A bovine CD18 signal peptide variant with increased binding activity to Mannheimia hemolytica leukotoxin

Ethics statement

All animal procedures were reviewed and approved by the U.S. Department of Agriculture, Agricultural Research Service, U.S. Meat Animal Research Center (USMARC) Institutional Animal Care and Use Committee (IACUC project number 2.2).

Panels of cattle DNA used for missense mutation discovery

Two panels of DNAs were used to determine ITGB2 genotypes from U.S. cattle. The first was a previously described panel of 96 unrelated beef cattle from 19 popular U.S. beef breeds that had already been characterized by whole-genome sequencing²⁰. This identified predicted coding changes throughout the ITGB2 gene. The second panel included a non-overlapping set of 1142 unrelated cattle from 46 breeds, on which targeted Sanger sequencing was performed to identify any predicted coding changes in the signal peptide region and the region containing the D128G variant causing BLAD (ITGB2 exons 2, 3, and 5). Briefly, the first panel of 96 beef cattle (USMARC Beef Cattle Diversity Panel version 2.9 [MBCDPv2.9]) was based on commercially-available purebred registered sires. Pedigrees were obtained from leading suppliers of U.S. beef cattle semen and analyzed to identify unrelated individuals for inclusion. The number of sires representing each breed (four, five, or six) was based on their numbers of registered progeny circa 2000: Angus (n = 6), Hereford (n = 6), Charolais (n = 6), Simmental (n = 6), Red Angus (n = 6), Limousin (n = 6), Gelbvieh (n = 6), Brangus (n = 5), Beefmaster (n = 5), Salers (n = 5), Shorthorn (n = 5), Maine-Anjou (n = 5), Brahman (n = 5), Chianina (n = 4), Texas Longhorn (n = 4), Santa Gertrudis (n = 4), Braunvieh (n = 4), Corriente (n = 4), and Tarentaise (n = 4). On the basis of the number of registered progeny, the breeds were estimated to represent greater than 99% of the germplasm used in the US beef cattle industry, contain more than 187 unshared haploid genomes, and allow a 95% probability of detecting any allele with a frequency greater than 0.016²¹.

The second panel of 1142 cattle consisted of samples from male and female registered purebred cattle with diverse pedigrees from 46 breeds. Samples were from semen, blood, or hair follicles, depending on gender and availability²². Where possible, animals within breed were chosen so they did not share parents or grandparents, and none were closely related to the 96 sires in the MBCDPv2.9. The breeds used in the second panel were: Angus (n = 24), Ankole-Watusi (n = 20), Ayrshire (n = 24), Beefmaster (n = 24), Belgian Blue (n = 24), Blonde d'Aquitaine (n = 24), Brahman (n = 23), Brahmousin (n = 24), Brangus (n = 24), Braunvieh (n = 24), Brown Swiss (n = 26), Charolais (n = 24), Chianina (n = 24), Corriente (n = 24), Devon (n = 23), Dexter (n = 22), Gelbvieh (n = 23), Guernsey (n = 23), Hereford (n = 24), Highland (n = 24), Holstein (n = 81), Indu-Brazil (n = 25), Jersey (n = 29), Limousin (n = 24), Maine-Anjou (n = 24), Marchigiana (n = 24), Mini-Hereford (n = 24), Mini-Zebu (n = 24), Montbeliard (n = 24), Murray Grey (n = 20), Nelore (n = 24), Piedmontese (n = 25), Pinzgauer (n = 23), Red Angus (n = 23), Red Poll (n = 24), Romagnola (n = 24), Salers (n = 24), Santa Gertrudis (n = 24), Senepol (n = 23), Shorthorn (n = 23), Simmental (n = 23), Tarentaise (n = 24), Texas Longhorn (n = 23), Texas Longhorn, Cattlemen’s Texas Longhorn Registry (CTLR, n = 19), Tuli (n = 23), and Wagyu (n = 22).

DNA sequencing and single nucleotide polymorphism (SNP) genotyping

Unless otherwise indicated, reagents were molecular-biology grade. DNA from whole blood samples was extracted by use of a solid-phase system incorporating either spin-columns or 96-well microtitration plates according to the manufacturer's instructions (Qiagen Inc., Germantown, MD, USA). DNA from liver, muscle, skin, or hair samples was extracted by standard procedures²². Briefly, minced tissue (35 mg) or hair follicles (100 trimmed bulbs) were suspended in 2.5 mL of a lysis solution containing 10 mM TrisCl, 400 mM NaCl, 2 mM EDTA, 1% wt/vol sodium dodecyl sulfate, RNase A (250 ug/ml; Sigma-Aldrich, St. Louis, MO, USA), pH 8.0. The solution was incubated at 37°C with gentle agitation. After 1 hour, 1 mg proteinase K was added (Sigma-Aldrich) and the solution was incubated overnight at 37°C with continued agitation. The solution was transferred to 15 ml tube containing 3 ml of a phase-separation gel (high-vacuum grease, Dow Corning Corporation, Midland, MI, USA) and extracted twice with 1 vol of phenol:chloroform:isoamyl alcohol (25:24:1), and once with 1 vol of chloroform before precipitation with 2 vol of 100% ethanol. The precipitated DNA was washed once in 70% ethanol, briefly air dried, and dissolved in a solution of 10 mM TrisCl, 1 mM EDTA (TE, pH 8.0).

DNA from commercial bull semen was extracted similarly, with slight modification²³. Briefly, three 0.5 ml straws of commercial semen from a single animal were pooled, and the cells were collected by centrifugation for 5 min at 1000 x g. The cell pellet was washed three times in 1 ml of a wash solution (TE with 100 mM NaCl, TNE) and suspended in 1 ml of the same solution with 1% wt/vol sodium dodecyl sulfate, 1 mg proteinase K (Sigma-Aldrich), and 40 mM dithiothreitol (DTT). This 1 ml lysis solution was incubated overnight at 37°C, transferred to a 15 ml tube containing 1.5 ml of TNE with 40 mM DTT, and 3 ml of a phase-separation gel, extracted twice with 1 vol of phenol:chloroform:isoamyl alcohol (25:24:1), and once with 1 vol of chloroform before precipitation with 0.1 vol of 3 M sodium acetate (pH 5.2) and 2 vol of 100% ethanol. The precipitated DNA was washed once in 70% ethanol, briefly air dried, and dissolved in a solution TE.

