
  • the immunosuppressive effect of latent infections with lymphoid leukosis exacerbates the course of other infections.
  • the ALV-J virus When infecting the poultry, the ALV-J virus enters the cells via chNHEI receptor. The retrovirus is then transcribed by reverse transcription and integrates as a provirus into the nuclear DNA of the host cell. The proviral DNA is transcribed to viral RNA, which is translated in the cytoplasm and enveloped into newly formed particles. The release of the particles from the infected cells leads to infection spread to permissive cells in the body of the individual, unless the fowls are either resistant, or protected by restriction factors.
  • the chNHEI receptor is a cellular glycoprotein with ion exchange function, which occurs as a homotrimer. Its prominent first extracellular loop contains amino acid residues critical for interaction with ALV-J. Chicken cells devoid of this glycoprotein are not permissive to ALV-J infection. Similarly, deletion of an amino acid, W38, results in resistance to ALV-J, but not to all other ALV subgroups.
  • the above-mentioned problems are removed by the method of preparing genetically modified poultry resistant to the subgroup J avian leucosis virus according to the present invention, which is based on the fact that this poultry carries the W38 deletion introduced into the chNHEI gene using CRISPR/Cas9-mediated homologous recombination, or optionally, carries the W38 deletion introduced using CRISPR/Cas9 and a specific sgRNA, to yield domestic chicken or domestic turkey resistant to subgroup J avian leukosis virus (ALV).
  • the inventors have created genetically modified poultry individuals, where using genome editing of primordial germ cells (PGC), the tryptophan codon at position 38 (W38) in the chNHEI ion exchanger gene has been deleted. Since chNHEI serves as ALV-J receptor and W38 is an amino acid critical for its receptor but not ion exchanger function, this results in induction of full resistance to ALV-J.
  • PPC primordial germ cells
  • W38 is an amino acid critical for its receptor but not ion exchanger function
  • transgenic individuals can be constructed using poultry embryonic cells,‘primordial germ cells’ (PGC), which can be cultured in vitro, genetically manipulated, and then transplanted into the irradiation-sterilized testes of cockerels.
  • PGC poultry embryonic cells
  • the introduced cells restore spermiogenesis, and this may result in progeny carrying the genetic modification identical with the transplanted PGC.
  • PGC poultry embryonic cells
  • the chHNEI receptor induces full resistance to avian leucosis in an in vitro model of chicken fibroblasts.
  • the method of the present invention in fact represents a combination of results of these two above-mentioned Czech patents, creating a genetically modified line of domestic chicken carrying the W38 deletion.
  • This protection is genetically determined in these chickens, and therefore transmissible to further generations.
  • Inclusion of these resistant modified individuals into a breeding programme may transfer the said property to all individuals, thus significantly increasing the quality of the breeding flock, finally resulting in significant economy in production of eggs, or poultry meet.
  • This novel method may have a worldwide impact on the poultry health, and is particularly relevant to domestic chicken and domestic turkey (collectively referred to as poultry)
  • the method of the present invention related to subgroup J avian leukosis refers to the model of genetically modified individuals with permanent resistance to ALV-J infection created by the inventors. It thus represents a route to eradication of this disease not only in China and Southeast Asia, but also in other parts of the world, because there is a risk of reintroduction of new and more difficult to eradicate Chinese ALV-J strains into regions where this disease is not found at present, including Europe and the United States.
  • the Czech patent No. 307285 specifically refers to the sensitivity and resistance to ALV-J infection in domestic chicken. It constitutes the claim for an isolated DNA molecule encoding mutated protein chNHEI , or its fragment, where tryptophan in position 38 has been deleted, and additionally for an isolated DNA molecule encoding mutated chNHEI , or its fragment, where tryptophan in position 38 has been substituted with glycine or glutamate.
  • This patent describes experimental cell-based verification that the NHE1 sequence of domestic chicken containing mutant W38 confers full resistance to ALV-J infection!
  • Fig. 1 shows a diagram of homologous recombination resulting in W38 deletion in the chicken NHE1 gene.
  • Exon 1 contains the gRNA target sequence (middle) with denoted TGG triplet for W38 (yellow) as a restriction site for Cas9 cleavage (scissors).
