www.modernpathology.org
Open in
urlscan Pro
104.18.123.114
Public Scan
URL:
https://www.modernpathology.org/article/S0893-3952(22)01780-X/fulltext
Submission: On August 07 via api from US — Scanned from DE
Submission: On August 07 via api from US — Scanned from DE
Form analysis 2 forms found in the DOM
POST /action/doLogin?redirectUri=https%3A%2F%2Fwww.modernpathology.org%2Farticle%2FS0893-3952%2822%2901780-X%2Ffulltext
<form action="/action/doLogin?redirectUri=https%3A%2F%2Fwww.modernpathology.org%2Farticle%2FS0893-3952%2822%2901780-X%2Ffulltext" method="post"><input type="hidden" name="redirectUri"
value="https://www.modernpathology.org/article/S0893-3952(22)01780-X/fulltext"><input type="hidden" name="referer" value="/article/S0893-3952(22)01780-X/fulltext"><input type="hidden" name="ecommRedirect"><input type="hidden" name="code"
value="modpat-site"><input type="hidden" name="UX3LoginWidget" value="true"><input type="hidden" name="isPopup" value="true">
<div class="input-group">
<div class="label"><label for="login">Email/Username</label></div><input id="login" type="text" name="login" value="" size="15" class="login">
</div>
<div class="input-group">
<div class="label"><label for="password">Password</label></div><input id="password" type="password" name="password" value="" autocomplete="off" class="password"><a href="#" class="login__field__action js-show-password">Show</a>
<div class="actions"><a href="https://www.modernpathology.org/action/requestResetPassword" class="link show-request-reset-password">Forgot password?</a></div>
</div>
<div class="remember"><input type="checkbox" name="savePassword" id="6ee85045-2441-4b5c-8a4b-4c078d548375-remember" value="1" checked="checked"><label for="6ee85045-2441-4b5c-8a4b-4c078d548375-remember">Remember me</label></div>
<div class="submit" disabled="disabled"><input type="submit" name="submit" value="Log in" class="button submit primary" disabled="disabled"></div>
</form>POST /action/requestResetPassword
<form action="/action/requestResetPassword" method="post" class="request-reset-password-form"><input type="hidden" name="platform"><input type="hidden" name="requestResetPassword" value="true"><input type="hidden" name="websiteName"
value="Modern Pathology"><input type="hidden" name="codeSite" value="modpat-site">
<div class="input-group">
<div class="label"><label for="reset-password-email">Email*</label></div><input id="reset-password-email" type="text" name="email" value="" size="15" class="email">
</div>
<div class="submit" disabled="disabled"><input type="submit" name="submit" value="Submit" disabled="disabled" class="button primary submit"></div>
</form>Text Content
Skip to Main Content
LOGIN TO YOUR ACCOUNT
Email/Username
Password
Show
Forgot password?
Remember me
Don’t have an account?
Create a Free Account
If you don't remember your password, you can reset it by entering your email
address and clicking the Reset Password button. You will then receive an email
that contains a secure link for resetting your password
Email*
If the address matches a valid account an email will be sent to __email__ with
instructions for resetting your password
Cancel
Open GPT Console
Open Oracle Keywords
Refresh Values
Property Value Status
Version
Ad File
Disable Ads Flag
Environment
Moat Init
Moat Ready
Contextual Ready
Contextual URL
Contextual Initial Segments
Contextual Used Segments
AdUnit
SubAdUnit
Custom Targeting
Ad Events
Invalid Ad Sizes
* Submit USCAP Access
* Log in
* Register
* Log in
* Submit USCAP Access
* Log in
* Subscribe
* Claim
Access provided by
Article| Volume 19, ISSUE 12, P1546-1554, January 2006
Download Full Issue
Download started.
Ok
Positional expression profiling indicates candidate genes in deletion hotspots
of hepatocellular carcinoma
* PDF [755 KB]PDF [755 KB]
* Figures
* Figure Viewer
* Download Figures (PPT)
* Save
* Add To Online LibraryPowered ByMendeley
* Add To My Reading List
* Export Citation
* Create Citation Alert
* Share
Share on
* Twitter
* Facebook
* Linked In
* Sina Weibo
* Email
* more
* Reprints
* Request
* Top
POSITIONAL EXPRESSION PROFILING INDICATES CANDIDATE GENES IN DELETION HOTSPOTS
OF HEPATOCELLULAR CARCINOMA
* Kathy Y-Y Chan
Kathy Y-Y Chan
Affiliations
Department of Anatomical and Cellular Pathology, The Chinese University of
Hong Kong, Shatin, NT, SAR Hong Kong, China
Search for articles by this author
* Paul B-S Lai
Paul B-S Lai
Affiliations
Department of Surgery, The Chinese University of Hong Kong, Shatin, NT, SAR
Hong Kong, China
Search for articles by this author
* Jeremy A Squire
Jeremy A Squire
Affiliations
Department of Medical Biophysics and Laboratory Medicine and Pathobiology,
University of Toronto, Toronto, Ontario, Canada
Search for articles by this author
* Ben Beheshti
Ben Beheshti
Affiliations
Department of Medical Biophysics and Laboratory Medicine and Pathobiology,
University of Toronto, Toronto, Ontario, Canada
Search for articles by this author
*
* Navy L-Y Wong
Navy L-Y Wong
Affiliations
Department of Anatomical and Cellular Pathology, The Chinese University of
Hong Kong, Shatin, NT, SAR Hong Kong, China
Search for articles by this author
* Shirley M-H Sy
Shirley M-H Sy
Affiliations
Department of Anatomical and Cellular Pathology, The Chinese University of
Hong Kong, Shatin, NT, SAR Hong Kong, China
Search for articles by this author
* Nathalie Wong
Nathalie Wong
Contact
Affiliations
Department of Anatomical and Cellular Pathology, The Chinese University of
Hong Kong, Shatin, NT, SAR Hong Kong, China
Search for articles by this author
* Show all authors
Open AccessDOI:https://doi.org/10.1038/modpathol.3800674
Plum Print visual indicator of research metrics
PlumX Metrics
* Citations
* Citation Indexes: 41
* Captures
* Exports-Saves: 1
* Readers: 20
see details
Previous ArticleChronic myelomonocytic leukemia: the role of bone …
Next ArticleExpression of the plasmacytoid dendritic cell marker …
* Abstract
* Main
* Materials and methods
* Results
* Discussion
* Accession codes
* References
* Article info
* Figures
* Tables
* Related Articles
ABSTRACT
Molecular characterizations of hepatocellular carcinoma have indicated frequent
allelic losses on chromosomes 4q, 8p, 16q and 17p, where the minimal deleted
regions have been further defined on 4q12–q23, 4q31–q35, 8p21–p22, 16q12.1–q23.1
and 17p13. Despite these regions are now well-recognized in early liver
carcinogenesis, few underlying candidate genes have been identified. In an
effort to define affected genes within common deleted loci of hepatocellular
carcinoma, we conducted transcriptional mapping by high-resolution cDNA
microarray analysis. In 20 hepatocellular carcinoma cell lines and 20 primary
tumors studied, consistent downregulations of novel transcripts were highlighted
throughout the entire genome and within sites of frequent losses. The
array-derived candidates including fibrinogen gamma peptide (FGG, at 4q31.3),
vitamin D binding protein (at 4q13.3), fibrinogen-like 1 (FGL1, at 8p22),
metallothionein 1G (MT1G, at 16q12.2) and alpha-2-plasmin inhibitor (SERPINF2,
at 17p13) were confirmed by quantitative reverse transcription–polymerase chain
reaction, which also indicated a more profound downregulation of FGL1, MT1G and
SERPINF2 relative to reported tumor-suppressor genes, such as DLC1 (8p22),
E-cadherin (16q22.1) and TP53 (17p13.1). In primary hepatocellular carcinoma
examined, a significant repression of MT1G by more than 100-fold was indicated
in 63% of tumors compared to the adjacent nonmalignant liver (P=0.0001).
Significant downregulations of FGG, FGL1 and SERPINF2 were also suggested in 30,
23 and 33% of cases, respectively, compared to their nonmalignant counterparts
(P<0.016). In summary, transcriptional mapping by microarray indicated a number
of previously undescribed downregulated genes in hepatocellular carcinoma, and
highlighted potential candidates within common deleted regions.
ADVERTISEMENT
SCROLL TO CONTINUE WITH CONTENT
* hepatocellular carcinoma
* deletion hotspots
* cDNA array
* transcriptional mapping
MAIN
Hepatocellular carcinoma currently ranks the fifth most common malignancy
worldwide.
1
* Okuda K
Hepatocellular carcinoma.
J Hepatol. 2000; 32: 225-237
10.1016/S0168-8278(00)80428-6
* Abstract
* Full Text PDF
* PubMed
* Google Scholar
,
2
* Lau WY
Primary liver tumors.
Semin Surg Oncol. 2000; 19: 135-144
10.1002/1098-2388(200009)19:2<135::AID-SSU6>3.0.CO;2-A
* Crossref
* PubMed
* Scopus (56)
* Google Scholar
It carries a high cancer morbidity and mortality because by the time of clinical
presentation, more than 80% of patients are at the advance inoperable stage.
2
* Lau WY
Primary liver tumors.
Semin Surg Oncol. 2000; 19: 135-144
10.1002/1098-2388(200009)19:2<135::AID-SSU6>3.0.CO;2-A
* Crossref
* PubMed
* Scopus (56)
* Google Scholar
,
3
* Lai EC
* Fan ST
* Lo CM
Hepatic resection for hepatocellular carcinoma. An audit of 343 patients.
