Rewiring of Gene Expression in Circulating White Blood Cells is Associated with Pregnancy Outcome in Heifers (Bos Taurus)

Overview

Journal Sci Rep

Specialty Science

Date 2020 Oct 9

PMID 33033295

Citations 13

Authors

Sarah E Moorey

Bailey N Walker

Michelle F Elmore

Joshua B Elmore

Soren P Rodning

Fernando H Biase

Affiliations

Soon will be listed here.

Abstract

Infertility is a challenging phenomenon in cattle that reduces the sustainability of beef production worldwide. Here, we tested the hypothesis that gene expression profiles of protein-coding genes expressed in peripheral white blood cells (PWBCs), and circulating micro RNAs in plasma, are associated with female fertility, measured by pregnancy outcome. We drew blood samples from 17 heifers on the day of artificial insemination and analyzed transcript abundance for 10,496 genes in PWBCs and 290 circulating micro RNAs. The females were later classified as pregnant to artificial insemination, pregnant to natural breeding or not pregnant. We identified 1860 genes producing significant differential coexpression (eFDR < 0.002) based on pregnancy outcome. Additionally, 237 micro RNAs and 2274 genes in PWBCs presented differential coexpression based on pregnancy outcome. Furthermore, using a machine learning prediction algorithm we detected a subset of genes whose abundance could be used for blind categorization of pregnancy outcome. Our results provide strong evidence that transcript abundance in circulating white blood cells is associated with fertility in heifers.

Citing Articles

Higher abundance of 2-dehydro-d-gluconate in the plasma of sub-fertile or infertile Bos taurus heifers.

Marrella M, Moorey S, Campagna S, Sarumi Q, Biase F J Anim Sci. 2024; 102.

PMID: 38720650 PMC: 11247527. DOI: 10.1093/jas/skae126.

Harnessing Genomics and Transcriptomics Approaches to Improve Female Fertility in Beef Cattle-A Review.

Kertz N, Banerjee P, Dyce P, Diniz W Animals (Basel). 2023; 13(20).

PMID: 37894009 PMC: 10603720. DOI: 10.3390/ani13203284.

A multi-omics analysis identifies molecular features associated with fertility in heifers (Bos taurus).

Marrella M, Biase F Sci Rep. 2023; 13(1):12664.

PMID: 37542054 PMC: 10403585. DOI: 10.1038/s41598-023-39858-0.

Robust identification of regulatory variants (eQTLs) using a differential expression framework developed for RNA-sequencing.

Marrella M, Biase F J Anim Sci Biotechnol. 2023; 14(1):62.

PMID: 37143150 PMC: 10161580. DOI: 10.1186/s40104-023-00861-0.

Sexing of cattle embryos using RNA-sequencing data or polymerase chain reaction based on a complete sequence of cattle chromosome Y.

Nix J, Schettini G, Biase F Front Genet. 2023; 14:1038291.

PMID: 37077537 PMC: 10106624. DOI: 10.3389/fgene.2023.1038291.

References

Dias M, Souza F, Takada L, Feitosa F, Costa R, Diaz I . Study of lipid metabolism-related genes as candidate genes of sexual precocity in Nellore cattle. Genet Mol Res. 2015; 14(1):234-43. DOI: 10.4238/2015.January.16.7. View

Jin W, Ibeagha-Awemu E, Liang G, Beaudoin F, Zhao X, Guan L . Transcriptome microRNA profiling of bovine mammary epithelial cells challenged with Escherichia coli or Staphylococcus aureus bacteria reveals pathogen directed microRNA expression profiles. BMC Genomics. 2014; 15:181. PMC: 4029070. DOI: 10.1186/1471-2164-15-181. View

Boddhireddy P, Kelly M, Northcutt S, Prayaga K, Rumph J, DeNise S . Genomic predictions in Angus cattle: comparisons of sample size, response variables, and clustering methods for cross-validation. J Anim Sci. 2014; 92(2):485-97. DOI: 10.2527/jas.2013-6757. View

Vegh P, Magee D, Nalpas N, Bryan K, McCabe M, Browne J . MicroRNA profiling of the bovine alveolar macrophage response to Mycobacterium bovis infection suggests pathogen survival is enhanced by microRNA regulation of endocytosis and lysosome trafficking. Tuberculosis (Edinb). 2015; 95(1):60-7. DOI: 10.1016/j.tube.2014.10.011. View

