Introduction
Materials and methods
Gene expression analysis using GeneChip@rat genome array
RNA amplification
Sample hybridization, array washing, staining and scanning
Array data analysis and visualization
Validation of differentially expressed genes
Gene bank acc. No
|
Gene symbol
|
Primer 5’ to 3’
|
bp
|
---|---|---|---|
NM_012536
|
CTRB1
|
F: CTGAAGATCGCACAGGTCTTT
|
185
|
R: TCTTGAGGGCATTGTATTTGG
| |||
NM_017239
|
MYH6
|
F: AAGCTGCAGTTGAAGGTGAAG
|
214
|
R: TGGACAGGTTATTCCTCATCG
| |||
NM_013085
|
PLAU
|
F: GAGGGTGCTTGTCCAATATGA
|
189
|
R: CAGGAATACACCAGCTTTGCT
| |||
NM_207602
|
ST3GAL6
|
F: TGCGTATCACAATCTGACTGC
|
200
|
R: AATCACCAGGCAGCAACAG
| |||
NM_017128
|
INHBA
|
F: TAGGCAGTCTGAAGACCATCC
|
199
|
R: TGAGTGGAAGGAGAGTGAGGA
| |||
NM_031558
|
STAR
|
F: CTCACGTGGCTGCTCAGTAT
|
221
|
R: CTTGGCTGAAGGTGAACAGA
| |||
NM_017235
|
HSD17B7
|
F: CTTTTAGTCCCAGCGAGGAG
|
188
|
R: TGGCCCAAACACAAACATAC
| |||
NM_138504
|
OSGIN1
|
F: CAATCCCTGAGGAGGAAGAG
|
217
|
R: CCCCTCTGGTCTATGGCTAC
| |||
NM_013413
|
RLN1
|
F: CGTTCCCAGAGCTACAACAAC
|
249
|
R:CCATTAGCTCCGTATCAGCAG
| |||
NM_031144
|
ACTB
|
F: ACTGGGACGATATGGAGAAGA
|
202
|
R:AGAGGCATACAGGGACAACAC
|
Results
Ovarian polycystic syndrome is associated with dysregulation of gene expression
Gene transcripts repressed in DHT-treated rats
Functional classification of the genes repressed in ovaries of DHT-treated rats
Gene transcripts activated in ovaries of DHT-treated rats
Molecular functions activated in ovaries of DHT-treated rats
Zinc ion binding
|
NR2F2,MAP3K1,PTGR1,CPA1,VEZF1,ACY3,SLC39A8,CPA2,RBM5,ZFP278,ZNF574, ZEB2, JARID1A, PHC1, ZCCHC11, KLF11, ZFPM2, OSR2, MSL2L1, TRIM37, PAN3, ZC3H11A, RGNEF, CRYZ, SIVA1, ZFP26, TRIM35, ZFP61, FOXP2, DTX3, ZNF292, GATA4, KLF15, RNF138, MMP23
|
Transcription regulator activity
|
NR2F2, CITED2, CRYM, ARNT2, NFIA, NR3C2, BMP2, SMARCD3, RPL7, MYCN, ZFP278, ZEB2, KLF11, ZFPM2, ARX, TLE1, FOXP2, ZNF292, GATA4, NR0B1,RBPJ, MEIS1, HOXD9, CDH1, FOXO1,TWIST, KLF15
|
Receptor binding
|
INSL3, INHA, JAK2, AKAP9, CXCL12, INHBB, ARNT2, INHBA, PENK, BMP2,SMARCD3, SEMA3C, EPHA4,SEMA6A, SIVA1, NR0B1, GAS6, ANGPTL1, MDK,STC1, IRS3
|
Protein dimerization activity
|
INHA, INHBB, GHR, ARNT2, NR3C2, SHMT1, INHBA, BMP2, MYH6, MYH7, RPL7, PON3, GUCY1A3, FOXP2, NR0B1, MEIS1, ROBO2
|
Growth factor activity
|
INHA, JAK2, INHBB, INHBA, BMP2, GAS6, MDK
|
Carboxylic acid transmembrane transporter activity
|
SLCO1A4, SLC13A5, SLC1A3, SLC7A5, SLC7A8
|
Growth factor binding
|
FGFR2, IGFBP6, CRIM1,HTRA3, CYR61
|
Insulin-like growth factor binding
|
IGFBP6, CRIM1, HTRA3, CYR61
|
Protein phosphatase binding
|
GHR, PHACTR1, JUP, CDH1
|
Extracellular matrix binding
|
VTN, RPSA, CYR61
|
L-amino acid transmembrane transporter activity
|
SLC1A3,SLC7A5, SLC7A8
|
Semaphorin receptor binding
|
SEMA3C, SEMA6A
|
Protein tyrosine phosphatase-like protein binding
