Gene expression profiling in patients with carcinoma of unknown primary site: from translational research to standard of care

A case report of challenges in distinguishing gastroesophageal junction hepatoid adenocarcinoma from testicular germ cell tumor: Insights for improved diagnosis with gene expression profiling

Gastroesophageal junction hepatoid adenocarcinoma is a rare form of gastroesophageal cancer. We present a case of a 38-year-old man with no significant medical history who was diagnosed with gastroesophageal junction hepatoid adenocarcinoma but initially misdiagnosed with a testicular germ cell tumor, given the elevated alpha-feto protein and poorly differentiated pathology. We will elaborate on the importance of gene expression profiling in modern oncology to better define the tumor of origin in patients with cancer of unknown primary origin, how it helped us to diagnose gastroesophageal junction hepatoid adenocarcinoma and how it can help identify potential additional therapeutic targets in some cases. Due to the rarity of this subtype of gastroesophageal junction cancer there is a lack of standard therapeutic options, and we will discuss the most commonly used treatment regimens. The patient underwent three lines of antineoplastic therapy and unfortunately passed after 51 weeks of follow-up.

[Breast-like cancer of unknow primary : Implications for radiological diagnostics]

BACKGROUND

Cancer of unknown primary (CUP) is defined by the presence of metastatic disease with an undetectable primary tumor at the time of presentation despite standard-of-care imaging. Although the prognosis of most CUP patients is poor, certain subgroups with more favorable prognosis have been defined.

DIAGNOSTICS

Women with isolated axillary lymph node metastases and confirmed histologic adenocarcinoma or poorly differentiated subtype, no other distant metastases, and no evidence of a primary cancer including primary breast carcinoma evaluated by clinical examination, computed tomography of thorax and abdomen, mammography, breast ultrasound, and breast magnetic resonance imaging (MRI) represent a potentially curable subgroup of patients with CUP. Breast MRI is the most important radiological modality in the diagnostic workup of breast-like CUP to exclude a primary cancer in the breast.

THERAPY

Breast-like CUP patients are treated according to guidelines for patients with node-positive breast cancer. Standard-of-care adjuvant systemic therapy should be given. Axillary lymph node dissection (ALND) is indicated. If no primary cancer in the breast is detected, surgery of the ipsilateral breast should not be performed. Radiotherapy of the ipsilateral breast and supra-/infraclavicular lymph nodes should be discussed.

A comparison of DNA sequencing and gene expression profiling to assist tissue of origin diagnosis in cancer of unknown primary

Cancer of unknown primary (CUP) is a syndrome defined by clinical absence of a primary cancer after standardised investigations. Gene expression profiling (GEP) and DNA sequencing have been used to predict primary tissue of origin (TOO) in CUP and find molecularly guided treatments; however, a detailed comparison of the diagnostic yield from these two tests has not been described. Here, we compared the diagnostic utility of RNA and DNA tests in 215 CUP patients (82% received both tests) in a prospective Australian study. Based on retrospective assessment of clinicopathological data, 77% (166/215) of CUPs had insufficient evidence to support TOO diagnosis (clinicopathology unresolved). The remainder had either a latent primary diagnosis (10%) or clinicopathological evidence to support a likely TOO diagnosis (13%) (clinicopathology resolved). We applied a microarray (CUPGuide) or custom NanoString 18-class GEP test to 191 CUPs with an accuracy of 91.5% in known metastatic cancers for high-medium confidence predictions. Classification performance was similar in clinicopathology-resolved CUPs - 80% had high-medium predictions and 94% were concordant with pathology. Notably, only 56% of the clinicopathology-unresolved CUPs had high-medium confidence GEP predictions. Diagnostic DNA features were interrogated in 201 CUP tumours guided by the cancer type specificity of mutations observed across 22 cancer types from the AACR Project GENIE database (77,058 tumours) as well as mutational signatures (e.g. smoking). Among the clinicopathology-unresolved CUPs, mutations and mutational signatures provided additional diagnostic evidence in 31% of cases. GEP classification was useful in only 13% of cases and oncoviral detection in 4%. Among CUPs where genomics informed TOO, lung and biliary cancers were the most frequently identified types, while kidney tumours were another identifiable subset. In conclusion, DNA and RNA profiling supported an unconfirmed TOO diagnosis in one-third of CUPs otherwise unresolved by clinicopathology assessment alone. DNA mutation profiling was the more diagnostically informative assay. © 2022 The Authors. The Journal of Pathology published by John Wiley & Sons Ltd on behalf of The Pathological Society of Great Britain and Ireland.

