Bovine neonate is deficient in innate immunity at birth.

With an objective to understand acquisition of innate immunity in bovine neonates, we analyzed perinatal expression of cytokine, adhesion molecule and complement component genes involved in innate and adaptive immune functions. Statistically robust transcriptomic analysis of 27 cytokines showed low IL1B, IL2 and IL7 but high IL23, TGFB1 and TGFB2 expression in bovine neonates post-birth. Unlike mice and humans, no TH2 polarizing cytokine expression occurs in bovine neonates. Further, TH17 and Treg differentiation in bovine neonates may differ from other species like mice and humans. Decreased IL7, IL23R, CXCR3 and increased TGFB1 and TGFB2 expression provides an immunosuppressive environment in the bovine neonate at birth. Transcriptomic analysis of 31 adhesion molecules showed rapid increase in ITGAL expression within a week post-birth in bovine neonates that permits acquisition of innate cytotoxic functions by granulocytes (antibody-mediated), cytotoxic T and NK cells. However, innate immune functions involving phagocytosis and platelet aggregation are deficient in bovine neonates at birth. Of twenty-seven, 18 complement component genes show no significant differential gene expression in neonates post-birth. But low expression of C1QA, C1QB, CQC, C1R and C2 compromises classical and lectin complement pathways mediated lytic function in bovine neonates. The complement-mediated cytotoxic functions, however, normalize between days 7 and 28 post-birth. To conclude, bovine neonate is immunosuppressed and deficient in innate immune competence at birth. Such differences with regard to global innate immune deficiency and lack of TH2 polarization in bovine neonates have profound implications for designing vaccines to prevent neonatal infections. To conclude, species-specific unique characteristics of developing innate and adaptive immune system need to be taken into consideration while designing new immunization strategies to prevent neonatal mortality from infections.

Somatic hypermutations and isotype restricted exceptionally long CDR3H contribute to antibody diversification in cattle.

Antibody diversification in IgM and IgG antibodies was analyzed in an 18-month old bovine (Bos taurus) suffering from naturally occurring chronic and recurrent infections due to bovine leukocyte adhesion deficiency (BLAD). The BLAD, involving impaired leukocyte beta2 integrin expression on leukocytes, develops due to a single point mutation in conserved region of the CD18 gene resulting in substitution of aspartic acid128 with glycine (D128G). Twenty four VDJCmu and 25 VDJCgamma recombinations from randomly constructed cDNA libraries, originating from peripheral blood lymphocytes, were examined for the variable-region structural characteristics in IgM and IgG antibody isotypes. These analyses led to conclude that: (a) expression of exceptionally long CDR3H is isotype restricted to cattle IgM antibody; (b) VDJ recombinations encoding IgM with exceptionally long CDR3H undergo clonal selection and affinity maturation via somatic mutations similar to conventional antibodies; (c) somatic mutations contribute significantly to both IgM and IgG antibody diversification but significant differences exist in the patterns of 'hot spot' in the FR1, FR3 and CDR1H and, also, position-dependant amino acid diversity; and (d) transition nucleotide substitutions predominate over transversions in both VDJCmu and VDJCgamma recombinations consistent with the evolutionary conservation of somatic mutation machinery. Overall, these studies suggest that both somatic mutations and exceptional CDR3H size generation contribute to IgM and IgG antibody diversification in cattle during the development of immune response to naturally occurring chronic and multiple microbial infections.

Bovine T cell receptors and γδ WC1 co-receptor transcriptome analysis during the first month of life.