  • TGG triplet for W38 yellow
  • scissors a restriction site for Cas9 cleavage
  • nucleotides whose synonymous mutation creates the recognition site for Bsal endonuclease, which then serves for detection of the modified allele.
  • sequencessODN single-stranded oligonucleotides
  • Fig. 2 shows a comparison of the sequence of wild-type chNHEI allele (A) and the sequence after deletion of the codon for W38 (B). Only the immediate vicinity of W38 is shown, denoted by an arrow. The sequence is represented as a chromatogram with transcribed both nucleotide and amino acid sequence.
  • Fig. 3 shows GFP positivity after infection of fibroblasts from the embryos of genotypes W38 -/- (top left), W38 +/- (top right) and W38 +/+ (bottom left) measured by flow cytometry.
  • the x axis GFP fluorescence intensity
  • the y axis cell counts. Percentages of GFP-positive cells are shown in the bottom right corner of the histograms. Bottom right, graph summarising percentages of GFP-positive cells in all examined embryos (four for each genotype).
  • Fig. 4 shows viremia quantification in the chickens of genotypes W38 -/-, +/-, and +/+ (marked on the x axis) after infection with reporter vector RCASBP(J)GFP. Viremia was assessed (on the y axis) in relative units (fold) of negative controls (infection by non-specific RCAS-A virus) after quantitative RT PCR.
  • the preparation of genetically modified lines of poultry is based on the derivation of primordial germ cells from chicken embryos at the age of 24 to 96 hours. These cells were cultured from the samples of collected embryonic blood, or from the head part of the embryo, and expanded in vitro.
  • the W38 deletion was introduced into the PGC genome using CRISPR/Cas9 with gRNA specific for the W38 region in the chNHEI gene and the template for homologous recombination containing the W38 region (Fig. 1).
  • the construct encoding CRISPR/Cas9 with the appropriate gRNA and the template for homologous recombination were introduced into PGC by electroporation in the Amaxa system.
  • Embryos of G2 individuals were incubated until day 10 of development and cultures of embryonic fibroblasts were then prepared. The W38 genotype was verified by DNA isolation, PCR and sequencing. Cultures of embryonic fibroblasts were infected with a virus with ALV-J receptor specificity, in particular, with reporter vector RCASBP(J)GFP, which for easy virus detection transduces the reporter gene for green fluorescent protein (GFP). Quantitative assessment of GFP was done using flow cytometry. Embryonic fibroblasts with W38+/+ and W38+/- genotypes showed identical GFP positivity in about 90 % cells, which indicates almost complete virus spread.
  • Chickens of W38 +/+, W38 +/- and W38 -/- genotypes were infected at the age of several days to two months with reporter vector RCASBP(J)GFP, which maintains the ALV-J receptor specificity while being more aggressive than the prototype strains of ALV-J such as, e.g., HPRS103.
  • the normal course of ALV-J infection is manifested by transient viremia, which according to the age of infected individual develops after several days, typically culminates within 10 days and remains one to two weeks after the culmination.
  • RT-qPCR reverse transcriptase quantitative polymerase chain reaction
  • a complementation assay in which a replication-competent introduced virus complements a defective virus that is then secondarily quantified based on the number of focus-forming transformed cells.
  • the second method of detection verifies the presence of biologically active virus, not just the RNA.
  • the material tested was represented by the serum of infected animals collected at two time points, one and two weeks post infection. Using RT-qPCR, all chickens of the W38-/- genotype (5 chickens in total) were tested negative at both time points.
  • the W38 +/+ and W38 +/- genotypes (10 chickens in total) were, with one exception, positive at the later time point; at the first time point of collection, three chickens were negative, which means a slow onset of viremia during the first week and increase of viremia during the second week.
  • the only negative case may mean here unsuccessful infection, e.g., due to defective inoculation.
  • deletion W38 induces perfect resistance to ALV-J when the virus is inoculated to the circulating blood of juvenile individuals. This type of infection best simulates infection in the conditions of home breeding.
  • Table 1 shows verification of viremia in chickens of genotypes W38 -/-, +/- and +/+ (control wild-type genotype) after infection with reporter vector RCASBP(J)GFP. Viremia was determined as a titre of complemented defective virus 16Q and terminal dilution in two serum samples, 6 and 13 days post infection.
