Background
Results
Gene expression analysis of Cf and validation by real time RT-PCR
Gene | Abbreviation | Intensity | Mismatch | Ratio |
---|---|---|---|---|
Common up-regulated genes | of Cf | binding | Cf/Lfs | |
arylacetamide deacetylase (esterase) |
DAC
| 115.92 | P | 956.45 |
sparc/osteonectin (testican 3) |
SPOCK3
| 16.70 | P | 669.24 |
neuropeptide Y receptor Y1 |
NPYR
| 20.86 | P | 416.71 |
collagen, type XIV, alpha 1 (undulin) |
COL14A1
| 47.74 | P | 245.03 |
growth associated protein 43 |
B-50
| 23.52 | P | 232.10 |
procollagen C-endopeptidase enhancer 2 |
PCPE2
| 117.81 | P | 224.83 |
sorbin and SH3 domain containing 2 |
SORB2
| 10.65 | P | 192.25 |
myozenin 2 |
MYOZ2
| 6.53 | P | 139.50 |
serpin peptidase inhibitor, clade B (ovalbumin), member 2 transcript variant 2 |
PAI2
| 260.13 | P | 133.32 |
doublecortin-like kinase 1 |
DCLK
| 19.11 | P | 112.57 |
formyl peptide receptor-like 2 |
FPRL2
| 3.24 | P | 111.02 |
contactin associated protein-like 3 |
CASPR3
| 5.09 | P | 106.75 |
integrin, beta-like 1 (with EGF-like repeat domains) |
ITGBL1
| 13.35 | P | 82.92 |
collagen, type IV, alpha 6 |
COL4A6
| 76.71 | P | 77.06 |
myc target 1 |
MYCT1
| 28.15 | P | 73.88 |
S100 calcium binding protein A4 |
S100A4
| 103.88 | P | 72.30 |
phosphodiesterase 1A, calmodulin-dependent |
HSPDEA1
| 12.50 | P | 71.51 |
neurofilament, light polypeptide 68 kDa |
NEFL
| 5.71 | P | 69.33 |
ADAMTS-like 1 |
ADAMTSR1
| 3.24 | P | 68.55 |
early B-cell factor 1 |
EBF
| 4.57 | P | 60.80 |
ST6 (alpha-N-acetyl-neuraminyl-2,3-beta-galactosyl-1,3)-N-acetylgalactosaminide alpha-2,6-sialyltransferase 5 |
SIAT7E
| 0.02 | P | 3943.41 |
fibrillin 2 (congenital contractural arachnodactyly) |
FBN2
| 0.05 | P | 1035.17 |
fibroblast growth factor receptor 2 |
FGFR2
| 0.04 | P | 684.03 |
pregnancy specific beta-1-glycoprotein 5 |
PSG
| 0.07 | P | 349.77 |
Sal-like 1 (Drosophila) |
SALL1
| 0.03 | P | 312.29 |
membrane metallo-endopeptidase |
MME
| 0.05 | P | 274.25 |
odz, odd Oz/ten-m homolog 2 (Drosophila) |
TEN-M2
| 0.93 | P | 134.10 |
R-spondin 3 homolog (Xenopus laevis) |
RSPO3
| 0.4 | P | 70.16 |
bone morphogenetic protein 2 |
BMP2A
| 1.19 | P | 68.96 |
neuroligin 4, Y-linked |
NLGN4Y
| 0.09 | P | 68.62 |
matrix-remodelling associated 5 |
DKFZp564I1922
| 1.31 | P | 57.89 |
collagen, type IV, alpha 4 |
COL4A4
| 0.67 | P | 49.71 |
bradykinin receptor B1 |
BRADYB1
| 1.61 | P | 48.96 |
microfibrillar-associated protein 4 |
MFAP4
| 0.3 | P | 32.40 |
matrix metallopeptidase 3 (stromelysin 1, progelatinase) |
MMP-3
| 0.85 | P | 30.01 |
chromosome 13 open reading frame 15 |
RGC32
| 1.69 | P | 28.40 |
fibroblast growth factor 13 |
FGF13
| 0.38 | P | 28.15 |
ephrin receptor A5 |
EPHA5
| 0.40 | P | 25.68 |
interleukin 24 |
IL-24
| 1.68 | P | 25.27 |