Here we evaluated neonatal transcription of α, ß, γ and δ TCR and the γδ T cell co-receptor family WC1 in peripheral blood mononuclear cells. A previous report showed a rapid and global shift in transcription of immunoglobulin genes in neonatal calves during the first month after birth but this was not found here for the T cell genes. Transcription frequency of genes within TRAV subgroups correlated with the number of members, indicating a stochastic choice. In contrast, of the approximately 60 TRDV genes those in two of eleven TRDV1 clades and TRDVb3 were transcribed significantly more than the others while those in only one TRBV subgroup were. Transcription of genes in the TRGV5-containing cassette predominated among TRGV genes as a result of their exclusive usage by the WC1+ γδ T cells with a preference for transcription of two of four TRGV genes in that cassette. Finally, we report no large differences in transcription frequencies among the 13 WC1 genes.

Preferential expression of IGHV and IGHD encoding antibodies with exceptionally long CDR3H and a rapid global shift in transcriptome characterizes development of bovine neonatal immunity.

With an objective to understand natural development of bovine neonatal immunity, we analyzed 18 RNA-seq libraries from peripheral blood lymphocytes of three neonatal calves pre- (day 0) and post-colostrum (7, 14 and 28) uptake as compared to their dams. A significant global shift in neonatal transcriptome occurs within first week post-birth, in contrast to dams, with an upregulation of 717 genes. Global pathway analysis of the transcriptome revealed 110 differentially expressed immune-related genes, such as, complement, MHCII, chemokine receptors, defensins and cytokines, at birth. The signaling molecules (LAX1, BLK) and transcription factors (GATA3, FOXP3) are expressed at high levels. High expression of GATA3 transcription factor at birth seems to skew the neonatal immune response towards TH2 type. The high levels of T-cell signaling molecules, CD3G and CD3D, at birth are important in neonatal T cell development. Unlike adults, IGKC expression is high in the neonates where IGKV12 is preferentially expressed at birth. But IGLC is predominant in both neonates and adult where IGLV3.4 is preferentially expressed in B cells at birth. Both IGHM and IGHD are expressed at birth and IGHM achieves adult levels by day 7. This is followed by IGHA and IGHG expression 14-28 days post-birth. Importantly, preferential expression of IGHV1S1(BF4E9) and longest IGHD2(DH2) genes that encode immunoglobulin with exceptionally long CDR3H at birth indicates their critical role, as B cell antigen receptor, in the B cell development via idiotype-anti-idiotype interactions. The transcriptome signatures described here permit assessment bovine neonatal immunocompetence. Bovine neonates acquire innate and IgM-mediated humoral immunocompetence within first week post-birth.

T lymphocyte subpopulations diverge in commercially raised chickens.

To evaluate immunocompetence in commercially raised chickens, we immunophenotyped Dekalb Delta and H&N White Leghorn (WLH) hybrids, 20 chickens in each of 3 age groups (9 wk [juvenile], 25 wk [young adult], and 79 or 80 wk [adult]), for circulating CD3+, CD4+, CD8+, TCR1+, TCR2+, and TCR3+ lymphocytes. The proportion of CD3+ T cells, including CD4+ and CD8+ subsets, was increased in the hybrids as compared with published values for laboratory-raised outbred WLH chickens. The proportion of the TCR2+ (Vbeta1) T cell subpopulation was also increased. An age-related decrease in the proportion of TCR1+ (gammasigma) T cells was noted in both hybrids. Further, a remarkably low CD4:CD8 ratio was evident in all age groups of both hybrids, indicating decreased immunocompetence. Overall, these experiments provide age-related proportions of various peripheral-blood T lymphocyte subpopulations in commercially raised Dekalb Delta and H&N chickens that diverge from the proportions in laboratory-raised outbred WLH chickens and suggest reduced immunocompetence. Such a decline in immunocompetence, including humoral immune capacity, could be attributed to genetic selection for production traits, environmental factors associated with commercial operations, and intense immunization.

Exceptionally long CDR3H of bovine scFv antigenized with BoHV-1 B-epitope generates specific immune response against the targeted epitope.

