Transcriptome analysis identifies genes involved with the development of umbilical hernias in pigs.
Journal
PloS one
ISSN: 1932-6203
Titre abrégé: PLoS One
Pays: United States
ID NLM: 101285081
Informations de publication
Date de publication:
2020
2020
Historique:
received:
06
12
2019
accepted:
16
04
2020
entrez:
8
5
2020
pubmed:
8
5
2020
medline:
29
7
2020
Statut:
epublish
Résumé
Umbilical hernia (UH) is one of the most frequent defects affecting pig production, however, it also affects humans and other mammals. UH is characterized as an abnormal protrusion of the abdominal contents to the umbilical region, causing pain, discomfort and reduced performance in pigs. Some genomic regions associated to UH have already been identified, however, no study involving RNA sequencing was performed when umbilical tissue is considered. Therefore, here, we have sequenced the umbilical ring transcriptome of five normal and five UH-affected pigs to uncover genes and pathways involved with UH development. A total of 13,216 transcripts were expressed in the umbilical ring tissue. From those, 230 genes were differentially expressed (DE) between normal and UH-affected pigs (FDR <0.05), being 145 downregulated and 85 upregulated in the affected compared to the normal pigs. A total of 68 significant biological processes were identified and the most relevant were extracellular matrix, immune system, anatomical development, cell adhesion, membrane components, receptor activation, calcium binding and immune synapse. The results pointed out ACAN, MMPs, COLs, EPYC, VIT, CCBE1 and LGALS3 as strong candidates to trigger umbilical hernias in pigs since they act in the extracellular matrix remodeling and in the production, integrity and resistance of the collagen. We have generated the first transcriptome of the pig umbilical ring tissue, which allowed the identification of genes that had not yet been related to umbilical hernias in pigs. Nevertheless, further studies are needed to identify the causal mutations, SNPs and CNVs in these genes to improve our understanding of the mechanisms of gene regulation.
Identifiants
pubmed: 32379844
doi: 10.1371/journal.pone.0232542
pii: PONE-D-19-33848
pmc: PMC7205231
doi:
Types de publication
Journal Article
Research Support, Non-U.S. Gov't
Langues
eng
Sous-ensembles de citation
IM
Pagination
e0232542Déclaration de conflit d'intérêts
The authors have declared that no competing interests exist.
Références
Mol Vis. 2009 Oct 15;15:2045-9
pubmed: 19844586
Int Arch Allergy Immunol. 2005 Apr;136(4):385-400
pubmed: 15775687
J Mol Biol. 2017 Feb 17;429(4):515-530
pubmed: 27932295
Bioinformatics. 2015 Jan 15;31(2):166-9
pubmed: 25260700
Genomics. 1998 May 1;49(3):467-71
pubmed: 9615235
J Biol Chem. 2013 Mar 22;288(12):8053-60
pubmed: 23344953