Gene ontology (%) | Accession no. | Description | Ratio |
---|---|---|---|
Cellular metabolism (23.7%) | NM_000909 | neuropeptide Y receptor Y1 | 416.71 |
NM_004734 | doublecortin-like kinase 1 | 112.57 | |
NM_002961 | S100 calcium binding protein A4 | 72.30 | |
AF208502 | early B-cell factor 1 | 60.80 | |
AW004016 | ST6 beta-galactosamide alpha-2,6 sialyltransferase 2 | 59.04 | |
Protein binding (20.8%) | BF449063 | collagen, type XIV, alpha 1 (undulin) | 245.03 |
NM_002045 | growth associated protein 43 | 232.10 | |
AI659533 | sorbin and SH3 domain containing 2 | 192.25 | |
BF939176 | myozenin 2 | 139.5 | |
AF333769 | contactin associated protein-like 3 | 106.75 | |
Signal transduction (10.9%) | AW026543 | formyl peptide receptor-like 2 | 111.02 |
NM_004791 | integrin, beta-like 1 | 82.92 | |
NM_005019 | phosphodiesterase 1A | 71.51 | |
AF159570 | regulator of G-protein signalling 5 | 49.64 | |
W67461 | angiopoietin-like 1 | 49.16 | |
Extracellular region (7.8%) | NM_001086 | arylacetamide deacetylase (esterase) | 956.45 |
AI808090 | Sparc/osteonectin, cwcv and kazal-like domains proteoglycan (testican) 3 | 669.24 | |
NM_013363 | procollagen C-endopeptidase enhancer 2 | 224.83 | |
AI889941 | collagen, type IV, alpha 6 | 77.06 | |
NM_052866 | a disintegrin and metalloproteinase with thrombospondin motif-like 1 | 68.55 | |
Transcription factor (7.5%) | AF332197 | sine oculis homeobox homolog 2 | 44.20 |
AI681917 | iroquois homeobox protein 3 | 35.34 | |
NM_020639 | receptor-interacting serine-threonine kinase 4 | 29.41 | |
AK023792 | PBX/knotted 1 homeobox 2 | 29.40 | |
AF208967 | paternally expressed 3 | 26.74 | |
Protein modification (5.5%) | AW975934 | Titin | 32.01 |
NM_020639 | receptor-interacting serine-threonine kinase 4 | 29.41 | |
NM_000222 | v-kit Hardy-Zuckerman 4 feline sarcoma viral oncogene homolog | 25.21 | |
BF446673 | hemicentin 1 | 18.96 | |
NM_002848 | protein tyrosine phosphatase, receptor type, O | 14.58 | |
Receptor (4.8%) | BF941499 | G protein-coupled receptor 116 | 35.62 |
L35594 | ectonucleotide pyrophosphatase/phosphodiesterase 2 | 32.11 | |
NM_002820 | parathyroid hormone-like hormone | 30.44 | |
U61276 | jagged 1 (Alagille syndrome) | 19.60 | |
AK022548 | integrin, alpha 7 | 15.62 | |
Cell differentiation (4.3%) | AA343027 | Sema domain, immunoglobulin domain (Ig), short basic domain, secreted, (semaphorin) 3D | 67.06 |
NM_000216 | Kallmann syndrome 1 sequence | 27.91 | |
AL560266 | Fc receptor-like A | 19.61 | |
AA127691 | neuropilin 2 | 19.35 | |
NM_002506 | nerve growth factor, beta polypeptide | 19.11 | |
Cell adhesion (3.5%) | NM_006727 | cadherin 10, type 2 (T2-cadherin) | 55.43 |
NM_000072 | CD36 molecule (thrombospondin receptor) | 40.71 | |
AL573851 | endothelial cell adhesion molecule | 22.52 | |