We discovered that some bovine antibodies are amongst the largest known to exist due to the presence of an exceptionally long CDR3H (≥49 amino acids) with multiple cysteines that provide a unique knob and stalk structure to the antigen binding site. The large CDR3H size, unlike mouse and human, provides a suitable platform for antigenization with large configurational B-epitopes. Here we report the identification of a B-epitope on the gC envelope protein of bovine herpes virus type-1 (BoHV-1) recognized by a bovine IgG1 antibody. The identified 156 amino acid long gC fragment (gC156) was expressed as a recombinant protein. Subsequently, a functional scFv fragment with a 61 amino-acid long CDR3H (scFv1H12) was expressed such that gC156 was grafted into the CDR3H, replacing the "knob" region (gC156scFv1H12 or Ag-scFv). Importantly, the Ag-scFv could be recognized by a neutralizing antibody fragment (scFv3-18L), which suggests that the engraftment of gC156 into the CDR3H of 1H12 maintained the native conformation of the BoHV-1 B-epitope. A 3D model of gC156 was generated using fold-recognition approaches and this was grafted onto the CDR3H stalk of the 1H12 Fab crystal structure to predict the 3D structure of the Ag-scFv. The grafted antigen in Ag-scFv is predicted to have a compact conformation with the ability to protrude into the solvent. Upon immunization of bovine calves, the antigenized scFv (gC156scFv1H12) induced a higher antibody response as compared to free recombinant gC156. These observations suggest that antigenization of bovine scFv with an exceptionally long CDR3H provides a novel approach to developing the next generation of vaccines against infectious agents that require induction of protective humoral immunity.

Unusually long germline DH genes contribute to large sized CDR3H in bovine antibodies.

We demonstrated earlier the existence of an exceptionally long third complementarity-determining region of the heavy chain (CDR3H) (up to 61 amino acids (aa)), with multiple cysteine residues, in some functional IgM antibodies of cattle. To understand the origin of such a long CDR3H, we have now characterized the germline diversity gene (D(H)) of the cattle. A 2.3kb genomic DNA fragment hybridizing with a newly developed DNA probe to putative bovine D(H) gene sequences was isolated, cloned and its nucleotide sequence determined. Inspection of the nucleotide sequence led to identification of three bovine germline D(H) gene segments of varying size: 42bp (14 possible codons), 58bp (19 possible codons) and 148bp (49 possible codons). The characteristic repetitive GGT and TAT codons, remarkable in the CDR3H region of fetal VDJ rearrangements likely encoded by germline genes, are noted in two of the identified germline D(H) genes. These D(H) genes are preferentially expressed in the third reading frame to encode hydrophilic glycine and tyrosine residues in the CDR3H region. Phylogenetic analysis suggests that bovine D(H) genes are closest to rabbit and chicken D(H) genes. Thus, both short and long germline D(H) genes exist in cattle and these are capable of directly contributing to CDR3H size heterogeneity including the exceptionally long CDR3H region, apart from recombination associated mechanistic factors.

Enhanced bovine herpesvirus type 1 neutralization by multimerized single-chain variable antibody fragments regardless of differential glycosylation.

Single-chain variable antibody fragments (scFvs) with a 2-amino-acid linker capable of multimerization as di-, tri-, or tetrabodies that neutralize bovine herpesvirus type 1 (BoHV-1) in vitro were constructed and expressed in Pichia pastoris. In contrast to the monomeric form, multimeric scFvs had a higher virus neutralization potency, as evidenced by a 2-fold increase in their ability to neutralize BoHV-1 due to avidity effects. Mass spectrum (quadrupole time of flight [Q-TOF]) analyses of multimeric scFv demonstrated extensive heterogeneity due to differential cleavage, variable glycosylation (1 to 9 mannose residues), and the incorporation of minor unidentified adducts. Regardless of the differential glycosylation patterns, the scFvs recognized non-gB or -gE target viral epitopes in the BoHV-1 envelope fraction in a Western blot and also neutralized BoHV-1 in infected Madin-Darby kidney (MDBK) cells in vitro. Indirect evidence for the noncovalent multimerization of scFv was the presence of a major peak of multimerized scFv without a His tag (due to differential cleavage) in the Q-TOF profile, unlike monomeric scFv, which copurified with normally His-tagged scFv and recognized the target antigen. Overall, differentially glycosylated recombinant scFvs against BoHV-1 with a short linker (2 amino acids) are capable of assembly into functional multimers that confer high avidity, resulting in increased virus neutralization in vitro compared to that of monovalent scFv with a long (18-amino-acid) flexible linker. Overall, recombinant multimerized scFv5-2L potentially provides a high-potency therapeutic and immunodiagnostic reagent against BoHV-1, which is suitable for passive immunization and topical application.

