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Mol Diagn Ther 2009; 13 (6): 367-373

REVIEW ARTICLE 1177-1062/09/0006-0367/$49.95/0

2009 Adis Data Information BV. All rights reserved.

Molecular Classification of Cancers of


Unknown Primary Site
F. Anthony Greco1 and Mark G. Erlander2
1 Sarah Cannon Cancer Center, Nashville, Tennessee, USA
2 bioTheranostics, Inc., San Diego, California, USA

Contents

Abstract . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . 367
1. Molecular Profiling in Human Cancers . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . 368
2. Molecular Profiling in CUP . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . 370
3. Discussion . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . 372

Abstract Cancer of unknown primary site is a common metastatic cancer, diagnosed in about 50 000 patients per
year in the US. The diagnosis, classification, and management of patients with carcinoma of unknown
primary site has been difficult and frustrating. The therapy has usually been empiric for the majority of
patients, and their prognosis has been poor.
Molecular classification of metastatic cancers with known primary sites has been accurate (7689%), as
reported from several studies. Molecular profiling of initial biopsy specimens has tremendous potential as a
test to diagnose the site of tumor origin in patients with unknown primary cancer. Several retrospective
studies of molecular profiling assays have provided indirect validation of the accuracy of primary site
prediction, based on correlations with clinicopathologic features. One additional study of initial diagnostic
biopsies in unknown primary cancer patients, where primary tumor sites were identified months to years
later, has provided more direct validation of the accuracy of molecular classification (the primary tumor sites
of 15 of 20 patients were correctly predicted). The ability to diagnose and classify unknown primary cancer
more precisely would allow for more site-specific or targeted therapy, and likely improve patient outcomes.
Several clinical studies are in progress or planned to test this concept.

Cancer of unknown primary site (CUP) is a common me- lymphoma, sarcoma, or melanoma) can be defined. The large
tastatic cancer, accounting for about 5% (50 000 patients) of all majority of CUP patients have carcinoma. Although the anato-
advanced cancer each year in the US.[1] These patients are mical primary tumor site is not found at the time of diagnosis,
unique in that they have no clinically apparent primary cancer the clinicopathologic evaluation of the patients has frequently
to explain the source of their metastasis. CUP is not a single varied and, therefore, studies in CUP have often been difficult
neoplasm with a defined natural history, but a very hetero- to interpret and compare. This difficulty is understandable
geneous group with variable clinical features and histopatho- since the evaluation of these patients has changed over the years
logies. Diagnosis, classification, and management of these as diagnostic technology has improved. A standard CUP de-
patients has been difficult and frustrating. finition has been published[1] but remains dynamic and con-
The definition of CUP by clinicians and investigators has not tinues to evolve. Unless an anatomical primary tumor site is
been the same over the years. All cell types are included in the identified at the time of diagnosis, the patients by our definition
definition but, with rare exceptions, the lineage (carcinoma, have CUP, regardless of the immunohistochemistry (IHC)
368 Greco & Erlander