  • the novel method of producing genetically modified poultry resistant to subgroup J avian leucosis virus brings a novel, original solution to eradication of avian leukosis ALV of type J and offers a newly created model of genetically modified individuals with permanent resistance to ALV-J infection. Therefore, it represents a totally revolutionary method of eradication of this disease not only in strong poultry farming countries such as China and Southeast Asia, but also in other parts of the world, because this disease poses a potential risk of being reintroduced into regions where its aetiological agent has already been eradicated.

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Abstract

The present invention refers to the method of preparing genetically modified poultry resistant to subgroup J avian leukosis virus, which is characterised by the fact that this poultry carries the W38 deletion introduced into the chNHE1 gene using CRISPR/Cas9-mediated homologous recombination, or optionally, carries the W38 deletion introduced using CRISPR/Cas9 and a specific sgRNA, to yield domestic chicken or domestic turkey resistant to subgroup J avian leukosis virus (ALV).

Description

l
Method of preparing genetically modified poultry resistant to subgroup J avian leukosis virus
Technical field
The present invention relates to engineered, permanent, and genetically determined resistance of poultry to a severe poultry disease - avian leukosis, induced by subgroup J ALV virus.
Background
Avian leukosis is a neoplastic disease of the haematopoietic system of poultry caused by avian leukosis viruses.
The aetiology of avian leukosis is associated with avian leukosis viruses (ALV) of family Retroviridae, most often of subgroups A and B, more recently of subgroup J, and most recently of subgroup K. Infections with exogenous ALV are encountered in the poultry population very frequently (Jurajda,V., 2002), but the incidence of clinical disease is, in general, markedly lower (1 to 5 % of infected animals) than, e.g., in the case of Mark disease. Of leukosis forms, the relatively most frequent is lymphoid leukosis (LL); other pathological manifestations of ALV including osteopetrosis, sarcomas and related tumours are found in the field sporadically, or even rarely. An exception is myelocytomatosis, induced by subgroup J ALV, which in the 1990 started to occur in the meat-type breeds and broilers in many countries worldwide, including the Czech Republic. The economic impact of type J ALV is not only reflected in direct loss by death, but mostly in the negative effect on breeding yields (lower weight gain and laying). Moreover, the immunosuppressive effect of latent infections with lymphoid leukosis exacerbates the course of other infections.
When infecting the poultry, the ALV-J virus enters the cells via chNHEI receptor. The retrovirus is then transcribed by reverse transcription and integrates as a provirus into the nuclear DNA of the host cell. The proviral DNA is transcribed to viral RNA, which is translated in the cytoplasm and enveloped into newly formed particles. The release of the particles from the infected cells leads to infection spread to permissive cells in the body of the individual, unless the fowls are either resistant, or protected by restriction factors.
In the retrovirus lifecycle, the sensitivity or resistance to the virus is decided upon by the presence of the appropriate receptor molecule on the surface of the target cell. The chNHEI receptor is a cellular glycoprotein with ion exchange function, which occurs as a homotrimer. Its prominent first extracellular loop contains amino acid residues critical for interaction with ALV-J. Chicken cells devoid of this glycoprotein are not permissive to ALV-J infection. Similarly, deletion of an amino acid, W38, results in resistance to ALV-J, but not to all other ALV subgroups. Deletions or substitutions of W38 have been found in NHE1 of pheasants and most galliform birds; sensitive species thus only include domestic chicken, four wild fowl species, turkey, and several species of New World quails from the genera Calipepla, Colinus a Oreortyx (Plachy J, Reinisova M, Kucerova D, Senigl F, Stepanets V, Hron T, Trejbalova K, Elleder D, Hejnar J.: Identification of New World quails susceptible to infection with avian leukosis virus subgroup J. Journal of Virology 91(3): e02002-16, 2017). According to our research, neither the breeds of domestic hens nor primitive domestic chicken stocks contain alleles with the W38 deletion. As a result, there is no natural source of genetic variability to be used to selectively breed resistant animals (Reinisova M, Plachy J, Kucerova D, Senigl F, Vinkler M, Hejnar J.: Genetic Diversity of NHE1, Receptor for Subgroup J Avian Leukosis Virus, in Domestic Chicken and Wild Anseriform Species. PloS One 11 (3):e0150589).