Tumor Genomic Profiling to Determine Tissue Origin of Cancers of Unknown Primary: A Single Institute Experience With its Utility and Impact on Patient Management

Tumor genomic profiling represents a promising tool in diagnosis and management of cancer of unknown primary. We report our experience on the impact of genomic profiling in elucidating primary tumor site, correlation with pathologic findings and patient management. Tissue or cytology specimens from 22 cancers of unknown primary were referred for genomic profiling. Reports were available to review in 18 cases; 3 samples were inadequate for analysis. Of the remaining 15 cases, primary tumor site was suggested in 12 cases (80%), whereas it remained indeterminate in 3 (20%). Of the 12 cases, molecular profiling was concordant with light microscopy findings in 3 patients, whereas in 2 cases molecular testing identified a sarcoma, contradicting light microscopy and immunohistochemistry findings. The suggested primary was confirmed by additional immunohistochemistry in 1 case and by endoscopic biopsy in another. In 5 cases, follow-up biopsy or additional testing were not considered necessary for patient management. Three patients received palliative care and 12 received various chemotherapy regimens. Five patients died within a year, whereas 9 were alive more than a year after diagnosis, 3 of who were alive >3 years after diagnosis. In conclusion, genomic profiling helped confirm the original diagnosis and suggested primary sites in two third of our cases. Although many patients may be at a disease stage too advanced to withstand further investigations or underg aggressive therapy, molecular testing improves diagnostic accuracy and may thus assist in selection of the most appropriate therapy.

Carcinoma of Unknown Primary Origin: Application of Immunohistochemistry With Emphasis to Different Cytokeratin 7 and 20 Staining Patterns

BACKGROUND

Although the primary origin of some carcinomas may be obscure to clinicians, its identification is crucial as it affects prognosis and treatment (especially novel targeted therapies). Immunohistochemistry (IHC) may be helpful in identifying the primary origin of carcinomas. This retrospective survey aimed to evaluate the frequency and accuracy of each IHC marker used to determine the origin of carcinomas.

METHODS

The review of pathology department archives revealed 307 cases of cancer of unknown primary origin (CUP) between 2015 and 2020, which were accessible in the department archives. Demographic information, site of biopsy, clinical and pathologic diagnoses, and IHC results of the patients were collected.

RESULTS

The patients included 157 (51.15%) men and 150 (48.85%) women. The age of the patients ranged from 14 to 92 years, including 106 (34.5%) expired cases. In 27% of cases, the primary origin of carcinoma remained unknown. The agreement between pathologic and clinical diagnoses was 59%. The most common pattern of cytokeratin (CK) expression in CUP was CK7+/CK20- (55.3%), followed by CK7-/CK20- (19%), CK7+/CK20+ (15%), and CK7-/CK20+ (10.7%), respectively.

CONCLUSION

The IHC analysis may improve the diagnosis of CUPs. However, the origin of some cases remains unknown despite an IHC analysis, thereby necessitating the use of more diagnostic procedures or gene expression studies for reaching a definitive diagnosis.

Case Report: Successful Immunotherapy Improved the Prognosis of the Unfavorable Subset of Cancer of Unknown Primary

Background

Cancer of unknown primary (CUP) is heterogeneous and has a wide variety of clinical presentations and a poor prognosis in most patients, with a median overall survival of only 6 months. The development of molecular profiling contributes to precision therapy, and targeted drugs and immune checkpoint inhibitors (ICIs) greatly promote individualized treatment.

Case presentation

Here, we reported a case of an unfavorable subset of CUP who had a long time of survival after the immunotherapy-prominent comprehensive treatment. A 48-year-old man presented with back pain and a cough. A diagnostic work-up showed bone marrow, multiple bones, and lymph node metastasis. Lymph node pathology implies metastatic poorly differentiated cancer. Next-generation sequencing (NGS) showed no special targets, but the tumor proportion score (TPS) of programmed death-ligand 1 (PD-L1) was 80% and the tumor mutation burden (TMB) was 16.7 per million bases. After two cycles of pembrolizumab 200 mg D1 plus nanoparticle albumin-bound (nab)-paclitaxel 200 mg D1&8 (q3w), PET-CT and bone marrow aspiration cytology showed a complete response (CR). Subsequently, pembrolizumab alone was used for three months. The left inguinal lymph nodes showed new metastasis. After two cycles of the combination treatment of pembrolizumab and (nab)-paclitaxel, a partial response (PR) was achieved. After seven months, retroperitoneal lymph nodes showed new metastasis, and the sequential treatment with radiotherapy and pembrolizumab exhibited encouraging efficacy. To date, the patient has survived nearly 40 months with the combination therapy.