stains or molecular profile predictions. Until these important the repertoire of cell-type IHC markers has substantially in-
diagnostic tests are clinically validated in CUP with compari- creased. The issue of validation of IHC in reference to the
sons between outcome data and known primary cancers, the primary site in patients with CUP remains an important con-
primary site in CUP remains only a prediction rather than sideration. Most of the IHC markers have been validated for
an absolute identification of the origin of the cancers in these patients with known primary cancer. Frequently, it is assumed
patients. that if an IHC marker is present in CUP, this indicates the
Over the past 30 years, some patients have been classified specific primary cancer derived from validation studies of the
into subsets according to clinical features and classic histo- marker in known cancer types. In our experience, a definitive
pathology. A minority of patients (20%) are within these several primary site diagnosis based on IHC findings is not common in
subsets that are more treatable and have a better prognosis than patients with CUP, and in one small autopsy series, histo-
the group as a whole with CUP.[2] The majority of CUP patients chemical or IHC stains were helpful in revealing the diagnosis
have carcinoma and most of these are adenocarcinomas. Al- of the primary tumor site (verified at autopsy) in only four of
though the pathogenesis and biology of CUP is poorly under- 27 patients.[6]
stood, most patients harbor a clinically undetectable or occult The amount of tissue available for IHC workup is often
primary site, which gives rise to the detectable metastasis. limited, given the increased use of core needle biopsies and fine
Several autopsy series have documented occult primary sites needle aspirates to obtain diagnostic material. Therefore,
in about 75% of all patients examined, most commonly in the sometimes a complete IHC workup is difficult and can lead the
lung, pancreas, kidney/adrenal gland, liver/bile duct, and colon/ IHC analysis down an incorrect line of investigation. Each IHC
rectum.[3] Since the majority of CUP patients have a small, marker has a sensitivity and specificity for a given cancer type,
clinically undetectable primary site, they represent a large and these statistical parameters can change, depending on the
number of different cancers. Diagnosis of the primary tumor number and type/subtype of different tumors examined. Fi-
site at the time of clinical presentation has not been possible for nally, IHC is a subjective technique requiring an experienced
most patients. IHC has been helpful in suggesting or predicting pathologist for interpretation. Therefore, there is a need for
the possible primary sites in some patients by the demonstra- other classification methods. In particular, gene expression
tion of various markers in the tumor cells.[4] However, there are profiling may compliment IHC methods because it is quanti-
only a few IHC markers specific enough to confidently identify tative and can classify tumors that IHC has difficulty with, and
the primary site. In most patients with CUP, the primary site it uses small amounts of tissue (3001000 cells) to generate a
remains speculative, even after extensive IHC study of the prediction for cancer classification.
tumor with multiple markers. Diagnosis of the primary site Molecular profiling is a relatively new technology with tre-
is a critical issue, since therapy is more likely to be effective if mendous potential in CUP classification and diagnosis.[7] There
site-specific therapy is administered, rather than empirical is no other large group of cancer patients with an obscure or
single regimens for all patients. The therapy for many advanced undefined site of origin. In the setting of CUP, the appropriate
cancer patients has improved, and the types of therapies are use of molecular profiling may provide critical information
different for many of these specific cancers. Therefore, accurate relevant to the specific type of cancer present, particularly when
classification and diagnosis of the type of cancer present in considered with the clinical and pathologic features. Accurate
CUP patients is important. classification and diagnosis will likely improve the outcome of
Pathologic evaluation specifically, standard light micro- many CUP patients, since more appropriate, tailored therapy
scopy and IHC stains has been one of the essential steps in would be administered to each patient.
predicting the possible primary site of origin in CUP.[4] Al-
though there is no question that IHC has revolutionized cancer
pathology, studies reporting qualitative metrics of the success 1. Molecular Profiling in Human Cancers
of IHC to identify the primary site in CUP are rather scant. A
major reason for this is the difficulty of documenting the pri- The invention of microarrays about 15 years ago enabled the
mary tumor site. A commonly cited study regarding the ability simultaneous quantification of whole-genome gene expression
of IHC to diagnose the primary site is by DeYoung and Wick,[5] and has led to unprecedented advancements in genomic-related
in which there was a reported 67% success rate in identifying computational technologies, a continued unraveling of cancer-
the primary site by using IHC. However, data were not dis- activated pathways, and discovery of diagnostic, prognostic,
closed, and also the study was reported 9 years ago. Since then, and drug response signatures in a multitude of cancer types.[8,9]