Ann Surg. 1995; 221: 291-298
10.1097/00000658-199503000-00012
* Crossref
* PubMed
* Scopus (404)
* Google Scholar
The low efficacy of current screening regime by serum alpha-fetoprotein
measurements and transabdominal ultrasound imaging has rendered most patients
not being diagnosed in time for curative surgery. Thus, underpinning the genetic
events associated with hepatocellular carcinoma is expected to improve our
understanding on liver carcinogenesis and also potentially provide biomarkers
that are of diagnosis and prognostic values.
Molecular studies using loss of heterozygosity analysis and comparative genomic
hybridization have revealed recurrent chromosomal changes in hepatocellular
carcinoma including losses on 1p, 4q, 6q, 8p, 11q, 13q, 16q and 17p.
4
* Wong N
* Lai P
* Lee SW
Assessment of genetic changes in hepatocellular carcinoma by comparative genomic
hybridization analysis: relationship to disease stage, tumor size, and
cirrhosis.
Am J Pathol. 1999; 154: 37-43
10.1016/S0002-9440(10)65248-0
* Abstract
* Full Text
* Full Text PDF
* PubMed
* Scopus (257)
* Google Scholar
,
5
* Marchio A
* Meddeb M
* Pineau P
Recurrent chromosomal abnormalities in hepatocellular carcinoma detected by
comparative genomic hybridization.
Genes Chromosomes Cancer. 1997; 18: 59-65
10.1002/(SICI)1098-2264(199701)18:1<59::AID-GCC7>3.0.CO;2-0
* Crossref
* PubMed
* Scopus (261)
* Google Scholar
,
6
* Kusano N
* Shiraishi K
* Kubo K
Genetic aberrations detected by comparative genomic hybridization in
hepatocellular carcinomas: their relationship to clinicopathological features.
Hepatology. 1999; 29: 1858-1862
10.1002/hep.510290636
* Crossref
* PubMed
* Scopus (197)
* Google Scholar
As diminutions on 4q, 8p, 16q and 17p have been described in the nontumorous
cirrhotic nodules and early preneoplastic liver dysplasia, these changes have
been further implicated in the early carcinogenetic events of hepatocellular
carcinoma.
4
* Wong N
* Lai P
* Lee SW
Assessment of genetic changes in hepatocellular carcinoma by comparative genomic
hybridization analysis: relationship to disease stage, tumor size, and
cirrhosis.
Am J Pathol. 1999; 154: 37-43
10.1016/S0002-9440(10)65248-0
* Abstract
* Full Text
* Full Text PDF
* PubMed
* Scopus (257)
* Google Scholar
,
5
* Marchio A
* Meddeb M
* Pineau P
Recurrent chromosomal abnormalities in hepatocellular carcinoma detected by
comparative genomic hybridization.
Genes Chromosomes Cancer. 1997; 18: 59-65
10.1002/(SICI)1098-2264(199701)18:1<59::AID-GCC7>3.0.CO;2-0
* Crossref
* PubMed
* Scopus (261)
* Google Scholar
,
6
* Kusano N
* Shiraishi K
* Kubo K
Genetic aberrations detected by comparative genomic hybridization in
hepatocellular carcinomas: their relationship to clinicopathological features.
Hepatology. 1999; 29: 1858-1862
10.1002/hep.510290636
* Crossref
* PubMed
* Scopus (197)
* Google Scholar
It has been long recognized that delineation of the smallest overlapping regions
in nonrandom genomic regions holds value in defining critical loci that are
likely to harbor causative tumor-suppressor or proto-oncogene(s). In the case of
hepatocellular carcinoma, only few tumor-suppressor genes have been described to
the smallest overlapping regions. For example, deleted in liver cancer 1 (DLC1)
on 8p21–p22,
7
* Yuan BZ
* Miller MJ
* Keck CL
Cloning, characterization, and chromosomal localization of a gene frequently
deleted in human liver cancer (DLC-1) homologous to rat RhoGAP.
Cancer Res. 1998; 58 (9605766): 2196-2199
* PubMed
* Google Scholar
E-cadherin (CDH1) on 16q12.1–q23.1
8
* Lau SH
* Guan XY
Cytogenetic and molecular genetic alterations in hepatocellular carcinoma.
Acta Pharmacol Sin. 2005; 26: 659-665
10.1111/j.1745-7254.2005.00126.x
* Crossref
* PubMed
* Scopus (34)
* Google Scholar
and tumor protein p53 (TP53) on 17p13.
9
* Zondervan PE
* Wink J
* Alers JC
Molecular cytogenetic evaluation of virus-associated and non-viral
hepatocellular carcinoma: analysis of 26 carcinomas and 12 concurrent
dysplasias.
J Pathol. 2000; 192: 207-215
10.1002/1096-9896(2000)9999:9999<::AID-PATH690>3.0.CO;2-#
* Crossref
* PubMed
* Scopus (89)
* Google Scholar
Candidate genes in the smallest overlapping regions 4q12–q23
10
* Yeh SH
* Chen PJ
* Lai MY
Allelic loss on chromosomes 4q and 16q in hepatocellular carcinoma: association
with elevated alpha-fetoprotein production.
Gastroenterology. 1996; 110: 184-192
10.1053/gast.1996.v110.pm8536855
* Abstract
* Full Text PDF
* PubMed
* Scopus (81)
* Google Scholar
and 4q31–q35, on the other hands, remains undescribed.
11
* Chang J
* Kim NG
* Piao Z
Assessment of chromosomal losses and gains in hepatocellular carcinoma.
Cancer Lett. 2002; 182: 193-202
10.1016/S0304-3835(02)00083-6
* Crossref
* PubMed
* Scopus (33)
* Google Scholar
,
12
* Yasui K
* Arii S
* Zhao C
TFDP1, CUL4A, and CDC16 identified as targets for amplification at 13q34 in
hepatocellular carcinomas.
Hepatology. 2002; 35: 1476-1484
10.1053/jhep.2002.33683
* Crossref
* PubMed
* Scopus (153)
* Google Scholar
As regions of aberrant genomic loci can harbor more than one tumor-related
genes, such as RASSF1A, MLH1, TGFBR2 and BLU on chromosome 3p21,
13
* Chow LS
* Lo KW
* Kwong J
RASSF1A is a target tumor suppressor from 3p21.3 in nasopharyngeal carcinoma.
Int J Cancer. 2004; 109: 839-847
10.1002/ijc.20079
* Crossref
* PubMed
* Scopus (99)
* Google Scholar
,
14
* Wong TS
* Tang KC
* Kwong DL
Differential gene methylation in undifferentiated nasopharyngeal carcinoma.
Int J Oncol. 2003; 22 (12632081): 869-874
* PubMed
* Google Scholar
,
15
* Kok K
* Naylor SL
* Buys CH
Deletions of the short arm of chromosome 3 in solid tumors and the search for
suppressor genes.
Adv Cancer Res. 1997; 71: 27-92
10.1016/S0065-230X(08)60096-2
* Crossref
* PubMed
* Google Scholar
,
16
* Qiu GH
* Tan LK
* Loh KS
The candidate tumor suppressor gene BLU, located at the commonly deleted region
3p21.3, is an E2F-regulated, stress-responsive gene and inactivated by both
epigenetic and genetic mechanisms in nasopharyngeal carcinoma.
Oncogene. 2004; 23: 4793-4806
10.1038/sj.onc.1207632
* Crossref
* PubMed
* Scopus (122)
* Google Scholar
the existence of more than one tumor-suppressor gene within common deleted sites
of hepatocellular carcinoma cannot be ruled out.
The microarray technology has greatly facilitated the investigation of whole
genome expression analysis. Large-scale transcriptional profiling has so far
been reported in multiple cancers including hepatocellular carcinoma.
17
* Alon U
* Barkai N
* Notterman DA
Broad patterns of gene expression revealed by clustering analysis of tumor and
normal colon tissues probed by oligonucleotide arrays.
Proc Natl Acad Sci USA. 1999; 96: 6745-6750
10.1073/pnas.96.12.6745
* Crossref
* PubMed
* Scopus (3385)
* Google Scholar
,
18
* Nagai H
* Terada Y
* Tajiri T
Characterization of liver-cirrhosis nodules by analysis of gene-expression
profiles and patterns of allelic loss.
J Hum Genet. 2004; 49: 246-255
10.1007/s10038-004-0141-8
* Crossref
* PubMed
* Scopus (11)
* Google Scholar
,
19
* Okabe H
* Satoh S
* Kato T
Genome-wide analysis of gene expression in human hepatocellular carcinomas using
cDNA microarray: identification of genes involved in viral carcinogenesis and
tumor progression.
Cancer Res. 2001; 61 (11280777): 2129-2137
* PubMed
* Google Scholar
,
20
* Xu XR
* Huang J
* Xu ZG
Insight into hepatocellular carcinogenesis at transcriptome level by comparing
gene expression profiles of hepatocellular carcinoma with those of corresponding
noncancerous liver.
Proc Natl Acad Sci USA. 2001; 98: 15089-15094
10.1073/pnas.241522398
* Crossref
* PubMed
* Scopus (326)
* Google Scholar
With regard to hepatocellular carcinoma, most microarray studies have emphasized
on determining the profiles that allow differentiation of stepwise progressions
from the preneoplastic lesions and in defining expression patterns associated
with clinical subsets such as the prediction of drug resistance.