A single point mutation in framework region 3 of heavy chain affects viral neutralization dynamics of single-chain Fv against bovine herpes virus type 1.

We constructed functional recombinant single chain Fv (scFv) against bovine herpes virus type 1 (BoHV-1), aetiological agent of respiratory and genital diseases in cattle for which available vaccines do not provide adequate protection. The scFv against BoHV-1 with 18 amino acid long flexible linker (scFv3-18L; monomeric form) recognized target antigen and, also, neutralized BoHV-1 in vitro. A comparison with recombinant scFv with 7 amino acid linker against BoHV-1 (scFv1-7L), capable of forming diabodies, indicated that a relatively higher concentration (two-fold) of monomer scFv3-18L is needed for virus neutralization as compared to scFv1-7L. A single point replacement mutation (Asp98 to Gly98) in the framework-3 (FR3) variable-region of scFv with 18 amino acid linker (scFv4m-18L), however, affected the viral neutralization in a dose-dependent manner where 2.7 fold higher mutant scFv concentration was required to achieve virus neutralization. Despite differences in dose-dependent viral neutralization of the mutant scFv-18L, it detected viral antigen in an immunofluorescent assay. The outlined experiments demonstrate that recombinant scFv against BoHV-1, whether expressed as scFv or diabody, provide an effective antibody based therapeutic and immunodiagnostic protein. Further, single point substitution mutation in the FR3 can affect viral neutralization dynamics without affecting qualitative viral antigen recognition.

Novel atypical nucleotide insertions specifically at VH-DH junction generate exceptionally long CDR3H in cattle antibodies.

Some IgM cattle antibodies are amongst the largest known to exist in jawed vertebrates where CDR3H size may extend up to 61 amino acids. To understand the origin of such an exceptionally long CDR3H, bovine D(H) gene locus was completely characterized from Holstein cattle that revealed the presence of a total of eight D(H) genes, including D(H)Q52, with a distinct organization in sub-clusters. However, a total of 10 D(H) genes are identified at the polymorphic D-gene locus in cattle that are classified into four families, designated as BovD(H)A, BovD(H)B, BovD(H)C and BovD(H)D. In fetal B-cells, VDJ recombinations encoding long CDR3H (>50 codons) are directly encoded by the single germline V(H) gl.110.20, the longest D(H)2 and the J(H)1 genes, apart from few N- and P-nucleotide additions at the junctions. Further, non J-proximal D(H)7 gene is preferentially expressed in fetal B cells. The adult VDJ recombinations, however, are distinctly remarkable for 'conserved short nucleotide sequence' ('CSNS'; 13-18 nucleotides), of non-V(H) or D(H) gene origin, inserted specifically at V(H)-D(H) junctions resulting in extension of CDR3H size up to 61 codons. Together with P-nucleotides, N-additions (1-9 nucleotides) are noted at both the V(H)-D(H) and D(H)-J(H) junctions. Such 'CSNS' insertions at V(H)-D(H) junction of adult VDJ recombinations encoding exceptionally long CDR3H provide novel mechanism of antibody diversification in cattle, not yet observed in other species. Further, analysis of V(H)-D(H)-J(H) recombinations originating from fetal B-cells reveals the presence of substitution, deletion or addition mutations without prior exposure to external antigen. Thus, somatic hypermutations may contribute towards diversification of the developing nascent antibody repertoire in cattle. In conclusion, the outlined experiments provide novel antibody diversification mechanism via 'CSNS' insertions, specifically at the V(H)-D(H) junction, in generating exceptionally long CDR3H extending up to 61 codons in cattle antibodies.