2009 Adis Data Information BV. All rights reserved. Mol Diagn Ther 2009; 13 (6)
Molecular Classification of CUP 369

With regard to cancer classification/diagnosis, Golub et al.[10] complete laser microdissection. CUP tumors by definition are
demonstrated that gene expression profiling could be used to predominantly metastatic, growing in other organs/tissues;
diagnostically discriminate between acute myeloid leukemia therefore, it is of paramount importance that the sample pro-
and acute lymphoblastic leukemia. This landmark study de- cess is highly enriched for the tumor cells. This point cannot
monstrated for the first time that cancer types could be classi- be overemphasized, given that these gene expression tests are
fied by measuring the differential expression of specific gene not measuring tumor specific markers but, rather, expression
sets. Subsequently, Ramaswamy et al.[11] and Su et al.[12] dynamics in relation to cell lineage, as described above. Third,
demonstrated that numerous cancer types could be classified by the test needs to be compatible with low numbers of tumor cells
gene expression profiling. (300500) since, in practical terms, many samples are core
Since these studies, there have been numerous additional needle biopsies or fine needle aspirates. Finally, the test needs to
reports demonstrating the ability to use gene expression to be able to discriminate between a large number of tumor types,
classify human tumors.[13-21] This approach has been successful given that CUP can arise from many primary sites. The number
because the 400-odd different cell types in the body have dif- of tumor types recognized by these various assays varies from 6
ferent gene expression profiles, which reflect their distinct to 39 (table I).
cellular functions (e.g. hepatocytes versus breast luminal epi- In the majority of clinical settings in patients with a known
thelium), and cancers developing from these different cell types primary cancer site, the diagnosis is secured by the clinical
retain some of their unique cell-type differences within their findings and the use of traditional pathologic methods. Gene
gene expression pattern. Furthermore, it has been shown expression profiles for diagnosis are not necessary. In CUP, the
through several validation studies that metastatic cancers retain potential role for gene expression profiling in classifying the
expression patterns found in their respective primary cancers primary tumor site is apparent. In the past decade, several
and that poorly differentiated and undifferentiated tumors of a molecular-based clinical assays for tumor classification in CUP
given cancer type often retain expression patterns observed in have been developed, based on the fundamental tenet that ef-
their respective well-differentiated tumors.[21] fective treatment for cancers relies on knowledge of the primary
A summary of selected gene expression studies in human anatomical origin/site of the tumor. In parallel with these ef-
cancers of known primary tumor sites is illustrated in table I. forts has been the emergence of biologic-targeted therapies that
From a technical point of view, a clinically viable test needs to inhibit specific signal transduction pathways active in parti-
be compatible with formalin-fixed, paraffin-embedded tissues, cular cancer types (e.g. human epidermal growth factor re-
given that nearly all tumor samples are preserved in this fash- ceptor-2 [HER2] and estrogen receptor expression in breast
ion. Second, the test should include the ability initially to cancer, epidermal growth factor receptor [EGFR] mutation in

Table I. Summary of selected gene expression studies in human cancers of known primary sites
Original study No. of samples Gene expression Tissue No. of cancers Accuracy Commercial entity
platform compatibility classified (%)
Tothill et al.[14] Training set: 229 tumors; Microarray Frozen 14 89 None
validation set the same but using (10 500 cDNAs)
leave-one-out cross-validation
Talantov et al.[15] Training set: 260 tumors; Real-time RT-PCR FFPE 6 plus other 76 www.veridex.com
validation set: 48 tumors (10 genes) cancers
Rosenfeld et al.[16] Training set: 253 tumors; Real-time RT-PCR FFPE 22 86 www.rosettagenomics.com
validation set: 83 tumors (48 micro-RNAs)
Monzon et al.[17] Validation set: 477 tumors Microarrays Frozen 15 89 www.pathworkdx.com
(1550 genes)
Pillai et al.[22] Validation set: 352 tumors Microarrays FFPE 15 89 www.pathworkdx.com
(1550 genes)
Ma et al.[21] Training set: 481 tumors; Real-time RT-PCR FFPE 39 87 in www.biotheranostics.com
validation set: 119 tumors (92 genes) 32 tumor
types
cDNA = complementary DNA; FFPE = formalin-fixed, paraffin-embedded; RT = reverse transcriptase.