Conclusions

The ICI-prominent comprehensive treatment provided clinical benefit for the reported case of CUP. Thus, CUP patients with markers of benefiting from immunotherapy should be actively treated with immunotherapy to improve their prognosis.

Cancer-of-Unknown-Primary-Origin: A SEER-Medicare Study of Patterns of Care and Outcomes among Elderly Patients in Clinical Practice

Simple Summary

Cancer-of-unknown-primary-origin (CUP) is challenging to diagnose and treat, and little is known about its diagnostic work-up, treatment, and outcomes in routine healthcare. We examined data from elderly patients (at least 66 years old) diagnosed with CUP in real-world US clinical practice, using the Surveillance, Epidemiology, and End Results–Medicare-linked database. Only half of elderly patients with CUP received all three diagnostic work-up procedures (biopsy, immunohistochemistry, and imaging), as recommended by guidelines. Patients who received all three diagnostic work-up procedures were more likely to receive any type of anticancer treatment, and patients who did not receive full diagnostic work-up had shorter median overall survival, particularly with increasing age. Overall, these results suggest that further studies are needed to understand why many patients given a diagnosis of CUP do not receive complete diagnostic work-up or treatment. Further research into improving diagnostic work-up and treatment effectiveness in patients diagnosed with CUP is required.

Abstract

Knowledge of contemporary patterns of cancer-of-unknown-primary-origin (CUP) diagnostic work-up, treatment, and outcomes in routine healthcare is limited. Thus, we examined data from elderly patients diagnosed with CUP in real-world US clinical practice. From the Surveillance, Epidemiology, and End Results–Medicare-linked database, we included patients ≥ 66 years old with CUP diagnosed between 1 January 2013 and 31 December 2015. We analyzed baseline demographics, clinical characteristics, methods of diagnostic work-up (biopsy, immunohistochemistry, imaging), treatment-related factors, and survival. CUP diagnosis was histologically confirmed in 2813/4562 patients (61.7%). Overall, 621/4562 (13.6%) patients received anticancer pharmacotherapy; among these, 97.3% had a histologically confirmed tumor and 83.1% received all three procedures. Among those with a histologically confirmed tumor, increasing age, increasing comorbidity score, not receiving all three diagnostic measures, and having a not-further specified histologic finding of only ‘malignant neoplasm’ were all negatively associated with receipt of anticancer pharmacotherapy. Median overall survival was 1.2 months for all patients. Median time between CUP diagnosis and treatment initiation was 41 days. Limited diagnostic work-up was common and most patients did not receive anticancer pharmacotherapy. The poor outcomes highlight a substantial unmet need for further research into improving diagnostic work-up and treatment effectiveness in CUP.

SEOM-GECOD clinical guideline for unknown primary cancer (2021)

Cancer of unknown primary site (CUP) is defined as a heterogeneous group of tumors that appear as metastases, and of which standard diagnostic work-up fails to identify the origin. It is considered a separate entity with a specific biology, and nowadays molecular characteristics and the determination of actionable mutations may be important in a significant group of patients. In this guide, we summarize the diagnostic, therapeutic, and possible new developments in molecular medicine that may help us in the management of this unique disease entity.

Site-specific therapy in cancers of unknown primary site: a systematic review and meta-analysis

Background

Cancer of unknown primary site (CUP) is a term applied to characterize pathologically confirmed metastatic cancer with unknown primary tumor origin. It remains uncertain whether patients with CUP benefit from site-specific therapy guided by molecular profiling.

Patients and methods

A systematic search in PubMed, Web of Science, Embase, Cochrane Library, and ClinicalTrials.gov, and of conference abstracts from January 1976 to January 2021 was performed to identify studies investigating the efficacy of site-specific therapy on patients with CUP. The quality of included studies was evaluated using the Cochrane risk of bias tool and Newcastle–Ottawa scale. Eligible studies were weighted and pooled for meta-analysis. Hazard ratios (HRs) for overall survival (OS) and progression-free survival (PFS) were assessed to compare the efficacy of site-specific therapy with empiric therapy in patients with CUP. In addition, subgroup analyses were conducted.