PCR-amplified fragments of genomic DNA from ITGB2 exons 2, 3 and 5, encoding the CD18 signal peptide sequence and the region containing the known variant causing BLAD, were produced for Sanger sequencing in 96 or 384-well plates. A standard 25 µl amplification reaction contained 2.5 µl of genomic DNA in TE (10 ng/µl), 12.5 µl of a concentrated PCR cocktail (Maxima Hot Start, Thermo Fisher Scientific, Waltham, MA, USA), 1.25 µl each of an oligonucleotide primer stock solution (100 uM, in TE), 1 µl dimethyl sulfoxide (Sigma-Aldrich), and 6.5 µl water. The sense and antisense primer sequences for exons 2 and 3 were 5'-AGG-GAG-ACT-GAC-CTG-TGT-G-3' and 5'-CTG-GGA-AGC-AGA-GTG-ATA-GT-3', respectively (USMARC primer no. 89878 and 89880). The sense and antisense primer sequences for exon 5 were 5'-AGA-GAG-ATC-CAG-GTA-GAA-CTG-3' and 5'-GTG-CAG-AGG-TGC-AGA-GGT-G-3', respectively (USMARC primer no. 89887 and 89889). The final concentration of each primer was of 5 uM (Integrated DNA Technologies, Inc., Coralville, IA, USA). PCR was performed with either the PTC 200, the PTC 220 Dyad, or the PTC 225 Tetrad thermal cycler chassis (MJ Research, Watertown, MA, USA). Reactions were denatured at 94°C for 15 min, subjected to 45 cycles of denaturation at 94°C for 20 s, annealed at 58°C for 30 s, and extended at 72°C for 1 min. After cycling the final products were extended at 72°C for 3 min before storage at 4°C. A 5 µl portion of each amplified product was analyzed by agarose gel electrophoresis (0.8%) in buffer containing 90 mM Tris-borate (pH 8.0), 2 mM ethylenediamine tetraacetic acid, and 0.1 µg/ml ethidium bromide. A 6 µl portion of each amplified product was treated with Exonuclease I (1.4 U, New England Biolabs Inc., Ipswich, MA, USA) at 37°C for 1 hr in a 13 µl reaction volume to digest single-stranded primer oligonucleotides. The Exonuclease I was inactivated with a 65°C incubation for 20 min and the DNA was precipitated with two volumes of 100% ethanol. The plates were centrifuged at 1800 x g for 30 min, decanted, and air dried.

Sequencing reactions were accomplished by dissolving air-dried DNA pellets in 5 µl of sequencing reaction cocktail containing 0.25 µl of dye terminators (DYEnamic ET Dye terminators, Amersham Biosciences, Piscataway, NJ, USA), 1.75 µl dye terminator dilution buffer (Amersham Biosciences), 2 µl oligonucleotide primer (1.6 µM stock solution in water), and 1 µl water according to the manufacturer’s instructions. The final oligonucleotide concentration was 640 nM. Reactions were denatured at 96°C for 30 s, subjected to 26 cycles of denaturation at 96°C for 10 s, annealed at 50°C for 5 s, and extended at 60°C for 4 min. After cycling the final products were stored at 4°C until the DNA was precipitated with 22 µl of 70% isopropyl alcohol. The plates were centrifuged, at 1800 x g for 30 min, decanted, and the samples were washed with 22 µl of 70% ethanol. The plates were centrifuged again, decanted, air dried, sealed with foil, and stored at -20°C until use. Sequencing reactions were resolved by capillary electrophoresis as described by the manufacturer (3730xl DNA Analyzer, Applied Biosystems, Foster City, CA, USA). Animal sequences from both strands were analyzed with polyphred software version 6.18²⁴ in conjunction with the phred/phrap/consed software version 29^25–27.

Whole genome sequencing of BL3 cells

Whole genome sequencing of BL3 cells (a bovine lymphoma cell line; kindly provided by Dr. Subramaniam Srikumaran) was accomplished with methods as described elsewhere²⁰. Briefly, genomic DNA was used to make a 500 bp paired-end library and sequenced with a massively parallel sequencing machine and high-output kits (NextSeq500, two by 150 paired-end reads, Illumina, San Diego, CA, USA) until a minimum of 40 GB of data with greater than Q20 quality, was collected. After sequencing, the raw reads were filtered to remove adaptor sequences, contaminating dimer sequences, and low-quality reads. The DNA sequence alignment process was similar to that previously reported²⁰. FASTQ files were aggregated for each sample and DNA sequences were aligned individually to the bovine reference assembly UMD3.1²⁸ with the Burrows-Wheeler aligner (BWA) aln algorithm version 0.7.12²⁹, then merged and collated with bwa sampe. The resulting sequence alignment map (SAM) files were converted to binary alignment map (BAM) files, and subsequently sorted via SAMtools version 0.1.18³⁰. Potential PCR duplicates were marked in the BAM files using the Genome Analysis Toolkit (GATK) version 1.5-32-g2761da9³¹. Regions in the mapped dataset that would benefit from realignment due to small indels were identified with the GATK module RealignerTargetCreator, and realigned using the module IndelRealigner. The BAM files produced at each of these steps were indexed using SAMtools. The resulting indexed BAM files were made available via the USMARC WGS browser and the raw reads for the BL3 cell line were deposited at NCBI BioProject PRJNA325058, BioSample number SAMN05217649. Mapped datasets for each sample were individually genotyped with the GATK UnifiedGenotyper with arguments “--alleles” set to the VCF file (Extended Data File S1)³², “--genotyping_mode” set to “GENOTYPE_GIVEN_ALLELES”, and “--output_mode” set to “EMIT_ALL_SITES”. Lastly, some SNP variants were identified manually by inspecting the sequence with IGV software version 2.1.28^33,34 (described in the Methods section entitled ‘Identifying protein variants encoded by ITGB2’). In these cases, read depth, allele count, allele position in the read, and quality score were considered when the manual genotype determination was made.