In countries with developed poultry industry, systematic and long-term selection of animals suffering from this disease is used for its eradication (e.g., the last focus of ALV-J infection in the United States was eliminated in 2007 (Malhotra S, Justice J 4th, Lee N, Li Y, Zavala G, Ruano M, Morgan R, Beemon K: Complete genome sequence of an American avian leukosis virus subgroup J isolate that causes hemangiomas and myeloid leukosis. Genome Announcements 3(2): pii: e01586-14, 2015). However, this requires rather a demanding and costly screening of animals during the breeding process, which can only be used in factory farming under full control of infectious diseases. In China, and in fact in the entire Asia and Africa, where poultry is commonly sold at markets at any age and fattening is also practiced at small family farms without any control, it is so far unrealistic to be rid of this disease despite the eradication programmes that have been launched in recent years.
Summary of the invention
The above-mentioned problems are removed by the method of preparing genetically modified poultry resistant to the subgroup J avian leucosis virus according to the present invention, which is based on the fact that this poultry carries the W38 deletion introduced into the chNHEI gene using CRISPR/Cas9-mediated homologous recombination, or optionally, carries the W38 deletion introduced using CRISPR/Cas9 and a specific sgRNA, to yield domestic chicken or domestic turkey resistant to subgroup J avian leukosis virus (ALV).
The inventors have created genetically modified poultry individuals, where using genome editing of primordial germ cells (PGC), the tryptophan codon at position 38 (W38) in the chNHEI ion exchanger gene has been deleted. Since chNHEI serves as ALV-J receptor and W38 is an amino acid critical for its receptor but not ion exchanger function, this results in induction of full resistance to ALV-J. The present invention isjjased on two already granted Czech patents Nos. 307102 and 307285.
According to the Czech patent No. 307102, we are aware that transgenic individuals can be constructed using poultry embryonic cells,‘primordial germ cells’ (PGC), which can be cultured in vitro, genetically manipulated, and then transplanted into the irradiation-sterilized testes of cockerels. The introduced cells restore spermiogenesis, and this may result in progeny carrying the genetic modification identical with the transplanted PGC. According to the Czech patent No. 307285, we are aware that the deletion of amino acid W38 in the chHNEI receptor induces full resistance to avian leucosis in an in vitro model of chicken fibroblasts.
The method of the present invention in fact represents a combination of results of these two above-mentioned Czech patents, creating a genetically modified line of domestic chicken carrying the W38 deletion. By preventing entry of leukosis viruses into the cells of these individuals, permanent resistance is induced. This protection is genetically determined in these chickens, and therefore transmissible to further generations. Inclusion of these resistant modified individuals into a breeding programme may transfer the said property to all individuals, thus significantly increasing the quality of the breeding flock, finally resulting in significant economy in production of eggs, or poultry meet. This novel method may have a worldwide impact on the poultry health, and is particularly relevant to domestic chicken and domestic turkey (collectively referred to as poultry)
The method of the present invention related to subgroup J avian leukosis refers to the model of genetically modified individuals with permanent resistance to ALV-J infection created by the inventors. It thus represents a route to eradication of this disease not only in China and Southeast Asia, but also in other parts of the world, because there is a risk of reintroduction of new and more difficult to eradicate Chinese ALV-J strains into regions where this disease is not found at present, including Europe and the United States.
As was already mentioned, the Czech patent No. 307285 specifically refers to the sensitivity and resistance to ALV-J infection in domestic chicken. It constitutes the claim for an isolated DNA molecule encoding mutated protein chNHEI , or its fragment, where tryptophan in position 38 has been deleted, and additionally for an isolated DNA molecule encoding mutated chNHEI , or its fragment, where tryptophan in position 38 has been substituted with glycine or glutamate. This patent describes experimental cell-based verification that the NHE1 sequence of domestic chicken containing mutant W38 confers full resistance to ALV-J infection! In this patent, the inventors have found that when tryptophan in the chHNEI receptor is substituted with glycine, this substitution causes full resistance to avian leukosis in an in vitro model of chicken fibroblasts. This fact could only be confirmed/rejected by creating transgenic poultry where this deletion or substitution has been introduced into the genome using CRISPR/Cas9 genome editing. For this purpose, the inventors used the newly created model of preparation of transgenic animals according to the Czech patent No. 307102, which is directly related to the method of producing avian sperm with fertilising capacity developed in the testis of a sterilised recipient cockerel after transplantation of donor primordial germ chicken cells, allowing perfectly feasible and practical creation of transgenic individuals with about 50% high efficiency.
