CLINICAL VALUE OF DNA COPY NUMBER CHANGES IN SOLID
TUMORS — DATA EXTRACTED FROM OUR ONLINE CGH DATA
COLLECTION http://www.helsinki.fi/cmg/CHG-data.htm
Sakari Knuutila, Departments of Pathology and Medical Genetics, Haartman Institute
and Helsinki University Central Hospital, University of Helsinki, Helsinki, Finland
CGH DATA COLLECTION ON OUR WEB SITE http://www.helsinki.fi/cmg
The comparative genomic hybridization (CGH) method was developed and documented
in 1992 by Anne Kallioniemi and coauthors (Kallioniemi et al., 1992). It turned out to be
a powerful means for screening DNA copy number changes in solid tumors. We have
collected CGH findings from 16,530 documented cases of some 80 tumor entities. The
diagram (Fig. 1) shows that year by year the number of publications has increased
almost exponentially. Figure 2 indicates the total number of cases in the main tumor
categories.
FROM COPY NUMBER CHANGES TO GENES
As a screening method, CGH has revealed an enormous amount of DNA copy number
losses, gains and amplifications that have pinpointed chromosomal areas with tumor
suppressor genes and oncogenes. Table 1 shows examples of genes that we have
characterized subsequent to a copy number change found by the CGH technique.
TABLE 1. From DNA copy number change to gene: examples from our studies.
CHANGE
TUMOR
GENE
dim(19p)
amp(18q)
LKB1
BCL2
amp(1q21)
Peutz-Jeghers
Diffuse large B-cell
lymphoma
Osteosarcoma
amp(17q12q21)
Gastric carcinoma
DARPP-32
COAS1, 2 and 3
REFERENCE
(Hemminki et al., 1997;
Hemminki et al., 1998)
(Monni et al., 1997)
(Meza-Zepeda et al.,
2002)
(Kokkola et al., 1997;
El-Rifai et al., 2002;
Varis et al., 2002)
COPY NUMBER CHANGES TELL TUMOR PROGRESSION AND MOLECULAR
PATHOGENESIS, AND HELP DIFFERENTIAL DIAGNOSES
In a great variety of malignancies, especially in carcinomas, gains are more frequent
than losses. The malignant nature of a tumor is usually indicated by numerous changes
(Knuutila et al., 1998; Knuutila et al., 1999; Knuutila et al., 2000). Nevertheless, lack of
changes does not rule out malignancy. Ewing's sarcoma, as an example, may not show
any changes (Armengol et al., 1997). In many tumors, such as colorectal and cervical
carcinomas, the number of changes, especially amplifications, increase during tumor
progression (Ried et al., 1999).
Are there any copy number profiles in tumor that help in routine pathologic diagnosis?
Differential diagnosis between mesothelioma and adenocarcinoma of the lung is difficult
but prognostically and therapeutically important. Our previous studies demonstrated that
different profiles in these tumors help in differential diagnosis (Björkqvist et al., 1998).
DNA copy number profile in leiomyosarcoma differs from that in gastrointestinal stromal
tumor (El-Rifai et al., 1998). Furthermore, copy number profiling has increased the
insight into the biological pathogenesis of tumors. For example, in gynecological tumors
a relevant question is whether serous tumors in the ovary, uterus and fallopian tube
have similar pathogenesis. We have showed that the profiles were similar in serous
tumors but distinct from those in other histological subtypes (Pere et al., 1998). This
suggests that serous ovarian, uterine and tubal carcinomas may have a common
molecular pathogenesis.
DNA COPY NUMBER CHANGES AS PROGNOSTIC AND PREDICTIVE MARKERS
Data extracted from our compilation of documented CGH findings indicate numerous
copy number changes that seem to have clinical value in establishing prognosis and
selecting therapy. Table 2 is by no means a comprehensive presentation of all changes
that have clinical value. Numerous findings, also those included in the table, need to be
verified on larger patient material. According to my critical evaluation, it is fully justified
to perform CGH analyses for clinical purposes, and this is also a practice that has been
adopted in our laboratory for glial tumors, neuroblastoma, Ewing's sarcoma,
mesothelioma/adenocarcinoma of the lung, and lipoma/lipoma-like liposarcoma. To
conclude, I should say that this listing is just the top of an iceberg, and many more wellconducted clinicopathological/CGH studies are needed to identify all clinically relevant
DNA copy number changes. Moreover, CGH array is an important novel technology
which is able to show the biologically essential target genes from the copy number
changes (Varis et al., 2002). In the future, the target genes can most probably be
studied by techniques other than CGH, such as FISH or PCR (see the Poster Abstract
by Varis et al.: Gene amplification and overexpression at 17q in gastric cancer).