J Invest Dermatol. 2011 Jan;131(1):99-107
pubmed: 20882040
Cell. 2000 Jan 21;100(2):209-19
pubmed: 10660044
Allergy. 2009 Sep;64(9):1286-91
pubmed: 19222422
Cancer Res. 2004 Aug 1;64(15):5245-50
pubmed: 15289330
BMC Genomics. 2018 May 29;19(1):412
pubmed: 29843603
Genome Biol. 2002 Jun 18;3(7):RESEARCH0034
pubmed: 12184808
J Vet Intern Med. 1999 May-Jun;13(3):202-5
pubmed: 10357109
J Allergy Clin Immunol. 2000 Dec;106(6):1124-31
pubmed: 11112896
Br J Cancer. 2008 Oct 21;99(8):1269-75
pubmed: 18854825
Am J Pathol. 2011 Jun;178(6):2641-53
pubmed: 21641387
PLoS One. 2017 Jul 24;12(7):e0181580
pubmed: 28742099
Biophys J. 1996 Dec;71(6):3030-45
pubmed: 8968574
Eur J Clin Invest. 2009 Nov;39(11):953-9
pubmed: 19656168
Meat Sci. 2010 Feb;84(2):244-7
pubmed: 20374782
PLoS One. 2014 Jun 18;9(6):e99269
pubmed: 24940735
Biochem J. 2000 Sep 15;350 Pt 3:771-6
pubmed: 10970791
Matrix. 1993 Jul;13(4):297-306
pubmed: 8412987
Cancer Res. 2018 Jul 15;78(14):4059-4072
pubmed: 29764866
Prostaglandins Leukot Essent Fatty Acids. 2009 Jan;80(1):51-6
pubmed: 19091535
Int J Mol Sci. 2015 Aug 05;16(8):18149-84
pubmed: 26251901
Dev Neurobiol. 2015 May;75(5):494-504
pubmed: 25331329
J Invest Dermatol. 2012 Nov 15;132(E1):E6-11
pubmed: 23154631
Nucleic Acids Res. 2019 Jan 8;47(D1):D701-D710
pubmed: 30407520
Am J Hum Genet. 2006 Oct;79(4):724-30
pubmed: 16960809
Spine J. 2013 Mar;13(3):299-317
pubmed: 23537453
J Pathol. 2008 Jan;214(2):199-210
pubmed: 18161745
Genet Test Mol Biomarkers. 2010 Jun;14(3):313-7
pubmed: 20367178
PLoS One. 2018 Sep 20;13(9):e0204348
pubmed: 30235332
Bioinformatics. 2007 Jul 1;23(13):1607-15
pubmed: 17483500
Hum Pathol. 1989 Nov;20(11):1071-7
pubmed: 2530150
J Clin Immunol. 2016 Jan;36(1):19-27
pubmed: 26686525
Scand J Immunol. 2007 Aug-Sep;66(2-3):143-58
pubmed: 17635792
Anim Genet. 2016 Jun;47(3):298-305
pubmed: 27028052
Anim Genet. 2018 Dec;49(6):641-644
pubmed: 30246406
Biochem Pharmacol. 2000 Oct 15;60(8):1091-9
pubmed: 11007946
J Clin Anesth. 2016 Sep;33:26-30
pubmed: 27555128
Am J Med Genet A. 2018 Dec;176(12):2858-2861
pubmed: 30450763
Proc Natl Acad Sci U S A. 2001 Jun 19;98(13):7516-21
pubmed: 11381124
J Clin Invest. 2015 Jun;125(6):2375-84
pubmed: 25961457
J Am Vet Med Assoc. 1994 May 15;204(10):1660-4
pubmed: 8050950
Glycoconj J. 2004;19(7-9):433-40
pubmed: 14758066
Hum Mutat. 2003 Apr;21(4):447
pubmed: 12655565
Cold Spring Harb Perspect Med. 2014 Nov 03;4(11):a015297
pubmed: 25368015
J Cell Sci. 2008 Feb 1;121(Pt 3):255-64
pubmed: 18216330
Cell Death Differ. 2004 Mar;11(3):270-9
pubmed: 14647238
Apoptosis. 2008 Jan;13(1):1-9
pubmed: 17990121
Can Vet J. 2017 Oct;58(10):1065-1072
pubmed: 28966356
J Pathol. 2012 Jan;226(2):158-71
pubmed: 21989576
Tohoku J Exp Med. 2016;240(1):67-78
pubmed: 27600583
Science. 1991 Mar 22;251(5000):1451-5
pubmed: 2006419