Results

Five studies comprising 1114 patients were identified, of which 454 patients received site-specific therapy, and 660 patients received empiric therapy. Our meta-analysis revealed that site-specific therapy was not significantly associated with improved PFS [HR 0.93, 95% confidence interval (CI) 0.74-1.17, P = 0.534] and OS (HR 0.75, 95% CI 0.55-1.03, P = 0.069), compared with empiric therapy. However, during subgroup analysis significantly improved OS was associated with site-specific therapy in the high-accuracy predictive assay subgroup (HR 0.46, 95% CI 0.26-0.81, P = 0.008) compared with the low accuracy predictive assay subgroup (HR 0.93, 95% CI 0.75-1.15, P = 0.509). Furthermore, compared with patients with less responsive tumor types, more survival benefit from site-specific therapy was found in patients with more responsive tumors (HR 0.67, 95% CI 0.46-0.97, P = 0.037).

Conclusions

Our results suggest that site-specific therapy is not significantly associated with improved survival outcomes; however, it might benefit patients with CUP with responsive tumor types.

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Studies evaluating the role of site-specific therapy guided by molecular profiling in CUP provided contradictory results.

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Site-specific therapy is not significantly associated with improved survival outcomes in the overall CUP population.

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Molecularly defined site-specific therapy may improve OS only when high-accuracy assays assign CUP to responsive tumor types.

Image-guided percutaneous needle biopsy for the diagnosis of cancer of unknown primary

AIM

This study aimed to assess the efficacy of image-guided percutaneous needle biopsy in patients with suspected cancer of unknown primary.

METHODS

We conducted a retrospective observational study. Among 291 patients with suspected cancer of unknown primary who were referred to our institution between April 2011 and March 2014, 89 who underwent image-guided percutaneous needle biopsy and 27 who underwent surgical biopsy were defined as the image-guided percutaneous needle biopsy group and the surgical group, respectively. Patient backgrounds, diagnostic yields, promptness of biopsy, general anesthesia rates, and severe complication rates were compared between the two groups.

RESULTS

There was no significant difference in the patient backgrounds of the two groups. The diagnostic yields were 98.9% (95% confidence interval, 93.9%-99.8%) in the image-guided percutaneous needle biopsy group and 100% (95% confidence interval, 87.5%-100%) in the surgical biopsy group (no significant difference; p = 1.0). The mean time to biopsy was significantly shorter (6.5 days vs. 21.3 days; p < .0001) and general anesthesia was used in significantly fewer patients (0% vs. 40.7%; p < .0001) in the image-guided percutaneous needle biopsy group. There was no significant difference in the rate of serious complications between the two groups (p = 1.0).

CONCLUSION

As a biopsy procedure for patients with suspected cancer of unknown primary, image-guided percutaneous needle biopsy is equally diagnostic and safe for surgical biopsy and might be preferable to surgical biopsy in terms of promptness and not requiring general anesthesia.

Molecular Pathology of Lung Cancer

This overview of the molecular pathology of lung cancer includes a review of the most salient molecular alterations of the genome, transcriptome, and the epigenome. The insights provided by the growing use of next-generation sequencing (NGS) in lung cancer will be discussed, and interrelated concepts such as intertumor heterogeneity, intratumor heterogeneity, tumor mutational burden, and the advent of liquid biopsy will be explored. Moreover, this work describes how the evolving field of molecular pathology refines the understanding of different histologic phenotypes of non-small-cell lung cancer (NSCLC) and the underlying biology of small-cell lung cancer. This review will provide an appreciation for how ongoing scientific findings and technologic advances in molecular pathology are crucial for development of biomarkers, therapeutic agents, clinical trials, and ultimately improved patient care.

Feasibility of prognosis assessment for cancer of unknown primary origin using texture analysis of 18F-fluorodeoxyglucose PET/computed tomography images of largest metastatic lymph node

OBJECTIVE

Cancers of unknown primary origin cannot be staged using images, making the prognosis difficult. We attempted to predict prognosis of patients with unknown primary origin using tumour heterogeneity recently introduced in F-fluorodeoxyglucose (F-FDG) PET/computed tomography (CT).