21
* Lee JS
* Thorgeirsson SS
Genetic profiling of human hepatocellular carcinoma.
Semin Liver Dis. 2005; 25: 125-132
10.1055/s-2005-871192
* Crossref
* PubMed
* Scopus (53)
* Google Scholar
Information on gene expression changes within regions of aberrant genomic loci,
on the other hand, has been minimal. In this study, we have attempted to
delineate the deregulated transcripts in regional imbalances of hepatocellular
carcinoma, and especially in common deletions that have been described in the
early carcinogenetic events. A detail investigation was undertaken using a
high-resolution 19K cDNA microarray that allowed an average mapping resolution
of ∼162 kb throughout the whole genome. Our array study examined a large panel
of hepatocellular carcinoma cell lines that included early passages of
hepatocellular carcinoma cultures and established cell lines. Analysis of cell
lines can potentially increase detection sensitivity by minimizing secondary
effects of the tumor microenvironments. However, despite cell lines represent a
homogenous population of malignant hepatocytes; induced gene expressions from
prolonged in vitro culture might correspond to a major inadequacy in identifying
representative genes. To compensate for this potential limitation, we have also
examined a cohort of primary hepatocellular carcinoma tumors, which is expected
to provide representative results of clinical situation. Consistent
downregulated transcripts found in both cell lines and tumors that were assigned
to regions of deletion hotspots were further subjected to quantitative reverse
transcription–polymerase chain reaction (qRT-PCR) validations. Results obtained
were also compared to recognize tumor-suppressor genes such as DLC1, CDH1 and
TP53.
MATERIALS AND METHODS
CELL LINES
Seven hepatocellular carcinoma cell lines, Hep3B, PLC/PRF/5, SNU387, SNU398,
SNU423, SNU449 and SNU475, were obtained from the American Type Culture
Collection (Rockville, MD, USA). According to recommendations, Hep3B and
PLC/PRF/5 were cultured in DMEM medium containing 10% fetal bovine serum (FBS)
and 100 IU/ml penicillin and 100 U/ml streptomycin (Gibco BRL, Grand Island, NY,
USA), while SNU387, SNU398, SNU423, SNU449, SNU475 were maintained in RPMI
median containing 10% FBS and 100 IU/ml penicillin and 100 U/ml streptomycin
(Gibco BRL). Thirteen hepatocellular carcinoma cell lines (HKCI-1 to 10, and -C1
to C3) were established from our laboratory, eight of which HKCI-1, -2, -3, -4,
-5 and HKCI-C1, -C2 and -C3 have been previously reported.
22
* Wong N
* Chan KY
* Macgregor PF
Transcriptional profiling identifies gene expression changes associated with
IFN-alpha tolerance in hepatitis C-related hepatocellular carcinoma cells.
Clin Cancer Res. 2005; 11 (15709204): 1319-1326
* Crossref
* PubMed
* Scopus (21)
* Google Scholar
,
23
* Pang E
* Wong N
* Lai PB
Consistent chromosome 10 rearrangements in four newly established human
hepatocellular carcinoma cell lines.
Genes Chromosomes Cancer. 2002; 33: 150-159
10.1002/gcc.1220
* Crossref
* PubMed
* Scopus (23)
* Google Scholar
,
24
* Pang E
* Wong N
* Lai PB
A comprehensive karyotypic analysis on a newly developed hepatocellular
carcinoma cell line, HKCI-1, by spectral karyotyping and comparative genomic
hybridization.
Cancer Genet Cytogenet. 2000; 121: 9-16
10.1016/S0165-4608(99)00247-2
* Abstract
* Full Text
* Full Text PDF
* PubMed
* Scopus (19)
* Google Scholar
,
25
* Chan KY
* Wong N
* Lai PB
Transcriptional profiling on chromosome 19p indicated frequent downregulation of
ACP5 expression in hepatocellular carcinoma.
Int J Cancer. 2005; 114: 902-908
10.1002/ijc.20684
* Crossref
* PubMed
* Scopus (19)
* Google Scholar
Using the same methodology described,
22
* Wong N
* Chan KY
* Macgregor PF
Transcriptional profiling identifies gene expression changes associated with
IFN-alpha tolerance in hepatitis C-related hepatocellular carcinoma cells.
Clin Cancer Res. 2005; 11 (15709204): 1319-1326
* Crossref
* PubMed
* Scopus (21)
* Google Scholar
,
23
* Pang E
* Wong N
* Lai PB
Consistent chromosome 10 rearrangements in four newly established human
hepatocellular carcinoma cell lines.
Genes Chromosomes Cancer. 2002; 33: 150-159
10.1002/gcc.1220
* Crossref
* PubMed
* Scopus (23)
* Google Scholar
,
24
* Pang E
* Wong N
* Lai PB
A comprehensive karyotypic analysis on a newly developed hepatocellular
carcinoma cell line, HKCI-1, by spectral karyotyping and comparative genomic
hybridization.
Cancer Genet Cytogenet. 2000; 121: 9-16
10.1016/S0165-4608(99)00247-2
* Abstract
* Full Text
* Full Text PDF
* PubMed
* Scopus (19)
* Google Scholar
we have newly established five additional cell lines (HKCI-6, -7, -8, -9 and
-10). The early passages 20–25 of the HKCI series of cell lines were utilized in
the microarray study. These cell lines were maintained in complete medium
containing RPMI 1640 glutamax with HEPES buffer supplemented with 10% FBS, 100
IU/ml penicillin, 100 U/ml streptomycin, 10 ng/ml selenium, 10 μg/ml transferrin
and 10 μg/ml insulin. All cultures were maintained in a humidified incubator at
37°C in an atmosphere of 5% CO2.
PATIENTS
Tumorous liver tissue was collected from 38 patients (aged 24–78 years, 84%
male) who underwent curative surgery for hepatocellular carcinoma at the Prince
of Wales Hospital, Hong Kong. A corresponding adjacent nonmalignant liver tissue
was secured for 30 patients. Informed consent was obtained from each patient
recruited. Patients were predominantly hepatitis B carriers (95%) with
underlying liver cirrhosis indicated in 84% of cases. According to the American
Joint Committee on Cancer tumor staging criteria,
26
* Fleming ID
American Cancer Society, American College of Surgeons, National Cancer Institute
(US), American Joint Committee on Cancer, American College of Radiology, College
of American Pathologists.
AJCC Cancer Staging Manual. Lippincott-Raven, Philadelphia1997
* Google Scholar
one case was graded as stage I, 20 cases as stage II, 11 as stage III and six as
stage IV.
Microarray analysis was conducted on 20 hepatocellular carcinoma tumors, of
which retrievable tumor RNA from 12 cases was further utilized in qRT-PCR
validations. An additional 18 cases was further investigated by qRT-PCR,
totaling 30 paired cases being assessed for the array-derived candidate genes.
MICROARRAY ANALYSIS
The expression array experiments were carried out according to the method
previously described from our laboratory.
25
* Chan KY
* Wong N
* Lai PB
Transcriptional profiling on chromosome 19p indicated frequent downregulation of
ACP5 expression in hepatocellular carcinoma.
Int J Cancer. 2005; 114: 902-908
10.1002/ijc.20684
* Crossref
* PubMed
* Scopus (19)
* Google Scholar
Briefly, 10 μg of Trizol extracted total RNA from cell lines and primary tumors
was reverse-transcribed by AncT mRNA primer using Superscript II reverse
transcriptase (Invitrogen, Carlsbad, CA, USA). A pool of three normal liver
samples was used as reference purchased from three different companies (Ambion,
Austin, TX, USA; Strategene, La Jolla, CA, USA; CloneTech, Pale Alto, CA, USA).
Following fluorescence labeling of the transcribed cDNAs with Cy5-dCTP or
Cy3-dCTP, the labeled cDNAs were mixed with calf thymus DNA, poly(dA), and yeast
tRNA in Dighyb buffer (Roche Diagnostics, Mannheim, Germany) and hybridized onto
cDNA microarray slides (Ontario Cancer Institute, Toronto, Canada). The 19K cDNA
microarray employed contains 19 008 sequence-verified human genes and EST
sequences that allowed an average resolution of ∼162 kb throughout the genome.
Hybridization was carried out at 37°C for 16 h. Following posthybridization
washes in 1 × SCC/0.1%SDS at 50°C, Cy5 and Cy3 hybridized signals were captured
by ScanArray 5000 (GSI Lumonics, Packard BioScience, Pangbourne, UK). Raw images
acquired were analyzed and quantified by the GenePix Pro 4.0 (Axon, Union City,
CA, USA). Custom software Normalize Suite v1.56 was used for normalization of
Cy3 and Cy5 intensities, data combination of dye swap experiments and
integration of signal ratios determined with physical map locations of cDNAs in
sequential order of megabase distances (http://www.utoronto.ca/cancyto/).
27
* Beheshti B
* Braude I
* Marrano P
Chromosomal localization of DNA amplifications in neuroblastoma tumors using
cDNA microarray comparative genomic hybridization.
