INTRODUCTION
Folate plays vital roles in cell growth and proliferation through regulating the synthesis and stabilization of deoxyribonucleic acid (DNA) and ribonucleic acid (RNA), and its deficiency may lead to many serious diseases [
1]. Moreover, the adequate levels of folate are crucial for the proper immune function, particularly during pregnancy. Ruminants synthesize folic acid due to bacteria in their rumen [
2]. In some conditions like the periparturient period, the dairy cows experience severe immune and metabolic depression due to pregnancy stress, which increases their susceptibility to mastitis and other infectious diseases [
3]. Interestingly, the secretion of folates is also increased six times greater in colostrum than in milk 39 days post-calving [
4]. Whether the demand for folic acid may increase or not for maintenance of immune system capacity during this period is still undefined.
The physiological responses of an individual to the environment and stress are driven by the modulation of its genes through the production of mRNAs or transcriptome [
5]. A combined supplement of vitamins B
9 and B
12 by intramuscular route significantly regulates the hepatic and mammary gland gene expression in lactating dairy cows [
6] and also facilitates the lactational performance and energy status in multiparous cows [
7]. Moreover, Graulet et al [
8], also reported that the intramuscular injection of folic acid facilitates metabolic efficiency and increases the milk production ability of dairy cows [
8]. However, the oral supplementation of coated folic acid is widely ignored particularly during the perinatal period in dairy cows. It is essential that the ruminant’s folate requirements must be adjusted particularly during the periparturient period to avoid any loss in production ability and to prevent the metabolic or infectious diseases.
To address whether the supplementation of folic acid is needed for health maintenance and animal production activities especially during the perinatal time in a dairy cow, we conducted first a molecular-based study, in which the influence of coated folic acid supplementation on the immune status of Holstein cows was tested. By taking the advantage of RNA-seq assay, we evaluated the transcriptomic profiles of bovine peripheral blood lymphocytes (PBLs) for immunity-associated genes and pathways in response to oral supplementation of coated folic acid.
MATERIALS AND METHODS
Sample population and folic acid treatment
A total of 123 perinatal cows having similar parity, weight and prenatal period were selected and divided into three groups; group A (n = 41, 240 mg/500 kg cow/d), group B (n = 40, 120 mg/500 kg cow/d) and group C (n = 42, 0 mg/cow/d) based on the quantity of folic acid fed during the perinatal stage. The folic acid treatment lasted 21 days, including 14 days before calving till seven days after the calving (
Figure 1A). As the amount of folic acid supplementation was small (mg level), it was necessary to mix it with a certain amount of palletized concentrate to ensure enough folic acid was supplied to each cow.
Sample collection
Blood samples were collected from each group of Chinese Holsteins treated with folic acid before the treatment and seven days post-calving. The blood samples were taken in coagulant tubes, kept for 10 minutes at room temperature and then centrifuged at 12,000 rpm/15 m. Furthermore, serum was collected and stored at −20°C and sent to Beijing Huaying Biological Technology Research Institute for the detection of serum cytokines interleukin 17 (IL-17) and interferon-gamma (IFN-γ) by performing radioimmunoassay (Sino-UK, Beijing, China). In brief, each serum sample was initially centrifuged at 3,000 rpm/min for 5 min at 4°C. Next, 100 μL “cold” antigen (supernatant), 100 μL antibody and 100 μL “hot” antigen (radiolabeled antigen, 125-I) were mixed thoroughly and kept at 4°C for 24 h. Then, 500 μL separating buffer was added and mixed well. The mixture stayed at room temperature for 20 min. Later, the mixture was centrifuged at 3,500 rpm/min for 25 min at 4°C. Finally, the supernatant was discarded, and the precipitate bound with antigen was used to measure the radioactivity by a gamma counter.
In addition, the white blood cells at seven days post-calving were collected into a tube containing one mL Trizol for RNA extraction.