Construction of single-chain Fv with two possible CDR3H conformations but similar inter-molecular forces that neutralize bovine herpesvirus 1.

Bovine herpesvirus 1 (BoHV-1) causes respiratory and genital diseases in cattle for which available vaccines do not confer adequate protection. Since passive immunization with antibodies permits disease prevention, single-chain fragment variable (scFv), originating from a monoclonal bovine IgG1 antibody against BoHV-1, were constructed and expressed in Pichia pastoris in V(lambda)-V(H) orientation via a flexible seven-amino acid linker. Similar to the intact IgG, the purified recombinant scFv neutralized BoHV-1 in vitro and recognized viral antigens in BoHV-1 infected MDBK cells by immunofluorescence. Homology modeling of the Fv predicts two distinct conformations for CDR3H. Firstly, a long protruding CDR3H conformation where no disulfide linkage occurred between two "non-canonical" Cys residues resulted in a large binding cavity between V(lambda) and V(H). Secondly, a smaller potential antigen-binding cavity is predicted with a disulfide linkage between the two Cys residues of CDR3H creating a six-membered loop in the ascending polypeptide, which fitted into the space between V(lambda) and V(H). Despite such potential configurational diversity of the antigen-binding site, the electrostatic surface potentials that would interact with the BoHV-1 epitope are largely similar for both the topographies where salt-bridge type electrostatic interactions likely occur at the edges of the binding site. Given that IgG1 antibody against BoHV-1 is clonally selected, it is likely that disulfide-stabilized broader and flatter surface topography is specifically generated to accommodate the predicted carbohydrate neutralizing B-epitope on BoHV-1. The specificity and neutralizing capacity for BoHV-1 of the scFv should make this bovine antibody fragment a useful diagnostic and potential therapeutic candidate for an important viral pathogen in cattle.

Organization and genomic complexity of bovine lambda-light chain gene locus.

Complete characterization and physical mapping of bovine lambda (lambda) light chain locus, spanning 412kbp, on chromosome 17, has revealed twenty-five V(lambda) genes, seventeen being functional, organized in three sub-clusters 23.7kbp 5' of the J(lambda)-C(lambda) units. Three V(lambda) sub-clusters are separated by two large introns of 126.8 and 138.3kbp. The predominantly expressed V(lambda)1 genes are present in the two 5' sub-clusters, while J(lambda)-proximal V(lambda) sub-cluster comprises rarely expressed V(lambda)2 and V(lambda)3 genes. The preferential expression of V(lambda)1 genes in the bovine immunoglobulin repertoire is influenced by the composition of recombination signal sequences (RSS). Of the J(lambda)-C(lambda) cluster, it is mainly J(lambda)3-C(lambda)3 unit that is expressed in reading frame 2, though J(lambda)2 and J(lambda)3 have identical RSS. The predominant expression of J(lambda)3-C(lambda)3 genes over J(lambda)2-C(lambda)2 is likely due to endogenous counter selection for J(lambda)2 encoded CDR3 and framework 4 regions. Differences in the genomic complexity of V(lambda) genes in Hereford and Holstein cattle are due to polymorphism at the lambda-light chain gene locus. Despite more potential germline encoded combinatorial diversity, restricted V(lambda)1-J(lambda)3-C(lambda)3 recombinations encode the most lambda-light chain repertoire in cattle.

Increased negative selection impairs neonatal B cell repertoire but does not directly lead to generation of disease-associated IgM auto-antibodies.