Identifying predicted protein variants encoded by bovine ITGB2

Aligned WGS data from 96 sires of MBCDPv2.9 were visually analyzed in the ITGB2 coding region to identify potential CD18 protein variants. Viewing the aligned sequences and detecting variants was accomplished with the IGV software and a browser developed for this purpose. Briefly, public internet sites at the USDA, ARS, USMARC were used in combination with open source software installed on a laptop computer and recorded manually in a spreadsheet as previously described²⁰. A Java Runtime Environment (Oracle Corporation, Redwood Shores, CA, USA) was first installed on the computer. When links to the data were selected by the user, IGV software^33,34 was loaded from a third-party site (University of Louisville, Louisville, KY, USA) and aligned DNA sequence reads were displayed in the context of the bovine UMD3.1 reference genome assembly. For viewing ITGB2 gene variants, WGS from a set of eight animals of different breeds was loaded, and the IGV browser was directed to the appropriate genome region by entering “ITGB2” in the search field. The IGV zoom function was used to view the first exon at nucleotide resolution with the [show translation] option selected in IGV. An example of the alignment view for ITGB2 codon 27 with eight animals is shown in Extended data, Figure S1³⁵.

The exon sequences were visually scanned for polymorphisms predicted to alter amino acid sequences, including missense, nonsense, frameshift, splice site, and insertion/deletion mutations. An in silico analysis of other potential splice-affecting variants was not performed as there are no consensus guidelines on the selection of programs or protocols to interpret the predicted results in cattle. Once identified, the variant nucleotide position was viewed and recorded for all 96 animals. The codons affected by SNP alleles were translated into their corresponding amino acids with IGV, codon tables, and knowledge of the CD18 protein sequence (NP_786975). Haplotype phases of predicted polypeptide variants were unambiguously assigned with homozygous individuals, and those with only one variant amino acid. A maximum parsimony phylogenetic tree was manually constructed from the unambiguously phased protein variants and used to infer phases in the remaining variants with maximum parsimony assumptions.

MALDI-TOF MS genotyping of 14 ITGB2 missense mutations

A single multiplex assay was designed for the 14 ITGB2 missense SNPs with software provided by the manufacturer (Agena Biosciences, San Diego, CA, USA). The oligonucleotide sequences and assay conditions are provided in Table S1. After design and validation with bovine control DNAs for each SNP, the DNA from the 96 bulls in the MBCDPv2.9 diversity panel were tested in a blinded experiment. Assay design and genotyping was performed at GeneSeek (Lincoln, NE, USA) with the MassARRAY platform and iPLEX Gold chemistry according to the manufacturer’s instructions (Agena Biosciences).

Lkt preparation, gel electophoresis, and protein immunoblotting

M. haemolytica strains for toxin production were isolated from cattle with severe fibrinous pleuropneumonia in feedlot environments and had complete closed whole genome sequence assemblies available at NCBI. M. haemolytica strain 89010807 N serotype A1 (lktA+) has been widely used for Lkt production for in vitro cytotoxicity assays and has the added advantage of being the parent strain of an isogenic leukotoxin deletion mutant (lktA-)^36,37. A second strain, M. haemolytica strain USDA-ARS-USMARC-183 serotype A1, was isolated from an animal that was part of a high-mortality respiratory disease outbreak in a Kansas feedlot in 1991 and represents the first strain with a complete closed genome assembly³⁸; however, it had not previously been used in in vitro assays.

Isolates were maintained on Brain Heart Infusion (BHI) agar (Sigma-Aldrich) frozen stocks were kept in BHI broth with 20% glycerol at -80°C. RPMI 1640 medium (without Phenol Red and L-glutamine, Sigma-Aldrich) and semi-defined medium 2 (SDM2) were used for batch culture production of Lkt. SDM2 is an amino acid-limited culture medium supplemented with cysteine, glutamine, ferric iron, and manganese and was previously shown to greatly improve Lkt production in aerobic batch culture³⁹. For Lkt production, a single, 24-hour colony isolate from BHI agar was inoculated into 5 ml BHI broth in a 10 ml culture tube and incubated overnight at 37°C in 5% CO₂ without shaking. The following morning, 1 ml of BHI liquid culture was inoculated into 100 ml of fresh culture medium in a 300 ml Delong-style Erlenmeyer flask with baffles (Corning, Inc., Corning, NY, USA) and incubated at 37°C, 250 rpm, in 5% CO₂. At intervals, 14 ml samples were removed and centrifuged at 13,100 x g for 10 min at 4°C. The clarified supernatant was decanted, flash frozen in liquid nitrogen and stored at -80°C until use.

Lkt and other proteins secreted into the growth media by M. haemolytica were analyzed by SDS-PAGE. Clarified supernatants were precipitated with one volume of acetone on ice for 30 min, followed by centrifugation at 20,800 x g for 5 minutes at room temperature, and air dried 30 min. Sedimented proteins were dissolved in a commercial sample buffer with lithium dodecyl sulfate and dithiothreitol and used per the manufacture instructions (Thermo Fisher Scientific). Samples were heated to 70°C for 10 minutes and loaded on 4–12% precast polyacrylamide Bis-Tris gels (Thermo Fisher Scientific) at run 160 volts for approximately 35 min in 2-[N-morpholino]ethanesulfonic acid (MES) SDS running buffer (Thermo Fisher Scientific). Proteins sorted by SDS PAGE were stained with coomassie-dye reagent (GelCode Blue, Thermo Fisher Scientific) and destained in water. Prestained protein standards (Novex Sharp, Thermo Fisher Scientific) were used to estimate molecular weights of M. haemolytica proteins from clarified supernatants. ImageJ software (version 1.52A) was used to estimate relative proportions of protein bands on coomassie-stained page gel⁴⁰.