Best Pract Res Clin Rheumatol. 2008 Mar;22(1):85-100
pubmed: 18328983
World J Surg. 2002 Apr;26(4):401-8
pubmed: 11910470
Mol Biol Cell. 2002 Oct;13(10):3369-87
pubmed: 12388743
Cell. 1996 Feb 9;84(3):345-57
pubmed: 8608588
Genome Res. 2003 Nov;13(11):2498-504
pubmed: 14597658
Exp Cell Res. 1994 Apr;211(2):391-9
pubmed: 8143788
Vet Rec. 2008 Mar 22;162(12):377-82
pubmed: 18359931
Oncotarget. 2016 Apr 5;7(14):18440-57
pubmed: 26943039
FASEB J. 1989 Jul;3(9):2042-51
pubmed: 2663581
Matrix Biol. 2012 Apr;31(3):187-96
pubmed: 22226732
Plast Reconstr Surg Glob Open. 2016 Oct 24;4(10):e1036
pubmed: 27826465
Surg Clin North Am. 2008 Feb;88(1):1-15, vii
pubmed: 18267158
Clin Dermatol. 2007 Jan-Feb;25(1):79-92
pubmed: 17276205
Bioinformatics. 2010 Jan 1;26(1):139-40
pubmed: 19910308
BMC Bioinformatics. 2012 Jun 18;13:134
pubmed: 22708584
Genet Sel Evol. 2015 Mar 21;47:18
pubmed: 25886970
Biotechnol Lett. 2004 Mar;26(6):509-15
pubmed: 15127793
J Biol Chem. 2002 Nov 15;277(46):43557-64
pubmed: 12218063
Trends Microbiol. 2017 Apr;25(4):257-266
pubmed: 28089324
J Comp Pathol. 2020 Feb;175:69-74
pubmed: 32138845
Proc Natl Acad Sci U S A. 2001 Jun 5;98(12):6686-91
pubmed: 11390996
Genes (Basel). 2020 Jan 21;11(2):
pubmed: 31973088
J Vasc Surg. 1994 Aug;20(2):209-17
pubmed: 8040944
Nat Cell Biol. 2002 May;4(5):E131-6
pubmed: 11988758
Bioinformatics. 2013 Jan 1;29(1):15-21
pubmed: 23104886
Nat Cell Biol. 1999 Sep;1(5):E131-8
pubmed: 10559956
Am J Vet Res. 2009 Aug;70(8):1006-12
pubmed: 19645582
Arthritis Rheum. 2006 Mar;54(3):808-17
pubmed: 16508957
Clin Genet. 2012 Jul;82(1):1-11
pubmed: 22353005
Genetika. 2015 Oct;51(10):1163-70
pubmed: 27169231
J Cell Sci. 2010 Dec 15;123(Pt 24):4195-200
pubmed: 21123617
Anim Genet. 2019 Apr;50(2):162-165
pubmed: 30746724
Biochem J. 1996 Sep 15;318 ( Pt 3):909-14
pubmed: 8836137
Virchows Arch. 2004 Mar;444(3):247-56
pubmed: 14749928
Genome Res. 1999 May;9(5):449-56
pubmed: 10330124
Chirurgia (Bucur). 2015 May-Jun;110(3):224-30
pubmed: 26158731
Arthritis Res. 2002;4(3):157-64
pubmed: 12010565
Hum Mutat. 2014 Dec;35(12):1506-1513
pubmed: 25230692
Hum Mutat. 2006 Jul;27(7):719-20
pubmed: 16786515
Hum Genet. 2010 Feb;127(2):231-41
pubmed: 19911200
J Anim Sci. 2009 Aug;87(8):2469-74
pubmed: 19359506
Biochem Biophys Res Commun. 2002 Jan 18;290(2):756-62
pubmed: 11785964
Kidney Int. 2002 May;61(5):1714-28
pubmed: 11967021
Science. 1987 Oct 30;238(4827):638-44
pubmed: 3672117
Biochim Biophys Acta. 2014 Sep;1842(9):1604-12
pubmed: 24907562
Am J Med Genet A. 2018 May;176(5):1166-1174
pubmed: 29681106
Exp Dermatol. 2004 Mar;13(3):185-91
pubmed: 14987259
Pharmacol Rev. 2009 Jun;61(2):198-223
pubmed: 19549927
Dev Biol. 2010 May 1;341(1):126-40
pubmed: 19854168
J Clin Invest. 1990 Aug;86(2):453-62
pubmed: 2200803
Nat Genet. 2009 Apr;41(4):396-8
pubmed: 19287381