N69091 | protocadherin 17 | 22.32 | |
AA489646 | protocadherin beta 13 | 19.36 | |
Cell cycle (2.4%) | NM_003914 | cyclin A1 | 34.8 |
NM_015714 | G0/G1switch 2 | 26.62 | |
NM_001759 | cyclin D2 | 16.45 | |
NM_001992 | coagulation factor II (thrombin) receptor | 13.90 | |
AK024082 | Tousled-like kinase 2 | 11.09 | |
Cell motility (2.2%) | NM_005045 | reelin | 17.30 |
NM_003062 | slit homolog 3 (Drosophila) | 5.12 | |
M21121 | chemokine (C-C motif) ligand 5 | 5.06 | |
NM_014795 | zinc finger E-box binding homeobox 2 | 4.85 | |
D45864 | protein kinase, cGMP-dependent, type I | 4.74 | |
Proteolysis (2.0%) | NM_001870 | carboxypeptidase A3 (mast cell) | 20.01 |
NM_024539 | ring finger protein 128 | 12.68 | |
AL574912 | protease, serine, 35 | 11.59 | |
NM_001873 | carboxypeptidase E | 9.45 | |
NM_000892 | kallikrein B, plasma (Fletcher factor) 1 | 6.40 | |
Cell proliferation (2.0%) | U77914 | jagged 1 (Alagille syndrome) | 16.76 |
NM_004624 | vasoactive intestinal peptide receptor 1 | 13.07 | |
BF514079 | Kruppel-like factor 4 (gut) | 12.89 | |
NM_001432 | epiregulin | 11.98 | |
BC003355 | laminin, alpha 5 | 10.36 | |
Apoptosis (1.6%) | NM_002575 | serpin peptidase inhibitor | 133.32 |
NM_000557 | growth differentiation factor 5 | 14.79 | |
NM_003728 | unc-5 homolog C (C. elegans) | 9.60 | |
BF432648 | tumor necrosis factor receptor superfamily | 8.73 | |
NM_003551 | non-metastatic cells 5, protein expressed in (nucleoside-diphosphate kinase) | 6.80 | |
ECM organization and biosynthesis (0.9%) | BC001186 | protocadherin beta 5 | 15.90 |
M25813 | tenascin XB | 12.46 | |
NM_002380 | matrilin 2 | 4.89 | |
AY140646 | periostin, osteoblast specific factor 2 | 4.89 | |
NM_004612 | transforming growth factor, beta receptor I (activin A receptor type II-like kinase, 53 kDa | 4.56 |
Gene ontology (%) | Accession no. | Description | Ratio |
---|---|---|---|
Cellular metabolism (31.6%) | NM_030965 | ST6 (alpha-N-acetyl-neuraminyl-2,3-beta-galactosyl-1,3)-N-acetylgalactosaminide alpha-2,6-sialyltransferase 5 | 3943.41 |
NM_022969 | fibroblast growth factor receptor 2 | 684.03 | |
AU152837 | Sal-like 1 (Drosophila) | 312.29 | |
NM_007287 | membrane metallo-endopeptidase | 73.38 | |
BF589322 | R-spondin 3 homolog (Xenopus laevis) | 70.16 | |
Signal transduction (17.8%) | NM_001200 | bone morphogenetic protein 2 | 68.96 |
NM_000710 | bradykinin receptor B1 | 48.96 | |
R72286 | microfibrillar-associated protein 4 | 32.40 | |
NM_004114 | fibroblast growth factor 13 | 28.15 | |
BE218107 | EPH receptor A5 | 25.68 | |
Transcription factor (11.5%) | AJ277914 | LIM homeobox 9 | 25.01 |
NM_001452 | forkhead box F2 | 18.08 | |
AA705845 | transducin-like enhancer of split 4 (E(sp1) homolog, Drosophila) | 17.16 | |
BG261252 | ecotropic viral integration site 1 | 11.58 | |