Neoplasia. 2003; 5: 53-62
10.1016/S1476-5586(03)80017-9
* Crossref
* PubMed
* Google Scholar
QRT-PCR
Trizol extracted total RNA from cell lines, primary hepatocellular carcinoma and
adjacent nonmalignant liver tissues was subjected to DNase treatment to
eliminate possible carryover of genomic DNA. Control experiments by minus-RT–PCR
were also performed to ensure RNA quality. First-strand cDNA was prepared from 2
μg total RNA using random hexanucleotide primer and MultiScribe reverse
transcriptase (Applied Biosystems, Foster City, CA, USA). Quantitative PCR
(qPCR) was performed in triplicate assays using the TaqMan Universal Master Mix
(Applied Biosystems). TaqMan assays targeting vitamin D binding protein
precursor (GC, Hs00167096_m1), alpha-2-plasmin inhibitor (SERPINF2,
Hs00168686_m1), deleted in liver cancer 1 (DLC1, Hs00183436_m1), E-cadherin
(CDH1, Hs00170423_m1) fibrinogen-like 1 (FGL1, Hs00189514_m1), tumor protein p53
(TP53, Hs00153349_m1) and fibrinogen gamma peptide (FGG, Hs00241038_m1) were
acquired (Applied Biosystems). TaqMan probes and primers for metallothionein 1G
(MT1G) (GenBank accession number NM_005950) was designed using the Primer
Express V2.0 software (forward primer 5′-TGCCGCTAGGTGTCT-3′, reverse primer
5′-CGATGCCCCTTTGCAGAT-3′, MGB probe 5′ FAM-CTGTGCCAAGTGTGC-3′). TaqMan gene
expression assay for 18 s rRNA (Hs99999901_s1) was used as endogenous control.
The two steps PCR conditions were 2 min at 50°C, 10 min at 95°C, 45 cycles with
30 s at 95°C, and 1 min at 55°C. The amplification for the predesign assays was
performed for 45 cycles with denaturation at 94°C for 30 s, annealing at 60°C
for 1 min. The emission intensity was detected by the iCycler detection system
(BioRad Laboratories, Hercules, CA, USA). Relative quantification values
expressed as threshold cycle (Ct) were averaged and subsequently used to
determine the relative expression ratios between cases. The median gene
expressions of 8 normal livers were used for comparison. A no template negative
control was also included in each experiment.
STATISTICAL ANALYSIS
The differences in gene expression levels between hepatocellular carcinoma
tumors and surrounding nonmalignant livers were analyzed by the Wilcoxon signed
rank test. The statistical significance between tumor stages was measured by the
Mann–Whitney U-test. All analysis was performed with Prism software (GraphPad
Software, San Diego, CA, USA). A P-value less than 0.05 was considered
significant.
RESULTS
DOWNREGULATED GENES IN DELETION HOTSPOTS
Gene expression profiling in primary tumors and cell lines indicated deregulated
transcripts throughout the whole genome. Remarkably, profound repressions of
distinct genes were indicated in common regions of allelic losses. Upregulated
expressions, on the other hand, were less prominent and often associated with a
high background-to-noise ratio. In 20 cell lines, 131 transcripts were found to
be commonly downregulated, whereas frequent downregulations of 126 genes were
suggested in 20 hepatocellular carcinoma tumors examined. To further define
important genes, concordant transcripts that were repressed in both primary
tumors and cell lines were scored. Using a median cutoff threshold of >3-fold
reduction and an occurrence of >50%, 35 common candidate genes were indicated in
both series (Table 1).
Table 1Common downregulated genes in hepatocellular carcinoma tumors and cell
lines from transcriptional profiling
CytobandAccession no.NameSymbol20 Tumors20 Cell linesMedian fold
reductionPercentage cases ≥3-fold (%)Median fold reductionPercentage cases
≥3-fold (%)1p13.3W91952Vav 3
oncogeneVAV33.50533.48671p12BI9183533-hydroxy-3-methylglutaryl-Coenzyme A
synthase
2HMGCS23.59606.89801q42.2H22747AngiotensinogenAGT4.10559.20752p24.1BG566740Apolipoprotein
BAPOB3.59603.24502p22.2W01373CCAAT/enhancer binding protein
zetaCEBPZ4.28603.76753p24.2W16685N-glycanase 1NGLY14.01683.15603q21.3H71112MCM2
minichromosome maintenance deficient
2MCM24.70655.58743q24–q25.1H86642CeruloplasminCP6.357512.25953q25.1T83911Transmembrane
4 superfamily member 4TM4SF43.30563.35533q25.32W17370G elongation factor,
mitochondrial 1GFM15.087728.71100*4q13.3R88884Vitamin D binding
proteinGC7.377410.1567*4q31.3BG616563Fibrinogen gamma
chainFGG11.799352.541004q32.1H38897Tryptophan
2,3-dioxygenaseTDO23.06504.56675p13.2T96003LMBR1 domain containing
2LMBRD24.91946.631006p21.33T87339Apolipoprotein
MAPOM3.11505.12686p12.2BE796134Glutathione S-transferase
A2GSTA24.00676.36957p15.3R69654Oxysterol binding protein-like
3OSBPL37.52653.51507q22.1R96774Cytochrome P450, family 3, subfamily A,
polypeptide 7CYP3A75.855613.8792*8p22–p21.3BG618635Fibrinogen-like
1FGL14.315310.88808q12.1BM925604RAB2, member RAS oncogene
familyRAB23.33623.165510q26.3T97051Mitochondrial short-chain enoyl-coenzyme
AECHS13.58633.065811p15.4H12367Beta globinHBB5.44747.649311p15.1H45773Serum
amyloid A2SAA13.10553.776512q13.3R35197Hydroxysteroid
dehydrogenaseRODH5.025812.319512q21.33R87181DecorinDCN7.307513.217712q24.13BM805738Serine
dehydrataseSDS6.48698.349014q12N46702Syntaxin binding protein
6STXBP63.56643.4957*16q12.2H57208Metallothionein
1GMT1G9.29753.1060*17p13.3H69261Alpha-2-plasmin
inhibitorSERPINF24.71557.699017q11.2H29155VitronectinVTN11.96757.237817q23.2BM471342Myotubularin
related protein 4MTMR47.17935.458018q12.1H25541Ring finger protein
138RNF13812.15687.559519q13.33R08306Activating transcription factor
5ATF55.21655.368020p12.3W91932Proliferating cell nuclear
antigenPCNA3.34574.096720q11.23H24115Transglutaminase 2TGM24.66703.0153
*Bold represents candidate genes identified within the common deleted regions of
hepatocellular carcinoma.
* Open table in a new tab
Alignment of cytogenetic information with expression profiling suggested the 35
genes located on 27 subchromosomal regions (Table 1). In particular, five genes
resided within the deletion hotspots that have implicated in the early
carcinogenetic events of hepatocellular carcinoma (Figure 1). These being
vitamin D binding protein (GC) within smallest overlapping region 4q12–q23,
fibrinogen gamma peptide (FGG) in 4q31–q35, FGL1 in 8p21–p22, metallothionein 1G
(MT1G) in 16q12.1–q23.1 and alpha-2-plasmin inhibitor (SERPINF2) in 17p13. A
parallel comparative genomic hybridization analysis on 20 hepatocellular
carcinoma cell lines indicated regional losses of 4q12–q23 and 4q31–q35 in 55%
(11/20 cell lines) and 75% (15/20 cell lines) of cases, respectively. Regional
chromosomal loss at 8p21–p22 was found in 45% of cases (9/20 cell lines),
whereas deletions on both 16q12–q23 and 17p13 were suggested in 30% (6/20 cell
lines). A concordant downregulation of candidate genes and regional loss in cell
lines was suggested in 65% for FGG, 45% for GC and FGL1, 27% for MT1G and 25%
for SERPINF2.
Figure 1Positional expression profiling on chromosomes 4q, 8p, 16q and 17p in
hepatocellular carcinoma cell lines and tumors. Relative expression levels as
fold reductions determined for each transcript by microarray analysis on 20
hepatocellular carcinoma cell lines and 20 tumors were plotted along physical
map location of each cDNA clone. Candidate genes that showed marked
downregulations in more than 50% of both primary tumors and cell lines were
highlighted by bracket. The smallest overlapping region of common losses was
indicated as green bar next to the ideogram of each chromosome arm.
* View Large Image
* Figure Viewer
* Download Hi-res image
* Download (PPT)
VALIDATION IN CELL LINES AND TUMORS
The mRNA levels of GC, FGG, FGL1, MT1G and SERPINF2 were verified using the same
array studied cell lines and 12 of the primary hepatocellular carcinomas.
Although downregulations of DLC1, CDH1 and TP53 were not suggested from our
array analysis, due to their reported tumor-suppressive role and their
localization in the smallest overlapping regions, the mRNA expression levels of
these genes were also investigated by qRT-PCR (Table 2). With the exception of
DLC1 and CDH1, a repressed gene expression relative to pooled normal livers was
confirmed in the majority of specimens examined (Table 2). A downregulation of
FGG was suggested in 60% of cases at 0.50-fold (<0.01–3.57) (median, quartiles)
and FGL1 in 53% at 0.68-fold (<0.01–14.36). Repressed GC and MT1G expressions at
less than 0.01-fold were suggested in 70% of cases and 97%, respectively. On
17p13, downregulations of SERPINF2 were suggested in 84% of cases at 0.10-fold
(<0.01–0.65) and TP53 in 88% at 0.01 (<0.01–0.47) (Table 2).