To determine if increased negative B cell selection, due to lowered signaling threshold of responsiveness to a ligand as a result of SHP-1 deficiency, during ontogeny leads to the origin of disease-associated IgM auto-antibodies (AAbs), 47 V(H)J558+ VDJCmu rearrangements from SHP-1-deficient viable motheaten (me(v)/me(v)) and 24 J558+ VDJCmu rearrangements from normal me(v)/+ neonatal (<24 h post-birth) B cells were examined for their structural properties. None of the J558+ VDJCmu rearrangements from autoimmune-prone me(v)/me(v) had the characteristic CDR3H size restriction or arginine residues noted in disease-associated IgM AAbs. However, the MVAR2/10 genes are expressed at a high frequency in me(v)/me(v) (31.9%) as compared with me(v)/+ (16.7%), and pM11 gene expression is exclusively (14.9%) noted in me(v)/me(v) B cells. Clearly, there is a trend toward higher expression of pM11 genes (P-value < or = 0.09) in autoimmune-prone me(v)/me(v) strain. The CDR2H region of J558+ VDJCmu recombinations from me(v)/me(v) has increased hotspot triplets predisposing to mutations as compared with me(v)/+ (P-value < or = 0.01) mice. A higher DFL D-gene expression is noted in J558+ VDJCmu rearrangements from me(v)/me(v) (P-value < or = 0.1) in contrast to me(v)/+. The sophisticated logistic regression and odds ratio analysis of V-, D- and J-gene expressions in neonatal B cells from me(v)/me(v) and me(v)/+ mice demonstrates differential composition of the germ line IgM repertoire as a result of SHP-1 deficiency. These observations suggest that increased negative B cell selection during ontogeny impairs the developing IgM antibody repertoire but does not directly lead to generation of disease-associated IgM AAbs.

Bovine IgM antibodies with exceptionally long complementarity-determining region 3 of the heavy chain share unique structural properties conferring restricted VH + Vlambda pairings.

Naturally occurring antibody repertoires of cattle (Bos taurus) include a group of IgMlambda antibodies with exceptionally long complementarity-determining region 3 of the heavy chain (CDR3H) segments, containing multiple Cys residues. These massive CDR3H segments will greatly influence the tertiary and quaternary structures of the bovine IgM combining sites. As an antibody's combining site is formed by both heavy and light chains, we have analyzed the nucleotide sequences and structural properties of the lambda-light chains that pair with micro -heavy chains containing exceptionally long CDR3H. There appears to be an exquisite selective pressure for the use of three V(lambda)1 genes (V(lambda)1x and two new V(lambda)1d and V(lambda)1e genes) in IgM with unusually long CDR3H. The V(lambda)1d and V(lambda)1e genes are similar to each other, but diverge from the other V(lambda)1 genes into two closely related subfamilies. The available bovine V(lambda) genes are classified into three V(lambda) gene families: V(lambda)1, V(lambda)2 and V(lambda)3 based on nucleotide similarity >/=80%. Further, analysis of total Ser content and positions of Ser residues in the sequences was found to be sufficient to classify the cattle V(lambda)1 subfamilies. Patterns of Ser residues differ for V(lambda) domains from ruminant species (e.g. cattle, sheep and goats) and other mammals (e.g. humans and mice). These 'Ser signatures' can be used to track divergent evolution in lambda-light chains. Interestingly, Ser90L in complementarity-determining region 3 of the light chain (CDR3L) occurred in all V(lambda) domains that pair with V(H) regions containing exceptionally long CDR3H. A structural role for Ser90L was revealed in homology models of V(lambda) domains, i.e. to hold the ascending polypeptide of CDR3L in a relatively tight space between the N-terminal segment and residues from CDR1L. The CDR3L of V(lambda) domains also occupied smaller volumes if paired to V(H) domains with extremely long CDR3H (>/=48 residues), and were more variable in their conformation and filled larger volumes if CDR3Hs were