Description of drawings
In the appended drawings, Fig. 1 shows a diagram of homologous recombination resulting in W38 deletion in the chicken NHE1 gene. Top, the intron- exon structure of the chNHEI gene. Exon 1 contains the gRNA target sequence (middle) with denoted TGG triplet for W38 (yellow) as a restriction site for Cas9 cleavage (scissors). In red are denoted nucleotides whose synonymous mutation creates the recognition site for Bsal endonuclease, which then serves for detection of the modified allele. Bottom, sequences of single-stranded oligonucleotides (ssODN) to be used as a template for homologous recombination in the chicken and turkey.
Fig. 2 shows a comparison of the sequence of wild-type chNHEI allele (A) and the sequence after deletion of the codon for W38 (B). Only the immediate vicinity of W38 is shown, denoted by an arrow. The sequence is represented as a chromatogram with transcribed both nucleotide and amino acid sequence.
Fig. 3 shows GFP positivity after infection of fibroblasts from the embryos of genotypes W38 -/- (top left), W38 +/- (top right) and W38 +/+ (bottom left) measured by flow cytometry. The x axis, GFP fluorescence intensity, the y axis, cell counts. Percentages of GFP-positive cells are shown in the bottom right corner of the histograms. Bottom right, graph summarising percentages of GFP-positive cells in all examined embryos (four for each genotype).
Fig. 4 shows viremia quantification in the chickens of genotypes W38 -/-, +/-, and +/+ (marked on the x axis) after infection with reporter vector RCASBP(J)GFP. Viremia was assessed (on the y axis) in relative units (fold) of negative controls (infection by non-specific RCAS-A virus) after quantitative RT PCR.
The method of the present invention has been well validated by the inventors in the laboratories of the Institute of Molecular Genetics of the Czech Academy of Sciences, v. v. i., Prague, CZ, and BIOPHARM a.s., Pohofi-Chotoun, CZ. The following examples of embodiments of the present invention are only for illustration, without limiting the invention in any way.
Examples
Example 1
Preparation of a domestic chicken line with modified receptor gene chNHEI
The preparation of genetically modified lines of poultry is based on the derivation of primordial germ cells from chicken embryos at the age of 24 to 96 hours. These cells were cultured from the samples of collected embryonic blood, or from the head part of the embryo, and expanded in vitro. The W38 deletion was introduced into the PGC genome using CRISPR/Cas9 with gRNA specific for the W38 region in the chNHEI gene and the template for homologous recombination containing the W38 region (Fig. 1). The construct encoding CRISPR/Cas9 with the appropriate gRNA and the template for homologous recombination were introduced into PGC by electroporation in the Amaxa system. After electroporation, cells positive for GFP fluorescence associated with CRISPR/Cas9 were selected by sorting of individual cells in a flow cytometer. A well-growing expanded clone with molecularly confirmed W38 deletion was then orthotopically transplanted to sterilised recipient cockerels according to CZ patent No. 307102. Five months later, restored spermiogenesis was observed, and the ejaculate of recipient cockerels was used for artificial insemination of hens, first intramagnally and then intravaginally. The offspring exclusively comprised individuals heterozygous for the W38 deletion. After reaching sexual maturity, the heterozygous animals were crossed and in G2, all genotypes, i.e., W38 +/+, W38 +/- and W38 -/-, segregated in the expected ratio. The accordance with the expected ratio suggests that the W38 deletion does not represent a significant burden for its carrier that would reduce its utility in the breed. The W38 deletion was verified at all levels (PGC clones, ejaculate of recipient cockerels, blood or feather pulp of G1 and G2 individuals) using molecular genetic methods, i.e., DNA isolation, amplification of the specific segment of chNHEI by polymerase chain reaction (PCR) and sequencing of the PCR product. Exemplary DNA sequences are shown in Fig. 2. Example 2
Demonstration of resistance of W38 deletion carriers to ALV-J
The resistance of W38 -/- individuals was demonstrated by three independent methods that are routine in the art of virology research and that have been specifically established for ALV-J.