4
TABLE 2. Clinical value of DNA copy number changes by CGH.
TUMOR*
CHANGE
CLINICAL SIGNIFICANCE
REFERENCE
BONE AND SOFT TISSUE
Leiomyoma vs. leiomyosarcoma
Normal vs. chaotic
Benign vs. malignant
Uterine leiomyosarcoma
Lipoma vs. lipoma-like liposarcoma
dim(10q)
Normal vs. amp(12q)
High grade, recurrent
Benign vs. malignant;
differential diagnosis
GIST
Chondroma vs. chondrosarcoma
No gains vs. numerous gains
Normal vs. numerous changes
Benign vs. malignant
Benign vs. malignant
Chondrosarcoma
dim(13q) as the sole change
enh(8q24qter)
Longer survival
Shorter overall survival
Ewing's
PNST
MFH
enh(1q)
dim(16q)
enh(7p15p21, 17q22qter)
enh(7q32)
Fibrosarcoma
enh(12q14q22)
Adverse overall survival
Event-free survival
Poor overall survival
Poor overall survival, worse
metastasis-free survival
Poor overall survival
(El-Rifai et al., 1998;
Sarlomo-Rikala et al.,
1998; Levy et al.,
2000)
(Hu et al., 2001)
(Szymanska et al.,
1997; Pedeutour et
al., 1999)
(El-Rifai et al., 2000)
(Larramendy et al.,
1997; Larramendy et
al., 1999)
(Hu et al.,2001;
(Larramendy et
al.,1999)
(Hattinger et al.,
2002)
(Schmidt et al., 1999)
(Skytting et al., 1999)
NEUROGENIC TUMORS
Astrocytic tumor
Oligodendroglial tumor
enh(7p) vs. end(8q)
Higher survival rate vs.
Lower survival rate
(Schmidt et al., 2002)
(Nishizaki et al.,
2000)
5
Anaplastic
dim(1p,19q), no TP53 mutation
PCV treatment sensitive (+)
Well-differentiated
dim(9p,10), enh(7)
TP53 pos., no dim(1p,19q)
dim(1p,19q), no TP53
No PCV+
Mixed gliomas
(oligodendrocytomas); astrocytic
TP53 pos., no dim(1p,19q)
and oligodendroglial elements
enh(17q21qter)
Neuroblastoma
enh(17q12),proximal to ERBB2
enh(17q23.1qter), distal to
ERBB2
RESPIRATORY TRACT
Mesothelioma vs. adenocarcinoma of dim(10,14) (loss profiling) vs.
gain profiling
the lung
DIGESTIVE TRACT
Esophageal squamous cell carcinoma
enh(5p)
Hepatoblastoma
enh(8q,20)
enh(2q24)
Hepatocellular carcinoma
dim(8p,13q), amp(11q13)
FEMALE GENITALS
Endometrioid carcinoma
Cervical squamous cell carcinoma
dim(9q32q34,11q23,Xq12q24)
dim(9p)
dim(11p,18p)
Oligodendroglial origin,
PCV+
Astrocytic origin, no PCV+
Poor overall survival
Suppresses progression
Promotes progression;
poorer survival
(Weber et al., 1996;
Bigner et al., 1999)
(Bown et al., 2001;
Brinkschmidt et al.,
2001)
(Lastowska et al.,
2002)
Differential diagnosis
(Björkqvist et al.,
1998)
Unfavorable prognosis;
independent prognostic
marker
Unfavorable prognosis
Unfavorable prognosis,
independent marker
Unfavorable prognosis
(Yen et al., 2001;
Ueno et al., 2002)
Lymph. node metastasis,
cervical involvement
Lymph. node metastasis,
poor prognosis
(Suehiro et al., 2000)
(Weber et al., 2000)
(Kumon et al., 2001)
(Kusano et al., 2002)
(Dellas et al., 1999)
PCV: procarbazine, cyclophosphamide, vincristine; * tumors in bold: CGH analyses performed in our laboratory for clinical
purposes
6
7
Figure 1
8
Figure 2
Barcelona, September 2002
9
REFERENCES
Armengol G, Tarkkanen M, Virolainen M, Forus A, Valle J, Böhling T, Asko-Seljavaara
S, Blomqvist C, Elomaa I, Karaharju E, Kivioja AH, Siimes MA, Tukiainen E,
Caballin MR, Myklebost O, Knuutila S (1997) Recurrent gains of 1q, 8 and 12 in
the Ewing family of tumours by comparative genomic hybridisation. Br J Cancer
75:1403-1409.