Yang H, Mei J, Chang K, Zhou W, Huang L, Li M . Autophagy in endometriosis. Am J Transl Res. 2017; 9(11):4707-4725. PMC: 5714760. View

Fang L, Cai W, Liu S, Canela-Xandri O, Gao Y, Jiang J . Comprehensive analyses of 723 transcriptomes enhance genetic and biological interpretations for complex traits in cattle. Genome Res. 2020; 30(5):790-801. PMC: 7263193. DOI: 10.1101/gr.250704.119. View

Robertson S, Sharkey D . The role of semen in induction of maternal immune tolerance to pregnancy. Semin Immunol. 2001; 13(4):243-54. DOI: 10.1006/smim.2000.0320. View

Gusev A, Ko A, Shi H, Bhatia G, Chung W, Penninx B . Integrative approaches for large-scale transcriptome-wide association studies. Nat Genet. 2016; 48(3):245-52. PMC: 4767558. DOI: 10.1038/ng.3506. View

Neupane M, Geary T, Kiser J, Burns G, Hansen P, Spencer T . Loci and pathways associated with uterine capacity for pregnancy and fertility in beef cattle. PLoS One. 2017; 12(12):e0188997. PMC: 5724891. DOI: 10.1371/journal.pone.0188997. View

10.

Ma S, Tong C, Ibeagha-Awemu E, Zhao X . Identification and characterization of differentially expressed exosomal microRNAs in bovine milk infected with Staphylococcus aureus. BMC Genomics. 2019; 20(1):934. PMC: 6896338. DOI: 10.1186/s12864-019-6338-1. View

11.

Liao Y, Smyth G, Shi W . featureCounts: an efficient general purpose program for assigning sequence reads to genomic features. Bioinformatics. 2013; 30(7):923-30. DOI: 10.1093/bioinformatics/btt656. View

12.

Hughes H, Carroll J, Burdick Sanchez N, Richeson J . Natural variations in the stress and acute phase responses of cattle. Innate Immun. 2013; 20(8):888-96. DOI: 10.1177/1753425913508993. View

13.

Du J, Yuan Z, Ma Z, Song J, Xie X, Chen Y . KEGG-PATH: Kyoto encyclopedia of genes and genomes-based pathway analysis using a path analysis model. Mol Biosyst. 2014; 10(9):2441-7. DOI: 10.1039/c4mb00287c. View

14.

Bullard J, Purdom E, Hansen K, Dudoit S . Evaluation of statistical methods for normalization and differential expression in mRNA-Seq experiments. BMC Bioinformatics. 2010; 11:94. PMC: 2838869. DOI: 10.1186/1471-2105-11-94. View

15.

Bayraktar R, Van Roosbroeck K, Calin G . Cell-to-cell communication: microRNAs as hormones. Mol Oncol. 2017; 11(12):1673-1686. PMC: 5709614. DOI: 10.1002/1878-0261.12144. View

16.

Roberts A, Geary T, Grings E, Waterman R, MacNeil M . Reproductive performance of heifers offered ad libitum or restricted access to feed for a one hundred forty-day period after weaning. J Anim Sci. 2009; 87(9):3043-52. DOI: 10.2527/jas.2008-1476. View

17.

Martin J, Creighton K, Musgrave J, Klopfenstein T, CLARK R, Adams D . Effect of prebreeding body weight or progestin exposure before breeding on beef heifer performance through the second breeding season. J Anim Sci. 2007; 86(2):451-9. DOI: 10.2527/jas.2007-0233. View

18.

Cushman R, Kill L, Funston R, Mousel E, Perry G . Heifer calving date positively influences calf weaning weights through six parturitions. J Anim Sci. 2013; 91(9):4486-91. DOI: 10.2527/jas.2013-6465. View

19.

Chory J, Pollard Jr J . Separation of small DNA fragments by conventional gel electrophoresis. Curr Protoc Mol Biol. 2008; Chapter 2:Unit2.7. DOI: 10.1002/0471142727.mb0207s47. View

20.

Koks S, Velthut A, Sarapik A, Altmae S, Reinmaa E, Schalkwyk L . The differential transcriptome and ontology profiles of floating and cumulus granulosa cells in stimulated human antral follicles. Mol Hum Reprod. 2009; 16(4):229-40. DOI: 10.1093/molehr/gap103. View