For protein immunoblots (western blots), proteins from SDS-PAGE gels were electrophoretically transferred to 0.2 µm polyvinylidene difluoride membranes (PVDF, Invitrolon, Thermo Fisher Scientific) with a Mini Blot Module (Thermo Fisher Scientific) per the manufacturer's instructions. PVDF membranes were wetted in 100% methanol prior to equilibrating in transfer buffer (Bolt transfer buffer, Thermo Fisher Scientific) and assembling in the blotting apparatus. Proteins were transferred to membranes for 60 min at a constant voltage of 20 V. Blots were removed from the apparatus and incubated in a blocking reagent (StartingBlock(PBS), Thermo Fisher Scientific), for 60 min at room temperature with gentle agitation. This solution was replaced with a fresh blocking reagent that had a rabbit polyclonal Ltk antibody at a concentration of 1 µg/ml (M. haemolytica Lkt Antibody, catalog number LS-C369014, LifeSpan, BioSciences, Inc, Seattle, WA, USA) and incubated as above for 60 min. The primary Lkt antibody was washed three times in for 10 min each in 25 mM Tris, 0.15 M NaCl, 0.05% Tween-20, pH 7.5 (TBS Tween-20, Thermo Fisher Scientific). After washing, a goat anti-rabbit IgG antibody conjugated to horseradish peroxidase (HRP) (catalog number ab97040, Abcam, Cambridge, MA, USA) was added at a concentration of 1 µg/ml in blocking reagent and incubated for 60 min at room temperature with gentle agitation. This secondary anti-rabbit antibody was washed three times for 10 min each in TBS Tween-20 prior to detection with chemiluminescent substrate (Pierce ECL Western Blotting substrate, Thermo Fisher Scientific). The immunoblot was incubated in chemiluminescent substrate for 1 min and imaged for approximately 5 min (ChemiDoc, Bio-Rad Laboratories, Inc. Hercules, CA, USA).

Cell culture and synthetic peptides

BL3 cells were propagated in RPMI 1640 medium (Gibco, Thermo Fisher Scientific) supplemented with 10% fetal bovine serum (Atlas Biologicals, Fort Collins, CO, USA),1x antibiotic/antimycotic (Gibco, Thermo Fisher Scientific) and 2 mM L-glutamine (Gibco, Thermo Fisher Scientific). Custom bovine CD18 signal peptides (Figure 4–Figure 7) were commercially synthesized, (Thermo Fisher Scientific) purified by preparative high-performance liquid chromatography, and lyophilized. Peptides were dissolved in dimethysulfoxide at a concentration of 10 mg/ml, aliquoted, and stored at −20°C.

PBMC and PMN cell isolation

Primary cells were collected from two mixed breed animals (kept as part of the USMARC cattle population) that were each homozygous for the most common ITGB2 haplotype (variant “1”). For isolation of primary bovine cells, 50 ml of blood were collected by jugular puncture using 16-guage needles into syringes containing EDTA as an anticoagulant. PMN were isolated using a standard hypotonic lysis procedure. Briefly, blood was spun for 25 min at 1000 x g at 4°C. Plasma and buffy coat layers were removed and discarded. Sterile water was added to the red blood cell (RBC) layer to lyse RBC followed by addition of 10X PBS to restore tonicity. PMN were isolated by centrifugation for 10 min at 250 x g at 4°C. The PMN cell pellet was washed three times with 1x PBS and the final cell pellet was resuspended in RPMI 1640 medium.

Peripheral blood mononuclear cells (PBMC) were isolated essentially as described⁴¹. Briefly, PBMC were isolated over Ficoll-Paque Plus (GE Healthcare Bio-Sciences AB, Uppsala, Sweden), as per the manufacturer’s instructions, with modification. Briefly, 15 ml of whole blood mixed 1:1 with PBS was underlayed beneath 14 ml of the density gradient in a 50 ml conical tube. The tubes were then centrifuged for 45 min at 900 x g at room temp and with no brake. The PBMC layer was carefully removed and brought up to 45 ml in PBS in a new 50 ml conical tube followed by centrifugation for 15 min at 400 x g at 4°C with high brake. Erythrocytes were removed using RBC lysing buffer (Sigma-Aldrich). The PBMC pellet was further washed three times with 1x PBS and the final pellet was resuspended in RPMI 1640 medium.

MTT dye-reduction cytotoxicity assay

The ability of different CD18 signal peptide variants to bind Lkt and inhibit Lkt-induced cytolysis was measured with the MTT dye-reduction cytotoxicity assay¹⁰. The BL3 cell line was selected because it is the most well-studied, readily available, immortalized cell line susceptible to Ltk-induced cytolysis. CD18 signal peptides were tested at concentrations ranging from 50 μM to 0.195 μM. CD18 signal peptides were diluted using serial 2-fold dilutions in 96-well round bottom plates containing 50 µl/well of Lkt at a 50% toxicity end point titer in colorless RPMI 1640 medium without phenol red (Sigma-Aldrich). Synthetic signal peptides and Lkt preparations were pre-incubated for 1 hr on ice prior to the addition of 5 × 10⁵ cells/wells. These cells were added as a 50 ul suspension with a density of 1 × 10⁷ cells/ml in colorless RPMI. Cells were incubated with synthetic signal peptides and Lkt for 1 hr at 37°C in 5% CO₂ and subsequently centrifuged at 600 x g for 7 min at 4°C and the supernatant was removed and discarded. Cells were resuspended in 100 µl of colorless RPMI and 20 µl 0.5% MTT (3-(4,5-dimethylthiazol-2-yl)-2,5-diphenyl-2H-tetrazolium bromide; Sigma-Aldrich) and incubated for 20 min at 37°C in 5% CO_2, centrifuged as before, and the supernatant was removed and discarded. The purple formazan precipitate was then dissolved in 100 µl of acid isopropanol (0.04N HCl in isopropanol). Following a 5 min incubation, cellular debris was pelleted and the supernatant was transferred to a new 96-well plate. The optical density (OD) of the samples was measured at 570 nm and 690 nm. The background measurement at 690 nm was then subtracted from the 570 nm measurement to give the background adjusted OD. The percent cytotoxicity was calculated as follows: (1-(OD of toxin treated cells/OD of cells without toxin)) x 100. The percent inhibition of cytotoxicity in the presence of synthetic CD18 peptides was calculated as follows: ((percent cytotoxicity in the absence of peptide – percent cytotoxicity in the presence of peptide)/percent cytotoxicity in the absence of peptide) x 100. Given normal variability in the assay, values were occasionally obtained outside the range of 0 to 100% inhibition. Negative values were replaced with 0 and values greater than 100 were replaced with 100 for graphical presentation.