Bigner SH, Matthews MR, Rasheed BKA, Wiltshire RN, Friedman HS, Friedman AH,
Stenzel TT, Dawes DM, McLendon RE, Bigner DD (1999) Molecular genetic
aspects of oligodendrogliomas including analysis by comparative genomic
hybridization. Am J Pathol 155:375-386.
Björkqvist A-M, Tammilehto L, Nordling S, Nurminen M, Anttila S, Mattson K, Knuutila S
(1998) Comparison of DNA copy number changes in malignant mesothelioma,
adenocarcinoma and large-cell anaplastic carcinoma of the lung. Br J Cancer
77:260-269.
Bown N, Lastowska M, Cotterill S, O'Neill S, Ellershaw C, Roberts P, Lewis I, Pearson
ADJ (2001) 17q gain in neuroblastoma predicts adverse clinical outcome. U.K.
Cancer Cytogenetics Group and the U.K. Children's Cancer Study Group. Med
Pediatr Oncol 36:14-19.
Brinkschmidt C, Christiansen H, Terpe HJ, Simon R, Lampert F, Boecker W, DockhornDworniczak B (2001) Distal chromosome 17 gains in neuroblastomas detected by
comparative genomic hybridization (CGH) are associated with a poor clinical
outcome. Med Pediatr Oncol 36:11-13.
Dellas A, Torhorst J, Jiang F, Proffitt J, Schultheiss E, Holzgreve W, Sauter G, Mihatsch
MJ, Moch H (1999) Prognostic value of genomic alterations in invasive cervical
squamous cell carcinoma of clinical stage IB detected by comparative genomic
hybridization. Cancer Res 59:3475-3479.
El-Rifai W, Sarlomo-Rikala M, Andersson LC, Knuutila S, Miettinen M (2000) DNA
sequence copy number changes in gastrointestinal stromal tumors: tumor
progression and prognostic significance. Cancer Res 60:3899-3903.
El-Rifai W, Sarlomo-Rikala M, Knuutila S, Miettinen M (1998) DNA copy number
changes in development and progression in leiomyosarcomas of soft tissues. Am J
Pathol 153:985-990.
El-Rifai W, Smith Jr MF, Li G, Beckler A, Carl VS, Montgomery E, Knuutila S, Moskaluk
CA, Frierson Jr HF, Powell SM (2002) Gastric cancers overexpress DARPP-32
and a novel isoform, t-DARPP. Cancer Res 62:4061-4064.
Hattinger CM, Pötschger U, Tarkkanen M, Squire J, Zielenska M, Kiuru-Kuhlefelt S,
Kager L, Thorner P, Knuutila S, Niggli FK, Ambros PF, Gadner H, Betts DR (2002)
Prognostic impact of chromosomal aberrations in Ewing tumors. Br J Cancer
86:1763-1769.
Hemminki A, Markie D, Tomlinson I, Avizienyte E, Roth S, Loukola A, Bignell G, Warren
W, Aminoff M, Höglund P, Järvinen H, Kristo P, Pelin K, Ridanpää M, Salovaara T,
Toro T, Bodmer W, Olschwang S, Olsen AS, Stratton MR, de la Chapelle A,
Aaltonen LA (1998) A serine/threonine kinase gene defective in Peutz-Jeghers
syndrome. Nature 391:184-187.
Hemminki A, Tomlinson I, Markie D, Jarvinen H, Sistonen P, Bjorkqvist A, Knuutila S,
Salovaara R, Bodmer W, Shibata D, de la Chapelle A, Aaltonen LA (1997)
Barcelona, September 2002
10
Localization of a susceptibility locus for Peutz-Jeghers syndrome to 19p using
comparative genomic hybridization and targeted linkage analysis. Nature Genetics
15:87-90.
Hu J, Khanna V, Jones M, Surti U (2001) Genomic alterations in uterine
leiomyosarcomas: potential markers for clinical diagnosis and prognosis. Genes
Chromosomes Cancer 31:117-124.