2009 Adis Data Information BV. All rights reserved. Mol Diagn Ther 2009; 13 (6)
370 Greco & Erlander

non-small-cell lung cancer, and KRAS mutation in colorectal Therefore, validation of the usefulness and accuracy of mole-
cancer). This has led to the prediction that oncologists in the cular profiling in CUP biopsy samples is important. Once this
future will make treatment decisions largely based on the mole- validation is acceptable in CUP, then the clinical use of a mole-
cular makeup (mutational status, pathway activation, etc.) of the cular profiling assay would be critical to help determine the type
patients cancer, irrespective of the primary site of origin. Cur- of cancer and therapy for each patient. Molecular classification
rently, however, knowledge of the type and primary site of cancer would become an essential element of the evaluation and classi-
is essential in determining the therapy and prognosis of patients. fication of CUP patients.
The initial validation of gene expression profiling assays was
done in known human primary tumors. The various assays are 2. Molecular Profiling in Cancer of
all quite accurate (7689%) at independently determining the Unknown Primary Site
tumor type by these methods (table I). Classification or diag-
nosis of the particular tumor type in CUP biopsy specimens has Few would disagree that accurate determination of the pri-
been more difficult to validate, as the primary site or specific mary tumor site in patients with CUP would be helpful. This
type of cancer is not known and usually never becomes known would provide a specific diagnosis and help formulate a prog-
in these patients. Based on the ability of molecular profiling to nosis for the patient, as well as specific site-directed treatment.
accurately identify both primary tumors and metastatic sites in The group of patients with CUP represents an ideal setting to
patients with known primary cancer, it would seem logical to employ an accurate and reproducible molecular classification
assume a similar accuracy rate for these assays in metastatic system for diagnosis. There have been several retrospective
sites in CUP. However, extension of these findings to CUP studies evaluating the possible usefulness of molecular profiling
assumes that knowing the site of origin translates into improved in the diagnosis or classification of the primary tumor site in
patient outcomes that are analogous to improvement observed CUP patients.[14,15,18-20,25,26] All of these data provide some
from treatments based on known tumors. This assumption validation of the usefulness and accuracy of molecular profiling
argues that (a) CUP is not an entirely specific biology per se[23] in predicting the primary tumor site. However, the validation
but, rather, a collection of unspecified sets of cancer types (except for one study thus far[26]) has been indirect and based on
which, given the correct technology, can be sorted out; and (b) correlation with clinical features, response to therapies, and
once the cancer type is identified, the patient will be treated and pathology (including IHC stains). In the retrospective studies,
will benefit similarly to a patient with a known primary tumor. the inclusion criteria were variable from study to study, in-
There is merit in this argument, since it has been previously cluding IHC-predicted or resolved cases,[15,18] limited IHC
recognized that certain subsets of CUP have a favorable prog- with mainly clinical correlations[19,20,25] and actual identifica-
nosis[2] (e.g. isolated axillary node adenocarcinoma in women tion of latent primary tumor sites.[26] The various studies did
usually represents occult breast cancer). More recently, CUP in not have the same inclusion criteria, leading to some difficulty
association with a molecular profile or IHC prediction of colo- in interpretation when comparing studies. Each of these studies
rectal cancer appears to have a clinical course and response to will now be reviewed briefly (table II).
treatment consistent with metastatic colorectal cancer.[19,24] Tothill et al.[14] tested a complementary DNA microarray on
On the other hand, CUP is in several ways different from the initial diagnosis biopsy specimens from 13 patients with
known advanced cancers. The absence of a clinically detectable CUP. The predictions of the primary tumor site of origin were
primary tumor (even though most have occult small primary compared with clinicopathologic features, and the most likely
tumors proven by autopsy studies) is obvious. In addition, in primary site was decided by a medical oncologist. In 11 of 13
CUP patients proven to have a specific primary tumor at autop- patients (85%), their molecular classification prediction was
sy, the pattern of metastasis is frequently atypical or different consistent with the most likely primary site as determined by the
from known primary cancer (e.g. bone metastasis is more clinical and pathologic data. The actual anatomical primary
frequent than liver metastasis in occult pancreatic carcinoma; tumor site was not verified in any of these patients.
lymph node and lung metastases are more frequent than bone Talantov et al.[15] included 33 patients with CUP in their
metastasis in occult prostate carcinoma). CUP may have a total tumor samples from 449 patients in their validation study
unique genetic profile, although no data yet support this pos- of their reverse transcriptase (RT)-PCR assay for known pri-
sibility. Patients with CUP and clinically undetectable pri- mary cancers. Their assay was capable of identifying six tumor
maries (occult primaries) may also have different molecular types, and the assay results were consistent in 17 of 22 patients,
profiles than patients with the same known overt primaries. with the prediction of the primary site made by IHC.