Fresh bovine PBMC or PMN were used for comparison to results obtained using immortalized BL3 cells. Cells were suspended in 50 µl colorless RPMI medium and 10 µl Biolog Redox Dye MB, containing 500 μM water-soluble tetrazolium (Biolog, Hayward, CA, USA). This dye was used because it was found to be more sensitive to changes in cellular respiration when assaying primary cells (data not shown). Cells were incubated for 3 hr at 37°C in 5% CO₂, centrifuged as before, and the supernatant was transferred to a clean 96 well plate prior to the OD being measured at 590 nm and 750 nm. Calculations for percent cytotoxicity and percent inhibition were calculated using background adjusted OD values as described above.

Statistical analyses of IC₅₀ values

The half maximal inhibitory concentration (IC50) was estimated for each signal peptide variant to compare the concentration of peptide needed to block 50% of Lkt-induced cytotoxicity of susceptible bovine cells. Univariate nonlinear regression (NLIN procedure, SAS 9.4, SAS Institute Inc., Cary, NC, USA) was used to fit data from three replicates to the following equation: Y_ijk = T + (B - T)/(1 + (C_j/IC50_i)^S_i) + e _ijk, where Y_ijk is the measured Lkt inhibition for the k^th replicate of the i^th peptide at the j^th concentration (C_j) of peptide. T is the estimated maximum, B is the estimated minimum of the fitted nonlinear relationship between peptide concentration and Lkt inhibition. S_i is the slope of the relationship at IC50_i, the estimated concentration that the i^th peptide inhibits Lkt-induced cytotoxicity by 50%. e _ijk is random variation. Standard errors of IC50_i were used for comparisons of estimates.

Identifying ITGB2 polymorphisms affecting the predicted amino acid sequence of CD18

Bovine ITGB2 consists of 16 exons spanning 29.1 kb of genomic DNA and encodes a 769 amino acid protein with multiple functional domains (Figure 1A,B). Using software to view the aligned genome sequences from 96 diverse bulls, 13 codons with 14 missense variants were identified (Extended Data Table S2)⁴². There were no frameshifts, splice sites, or indel polymorphisms observed that would affect the predicted amino acid sequence. Two ITGB2 regions of interest were further selected for additional Sanger sequencing in 1142 purebred cattle from 46 breeds: the signal peptide region (exon 2), and the region containing the D128G variant causing BLAD (exon 5). DNA sequence analyses revealed no additional polymorphisms that were predicted to alter the polypeptide sequence, except the previously described D128G variant in Holstein cattle (data not shown). The genotypes were independently verified with a single, multiplexed, MALDI-TOF MS assay for 14 SNPs in the 96 diverse bulls, and in 1142 of 1168 cattle from 46 breeds (Extended Data Table S3)⁴³. Thus, in total, there were 14 missense variants identified in 13 codons (Table 1).

Figure 1. Physical maps of ITGB2, CD18, and rooted maximum parsimony phylogenetic tree of CD18 protein variants in cattle.

(A) Genomic DNA map of ITGB2: blue arrows, coding regions of exons; orange arrows, untranslated regions of exons; grey horizontal lines, intron regions. (B) Map of CD18 domains in relationship to missense mutations found in cattle. (C) Rooted maximum parsimony phylogenetic tree of CD18 protein variants from 1142 cattle from 46 breeds with connections to closely-related species. The most frequent CD18 isoform (“variant 1”) was used as the reference amino acid sequence for the trees. For “variants 1” through “14”, each node in the tree represents a different isoform of CD18 that varies by one amino acid compared to adjacent nodes. The hash marks represent nodes that were inferred but not observed. The areas of the circles are proportional to the overall variant frequency in the cattle tested. Yak CD18 was identical to bovine CD18 “variant 3” and denoted as the most likely root of the phylogenetic tree based on the relationship of CD18 sequences in yak, gaur, banteng, and bison. SP, signal peptide; PSI, plexin-semaphorin-integrin domain; SH, spacer-hybrid domain; I-L, I-like domain; MR, mid-region hybrid domain; EGF, epidermal growth factor-like domain; BT, beta tail domain; TM, transmembrane domain; CP, cytoplasmic domain.