Kallioniemi A, Kallioniemi O-P, Sudan D, Rutovitz D, Gray JW, Waldman F, Pinkel D
(1992) Comparative genomic hybridization for molecular cytogenetic analysis of
solid tumors. Science 258:818-821.
Knuutila S, Autio K, Aalto Y (2000) Online access to CGH data of DNA sequence copy
number changes. Letter. Am J Pathol 157:689.
Knuutila S, Autio K, Björkqvist A-M, Aalto Y, El-Rifai W, Hemmer S, Huhta T, Kettunen
E, Kiuru-Kuhlefelt S, Larramendy ML, Lushnikova T, Monni O, Pere H, Tapper J,
Tarkkanen M, Varis A, Wasenius V-M, Wolf M, Zhu Y (1999) DNA copy number
losses in human neoplasms. Am J Pathol 155:683-694.
Knuutila S, Björkqvist A-M, Autio K, Tarkkanen M, Wolf M, Monni O, Szymanska J,
Larramendy ML, Tapper J, Pere H, El-Rifai W, Hemmer S, Wasenius V-M, Vidgren
V, Zhu Y (1998) DNA copy number amplifications in human neoplasms. Review of
comparative genomic hybridization studies. Am J Pathol 152:1107-1123.
Kokkola A, Monni O, Puolakkainen P, Larramendy ML, Victorzon M, Nordling S,
Haapiainen R, Kivilaakso E, Knuutila S (1997) 17q12-21 amplicon, a novel
recurrent genetic change in intestinal type of gastric carcinoma: a comparative
genomic hybridization study. Genes Chromosomes Cancer 20:38-43.
Kumon K, Kobayashi H, Namiki T, Tsunematsu Y, Miyauchi J, Kikuta A, Horikoshi Y,
Komada Y, Hatae Y, Eguchi H, Kaneko Y (2001) Frequent increase of DNA copy
number in the 2q24 chromosomal region and its association with a poor clinical
outcome in hepatoblastoma: cytogenetic and comparative genomic hybridization
analysis. Jpn J Cancer Res 92:854-862.
Kusano N, Okita K, Shirahashi H, Harada T, Shiraishi K, Oga A, Kawauchi S, Furuya T,
Sasaki K (2002) Chromosomal imbalances detected by comparative genomic
hybridization are associated with outcome of patients with hepatocellular
carcinoma. Cancer 94:746-751.
Larramendy M, Valle J, Tarkkanen M, Kivioja AH, Karaharju E, Salmivalli T, Elomaa I,
Knuutila S (1997) No DNA copy number changes in osteochondromas. A
comparative genomic hybridization study. Cancer Genet Cytogenet 97:76-78.
Larramendy ML, Mandahl N, Mertens F, Blomqvist C, Kivioja AH, Karaharju E, Valle J,
Böhling T, Tarkkanen M, Rydholm A, Åkerman M, Bauer H, Anttila J-P, Elomaa I,
Knuutila S (1999) Clinical significance of genetic imbalances revealed by
comparative genomic hybridization in chondrosarcomas. Hum Pathol 30:12471253.
Lastowska M, Cotterill S, Bown N, Cullinane C, Variend S, Lunec J, Strachan T,
Pearson ADJ, Jackson MS (2002) Breakpoint position on 17q identifies the most
aggressive neuroblastoma tumors. Genes Chromosomes Cancer 34:428-436.
Levy B, Mukherjee T, Hirschorn K (2000) Molecular cytogenetic analysis of uterine
leiomyoma and leiomyosarcoma by comparative genomic hybridization. Cancer
Genet Cytogenet 121:1-8.
Meza-Zepeda LA, Forus A, Lygren B, Dahlberg AB, Godager LH, South A, Serra M,
Nezetic D, Tarkkanen M, Knuutila S, Myklebost O (2002) Positional cloning
Barcelona, September 2002
11
identifies a novel cyclophilin as a candidate amplified oncogene in 1q21.
Oncogene 21:2261-2269.
Monni O, Joensuu H, Franssila K, Klefstrom J, Alitalo K, Knuutila S (1997) BCL2
overexpression associated with chromosomal amplification in diffuse large B-cell
lymphoma. Blood 90:1168-1174.
Nishizaki T, Kubota H, Harada K, Harada K, Ito H, Suzuki M, Sasaki K (2000) Clinical
evidence of distinct subgroups of astrocytic tumors defined by comparative
genomic hybridization. Hum Pathol 31:608-614.