2009 Adis Data Information BV. All rights reserved. Mol Diagn Ther 2009; 13 (6)
Molecular Classification of CUP 371

Table II. Summary of gene expression profile validation studies in cancers of unknown primary site (CUP)
Study Assay Validation of assay Validation of assay
by indirect correlationa by direct correlationb
Tothill et al.[14] Microarray[14] 13 patients, Not done
11 predicted (85%)
Talantov et al.[15] RT-PCR[15] 22 patients, Not done
17 primaries predicted (77%)
Varadhachary et al.[19] RT-PCR[15] 120 patients, Not done
63 primaries predicted (61%)
Monzon et al.[25] Microarray[17] 21 patients, Not done
16 primaries predicted (76%)
Bridgewater et al.[20] Microarray[27] 21 patients, Not done
18 primaries predicted (86%)
Horlings et al.[18] Microarray[27] 38 patients, Not done
29 primaries predicted (76%)
Greco et al.[26] RT-PCR[21] Not applicable, 20 patients,
latent primary site known 15 predicted accurately (75%)
a Clinical and/or pathologic (immunohistochemistry) features only; no primary tumor site documented.
b Primary tumor site of origin later definitely identified.
RT = reverse transcriptase.

Varadhachary et al.[19] used this same RT-PCR assay on pancreatic) were consistent with the clinical differential in
biopsies from 120 patients with CUP. In 63 of 120 patients these patients. Correlations with the assay results in the other
(61%), a primary site was predicted, and the clinicopathologic nine patients were not reported in the abstract.
features and response to treatment were compatible with the The validation of the accuracy of molecular profile assays in
predicted primary site in the majority of patients. A colorectal predicting the primary site in CUP patients in these five retro-
cancer profile was suggested as an important group of CUP spective studies (one in abstract form only) was indirect, with
patients to recognize, since their responses to treatment utili- correlations based on clinical and pathologic features. The
zing colorectal-specific chemotherapy were similar to those of question remains how accurate the assays are in predicting or
known colon cancer patients. diagnosing the actual primary tumor site. Greco et al.[26] re-
Bridgewater et al.[20] used a microarray assay on biopsies cently reported, in abstract form, a direct retrospective vali-
from 21 CUP patients. These primary site predictions were dation study in 20 CUP patients who later had their primary
correlated with clinical and pathologic features. The primary sites discovered (median 10 months later, range 254 months
site prediction was clinically feasible in 18 of 21 patients, and later following initial diagnosis of CUP). The inclusion criteria
in 12 patients the clinical management would have been influ- required a primary anatomical tumor site identification at least
enced by the assay results. 8 weeks or longer following the initial diagnosis of CUP. Their
Horlings et al.[18] studied a microarray assay on samples initial diagnostic biopsies were evaluated by an RT-PCR assay
from 38 CUP patients. Twenty-two of 38 tumor samples could capable of identifying 32 tumor types. In 15 of 20 specimens
not be classified by IHC, and in 14 a tissue of origin was pre- (75%) from these patients, the primary tumor was accurately
dicted (64%) by the microarray assay that was consistent with predicted, providing direct validation of this assay. This is very
the clinicopathologic features. The assay was in agreement with encouraging, but additional direct validation studies would be
15 of the 16 patients primaries (94%) predicted by IHC. The helpful in providing confirmation and reassurance of the use-
anatomical primary tumor site was not confirmed in any patient. fulness of molecular profiling assays in classifying the primary
Monzon et al.[25] evaluated a microassay-based expression tumor site in CUP patients. The value of these assays will likely
profile assay on fresh-frozen biopsy specimens from 21 patients be even more clinically helpful in primary site prediction when
with CUP. The primary site was predicted in 16 of 21 patients used in concert with clinical and IHC data for each patient.
(76%) and was indeterminate in five (24%). The results in six of In summary, the primary site prediction for CUP has been
seven gastrointestinal predictions (five colorectal and one examined by several of the molecular tests. Given the occult,