Extraction of RNA and sample preparation
Total RNA was isolated from white blood cells using the TRIzol reagent (Invitrogen, Carlsbad, CA, USA). Isolated RNA was purified by removing DNA through DNase I digestion (Qiagen, Heldon, Germany). RNA degradation and contamination were detected by 1% agarose gels. The RNA concentration was assessed using NanoPhotometer spectrophotometer (Implen, Westlake, CA, USA). The extracted RNA was stored at −80°C and a whole nine samples (three from each group) were sent to the company (Annoroad Gene Technology Co., Ltd, Beijing, China) for RNA sequencing.
Library preparation for RNA-Seq
Three samples for each group were selected for library preparation. A total amount of 2 μg RNA per sample was used as input material for the RNA sample preparations. Sequencing libraries were generated using NEBNext Ultra RNA Library Prep Kit for Illumina (#E7530L, NEB, Ipswich, MA, USA) following the manufacturer’s recommendations and index codes were added to attribute sequences to each sample. Briefly, mRNA was purified from total RNA using poly-T oligo-attached magnetic beads. Fragmentation was carried out using divalent cations under elevated temperature in NEBNext first-strand synthesis reaction buffer (5×). First strand cDNA was synthesized using random hexamer primer and RNase H. Second strand cDNA synthesis was subsequently performed using a buffer, dNTPs, DNA polymerase I and RNase H. The library fragments were purified with QiaQuick PCR kits and elution with elution buffer, then terminal repair A-tailing and adapter added were implemented. The aimed products were retrieved by agarose gel electrophoresis, and polymerase chain reaction (PCR) was performed, then the library was completed.
Library examination
RNA concentration of library was measured using Qubit RNA Assay Kit in Qubit 3.0 to preliminary quantify and then dilute to 1 ng/μL. Insert size was assessed using the Agilent Bioanalyzer 2100 system (Agilent Technologies, Santa Clara, CA, USA), and qualified insert size was accurately quantified using Step One Plus Real-Time PCR System (Library valid concentration >10 nM). The clustering of the index-coded samples was performed on a cBot cluster generation system using HiSeq PE Cluster Kit v4-cBot-HS (Illumina, USA) according to the manufacturer’s instructions. After cluster generation, the libraries were sequenced on an Illumina Hiseq 4000 platform, and 150 bp paired-end reads were generated.
Bioinformatics analysis for RNA-Seq
Reads obtained from the sequencing machine include raw reads containing adapters or low quality bases, which affect the following assembly and analysis. To get high quality reads, the data was filtered to remove adaptor sequences, unknown nucleotides (N), low-quality reads having more than 50% of low quality (Q<20) bases, using next generation sequencing quality control toolkit version 2.3.3. A set of genomic index files of reference genome was built using Bowtie version 2.2.5, and clean reads were mapped to the Bos taurus reference genome (UMD3.1) obtained from Ensembl (
ftp://ftp.ensembl.org/pub/release-73/fasta/bos_taurus/dna/) using Tophat version 2.1.0 [
9]. Then, the transcripts were assembled using Cufflinks version 2.2.1. Transcript files generated by Cufflinks were added to a single-merged transcriptome annotation using Cuffmerge version 2.2.1. differentially expressed genes (DEGs) and transcripts were identified between different sample groups using Cuffdiff version 2.2.1 [
10]. Gene expression values were calculated by counting the number of fragments per kilobase of transcript per million mapped fragments, and Cuffdiff was applied to measure significant differences among the three groups.
Biological process of gene ontology (GO) enrichment and Kyoto encyclopedia of genes and genomes (KEGG) pathway analyses were conducted with DEGs using the database for annotation, visualization and integrated discovery (DAVID) pathways analysis tool (
http://david.abcc.ncifcrf.gov/). The DEGs were administered into STRING v10 to generate a protein-protein interaction (PPI) network and to predict physical/functional PPIs.