Pedeutour F, Forus A, Coindre J-M, Berner J-M, Nicolo G, Michiels J-F, Terrier P,
Ranchere-Vince D, Collin F, Myklebost O, Turc-Carel C (1999) Structure of the
supernumerary ring and giant rod chromosomes in adipose tissue tumors. Genes
Chromosomes Cancer 24:30-41.
Pere H, Tapper J, Wahlström T, Knuutila S, Bützow R (1998) Distinct chromosomal
imbalances in uterine serous and endometrioid carcinomas. Cancer Res 58:892895.
Ried T, Heselmeyer-Haddad K, Blegen H, Schröck E, Auer G (1999) Genomic changes
defining the genesis, progression, and malignancy potential in solid human tumors:
a phenotype/genotype correlation. Genes Chromosomes Cancer 25:195-204.
Sarlomo-Rikala M, El-Rifai W, Lahtinen T, Andersson L, Miettinen M, Knuutila S (1998)
Different patterns of DNA copy number changes in gastrointestinal stromal tumors,
leiomyomas, and schwannomas. Hum Pathol 29:476-481.
Schmidt H, Taubert H, Würl P, Kappler M, Lange H, Bartel F, Bache M, Holzhausen HJ, Hinze R (2002) Gains of 12q are the most frequent genomic imbalances in adult
fibrosarcoma and are correlated with a poor outcome. Genes Chromosomes
Cancer 34:69-77.
Schmidt H, Würl P, Taubert H, Meye A, Bache M, Holzhausen H-J, Hinze R (1999)
Genomic imbalances of 7p and 17q in malignant peripheral nerve sheath tumors
are clinically relevant. Genes Chromosomes Cancer 25:205-211.
Skytting BT, Szymanska J, Aalto Y, Lushnikova T, Blomqvist C, Elomaa I, Larsson O,
Knuutila S (1999) Clinical importance of genomic imbalances in synovial sarcoma
evaluated by comparative genomic hybridization. Cancer Genet Cytogenet 115:3946.
Suehiro Y, Umayahara K, Ogata H, Numa F, Yamashita Y, Oga A, Morioka H, Ito T,
Kato H, Sasaki K (2000) Genetic aberrations detected by comparative genomic
hybridization predict outcome in patients with endometrioid carcinoma. Genes
Chromosomes Cancer 29:75-82.
Szymanska J, Virolainen M, Tarkkanen M, Wiklund T, Asko-Seljavaara S, Tukiainen E,
Elomaa I, Blomqvist C, Knuutila S (1997) Overrepresentation of 1q21-23 and
12q13-21 in lipoma-like liposarcomas but not in benign lipomas. A comparative
genomic hybridization study. Cancer Genet Cytogenet 99:14-18.
Ueno T, Tangoku A, Yoshino S, Abe T, Toshimitsu H, Furuya T, Kawauchi S, Oga A,
Oka M, Sasaki K (2002) Gain of 5p15 detected by comparative genomic
hybridization as an independent marker of poor prognosis in patients with
esophageal squamous cell carcinoma. Clinical Cancer Research 8:526-533.
Varis A, Wolf M, Monni O, Vakkari M-L, Kokkola A, Moskaluk C, Frierson Jr H, Powell
SM, Knuutila S, Kallioniemi A, El-Rifai W (2002) Targets of gene amplification and
overexpression at 17q in gastric cancer. Cancer Res 62:2625-2629.
Barcelona, September 2002
12
Weber RG, Pietsch T, von Schweinitz D, Lichter P (2000) Characterization of genomic
alterations in hepatoblastomas. A role for gains on chromosomes 8q and 20 as
predictors of poor outcome. Am J Pathol 157:571-578.
Weber RG, Sabel M, Reifenberger J, Sommer C, Oberstraß J, Reifenberger G,
Kiessling M, Cremer T (1996) Characterization of genomic alterations associated
with glioma progression by comparative genomic hybridization. Oncogene 13:983994.
Yen C-C, Chen Y-J, Chen J-T, Hsia J-Y, Chen P-M, Liu J-H, Fan FS, Chiou T-J, Wang
W-S, Lin C-H (2001) Comparative genomic hybridization of esophageal squamous
cell carcinoma. Correlations between chromosomal aberrations and disease
progression/prognosis. Cancer 92:2769-2777.