A. In vitro infection of embryonic fibroblasts
Embryos of G2 individuals were incubated until day 10 of development and cultures of embryonic fibroblasts were then prepared. The W38 genotype was verified by DNA isolation, PCR and sequencing. Cultures of embryonic fibroblasts were infected with a virus with ALV-J receptor specificity, in particular, with reporter vector RCASBP(J)GFP, which for easy virus detection transduces the reporter gene for green fluorescent protein (GFP). Quantitative assessment of GFP was done using flow cytometry. Embryonic fibroblasts with W38+/+ and W38+/- genotypes showed identical GFP positivity in about 90 % cells, which indicates almost complete virus spread. In contrast, embryonic fibroblasts with the W38-/- genotype displayed GFP positivity in less than 0.05 % cells, which represents the natural background given by autofluorescence (Fig. 3). It can be concluded that the W38-/- genotype is perfectly resistant to ALV-J infection at the level of embryonic fibroblasts.
B. In vivo infection of chickens
Chickens of W38 +/+, W38 +/- and W38 -/- genotypes were infected at the age of several days to two months with reporter vector RCASBP(J)GFP, which maintains the ALV-J receptor specificity while being more aggressive than the prototype strains of ALV-J such as, e.g., HPRS103. The normal course of ALV-J infection is manifested by transient viremia, which according to the age of infected individual develops after several days, typically culminates within 10 days and remains one to two weeks after the culmination. The virus presence in vivo was this time verified both molecularly, by quantitative detection of viral genomic RNA using reverse transcriptase quantitative polymerase chain reaction (RT-qPCR), and biologically, by a complementation assay in which a replication-competent introduced virus complements a defective virus that is then secondarily quantified based on the number of focus-forming transformed cells. The second method of detection verifies the presence of biologically active virus, not just the RNA. In both cases, the material tested was represented by the serum of infected animals collected at two time points, one and two weeks post infection. Using RT-qPCR, all chickens of the W38-/- genotype (5 chickens in total) were tested negative at both time points. The W38 +/+ and W38 +/- genotypes (10 chickens in total) were, with one exception, positive at the later time point; at the first time point of collection, three chickens were negative, which means a slow onset of viremia during the first week and increase of viremia during the second week. The only negative case may mean here unsuccessful infection, e.g., due to defective inoculation. These results are summarised in Fig. 4. In the complementation assay, at the first time point of collection, only sporadic cases of positivity were found in W38 +/+ and W38 +/- genotypes. At the second time point, samples of animals with these genotypes were positive with one exception (the same individual as in the previous experiment), while all W38 -/- genotypes remained negative (Table 1). In summary, we can conclude that deletion W38 induces perfect resistance to ALV-J when the virus is inoculated to the circulating blood of juvenile individuals. This type of infection best simulates infection in the conditions of home breeding.
Table 1
Chicken Chicken Age of chicken Virus titre (lU/ml) genotype number at the time of 6 days p.i. 13 days p.i.
infection (days)
W38 -/- 604 28 0 0 W38 -/- 606 28 0 0 W38 -/- 611 20 0 0 W38 -/- 612 20 0 0 W38 -/- 615 14 0 0
W38 +/- 601 28 0 101 W38 +/- 603 28 0 102 W38 +/- 605 28 0 101 W38 +/- 610 20 102 103 W38 +/- 616 20 0 103 W38 +/- 618 14 0 102 W38 +/- 619 14 101 103
W38 +/+ 617 14 102 103 Table 1 shows verification of viremia in chickens of genotypes W38 -/-, +/- and +/+ (control wild-type genotype) after infection with reporter vector RCASBP(J)GFP. Viremia was determined as a titre of complemented defective virus 16Q and terminal dilution in two serum samples, 6 and 13 days post infection.