Quantitative reverse transcription polymerase chain reaction validation for RNA-seq analysis
To verify the gene expression data gained by RNA sequencing analysis, quantitative reverse transcription PCR (RT-qPCR) was carried out on eight randomly selected DEGs namely mitogen-activated protein kinase 13 (
MAPK13), cluster difference 4 (
CD4), selectin P ligand (
SELPLG), C-X-C motif chemokine receptor 2 (
CXCR2), major histocompatibility complex antigen class II (
BLA-DQB), C-C motif chemokine ligand 5 (
CCL5), NF-kappa-B inhibitor alpha (
NFKBIA), and TNF superfamily 13 (
TNFSF13) using the total RNA used for RNA-seq. The primers were designed for all the targeted genes by using Primer5 software and were further validated through Oligo 6.0. The detail of the primers has been given in the
supplementary material (Supplementary file 1). The cDNA was prepared using PrimeScriptTM RT reagent kit according to the manufacturer’s instructions (Takara, Dalian, China). The RT-qPCR reactions were carried out in a final volume of 20 μL with the Roche SYBR Green PCR Kit (Roche, Hercules, CA, USA) according to the manufacturer’s protocol. The bovine housekeeping glyceraldehyde 3-phosphate dehydrogenase was used as the internal standard to adjust the input of cDNA and to normalize the expression of target genes. Duplicate RT-qPCRs were performed on each cDNA, and the average Ct value was used for further analyses.
Statistical analysis
SAS9.2 general linear model program was used for statistical analysis, the folic acid effect model was analyzed as follows;
Among them: y, cytokines; μ, population mean; α, parity effect; β, weight effect; γ, folic acid effect; e, random residuals.
Furthermore, Student’s t-test was used to assess the difference between pre and post-folic acid treated groups for cytokines IL-17 and IFN-γ as well as to analyze the RT-qPCR results.
DISCUSSION
Folate is known to be one of the most key nutrients having an essential role in the improvement of immunity and prevention of diseases for the pregnant mammals. However, in dairy cattle, external folate intake has been widely neglected especially during the perinatal period. The current research using RNA-seq analysis proved the importance of folic acid, a synthetic form of folate, in terms of immunity and health regulation in transition Holstein cows.
The periparturient period in mammals is known to be critical for fecundity and health. During the periparturient period, the preservation of health and the preparation for oncoming parturition is of supreme significance for dairy cows. Balanced nutrition is necessary for maintaining a functional immune system, while also for avoiding other causes of inflammation, such as tissue damage, digestive, metabolic disorders, and infectious diseases during the perinatal period [
11]. In the current study, we tested the influence of orally administered coated folic acid in Holstein cows during the periparturient period and observed that the serum cytokines IL-17 and IFN-γ were up-regulated after low folic acid supplementation. IL-17 plays a key role in the host defenses against bacterial and fungal infections [
12–
15]. Our recent work found that the mutations in IL-17 might serve as biomarkers for resistance against mastitis in Holstein cattle as well as Sanhe cattle, a dual purpose breed of China [
16]. Moreover, IFN-γ is important for immune regulation as well as for the promotion of T cell priming and antibodies production [
17–
19]. As during the periparturient period immunity is suppressed and dairy cows are prone to infection at this time [
20], the elevated levels of IL17 and IFN-γ in response to low folic acid treatment suggest that dairy cows during the periparturient period should be fed with folic acid as matter of prophylaxis.