Table 2Validation of candidate genes on hepatocellular carcinoma tumors and cell
lines
Chrom. armSORGenes, symbolLocationExpression ratioArray (median,
quartile)qRT-PCRa(median, quartile)4q4q12–q13Vitamin D binding protein,
GC4q13.30.17 (0.06–0.45)<0.01 (<0.01–1.06)4q31–q35Fibrinogen gamma peptide,
FGG4q31.30.04 (0.01–0.09)0.50 (<0.01–3.57)8p8p21–p22Fibrinogen-like 1,
FGL18p220.10 (0.05–0.40)0.68 (<0.01–14.36)Deleted in liver cancer 1,
DLC1b8p220.88 (0.71–1.00)11.78 (0.83–28.57)16q16q12.1–q23.1Metallothionein 1G,
MT1G16q12.20.27 (0.14–0.42)<0.01 (<0.01–0.02)E-cadherin, CDH1b16q22.11.03
(0.89–1.61)1.64 (0.17–12.56)17p17p13Alpha-2-plasmin inhibitor,
SERPINF217p13.30.16 (0.10–0.33)0.10 (<0.01–0.65)Tumor protein p53,
TP53b17p13.11.22 (1.04–1.53)0.01 (<0.01–0.47)
aqRT-PCR validations included 20 cell lines and 12 primary tumors that were
subjected to microarray analysis.
bKnown TSG located within region of frequent allelic losses found in HCC.
* Open table in a new tab
INVESTIGATION IN PRIMARY HEPATOCELLULAR CARCINOMA
The mRNA expression levels of FGG, GC, FGL1, MT1G and SERPINF2 were further
examined in primary HCC tumors and adjacent nontumorous livers by qRT-PCR. In 30
cases examined, downregulation of MT1G expression was most prominent with more
than100-fold reductions indicated in 63% of tumors (P=0.0001) (Table 3). A
significant reduction of FGG, FGL1 and SERPINF2 in tumors was also suggested
(Table 3). Statistical analysis of GC, FGG, FGL1, MT1G and SERPINF2 expressions
between early (T1/2) and advanced (T3/T4) tumor stages did not suggest
differences with disease progression (P>0.05) In our series of hepatocellular
carcinoma studied, five cases arose from a noncirrhotic background. The adjacent
nontumorous liver of these five noncirrhotic tumors demonstrated expressions of
FGG and FGL1 similar to that found in normal livers. For GC, MT1G and SERPINF2,
on the other hand, a downregulation of these genes was suggested. Nevertheless,
the median expressions of all tested genes were comparable between the cirrhotic
and noncirrhotic hepatocellular carcinoma tumors.
Table 3Expression of array-derived candidate genes in primary hepatocellular
carcinoma
SORGenes, symbolRatio of tumor to paired adjacent liverPercentage cases
(%)Median (quartiles)P-value4q12–q13Vitamin D binding Protein, GC200.12
(0.25–0.86)0.1254q31–q35Fibrinogen gamma peptide, FGG300.19
(0.02–0.32)0.00988p21–p22Fibrinogen like 1, FGL1230.10
(0.08–0.63)0.015616q12.1–q23.1Metallothionein 1G, MT1G630.01
(0.00–0.16)0.000117p13Alpha-2-plasmin inhibitor, SERPINF2330.28
(0.09–0.40)0.0034
* Open table in a new tab
DISCUSSION
In the present microarray study, early passages and established hepatocellular
carcinoma cell lines have been utilized as a homogenous source of malignant
hepatocytes to elucidate for differentially expressed transcripts in
hepatocellular carcinoma. Results derived were further evaluated against genes
determined from primary tumors, which indicated 35 candidates to be commonly
downregulated in both cell lines and tumors. As diminutions on 4q12–q23,
4q31–q35, 8p21–p22, 16q12.1–q23.1 and 17p13 have been suggested in the early
neoplastic changes of hepatocellular carcinoma,
9
* Zondervan PE
* Wink J
* Alers JC
Molecular cytogenetic evaluation of virus-associated and non-viral
hepatocellular carcinoma: analysis of 26 carcinomas and 12 concurrent
dysplasias.
J Pathol. 2000; 192: 207-215
10.1002/1096-9896(2000)9999:9999<::AID-PATH690>3.0.CO;2-#
* Crossref
* PubMed
* Scopus (89)
* Google Scholar
,
28
* Lin YW
* Sheu JC
* Huang GT
Chromosomal abnormality in hepatocellular carcinoma by comparative genomic
hybridisation in Taiwan.
Eur J Cancer. 1999; 35: 652-658
10.1016/S0959-8049(98)00430-4
* Abstract
* Full Text
* Full Text PDF
* PubMed
* Scopus (52)
* Google Scholar
,
29
* Okabe H
* Ikai I
* Matsuo K
Comprehensive allelotype study of hepatocellular carcinoma: potential
differences in pathways to hepatocellular carcinoma between hepatitis B
virus-positive and -negative tumors.
Hepatology. 2000; 31: 1073-1079
10.1053/he.2000.6409
* Crossref
* PubMed
* Scopus (90)
* Google Scholar
,
30
* Zhang SH
* Cong WM
* Xian ZH
Clinicopathological significance of loss of heterozygosity and microsatellite
instability in hepatocellular carcinoma in China.
World J Gastroenterol. 2005; 11: 3034-3039
10.3748/wjg.v11.i20.3034
* Crossref
* PubMed
* Scopus (33)
* Google Scholar
it was interesting to note that five consistently downregulated genes, FGG, GC,
FGL1, MT1G and SERPINF2, were consistently downregulated in these characteristic
regions of allelic losses. Parallel analysis by comparative genomic
hybridization on the 20 hepatocellular carcinoma cell lines studied indicated a
high concordance of regional loss and downregulations of FGG, GC and FGL1, while
downregulations of MT1G and SERPINF2 were more frequent than cell lines
harboring chromosomal losses. This discrepancy may be explained by the presence
of other inactivation mechanisms, such as hypermethylation at the promoter
region, that play a role in the control of gene expressions. Moreover, our group
has recently shown that the downregulation of a novel gene ACP5 on chromosome
19p13 was associated with chromosomal breakage, which might represent an
alternate inactivation mechanism.
25
* Chan KY
* Wong N
* Lai PB
Transcriptional profiling on chromosome 19p indicated frequent downregulation of
ACP5 expression in hepatocellular carcinoma.
Int J Cancer. 2005; 114: 902-908
10.1002/ijc.20684
* Crossref
* PubMed
* Scopus (19)
* Google Scholar
From our array analysis, a reduced expression of the proliferating cell nuclear
antigen (PCNA) gene was suggested in both hepatocellular carcinoma cell lines
and tumors, which would seem contrary to a recent study conducted by Chen et al.
31
* Chen ZM
* Crone KG
* Watson MA
Identification of a unique gene expression signature that differentiates
hepatocellular adenoma from well-differentiated hepatocellular carcinoma.
Am J Surg Pathol. 2005; 29: 1600-1608
10.1097/01.pas.0000176426.21876.a5
* Crossref
* PubMed
* Google Scholar
One possible explanation for this discrepancy would be the cDNA clone (IMAGE
clone: 415202) representing the PCNA gene on the Ontario array has an almost 90%
sequence homology to a region located on chromosome X. The hybridization signal
may therefore be one of the false positive errors that are commonly found in
microarray studies. Nevertheless, in line with our findings, downregulations of
FGG, FGL1, SERPINF2 and MT1G were also observed in the hepatocellular carcinoma
tumor relative to the nontumorous liver in the Chen et al study.
32
* Rhodes DR
* Yu J
* Shanker K
ONCOMINE: a cancer microarray database and integrated data-mining platform.
Neoplasia. 2004; 6: 1-6
10.1016/S1476-5586(04)80047-2
* Crossref
* PubMed
* Google Scholar
According to qPCR, the expression levels of FGG, GC, FGL1, MT1G and SERPINF2
were similar in early and advanced stages hepatocellular carcinoma. This might
in turn suggest that the inactivation of these genes occurred early in the tumor
development and have been maintained through progression. Moreover, FGL1 was
more profoundly repressed than another tumor-suppressor gene DLC1 located on the
same 8p22 region. This was also found for MT1G and SERPINF2, which displayed
more repressed expressions than well-known tumor-suppressor genes CDH1 and TP53
within the same physical location. Our finding may hence potentially underline a
value for these novel candidates in hepatocellular carcinoma development.
Allelic losses on 4q are common in hepatocellular carcinoma, although targeted
genes in the smallest overlapping regions have not been suggested. In this
study, we report on the novel finding of repressed FGG (on 4q31.3) expressions
in hepatocellular carcinoma tumors, despite this protein is primarily
synthesized in the liver.
33
* Straub PW
A study of fibrinogen production by human liver slices in vitro by an
immunoprecipitin method.
J Clin Invest. 1963; 42: 130-136
10.1172/JCI104690
* Crossref
* PubMed
* Scopus (16)
* Google Scholar
A downregulation of FGG was found in 95% of cases compared to normal livers
(Table 2), although in comparison to their adjacent nontumorous cirrhotic livers
significant reduction was suggested in only 30% (Table 3). This observation was
also noted for other candidate genes examined (Tables 2 and 3). Our findings may
therefore be interpreted as aberrant gene expressions are also present in the
adjacent putative premalignant cirrhotic liver, and may have constituted to the
early tumor development. Deposition of fibrin(ogen) into the extracellular
matrix serves as a scaffold to support adhesion, binding to growth factors and
facilitates migration during angiogenesis.
34
* Simpson-Haidaris PJ
* Rybarczyk B
Tumors and fibrinogen. The role of fibrinogen as an extracellular matrix
protein.