Determining ITGB2 haplotypes encoding different CD18 polypeptides

Identifying haplotypes that encode distinct combinations of missense variants on the CD18 polypeptide is important for evaluating their potential function. A total of 15 ITGB2 haplotypes were identified that, when translated, were predicted to encode different CD18 proteins (Table 2). These 15 predicted polypeptide sequences were placed in the context of a maximum parsimony phylogenetic tree (Figure 1C). Haplotypes encoding CD18 protein variants “1 to 7”, “9”, “13”, and “14” were confirmed by their presence in homozygous animals. Haplotypes encoding CD18 protein variants “8”, “10”, and “15” were unambiguously confirmed in animals with only one heterozygous site. However, haplotype phase was ambiguous when the distance between two heterozygous sites exceeds the length of the DNA sequence read (150 bp in these WGS data sets). Thus, haplotypes for the remaining CD18 protein variants “11” and “12” were tentatively inferred from additional breed-level frequency information. For example, the inferred phase for variant “12” (P₁₅₅L₆₅₆) was only observed in two of 27 Braunvieh cattle that were each heterozygous for both missense variants. However, all 25 of the other Braunvieh cattle sequenced were homozygous for the variant “1” (Table 3 and Extended Data Table S3)⁴³. Thus, it was reasonable to infer that P₁₅₅ (exon 5), and L₆₅₆ (exon 14) are present on one rare haplotype in two animals, rather than on two rare haplotypes in each animal. Similarly, the inferred phase for variant “11” (C₅L₆₅₆) was only observed in six of 22 Wagyu cattle and each were heterozygous at positions 5 and 656. Since the 22 Wagyu cattle have a variant “1” frequency of 0.8 it seems likely that C₅ and L₆₅₆ variants are present on the same chromosome (i.e. diplotype “1,11”) rather than split across two chromosomes (i.e., diplotype “5,15”). In spite of the potential for ambiguous haplotype phases with rare variants, the phylogenetic tree of predicted CD18 proteins provides a solid framework for further evaluation.

Evolutionary comparison of CD18 polypeptide sequences

Determining the most likely phylogenetic root of the CD18 tree is important for establishing the likely order of mutational events. Comparing cattle CD18 precursor protein variants to those from closely related species in the Bos genus indicated that variant “3” (K₂₇) was the most likely root of the phylogenetic tree (Figure 1C). Cattle are predicted to share a common ancestor with other species in the Bos genus approximately 5 million years ago. In addition, the K₂₇ variant was associated with indicine cattle breeds, while the N₂₇ variant was associated with taurine breeds. For example, the N₂₇ frequency in 840 cattle from 33 taurine breeds was 0.998, while the K₂₇ frequency in 70 Brahman, Indu Brazil, and Nelore cattle was 0.95. Thus, the structure of the rooted tree suggests that CD18 protein variants “1” and “3” are the ancestral polypeptide sequence of taurine and indicine breeds, respectively. The rooted tree also suggests that the distal nodes represent CD18 variants that have arisen sometime after the split between taurines and indicines, approximately 500,000 years ago.

The conservation of amino acid residues throughout vertebrate species is a measure of their potential impact on protein function. Highly conserved residues are more likely to be indispensable for function and thus, variation at these positions is assumed to be deleterious. The 769 amino acid sequence of cattle CD18 is highly similar to those from yak, sheep, whale, and humans (99, 95, 90, and 83% identity, respectively). The cattle CD18 sequence is also remarkably similar to chicken, frog, fish, lamprey, and fruit fly (63, 57, 49, 42, and 19% identity, respectively), and has some polypeptide regions that are invariant throughout the Bilateria (Extended Data Table S4)⁴⁴. The 13 variant amino acid positions in the bovine CD18 precursor protein were compared to those in 35 representative Bilateria species. The aspartate residue at position 128 (D₁₂₈) is invariant throughout the Bilateria, except in cattle wherein G₁₂₈ causes the complete loss of CD18 function and results in BLAD in homozygous individuals of the Holstein breed (Figure 2). CD18 positions 65, 104, and 155 are also conserved and the variant allele in cattle is rare. Based only on the degree of residue conservation across species, the proposed predicted order of negative impact on CD18 function in cattle was: G₁₂₈ > G₆₅ = M₁₀₄ > P₁₅₅. The CD18 K₂₇ indicine variant was conserved throughout the jawed vertebrates and thus, the major N₂₇ taurine variant was not observed in any other species. However, based on its high frequency in most taurines, the N₂₇ variant does not appear to be deleterious.

Figure 2. Evolutionary comparison of CD18 residues at their variant sites in U.S. cattle.

Aligned and gapped protein sequences from a representative set of 56 bilateria species were compared (Extended Data Table S4). At variant sites in cattle, the residues were summarized for a representative subset of 35 species. TMRCA, estimated time to most recent common ancestor in millions of years⁴⁷; letters, IUPAC/IUBMB codes for amino acids; dot, amino acid residues identical to those in cattle “variant 1”; dash, not enough sequence similarity for comparison or missing residue in that peptide region.

The conservation of arginine at positions 3 (R₃) and 5 (R₅) in CD18 signal peptides was of particular interest because this region binds bacterial Lkt in ruminant species, which includes the Bovids, Cervids, Giraffids, musk deer, chevrotains, and pronghorns. The R₃ residue was conserved throughout the Bovinae, but not in sheep and goat, which have proline at that position (Figure 2). The histidine residue at position 3 (H₃) was rare in cattle, not observed in other ruminants, and on a distal node of the phylogenetic tree (CD18 polypeptide variant “7“, Figure 1C). Two animals from the Brahman breed group were identified with the H₃ and one was homozygous, indicating that H₃ is not a lethal recessive variant (H₃,H₃, Extended Data Table S2⁴⁵, and R₃,H₃, Extended Data Table S3⁴³). Unlike R₃, the R₅ variant was not conserved in Bovinae, since eland have cysteine at this site (C₅). In addition, the C₅ variant was present on four distinct putative CD18 polypeptide variants: “9“, “11”, “13”, and “15” (Figure 1C), including both taurine- and indicine-influenced breeds. The presence of the C₅ variant on multiple but infrequent haplotypes indicates recombination has occurred between this and other CD18 missense variants.

Comparison of batch production methods of biologically-active Lkt with two reference strains of M. haemolytica

The discovery of missense variants in the CD18 signal peptide provided the opportunity to test these variants using in vitro cell assays with bacterial Lkt. However, producing sufficient and consistent batches of biologically-active Lkt from reference bacterial strains was a challenge with traditional cell culture medium (RPMI). In an effort to overcome this barrier, Lkt production in RPMI was compared with that in a semi-defined bacterial culture medium (SDM2, Methods) with two wild-type M. haemolytica strains. The total biological activity of Lkt excreted into SDM2 culture was up to 80-fold greater at its peak than that in RPMI for a given reference strain of M. haemolytica (e.g. Strain 183, Figure 3A). In both media, Lkt activity was induced in late log phase as batch cultures made the transition to stationary phase. Although the biological activity quickly diminished as the culture progressed to stationary phase, the total Lkt protein measured by SDS PAGE continued to increase and the level was stable for hours in the culture supernatant (Figure 3B). The Lkt of clarified SDM2 culture supernatants with the highest cytolytic activity (Strain 183, fraction C, Figure 3B) was estimated to be 90% pure based on gel densitometry imaging of coomassie-stained SDS-PAGE gels. Preparations of similar quality were used for in vitro assays. The cytolytic activity of these toxin preparations was stable at -80°C for more than 2 years.