2009 Adis Data Information BV. All rights reserved. Mol Diagn Ther 2009; 13 (6)
372 Greco & Erlander

clinically undetectable nature of the primary sites in most CUP mor type will improve patient outcomes after site-specific or
patients, it is extremely difficult to verify the accuracy of mole- tailored therapy. Preliminary data do suggest that CUP with
cular assays or IHC stains in predicting the true primary site. colorectal molecular profile signatures responds similarly to
The studies of CUP by Tothill et al.,[14] Talantov et al.,[15] known advanced colorectal cancer treated with colorectal site-
Monzon et al.,[25] Varadachary et al.,[19] Bridgewater et al.,[20] specific therapy.[19] However, the number of patients is too
and Horlings et al.[18] were all based on indirect comparisons small to feel confident that outcomes in these colorectal profile
with clinical and IHC correlations. It is important to note that CUP patients will routinely parallel those in patients with
these were simply correlations or indirect validation and may known colorectal cancer. The ability to classify and diagnose
not have reflected the true accuracy of the molecular assay or, patients more precisely allows appropriate clinical trials to be
for that matter, IHC. The actual primary tumor site was not designed to answer the ultimate question of whether CUP pa-
identified in any of these patients. To obtain a more direct tient outcomes will be improved. Several studies are now in
validation of the accuracy of molecular profiling to predict the progress and others are planned.
primary tumor site in CUP, patients with latent primary tumor The optimal CUP study design would require molecular
sites were evaluated to test the RT-PCR assay, as previously profiling of the biopsy specimen and random allocation of
reported by Ma et al.[21] As mentioned, this assay accurately patients to either a standard empiric systemic regimen or to site-
predicted the primary tumor site or origin in 15 of 20 CUP specific or tailored systemic therapy, as determined by the
patients from their initial diagnostic biopsies. This was direct assay. Other trials prospectively treating patients according to
validation in patients with primary tumor sites that were later the molecular profile classification will also be of value. If
found, and convincing evidence that gene expression profiling molecular classification is proven to impart the same prognosis
can add value in the clinical evaluation of CUP. All of these for CUP patients as for those with corresponding known pri-
studies provide support for this concept. mary cancer, then an advance will have been achieved for CUP
patients.
3. Discussion The ideal management of CUP patients in the immediate
future will likely be based upon accurate diagnosis or classifi-
The molecular classification of CUP continues to evolve. cation of the primary tumor site. Perhaps more importantly, the
These data specifically evaluating the accuracy of primary site stage is set for a more precise molecular understanding of each
prediction are difficult to generate, since most patients never patients tumor, which will likely result in the recognition of a
have verifiable primary sites found. Most of the molecular specific individualized therapeutic approach. This evolving role
profile validation studies available in CUP are indirect evidence of gene expression profiling of human cancers may be more
with clinicopathologic correlations (table II). The only direct important in determining therapy for patients in the future than
validation (latent primaries were known) was reported by knowledge of their primary tumor site of origin.
Greco et al.[26] and was accurate in 75% of the patients. Iro-
nically, the majority of patients with CUP do have small,
clinically undetected or occult primary sites, as documented in Acknowledgments
the past from autopsy series. However, most of these patients
Dr Greco has received consultancy fees and speakers honoraria from
never have a clinically detectable primary site found during bioTheranostics, Inc. Dr Erlander is an employee of bioTheranostics, Inc.
their lifetime. In those rare patients whose latent primary sites and holds stock options in the company.
have later been discovered, the accuracy of a molecular pro-
filing assay in predicting the primary was very reasonable.
Additional data from this group may be forthcoming. Corre- References
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Correspondence: F. Anthony Greco, MD, Sarah Cannon Research Institute,
identify the histogenetic origin of metastatic adenocarcinomas of unknown 250 25th Avenue North, Suite 110, Nashville, TN 37203, USA.
primary. J Clin Oncol 2008; 26: 4435-41 E-mail: fgreco@tnonc.com

2009 Adis Data Information BV. All rights reserved. Mol Diagn Ther 2009; 13 (6)
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