|
JUP, CDH1
|
Actin-dependent atpase activity
|
MYH6, MYH7
|
Glycine hydroxyl methyltransferase activity
|
SHMT1, GART
|
Peptide antigen binding
|
SLC7A5, SLC7A8
|
Metallocarboxypeptidase activity
|
CPA1, CPA2
|
Molecular pathways activated or repressed in DHT-treated rats
Biosynthesis of steroids
|
↓
CYP51, ↓HMGCR, ↓SQLE, ↓HSD17B7, ↓FDFT1, ↓LSS, MVD, ↓FDPS, ↓IDI1, ↓SC5DL, ↓EBP, ↓SC4MOL, ↓TM7SF2, ↓DHCR24, ↓NSDHL
|
TGF-beta signaling pathway
|
↑INHBB, ↑INHBA, ↑AMH, ↑BMP2, ↑FOXO1, ↑FOXP2, ↓FKBP1A,↑ INHA, ↑
BAMBI, ↑CITED1, ↓CITED2
|
Leukocyte transendothelial migration
|
↑CXCL12, ↓THY1, ↓BCAR1, ↓PECAM1,↓ CXCR4, ↑CLDN11, ↑MYL9, ↓SIPA1
|
Cholesterol biosynthesis
| ↓MVD, ↓HMGCR, ↓HMGCS1, ↓FDPS, ↓IDI1, ↓FDFT1
|
Pyruvate metabolism
| ↓ME1, ↓DLAT, ↑ALDH1B1, ↓ME2, ↓ACAT2, ↓ACSS2, ↑ME3
|
Glycerophospholipid metabolism
| ↓PLA2G1B, ↑PLA2G2A, ↓GPD1, ↓CDS1,↓ PCYT2, ↑ETNK2, ↑CRLS1
|
Complement and coagulation cascades
| ↓A2M, ↓C2, ↓PLAU, ↑TFPI, ↑MASP1,↓ CFB, ↓C1QA
|
Glycolysis/Gluconeogenesis
| ↓HK1, ↓HK2, ↓DLAT, ↑FBP2, ↑ALDH1B1,↓ACSS2
|
Adipocytokine signaling pathway
|
↑JAK2, ↓NFKBIB, ↑IRS3, ↓ACSL3, ↓ADIPOR, ↑STK11
|
Butanoate metabolism
| ↓HMGCS1, ↓AACS, ↑ALDH1B1, ↓ACAT2, ↑ACSM5
|
Terpenoid biosynthesis
| ↓SQLE, ↓FDFT1, ↓FDPS, ↓IDI1
|
Ether lipid metabolism
| ↓PLA2G1B, ↑PLA2G2A, ↑PAFAH1B3, ↑ENPP6
|
Citrate cycle (TCA cycle)
| ↓ACLY, ↓IDH1, ↓DLAT, ↓DLST
|
Androgen and estrogen metabolism
|
↑SRD5A1, ↓ HSD17B1, ↓HSD17B7, ↓HSD3B6
|
Androgen/estrogene/progesterone biosynthesis
| ↓HSD3B6, ↓CYP11A1, ↓NSDHL, ↓CYP19A1
|
Glutathione metabolism
| ↓GPX1, ↓IDH1, ↓GSTT1, ↑GPX7
|
Lysine degradation
|
↑ALDH1B1, ↓DLST, ↓ACAT2, ↑MGC109340
|
Fatty acid metabolism
|
↑ACSL3, ↓ACAA2, ↑ALDH1B1, ↓ACAT2
|
Valine, leucine and isoleucine degradation
| ↓HMGCS1, ↓ACAA2, ↑ALDH1B1, ↓ACAT2
|
Validation of microarray data using real time quantitative PCR (qPCR)
Gene name
|
Gene symbol
|
Acess. No
|
Array result
|
qPCR result
| ||
---|---|---|---|---|---|---|
FC
|
P value
|
FC
|
P value
| |||
Chymotrypsinogen b1
|
CTRB1
|
NM_012536
|
20 (↑)
|
0.00003
|
27.3 (↑)
|
0.0023
|
Myosin, heavy chain 6, cardiac muscle, alpha
|
MYH6
|
NM_017239
|
17 (↑)
|
0.0004
|
14 0 (↑)
|
0.06
|
Plasminogen activator, urokinase
|
PLAU
|
NM_013085
|
5.37 (↑)
|
0.0008
|
5.56 (↑)
|
0.13
|
St3 beta-galactoside alpha-2,3-sialyltransferase 6
|
ST3GAL6
|
NM_207602
|
4.9 (↑)
|
0.0126
|
5.28 (↑)
|
0.05
|
Inhibin beta-a
|
INHBA
|
NM_017128
|
5.43(↑)
|
0.002
|
28.9 (↑)
|
0.04
|
Steroidogenic acute regulatory protein
|
STAR
|
NM_031558
|
14.57 (↓)
|
0.001
|
25.5 (↓)
|
0.0018
|
Hydroxysteroid (17-beta) dehydrogenase 7
|
HSD17B7
|
NM_017235
|
30.52 (↓)
|
0.0003
|
47.67 (↓)
|
0.006
|
Oxidative stress induced growth inhibitor 1
|
OSGIN1
|
NM_138504
|
26.98 (↓)
|
0.000022
|
21.57 (↓)
|
0.0047
|
Relaxin 1
|
RLN1
|
NM_013413
|
133.9 (↓)
|
0.0014
|
255.8 (↓)
|
0.019
|