Ann NY Acad Sci. 2001; 936: 406-425
10.1111/j.1749-6632.2001.tb03525.x
* Crossref
* PubMed
* Scopus (237)
* Google Scholar
Early cirrhotic hepatocellular carcinoma nodules are always surrounded by a
sheath of fibrotic tissue deposited during the course of chronic infection. The
early loss of the FGG in a cirrhotic liver could have modulated the outgrowth of
early hepatocellular carcinoma by reducing the integrity of extracellular
matrix, and promoted cell growth by increasing the elasticity of matrix
structure. Besides an important element in blood coagulation, FGG is also a
structural component of fibrinogen E-fragment. Studies on endothethial cells
have demonstrated fibrinogen E-fragment as a potent inhibitor of angiogenesis
that can inhibit cell migration and tubule formation induced from strong
proangiogenic factors such as VEGF and bFGF.
35
* Bootle-Wilbraham CA
* Tazzyman S
* Marshall JM
Fibrinogen E-fragment inhibits the migration and tubule formation of human
dermal microvascular endothelial cells in vitro.
Cancer Res. 2000; 60 (10987275): 4719-4724
* PubMed
* Google Scholar
This inhibition is believed to have occurred through the binding of fibrinogen
E-fragment at postreceptor locus that is common to both VEGF and bFGF.
35
* Bootle-Wilbraham CA
* Tazzyman S
* Marshall JM
Fibrinogen E-fragment inhibits the migration and tubule formation of human
dermal microvascular endothelial cells in vitro.
Cancer Res. 2000; 60 (10987275): 4719-4724
* PubMed
* Google Scholar
It is therefore plausible that the loss of the FGG chain could lead to
structural alterations of fibrinogen E-fragment resulting in lost or reduced
binding inhibition on the growth factors related angiogenesis activity and
consequently early tumor growth.
In the context of extracellular matrix, it was also particularly interesting to
have identified common downregulations of SERPINF2 (also known as
alpha-2-anti-plasmin). SERPINF2 is the major inhibitor of the proteolytic enzyme
plasmin that digests fibrins.
36
* Lee KN
* Jackson KW
* Christiansen VJ
A novel plasma proteinase potentiates alpha2-antiplasmin inhibition of fibrin
digestion.
Blood. 2004; 103: 3783-3788
10.1182/blood-2003-12-4240
* Crossref
* PubMed
* Scopus (113)
* Google Scholar
,
37
* Owensby DA
* Morton PA
* Wun TC
Binding of plasminogen activator inhibitor type-1 to extracellular matrix of Hep
G2 cells. Evidence that the binding protein is vitronectin.
J Biol Chem. 1991; 266 (1705551): 4334-4340
* Abstract
* Full Text PDF
* PubMed
* Google Scholar
The plasmin activation system is known to play a key role in extracellular
matrix degradation.
38
* Dano K
* Behrendt N
* Hoyer-Hansen G
Plasminogen activation and cancer.
Thromb Haemost. 2005; 93: 676-681
10.1160/TH05-01-0054
* Crossref
* PubMed
* Scopus (393)
* Google Scholar
The reduced expressions of SERPINF2 might lead to an increased level of
activated plasmin, which could impair the stabilization of fibrin bundle and in
turn the integrity of liver extracellular matrix. In addition, FGL1 (also named
as LFIRE-1/HFREP-1) is also a member of the fibrinogen superfamily
39
* Yamamoto T
* Gotoh M
* Sasaki H
Molecular cloning and initial characterization of a novel fibrinogen-related
gene, HFREP-1.
Biochem Biophys Res Commun. 1993; 193: 681-687
10.1006/bbrc.1993.1678
* Crossref
* PubMed
* Scopus (51)
* Google Scholar
and a liver-specific gene that is frequently downregulated in hepatocellular
carcinoma at both the mRNA and protein levels.
40
* Yan J
* Yu Y
* Wang N
LFIRE-1/HFREP-1, a liver-specific gene, is frequently downregulated and has
growth suppressor activity in hepatocellular carcinoma.
Oncogene. 2004; 23: 1939-1949
10.1038/sj.onc.1207306
* Crossref
* PubMed
* Scopus (48)
* Google Scholar
Upon restoration of exogenous wild-type FGL1 expression in hepatocellular
carcinoma, functional examinations have indicated an inhibitory effect of FGL1
on cell proliferation, anchorage-dependent or independent growth in vitro, and
suppression of tumorigenicity in athymic nude mice.
40
* Yan J
* Yu Y
* Wang N
LFIRE-1/HFREP-1, a liver-specific gene, is frequently downregulated and has
growth suppressor activity in hepatocellular carcinoma.
Oncogene. 2004; 23: 1939-1949
10.1038/sj.onc.1207306
* Crossref
* PubMed
* Scopus (48)
* Google Scholar
Besides displaying tumor-suppressive characteristics, since downregulations of
FGL1 expression in hepatocellular carcinoma is frequently association with 8p
allelic losses, it has been further implicated as a tumor-suppressor gene on 8p.
40
* Yan J
* Yu Y
* Wang N
LFIRE-1/HFREP-1, a liver-specific gene, is frequently downregulated and has
growth suppressor activity in hepatocellular carcinoma.
Oncogene. 2004; 23: 1939-1949
10.1038/sj.onc.1207306
* Crossref
* PubMed
* Scopus (48)
* Google Scholar
Previous microarray studies have showed that several isoforms of metallothionein
such as MT1A and MT1F are frequently downregulated in hepatocellular carcinoma
compared to nontumorous livers.
41
* Iizuka N
* Oka M
* Yamada-Okabe H
Self-organizing-map-based molecular signature representing the development of
hepatocellular carcinoma.
FEBS Lett. 2005; 579: 1089-1100
10.1016/j.febslet.2004.10.113
* Crossref
* PubMed
* Scopus (36)
* Google Scholar
,
42
* Iizuka N
* Oka M
* Yamada-Okabe H
Comparison of gene expression profiles between hepatitis B virus- and hepatitis
C virus-infected hepatocellular carcinoma by oligonucleotide microarray data on
the basis of a supervised learning method.
Cancer Res. 2002; 62 (12124323): 3939-3944
* PubMed
* Google Scholar
,
43
* Lu DD
* Chen YC
* Zhang XR
The relationship between metallothionein-1F (MT1F) gene and hepatocellular
carcinoma.
Yale J Biol Med. 2003; 76 (PMCID 2582696; PMID 15369632): 55-62
* PubMed
* Google Scholar
However, none of these studies has attempted validation analysis. In this study,
our array finding concurred with qRT-PCR verifications, which also indicated the
repressions of MT1G corresponded to the highest incidence (63%) and magnitude in
hepatocellular carcinoma tumors relative to their adjacent nonmalignant liver
tissue (P=0.0001) (Table 3).
In conclusion, utilizing microarray technology as a tool, we have successfully
identified a number of candidate genes throughout the hepatocellular carcinoma
genome and within the deletion hotspots. As number of genes found including
SERPINF2, FGG, Decorin, Vitronectin (Table 1) are structural components of the
extracellular matrix, we postulate that common downregulations of these targets
may perturb the integrity or maintenance of extracellular matrix. Indeed,
breakdown of the extracellular matrix is contributory to cancer developments.
44
* Shekhar MP
* Pauley R
* Heppner G
Host microenvironment in breast cancer development: extracellular matrix-stromal
cell contribution to neoplastic phenotype of epithelial cells in the breast.
Breast Cancer Res. 2003; 5: 130-135
10.1186/bcr580
* Crossref
* PubMed
* Scopus (154)
* Google Scholar
Moreover, extracellular matrix also serves as a reservoir of growth factors that
can modulate cell morphology and proliferation.
44
* Shekhar MP
* Pauley R
* Heppner G
Host microenvironment in breast cancer development: extracellular matrix-stromal
cell contribution to neoplastic phenotype of epithelial cells in the breast.
Breast Cancer Res. 2003; 5: 130-135
10.1186/bcr580
* Crossref
* PubMed
* Scopus (154)
* Google Scholar
,
45
* Getzenberg RH
* Pienta KJ
* Huang EY
Modifications of the intermediate filament and nuclear matrix networks by the
extracellular matrix.
Biochem Biophys Res Commun. 1991; 179: 340-344
10.1016/0006-291X(91)91375-M
* Crossref
* PubMed
* Scopus (24)
* Google Scholar
Thus, deregulation of extracellular matrix components may have adverse effects
on homeostasis, which consequently enhances local tumor cells growth and
promotes hepatocellular carcinoma formation.
ACCESSION CODES
ACCESSIONS
GenBank/EMBL/DDBJ
* •
BE796134
* •
BG566740
* •
BG616563
* •
BG618635
* •
BI918353
* •
BM471342
* •
BM805738
* •
BM925604
* •
H12367
* •
H22747
* •
H24115
* •
H25541
* •
H29155
* •
H38897
* •
H45773
* •
H57208
* •
H69261
* •
H71112
* •
H86642
* •
N46702
* •
NM_005950
* •
R08306
* •
R35197
* •
R69654
* •
R87181
* •
R88884
* •
R96774
* •
T83911
* •
T87339
* •
T96003
* •
T97051
* •
W01373
* •
W16685
* •
W17370
* •
W91932
* •
W91952
REFERENCES
1. * Okuda K
Hepatocellular carcinoma.
J Hepatol. 2000; 32: 225-237
10.1016/S0168-8278(00)80428-6
View in Article
* PubMed
* Abstract
* Full Text PDF
* Google Scholar
2. * Lau WY
Primary liver tumors.
Semin Surg Oncol. 2000; 19: 135-144
10.1002/1098-2388(200009)19:2<135::AID-SSU6>3.0.CO;2-A
View in Article
* Scopus (56)
* PubMed
* Crossref
* Google Scholar
3. * Lai EC
* Fan ST
* Lo CM
Hepatic resection for hepatocellular carcinoma. An audit of 343 patients.