NM_020327 | activin A receptor, type IB | 9.32 | |
Protein modification (7.9%) | AF245505 | matrix-remodelling associated 5 | 57.89 |
AA725644 | ubiquitin specific peptidase 42 | 18.73 | |
NM_001982 | v-erb-b2 erythroblastic leukemia viral oncogene homolog 3 (avian) | 11.34 | |
AV727260 | protein tyrosine phosphatase, receptor type, D | 10.93 | |
NM_002570 | proprotein convertase subtilisin/kexin type 6 | 9.83 | |
Cell differentiation (6.2%) | NM_000641 | interleukin 11 | 17.51 |
BC006454 | growth arrest-specific 7 | 15.20 | |
M69148 | midkine (neurite growth-promoting factor 2) | 14.03 | |
NM_003991 | endothelin receptor type B | 10.85 | |
AI758962 | EPH receptor A4 | 7.15 | |
Cell adhesion (5.9%) | NM_001999 | fibrillin 2 | 1035.17 |
NM_014893 | neuroligin 4, Y-linked | 68.62 | |
AI694562 | collagen, type IV, alpha 3 | 22.21 | |
NM_005864 | embryonal Fyn-associated substrate | 8.44 | |
AU146651 | collagen, type XII, alpha 1 | 4.89 | |
Cell cycle (5.9%) | NM_014059 | chromosome 13 open reading frame 15 | 28.40 |
M19701 | retinoblastoma 1 (including osteosarcoma) | 4.93 | |
NM_002009 | fibroblast growth factor 7 | 4.44 | |
NM_014703 | Vpr (HIV-1) binding protein | 3.92 | |
AI983033 | DEAD/H box polypeptide 12 | 3.91 | |
Cell motility (4.7%) | NM_002784 | pregnancy specific beta-1-glycoprotein 9 | 69.22 |
X99268 | twist homolog 1 | 5.45 | |
NM_015180 | spectrin repeat containing, nuclear envelope 2 | 3.81 | |
AI990816 | laminin, alpha 1 | 3.59 | |
N90777 | neuropilin 2 | 3.57 | |
Cell proliferation (4.5%) | NM_016931 | NADPH oxidase 4 | 5.79 |
AF064826 | glypican 4 | 4.31 | |
NM_004525 | low density lipoprotein-related protein 2 | 3.85 | |
NM_001963 | epidermal growth factor (beta-urogastrone) | 3.70 | |
AF064103 | CDC14 cell division cycle 14 homolog A | 3.67 | |
Apoptosis (4.0%) | NM_006850 | interleukin 24 | 25.27 |
NM_002135 | nuclear receptor subfamily 4, group A, member 1 | 5.48 | |
NM_003823 | tumor necrosis factor receptor superfamily | 4.59 | |
AJ301610 | glutamate receptor, ionotropic, kainate 2 | 3.92 | |
NM_005809 | peroxiredoxin 2 | 3.90 |
Detection of PN expression in Cf and CCA tissues
Expression of PN in CCA tissues and clinicopathological relevance
Tissues | Total cases (n) | PN expression in fibroblasts | ||
---|---|---|---|---|
Negative | Positive | |||
Low | High | |||
CCA | 52 | 9 (17%) | 13 (25%) | 30 (58%) |
Benign liver tissue | 8 | 2 (25%) | 6 (75%) | 0 (0%) |
Hepatocellular carcinoma | 4 | 1 (25%) | 3 (75%) | 0 (0%) |
Variable (No. of patients) | No. of dead patients | Hazard ratio | 95% confidence interval |
P
|
---|---|---|---|---|
(5-yr survival cut-off) | (HR) | (CI) | ||
Age in years
| ||||
≤ 57 (25) | 21 | 1 | ||
>57 (26) | 22 | 1.25 | 0.62-2.48 | 0.533 |
PN expression
| ||||
Low (22) | 17 | 1 | ||