For more understanding, we conducted the transcriptomic study of PBLs for the three dairy cattle groups with high, low and none folic acid supplementation. Previous studies reported that many biological pathways play a key role by accelerating immune-relevant cells and provide a strong defense against any foreign pathogens [
21]. The nuclear factor (NF)-kappa B signaling pathway, hematopoietic cell lineage, and TNF signaling pathways were reported to respond to
Staphylococcus aureus (
S. aureus) in mammary epithelial cells [
22], and against porcine reproductive and respiratory syndrome virus post-vaccination in pregnant sows [
23]. Moreover, studies also revealed that the toll like receptor signaling pathway plays a significant role in adaptive immunity [
24,
25]. Interestingly, we documented the above immunity associated pathways such as chemokine signaling pathway, TNF signaling, and NF-kappa B signaling pathway significantly (p<0.05) responded to high and low coated folic acid supplementation. Using microarrays, Ouattara et al [
6] found that intra-muscular injection of vitamins B
9 (folate) and B
12 positively regulated the biological processes having fundamental importance in immune, anti-inflammation, cell adhesion and response to stress in hepatic and mammary gland gene expression profiles in lactating dairy cows. The antigen presentation and processing signaling, cytokine-cytokine receptor interaction, and
S. aureus infection which are regarded as the key immunity associated biological pathways [
23,
26] were also reported in our low folic acid treated cows. Especially, linear regression analyses showed moderate relationships between the expression levels of differentially expressed genes (
CX3CR1 and
CCR3 in cytokine-cytokine receptor interaction pathway, as well as
BoLA-DQA5 in antigen presentation and processing signaling pathway and
S. aureus infection pathway) and serum IL-17 (
Supplementary file 8). Our study revealed that immunity linked biological function processes, i.e., immune response, defense response to bacterium, inflammatory function, chemokines, and cytokines mediated functions were dominantly regulated by orally administered folic acid (high, low). These findings suggest that coated folic acid oral supplementation provoke the immunity-related pathways and biological processes which may preserve the health and improve production performance of dairy cattle.
To control the related traits normally, a close correlation of genes with each other within the pathways is obligatory. When these genes are influenced by any external or internal factor, it will create a series of changes in the function of the body. In the current research (
Figure 7), we proved that folic acid supplementation causes the down-regulation of
NFKBIA and TNF alpha-induced protein 3 (
TNFAIP3) which are involved in the negative mediation of NF-kappaB transcription factor activity. The suppressor of cytokine signaling 3 (
SOCS3) was also significantly down-regulated which is involved in the negative regulation of cytokines that signal through the JAK/STAT pathway. Additionally, the
MYD88, nucleotide-binding oligomerization domain containing 2 and
MAPK13 are the positive regulators of IL-6 were successfully up-regulated by the folate treatment. The folic acid supplementation also regulated many important genes associated with immune response such as MHC class II antigen (
BLA-DQB),
TNFRSF1A,
CXCL8,
CXCL10,
PTAFR,
CXCR1,
CXCR5, and
CCL5. Importantly, our previously published study [
22] documented the up-regulation of the
CXCR1,
NFKBIA,
SOCS3, Pim-1 proto-oncogene, serine/threonine kinase, dual specificity phosphatase 4, zinc finger CCCH-type containing 12A, and
NFKBIA in mammary epithelial cells after infection by
S. aureus in vitro, while these genes showed significantly downregulated status in folic acid treated cows. In addition,
NFKBIA was up-regulated in response to Duck Tampusu virus infection [
27]. Meanwhile, we also noticed several key up-regulated genes (
CD8A,
CCL3,
CD4,
BLA-DQB, etc.) which play important roles in the development of immunity (
Supplementary file 7) were only detected in low folic acid treatment. Taking the up-regulated
CD4 gene as an example, which has an important function in the development of immunity, was down-regulated in mastitis cows [
28]. Collectively, the data suggest that low folic acid supplementation (120 mg/500 kg cow/d) has key role in the mediation of immunity associated genes, which might be used as biomarkers for health regulation.
A few studies in humans reported that the dietary folic acid in a high dose for an extended period had an adverse effect on natural killer cell cytotoxicity [
29]. Controversially, we did not report any such kind of change related to genes reported in our selected Chinese Holstein cows. However, we noticed a higher level of cytokines and chemokines regulating genes in the comparison of high vs control which may be harmful to the body. In addition, it is alluring to contemplate that this variability might be due to the inconsistency in the period of folic acid supplementation. Although our study profiled for the first time the importance of folic acid in immune regulation signaling during the bovine perinatal period through transcriptomic analysis, however, there are still limitations in our research which need to be addressed in future studies. Firstly, the remarkably regulated pathways and DEGs need to be tested through further
in-vitro study. Secondly, we noticed that metabolic associated biological pathways were also significantly regulated by folic acid treatment; thus future research on the metabolic-related traits linked to folic acid supplementation is warranted.