Figure 3. Comparison of M. haemolytica leukotoxin (Lkt) production in cell culture medium and a semi-defined bacterial culture broth.

(A) Growth curves of M. haemolytica strains (black lines) and the cytolytic activity of their secreted Lkt (red lines). The strain abbreviations: 183 (ltkA+), USDA-ARS-USMARC-183 (ltkA+); N (ltkA+), 89010807N (lktA+); and N (ltkA-), 89010807N (lktA-). Clarified culture supernatants were collected at time points indicated on the x-axis as A through E. (B) Coomassie-stained SDS-PAGE of proteins from 50 µl each of clarified culture supernatants. (C) Western blot of SDS-PAGE from the same clarified SDM2 culture supernatants that were used in panel (B). The black arrow indicates the expected position of Lkt on SDS-PAGE.

Figure 4. Cattle CD18 signal peptide variants differentially inhibit leukotoxin (Lkt)-induced cytolysis of bovine BL3 cells.

CD18 signal peptide variants were tested for their ability to bind Lkt and inhibit Lkt-induced cytolysis of immortalized bovine BL3 cells using a MTT dye reduction assay. CD18 peptide variants representing amino acids 1 to 22 (A) or 5 to 17 (B) were tested using 2-fold serial dilutions at concentrations ranging from 50 μM to 0.195 μM. Half-maximal inhibitory concentration (IC50) for each peptide was determined using non-linear regression analyses. Data are expressed as the mean with standard deviation (n=3).

Figure 5. Cattle CD18 signal peptides inhibit leukotoxin (Lkt)-induced cytolysis of primary bovine cells.

The 13-mer synthetic signal peptides (from Figure 4B) containing cattle CD18 residues 5 to 17 were tested for their ability to inhibit Lkt-induced cytolysis of primary bovine peripheral blood mononuclear cells (PBMC) (A) and polymorphonuclear leukocytes (PMN) (B). Donor animals were genotyped at the CD18 locus and were homozygous for CD18 variant “1”. Peptides were tested using 2-fold dilutions at concentrations ranging from 50 μM to 0.098 μM. The half-maximal inhibitory concentration (IC50) for each peptide was determined using non-linear regression analyses. Data are expressed as the mean with standard deviation (n = 3).

CD18 signal peptide variant C₅ has enhanced binding to bacterial Lkt

Analysis of cattle ITGB2 haplotypes showed that three distinct polypeptide sequences are encoded in the 22-amino acid signal peptide region: the common variant with arginine at positions 3 and 5 (R₃R₅), a rare variant with histidine at position three (H₃R₅), and second rare variant with cysteine at position 5 (R₃C₅). Synthetic 22-mer peptides representing these three, full-length, signal peptides were tested for their ability to bind Lkt. The synthetic peptides were pre-incubated with M. haemolytica Lkt preparations to allow binding, and applied to Lkt-sensitive BL3 cell cultures in vitro (Figure 4A). The common R₃R₅ signal peptide was used as a reference since it has a frequency of approximately 0.98 in U.S. cattle, and is predicted to be present on 10 of the full-length CD18 sequences. The synthetic R₃R₅ signal peptide had a IC50 of 17.9 μM, which represents the concentration of peptide needed to block 50% of Lkt-induced cytolysis of BL3 cells. The rare H₃R₅ signal peptide variant, which is only found on one full-length CD18 variant (Figure 1C, variant 7), was similar to the reference, with an IC50 of 21.6 μM. In contrast, the rare R₃C₅ signal peptide found on full-length CD18 variants 9, 11, 13, and 15 had an IC50 of 5.9 μM, which was 3-fold lower that the reference, indicating an increased affinity for Lkt (Figure 4A).

The optimum blocking of Ltk-induced cytotoxicity has been previously reported to occur with the 13-mer peptide corresponding to CD18 signal peptide residues 5 to 17¹⁰. Thus, we tested the effect of cysteine at position 5 (C₅) in this shorter peptide. The synthetic 13-mer C₅ peptide was 3.6-fold more effective at blocking Lkt toxicity compared to the 22-mer R₃C₅ peptide (IC50 of 1.6 and 5.9 μM, respectively). When compared to the 13-mer reference peptide with arginine at position five (R₅), the 13-mer C₅ peptide was 8-fold better at blocking Lkt-induced cytotoxicity (IC50 13.0 and 1.6 μM, respectively; Figure 4B). A negative control 13-mer peptide containing randomly assorted amino acids from the reference peptide sequence failed to inhibit Lkt-induced cytolysis, even at the highest concentration tested (50 μM), indicating that inhibition of cytolysis was sequence specific (Extended Data File S2)⁴⁸. Together, these results suggest that peptide sequence and length affect Lkt binding.

Synthetic C₅ variant CD18 signal peptide blocks Lkt-induced cytolysis of primary bovine cells

The 13-mer C₅ synthetic signal peptide containing CD18 residues 5 to 17 were also tested for their ability to inhibit Lkt-induced cytolysis of primary cells isolated from cattle. The purpose was to demonstrate that the reduction in cytotoxicity observed with C₅ signal peptides was comparable between the immortalized cell line and freshly isolated leukocytes from cattle. Like the BL3 cell line, the animals used as donor were homozygous for CD18 variant “1”, and thus have the reference (R₃R₅) signal peptide. With primary PBMC (Figure 5A) or PMN (Figure 5B), the 13-mer C₅ synthetic signal peptide was significantly better at blocking Lkt-induced cytotoxicity compared to the R₅ signal peptide (7- and 14-fold respectively) and was similar to that for BL3 cells (8-fold).