High (29) | 26 | 2.02 | 1.02-4.02 | 0.045* |
Lymph node metastasis
| ||||
Absence (36) | 28 | 1 | ||
Presence (15) | 15 | 3.13 | 1.54-6.35 | 0.002* |
Histological type
| ||||
Well-differentiated (20) | 16 | 1 | ||
Moderately-differentiated (8) | 8 | 2.77 | 1.10-6.98 | 0.031* |
Poorly-differentiated (8) | 7 | 1.64 | 0.63-4.29 | 0.310 |
Papillary (15) | 12 | 0.60 | 0.25-1.44 | 0.254 |
Tumor size (cm)
| ||||
≤ 5 (28) | 23 | 1 | ||
>5 (23) | 20 | 1.49 | 0.76-2.94 | 0.251 |
Variable | n | PN expression (%) | Univariate analysis | Multivariate analysis | ||
---|---|---|---|---|---|---|
Low | High |
P
| HR |
P
| ||
Age in years
| 0.575 | |||||
≤ 57 | 26 | 10 (38.5) | 16 (61.5) | 1 | ||
>57 | 26 | 12 (46.2) | 14 (53.8) | 0.899 | 0.870 | |
Sex
| 0.375 | |||||
Female | 20 | 10 (50.0) | 10 (50.0) | 1 | ||
Male | 32 | 12 (37.5) | 20 (62.5) | 1.638 | 0.452 | |
Histological type
| 0.083 | |||||
Well-differentiated | 21 | 8 (38.1) | 13 (61.9) | 1 | ||
Moderately-differentiated | 8 | 1 (12.5) | 7 (87.5) | 3.720 | 0.271 | |
Poorly-differentiated | 8 | 6 (75.0) | 2 (25.0) | 0.184 | 0.86 | |
Papillary | 15 | 7 (46.7) | 8 (53.3) | 0.611 | 0.505 | |
Tumor size (cm)
| 0.123 | |||||
≤ 5 | 29 | 15 (51.7) | 14 (48.3) | 1 | ||
>5 | 23 | 7 (30.4) | 16 (69.6) | 2.493 | 0.161 | |
Lymph node metastasis
| 0.830 | |||||
Absence | 37 | 16 (43.2) | 21 (56.8) | 1 | ||
Presence | 15 | 6 (40.0) | 9 (60.0) | 1.459 | 0.590 |
PN promotes proliferation and invasion of CCA cells
Knockdown of ITGα5 attenuates PN-induced proliferation and invasion
Discussion
Conclusions
Methods
Cells and culture condition
Gene expression profiling study and data analysis
Semi-quantitative real time PCR
Gene | Forward Primer | Reverse Primer | Size | Accession no. |
---|---|---|---|---|
5'-3' | 5'-3' | (bp) | ||
ADAM12
| tttgggggtcaacagttttc | agagctgggttcccttttgt | 191 | NM_003474 |
AREG
| tggggaaaagtccatgaaaa | tttcgttcctcagcttctcc | 174 | NM_001657 |
AGN2
| ccacctgaggaactgtctcg | ggtcttgctttggtccgtta | 191 | NM_001147 |
ER
| catatgggagaagggggagt | aagtgcaattacagagtgcaaaa | 166 | NM_001432 |
JAGL1
| gcctgccttaagtgaggaaa | gccaagaacaacacatcaaaga | 169 | U77914 |
LAMA5
| gtgatgaaaagcgggaatgt | acctccacagagcgagtcat | 221 | BC003355 |
NOV
| tgcaattccaagaaaatatcactg | cttggatttggagcttggaa | 167 | NM_002514 |
PDGF-A
| acacgagcagtgtcaagtgc | tctggttggctgctttaggt | 250 | X03795 |
PN
| cactctttgctcccaccaat | tcaaagactgctcctcccata | 157 | AY140646 |
RL
| tgctgaatttggggctactt | gggagatagggtcttcatcca | 198 | NM_005045 |
SCG2
| cccgaagaatgatgataccc | aaatgttgggatttgcttgg | 195 | NM_003469 |
ITGα
5
| agttgcatttccgagtctgg | ccaaacaggatggctaggat | 223 | NM_002205 |
β-actin
| cacactgtgcccatctacga | ctccttaatgtcacgcacga | 162 | X00351 |
gapdh
| ctcctcctgttcgacagtca | gttaaaagcagccctggtga | 140 | NM_002046 |