C. Tumour induction by ALV-J-pseudotyped virus
To simulate formation of solid tumours after ALV-J infection, we pseudotyped the transforming virus present in quail cell line 16Q and containing the -src oncogene by a virus with ALV-J receptor specificity, namely by the RCASBP(J)GFP vector. This results in acutely transforming virus, with oncogene v-src enveloped with the ALV-J viral glycoprotein, which is capable of inducing fast growing sarcomas in the site of inoculation, in our case in the wing web. We inoculated chickens at the age of 10 days to two months, and the incidence and growth of sarcomas were monitored during one month. All chickens of genotypes W38 +/+ and W38 +/- developed progressively growing sarcomas, whereas chickens of genotype W38 -/- did not develop any tumour in any one of the cases. Tumours in animals of the W38 +/+ genotype grew faster than tumours in chickens of the W38 +/- genotype, which indicates a mild negatively dominant effect of the allele carrying the W38 deletion. This is probably associated with chNHEI trimerization. It can be concluded that this experiment has demonstrated (perfect) full resistance to ALV-J in case of homozygous W38 deletion.
The above-mentioned examples (recently in extenso published in Koslova A, Trefil P, Mucksova J, Reinisova M, Plachy J, Kalina J, Kucerova D, Geryk J, Krchlikova V, Lejckova B, Hejnar J: Precise CRISPR/Cas9 Editing of the NHE1 Gene Renders Chickens Resistant to the J Subgroup of Avian Leukosis Virus. Proc Natl Acad Sci U S A. 117::2108-2112, 2020) conclusively document that the new line of domestic chicken created using the method of the present invention, which carries a homozygous deletion W38 in the chNHEI gene, is perfectly resistant to pathogenic virus ALV-J while preserving its normal growth, reproductive and utility properties, and without any apparent side effects, thus bringing a great economic effect.
Industrial applicability
The novel method of producing genetically modified poultry resistant to subgroup J avian leucosis virus brings a novel, original solution to eradication of avian leukosis ALV of type J and offers a newly created model of genetically modified individuals with permanent resistance to ALV-J infection. Therefore, it represents a totally revolutionary method of eradication of this disease not only in strong poultry farming countries such as China and Southeast Asia, but also in other parts of the world, because this disease poses a potential risk of being reintroduced into regions where its aetiological agent has already been eradicated.
References:
JURAJDA, Vladimir. Nemoci drubeze a ptactva - virove infection. 1. vyd. Brno: Edicni stfedisko VFU. Brno, 2002. 184 s. ISBN 80-7305-436-1.
Malhotra S, Justice J 4th, Lee N, Li Y, Zavala G, Ruano M, Morgan R, Beemon K: Complete genome sequence of an american avian leukosis virus subgroup j isolate that causes hemangiomas and myeloid leukosis. Genome Announcements 3(2): pii: e01586-14, 2015
Plachy J, Reinisova M, Kucerova D, Senigl F, Stepanets V, Hron T, Trejbalova K, Elleder D, Hejnar J.: Identification of New World quails susceptible to infection with avian leukosis virus subgroup J. Journal of Virology 91(3): e02002-16, 2017
Reinisova M, Plachy J, Kucerova D, Senigl F, Vinkler M, Hejnar J.: Genetic Diversity of NHE1 , Receptor for Subgroup J Avian Leukosis Virus, in Domestic Chicken and Wild Anseriform Species. PloS One 11(3):e0150589), 2016
Koslova A, Trefil P, Mucksova J, Reinisova M, Plachy J, Kalina J, Kucerova D, Geryk J, Krchlikova V, Lejckova B, Hejnar J: Precise CRISPR/Cas9 Editing of the NHE1 Gene Renders Chickens Resistant to the J Subgroup of Avian Leukosis Virus. Proc Natl Acad Sci U S A. 117::2108-2112, 2020
CZ patent No. 307102
CZ patent No. 307285

Claims

C L A I M S
1. The method of preparing genetically modified poultry resistant to subgroup J avian leukosis virus, which is characterised by the fact that this poultry carries the W38 deletion introduced into the chNHEI gene using CRISPR/Cas9-mediated homologous recombination, or optionally, carries the W38 deletion introduced using CRISPR/Cas9 and a specific sgRNA, to yield domestic chicken or domestic turkey resistant to subgroup J avian leukosis virus (ALV).
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