Ann Surg. 1995; 221: 291-298
10.1097/00000658-199503000-00012
View in Article
* Scopus (404)
* PubMed
* Crossref
* Google Scholar
4. * Wong N
* Lai P
* Lee SW
Assessment of genetic changes in hepatocellular carcinoma by comparative
genomic hybridization analysis: relationship to disease stage, tumor size,
and cirrhosis.
Am J Pathol. 1999; 154: 37-43
10.1016/S0002-9440(10)65248-0
View in Article
* Scopus (257)
* PubMed
* Abstract
* Full Text
* Full Text PDF
* Google Scholar
5. * Marchio A
* Meddeb M
* Pineau P
Recurrent chromosomal abnormalities in hepatocellular carcinoma detected by
comparative genomic hybridization.
Genes Chromosomes Cancer. 1997; 18: 59-65
10.1002/(SICI)1098-2264(199701)18:1<59::AID-GCC7>3.0.CO;2-0
View in Article
* Scopus (261)
* PubMed
* Crossref
* Google Scholar
6. * Kusano N
* Shiraishi K
* Kubo K
Genetic aberrations detected by comparative genomic hybridization in
hepatocellular carcinomas: their relationship to clinicopathological
features.
Hepatology. 1999; 29: 1858-1862
10.1002/hep.510290636
View in Article
* Scopus (197)
* PubMed
* Crossref
* Google Scholar
7. * Yuan BZ
* Miller MJ
* Keck CL
Cloning, characterization, and chromosomal localization of a gene
frequently deleted in human liver cancer (DLC-1) homologous to rat RhoGAP.
Cancer Res. 1998; 58 (9605766): 2196-2199
View in Article
* PubMed
* Google Scholar
8. * Lau SH
* Guan XY
Cytogenetic and molecular genetic alterations in hepatocellular carcinoma.
Acta Pharmacol Sin. 2005; 26: 659-665
10.1111/j.1745-7254.2005.00126.x
View in Article
* Scopus (34)
* PubMed
* Crossref
* Google Scholar
9. * Zondervan PE
* Wink J
* Alers JC
Molecular cytogenetic evaluation of virus-associated and non-viral
hepatocellular carcinoma: analysis of 26 carcinomas and 12 concurrent
dysplasias.
J Pathol. 2000; 192: 207-215
10.1002/1096-9896(2000)9999:9999<::AID-PATH690>3.0.CO;2-#
View in Article
* Scopus (89)
* PubMed
* Crossref
* Google Scholar
10. * Yeh SH
* Chen PJ
* Lai MY
Allelic loss on chromosomes 4q and 16q in hepatocellular carcinoma:
association with elevated alpha-fetoprotein production.
Gastroenterology. 1996; 110: 184-192
10.1053/gast.1996.v110.pm8536855
View in Article
* Scopus (81)
* PubMed
* Abstract
* Full Text PDF
* Google Scholar
11. * Chang J
* Kim NG
* Piao Z
Assessment of chromosomal losses and gains in hepatocellular carcinoma.
Cancer Lett. 2002; 182: 193-202
10.1016/S0304-3835(02)00083-6
View in Article
* Scopus (33)
* PubMed
* Crossref
* Google Scholar
12. * Yasui K
* Arii S
* Zhao C
TFDP1, CUL4A, and CDC16 identified as targets for amplification at 13q34 in
hepatocellular carcinomas.
Hepatology. 2002; 35: 1476-1484
10.1053/jhep.2002.33683
View in Article
* Scopus (153)
* PubMed
* Crossref
* Google Scholar
13. * Chow LS
* Lo KW
* Kwong J
RASSF1A is a target tumor suppressor from 3p21.3 in nasopharyngeal
carcinoma.
Int J Cancer. 2004; 109: 839-847
10.1002/ijc.20079
View in Article
* Scopus (99)
* PubMed
* Crossref
* Google Scholar
14. * Wong TS
* Tang KC
* Kwong DL
Differential gene methylation in undifferentiated nasopharyngeal carcinoma.
Int J Oncol. 2003; 22 (12632081): 869-874
View in Article
* PubMed
* Google Scholar
15. * Kok K
* Naylor SL
* Buys CH
Deletions of the short arm of chromosome 3 in solid tumors and the search
for suppressor genes.
Adv Cancer Res. 1997; 71: 27-92
10.1016/S0065-230X(08)60096-2
View in Article
* PubMed
* Crossref
* Google Scholar
16. * Qiu GH
* Tan LK
* Loh KS
The candidate tumor suppressor gene BLU, located at the commonly deleted
region 3p21.3, is an E2F-regulated, stress-responsive gene and inactivated
by both epigenetic and genetic mechanisms in nasopharyngeal carcinoma.
Oncogene. 2004; 23: 4793-4806
10.1038/sj.onc.1207632
View in Article
* Scopus (122)
* PubMed
* Crossref
* Google Scholar
17. * Alon U
* Barkai N
* Notterman DA
Broad patterns of gene expression revealed by clustering analysis of tumor
and normal colon tissues probed by oligonucleotide arrays.
Proc Natl Acad Sci USA. 1999; 96: 6745-6750
10.1073/pnas.96.12.6745
View in Article
* Scopus (3385)
* PubMed
* Crossref
* Google Scholar
18. * Nagai H
* Terada Y
* Tajiri T
Characterization of liver-cirrhosis nodules by analysis of gene-expression
profiles and patterns of allelic loss.
J Hum Genet. 2004; 49: 246-255
10.1007/s10038-004-0141-8
View in Article
* Scopus (11)
* PubMed
* Crossref
* Google Scholar
19. * Okabe H
* Satoh S
* Kato T
Genome-wide analysis of gene expression in human hepatocellular carcinomas
using cDNA microarray: identification of genes involved in viral
carcinogenesis and tumor progression.
Cancer Res. 2001; 61 (11280777): 2129-2137
View in Article
* PubMed
* Google Scholar
20. * Xu XR
* Huang J
* Xu ZG
Insight into hepatocellular carcinogenesis at transcriptome level by
comparing gene expression profiles of hepatocellular carcinoma with those
of corresponding noncancerous liver.
Proc Natl Acad Sci USA. 2001; 98: 15089-15094
10.1073/pnas.241522398
View in Article
* Scopus (326)
* PubMed
* Crossref
* Google Scholar
21. * Lee JS
* Thorgeirsson SS
Genetic profiling of human hepatocellular carcinoma.
Semin Liver Dis. 2005; 25: 125-132
10.1055/s-2005-871192
View in Article
* Scopus (53)
* PubMed
* Crossref
* Google Scholar
22. * Wong N
* Chan KY
* Macgregor PF
Transcriptional profiling identifies gene expression changes associated
with IFN-alpha tolerance in hepatitis C-related hepatocellular carcinoma
cells.
Clin Cancer Res. 2005; 11 (15709204): 1319-1326
View in Article
* Scopus (21)
* PubMed
* Crossref
* Google Scholar
23. * Pang E
* Wong N
* Lai PB
Consistent chromosome 10 rearrangements in four newly established human
hepatocellular carcinoma cell lines.
Genes Chromosomes Cancer. 2002; 33: 150-159
10.1002/gcc.1220
View in Article
* Scopus (23)
* PubMed
* Crossref
* Google Scholar
24. * Pang E
* Wong N
* Lai PB
A comprehensive karyotypic analysis on a newly developed hepatocellular
carcinoma cell line, HKCI-1, by spectral karyotyping and comparative
genomic hybridization.
Cancer Genet Cytogenet. 2000; 121: 9-16
10.1016/S0165-4608(99)00247-2
View in Article
* Scopus (19)
* PubMed
* Abstract
* Full Text
* Full Text PDF
* Google Scholar
25. * Chan KY
* Wong N
* Lai PB
Transcriptional profiling on chromosome 19p indicated frequent
downregulation of ACP5 expression in hepatocellular carcinoma.
Int J Cancer. 2005; 114: 902-908
10.1002/ijc.20684
View in Article
* Scopus (19)
* PubMed
* Crossref
* Google Scholar
26. * Fleming ID
American Cancer Society, American College of Surgeons, National Cancer
Institute (US), American Joint Committee on Cancer, American College of
Radiology, College of American Pathologists.
AJCC Cancer Staging Manual. Lippincott-Raven, Philadelphia1997
View in Article
* Google Scholar
27. * Beheshti B
* Braude I
* Marrano P
Chromosomal localization of DNA amplifications in neuroblastoma tumors
using cDNA microarray comparative genomic hybridization.
Neoplasia. 2003; 5: 53-62
10.1016/S1476-5586(03)80017-9
View in Article
* PubMed
* Crossref
* Google Scholar
28. * Lin YW
* Sheu JC
* Huang GT
Chromosomal abnormality in hepatocellular carcinoma by comparative genomic
hybridisation in Taiwan.
Eur J Cancer. 1999; 35: 652-658
10.1016/S0959-8049(98)00430-4
View in Article
* Scopus (52)
* PubMed
* Abstract
* Full Text
* Full Text PDF
* Google Scholar
29. * Okabe H
* Ikai I
* Matsuo K
Comprehensive allelotype study of hepatocellular carcinoma: potential
differences in pathways to hepatocellular carcinoma between hepatitis B
virus-positive and -negative tumors.