Arginine at position 4 (R₄) in the eland CD18 signal peptide disrupts the enhanced Lkt binding attributed by C₅

Some bovid species have CD18 signal peptide sequences that are slightly different from those in cattle (Figure 6A and Table S3). In water buffalo, the 13-mer peptide sequence corresponding to CD18 signal peptide amino acids 5 to 17 differs at position 16 (S₁₆), while the same region in sheep differs at positions 10 and 12 (F₁₀S₁₂). However, synthetic peptides corresponding to the water buffalo and sheep sequences were similar to the R₅ reference cattle signal peptide when tested for their ability to bind Lkt and inhibit cytolysis of BL3 cells in vitro. In contrast, the eland signal peptide was variant at three positions in this region compared to cattle (C₅V₈G₁₆), and its 13-mer synthetic signal peptide had a 24-fold decrease in IC50 compared to the reference cattle R₅ signal peptide and a similar IC50 compared to the reference cattle C₅ signal peptide (Figure 6A). However, if the synthetic peptide is expanded to include the eland residue at position 4, the results were different. Eland have an arginine residue at position 4 (R₄) where other ruminants have a glutamine (Q₄). A synthetic 14-mer signal peptide with R₄ (i.e., Eland R₄C₅V₈G₁₆) caused a 66-fold reduction in the ability of the eland signal peptide to bind Lkt compared to the 13-mer (C₅V₈G₁₆) as measured by IC50 (Figure 6B). When R₄ was replaced with the Q₄ normally found in cattle and other ruminants (i.e. Eland Q₄C₅V₈G₁₆ versus R₄C₅V₈G₁₆), Lkt binding was restored. Similarly, when Q₄ in the cattle signal peptide (Q₄C₅) was replaced with R₄ (R₄C₅) there was a significant reduction in the ability of this peptide to bind Lkt (5.6-fold increase in IC50). These results suggest that the amino acid position 4 in the signal peptide can affect Lkt binding and that R₄ amino acid sequence in eland may disrupt the enhanced Lkt binding conferred by the C₅ variant residue.

A truncated CD18 C₅ signal peptide has high affinity for Lkt

Toxin inhibitors represent a potentially potent class of therapeutics that could protect animals during acute lung infection. Since truncated synthetic C₅ signal peptides showed increase affinity for Lkt, various peptide lengths were tested to identify those with maximum Lkt binding. Removing the first four N-terminal amino acids (MLRQ) resulted in no significant difference in Lkt binding for the C₅ or reference R₅ signal peptides (Extended Data Figure S2)⁴². In contrast, stepwise deletions of C-terminal residues of the C₅ signal peptide had a significant impact on Lkt binding with the highest affinity being a 12-mer C₅ signal peptide with amino acids 5 to 16. The IC50 of this 12-mer C₅ peptide (CPQLLLLAGLLA) was 23-fold lower than the 13-mer reference R₅ signal peptide (residues 5 to 17) and 30-fold lower than the 12-mer R₅ signal peptide. Thus, the 12-mer C₅ peptide (CPQLLLLAGLLA) represents the minimal naturally-occurring peptide sequence with maximal inhibition of Lkt-induced BL3 cell lysis (Figure 7).

Underlying data

Whole genome sequence files (FASTQ) for the BL3 cell line are available in the NCBI SRA under accession number SRX4645762.

The BL3 sequence data have also been deposited with links to BioProject accession number PRJNA325058 (BioSample SAMN05217649) in the NCBI BioProject database.

In addition, access to the aligned sequences is available via the USDA internet site: https://www.ars.usda.gov/plains-area/clay-center-ne/marc/wgs/celllines/ as described in the Methods.

Extended data

Table S1. MALDI-TOF MS assay design for 14 ITGB2 missense SNPs. DOI: https://doi.org/10.6084/m9.figshare.7449374.v1⁵³.

Table S2. ITGB2 genotypes recorded manually from WGS reads mapped to UMDv3.1 assembly for the USMARC Beef Cattle Diversity Panel v2.9. DOI: https://doi.org/10.6084/m9.figshare.7449989.v1⁴⁵.

Table S3. Haplotype-phased genotypes (diplotypes) for ITGB2 from MALDI-TOF MS assays for 1142 cattle. DOI: https://doi.org/10.6084/m9.figshare.7450673.v1⁴³.

Table S4. Alignment of CD18 sequences from Bilateria species. DOI: https://doi.org/10.6084/m9.figshare.7450796.v1⁴⁴.

Figure S1. Screen image of Integrated Genome Viewer software displaying ITGB2 N27KI genotype data for eight bulls. DOI: https://doi.org/10.6084/m9.figshare.7450814.v1³⁵.

Figure S2. Effect of N-terminal truncations of synthetic CD18 signal peptides on Lkt binding. Synthetic CD18 signal peptides were synthesized with four amino acids removed from N-terminus (MLRQ). The common R₃R₅ (A) or the rare R₃C₅ variant (B) signal peptides were tested for their ability to inhibit leukotoxin-induced cytolysis of bovine BL3 cells using a MTT cytotoxicity assay. Peptides were tested at concentrations ranging from 50 μM to 0.195 μM. Data are expressed as the mean with standard deviation (n=3). DOI: https://doi.org/10.6084/m9.figshare.7450823.v1⁴².

File S1. VCF file with SNPs from BL3 WGS aligned to the bovine UMD3.1 reference assembly. https://doi.org/10.6084/m9.figshare.7450826.v1³².

File S2. MTT dye-reduction cytotoxicity assay results. Percent inhibition of cytotoxicity was calculated as described in the Methods. Shown are the results used for statistical analyses of data and for generating Figure 1–Figure 3, Figure 7. DOI: https://doi.org/10.6084/m9.figshare.7451039⁴⁸.