Hepatology. 2000; 31: 1073-1079
10.1053/he.2000.6409
View in Article
* Scopus (90)
* PubMed
* Crossref
* Google Scholar
30. * Zhang SH
* Cong WM
* Xian ZH
Clinicopathological significance of loss of heterozygosity and
microsatellite instability in hepatocellular carcinoma in China.
World J Gastroenterol. 2005; 11: 3034-3039
10.3748/wjg.v11.i20.3034
View in Article
* Scopus (33)
* PubMed
* Crossref
* Google Scholar
31. * Chen ZM
* Crone KG
* Watson MA
Identification of a unique gene expression signature that differentiates
hepatocellular adenoma from well-differentiated hepatocellular carcinoma.
Am J Surg Pathol. 2005; 29: 1600-1608
10.1097/01.pas.0000176426.21876.a5
View in Article
* PubMed
* Crossref
* Google Scholar
32. * Rhodes DR
* Yu J
* Shanker K
ONCOMINE: a cancer microarray database and integrated data-mining platform.
Neoplasia. 2004; 6: 1-6
10.1016/S1476-5586(04)80047-2
View in Article
* PubMed
* Crossref
* Google Scholar
33. * Straub PW
A study of fibrinogen production by human liver slices in vitro by an
immunoprecipitin method.
J Clin Invest. 1963; 42: 130-136
10.1172/JCI104690
View in Article
* Scopus (16)
* PubMed
* Crossref
* Google Scholar
34. * Simpson-Haidaris PJ
* Rybarczyk B
Tumors and fibrinogen. The role of fibrinogen as an extracellular matrix
protein.
Ann NY Acad Sci. 2001; 936: 406-425
10.1111/j.1749-6632.2001.tb03525.x
View in Article
* Scopus (237)
* PubMed
* Crossref
* Google Scholar
35. * Bootle-Wilbraham CA
* Tazzyman S
* Marshall JM
Fibrinogen E-fragment inhibits the migration and tubule formation of human
dermal microvascular endothelial cells in vitro.
Cancer Res. 2000; 60 (10987275): 4719-4724
View in Article
* PubMed
* Google Scholar
36. * Lee KN
* Jackson KW
* Christiansen VJ
A novel plasma proteinase potentiates alpha2-antiplasmin inhibition of
fibrin digestion.
Blood. 2004; 103: 3783-3788
10.1182/blood-2003-12-4240
View in Article
* Scopus (113)
* PubMed
* Crossref
* Google Scholar
37. * Owensby DA
* Morton PA
* Wun TC
Binding of plasminogen activator inhibitor type-1 to extracellular matrix
of Hep G2 cells. Evidence that the binding protein is vitronectin.
J Biol Chem. 1991; 266 (1705551): 4334-4340
View in Article
* PubMed
* Abstract
* Full Text PDF
* Google Scholar
38. * Dano K
* Behrendt N
* Hoyer-Hansen G
Plasminogen activation and cancer.
Thromb Haemost. 2005; 93: 676-681
10.1160/TH05-01-0054
View in Article
* Scopus (393)
* PubMed
* Crossref
* Google Scholar
39. * Yamamoto T
* Gotoh M
* Sasaki H
Molecular cloning and initial characterization of a novel
fibrinogen-related gene, HFREP-1.
Biochem Biophys Res Commun. 1993; 193: 681-687
10.1006/bbrc.1993.1678
View in Article
* Scopus (51)
* PubMed
* Crossref
* Google Scholar
40. * Yan J
* Yu Y
* Wang N
LFIRE-1/HFREP-1, a liver-specific gene, is frequently downregulated and has
growth suppressor activity in hepatocellular carcinoma.
Oncogene. 2004; 23: 1939-1949
10.1038/sj.onc.1207306
View in Article
* Scopus (48)
* PubMed
* Crossref
* Google Scholar
41. * Iizuka N
* Oka M
* Yamada-Okabe H
Self-organizing-map-based molecular signature representing the development
of hepatocellular carcinoma.
FEBS Lett. 2005; 579: 1089-1100
10.1016/j.febslet.2004.10.113
View in Article
* Scopus (36)
* PubMed
* Crossref
* Google Scholar
42. * Iizuka N
* Oka M
* Yamada-Okabe H
Comparison of gene expression profiles between hepatitis B virus- and
hepatitis C virus-infected hepatocellular carcinoma by oligonucleotide
microarray data on the basis of a supervised learning method.
Cancer Res. 2002; 62 (12124323): 3939-3944
View in Article
* PubMed
* Google Scholar
43. * Lu DD
* Chen YC
* Zhang XR
The relationship between metallothionein-1F (MT1F) gene and hepatocellular
carcinoma.
Yale J Biol Med. 2003; 76 (PMCID 2582696; PMID 15369632): 55-62
View in Article
* PubMed
* Google Scholar
44. * Shekhar MP
* Pauley R
* Heppner G
Host microenvironment in breast cancer development: extracellular
matrix-stromal cell contribution to neoplastic phenotype of epithelial
cells in the breast.
Breast Cancer Res. 2003; 5: 130-135
10.1186/bcr580
View in Article
* Scopus (154)
* PubMed
* Crossref
* Google Scholar
45. * Getzenberg RH
* Pienta KJ
* Huang EY
Modifications of the intermediate filament and nuclear matrix networks by
the extracellular matrix.
Biochem Biophys Res Commun. 1991; 179: 340-344
10.1016/0006-291X(91)91375-M
View in Article
* Scopus (24)
* PubMed
* Crossref
* Google Scholar
ARTICLE INFO
PUBLICATION HISTORY
Accepted: July 18, 2006
Received in revised form: July 10, 2006
Received: March 21, 2006
IDENTIFICATION
DOI: https://doi.org/10.1038/modpathol.3800674
COPYRIGHT
© 2006 United States & Canadian Academy of Pathology.
SCIENCEDIRECT
Access this article on ScienceDirect
Positional expression profiling indicates candidate genes in deletion hotspots
of hepatocellular carcinoma
*
Hide CaptionDownloadSee figure in article
Toggle Thumbstrip
* Fig. 1
* View Large Image
* Download Hi-res image
* Download .PPT
FIGURES
* Figure 1Positional expression profiling on chromosomes 4q, 8p, 16q and 17p in
hepatocellular carcinoma cell lines and tumors. Relative expression levels as
fold reductions determined for each transcript by microarray analysis on 20
hepatocellular carcinoma cell lines and 20 tumors were plotted along physical
map location of each cDNA clone. Candidate genes that showed marked
downregulations in more than 50% of both primary tumors and cell lines were
highlighted by bracket. The smallest overlapping region of common losses was
indicated as green bar next to the ideogram of each chromosome arm.
TABLES
* Table 1Common downregulated genes in hepatocellular carcinoma tumors and cell
lines from transcriptional profiling
* Table 2Validation of candidate genes on hepatocellular carcinoma tumors and
cell lines
* Table 3Expression of array-derived candidate genes in primary hepatocellular
carcinoma
RELATED ARTICLES
Hide CaptionDownloadSee figure in Article
Toggle Thumbstrip
* Download Hi-res image
* Download .PPT
* Home
* Articles & Issues
* Current Issue
* Issues in Progress
* Articles In Press
* List of Issues
* Multimedia
* ModPath Chat Podcast
* Collections
* Controversies in Pathology
* Monthly Readers' Choice
* For Authors
* About Open Access
* Researcher Academy
* Submit a Manuscript
* Author Information
* Permissions
* Journal Info
* About the Journal
* About Open Access
* About USCAP Member Access
* Activate Online Access
* Career Opportunities
* Contact Us
* Editorial Board
* Info for Advertisers
* Pricing
* Reprints
* New Content Alerts
* Society Information
* USCAP Annual Meeting
* USCAP Learning
* USCAP Membership
* USCAP
* Join us on Social Media
* Facebook
* Twitter
* LinkedIn
--------------------------------------------------------------------------------
The content on this site is intended for healthcare professionals.
--------------------------------------------------------------------------------
We use cookies to help provide and enhance our service and tailor content. To
update your cookie settings, please visit the Cookie Settings for this site.
Copyright © 2023 Elsevier Inc. except certain content provided by third parties.
* Privacy Policy
* Terms and Conditions
* Accessibility
* Help & Contact
✓
Thanks for sharing!
AddToAny
More…
Click to get updates and verify authenticity.
We use cookies that are necessary to make our site work. We may also use
additional cookies to analyze, improve, and personalize our content and your
digital experience. For more information, see ourCookie Policy
Cookie Settings Accept all cookies
COOKIE PREFERENCE CENTER
We use cookies which are necessary to make our site work. We may also use
additional cookies to analyse, improve and personalise our content and your
digital experience. For more information, see our Cookie Policy and the list of
Google Ad-Tech Vendors.
You may choose not to allow some types of cookies. However, blocking some types
may impact your experience of our site and the services we are able to offer.
See the different category headings below to find out more or change your
settings.
Allow all
MANAGE CONSENT PREFERENCES
STRICTLY NECESSARY COOKIES
Always active
These cookies are necessary for the website to function and cannot be switched
off in our systems. They are usually only set in response to actions made by you
which amount to a request for services, such as setting your privacy
preferences, logging in or filling in forms. You can set your browser to block
or alert you about these cookies, but some parts of the site will not then work.
These cookies do not store any personally identifiable information.
Cookies details
Back Button
COOKIE LIST
Search Icon
Filter Icon
Clear
checkbox label label
Apply Cancel
Consent Leg.Interest
checkbox label label
checkbox label label
checkbox label label
Confirm my choices