METHODS

Overall, 30 patients with unknown primary origin who underwent whole-body F-FDG PET/CT scans were retrospectively enrolled for texture analysis. The volume of interest was placed in the largest metastatic lymph nodes and conventional parameters and grey-level co-occurrence matrix (GLCM) were calculated. Statistical analysis of image-based variables was performed using Cox regression analyses. Patients were stratified into two groups based on cutoff values of GLCMentropy obtained using receiver operating characteristics (ROCs). Patients were analyzed, and overall survival (OS) was compared using Kaplan-Meier analysis.

RESULTS

Univariate Cox regression analysis showed significant differences in prognosis for parenchymal organ metastasis (P < 0.01), GLCM homogeneity (P = 0.01), GLCMcontrast (P < 0.01), GLCMentropy (P < 0.01) and GLCMdissimilarity (P < 0.01). Multivariate Cox regression analysis showed a significant difference in reduced prognosis for GLCMentropy positive (P < 0.01). Stratification was performed based on the GLCMentropy cutoff value, determined using ROCs analysis, with smaller groups showing better OS.

CONCLUSIONS

Despite previous difficulties in predicting prognosis in patients with unknown primary origin, F-FDG PET/CT texture features may enable stratification of prognosis. This could be useful for appropriate patient selection and management and help identify a subset of patients with favourable outcomes. These novel findings may be helpful for prognostication and improving patient care.

Cell-blocks and immunohistochemistry

The interpretation of results on immunostained cell-block sections has to be compared with the cumulative published data derived predominantly from formalin-fixed paraffin-embedded (FFPE) tissue sections. Because of this, it is important to recognize that the fixation and processing protocol should not be different from the routinely processed FFPE surgical pathology tissue. Exposure to non-formalin fixatives or reagents may interfere with the diagnostic immunoreactivity pattern. The immunoprofile observed on such cell-blocks, which are not processed in a manner similar to the surgical pathology specimens, may not be representative resulting in aberrant results. The field of immunohistochemistry (IHC) is advancing continuously with the standardization of many immunomarkers. A variety of technical advances such as multiplex IHC with refined methodologies and automation is increasing its role in clinical applications. The recent addition of rabbit monoclonal antibodies has further improved sensitivity. As compared to the mouse monoclonal antibodies, the rabbit monoclonal antibodies have 10 to 100 fold higher antigen affinity. Most of the scenarios involve the evaluation of coordinate immunostaining patterns in cell-blocks with relatively scant diagnostic material without proper orientation which is usually retained in most of the surgical pathology specimens. These challenges are addressed if cell-blocks are prepared with some dedicated methodologies such as NextGen CelBloking™ (NGCB) kits. Cell-blocks prepared by NGCB kits also facilitate the easy application of the SCIP (subtractive coordinate immunoreactivity pattern) approach for proper evaluation of coordinate immunoreactivity. Various cell-block and IHC-related issues are discussed in detail.

A Machine Learning Approach for Tracing Tumor Original Sites With Gene Expression Profiles

Some carcinomas show that one or more metastatic sites appear with unknown origins. The identification of primary or metastatic tumor tissues is crucial for physicians to develop precise treatment plans for patients. With unknown primary origin sites, it is challenging to design specific plans for patients. Usually, those patients receive broad-spectrum chemotherapy, while still having poor prognosis though. Machine learning has been widely used and already achieved significant advantages in clinical practices. In this study, we classify and predict a large number of tumor samples with uncertain origins by applying the random forest and Naive Bayesian algorithms. We use the precision, recall, and other measurements to evaluate the performance of our approach. The results have showed that the prediction accuracy of this method was 90.4 for 7,713 samples. The accuracy was 80% for 20 metastatic tumors samples. In addition, the 10-fold cross-validation is used to evaluate the accuracy of classification, which reaches 91%.

The role of molecular profiling in the diagnosis and management of metastatic undifferentiated cancer of unknown primary✰: Molecular profiling of metastatic cancer of unknown primary

Cancer of unknown primary (CUP) refers to metastatic tumors for which the primary tumor of origin cannot be determined at the time of diagnosis, despite extensive clinicopathologic investigations. Molecular profiling is increasingly able to predict a probable primary tumor type for CUP when clinicopathologic workup is inconclusive. Numerous studies have explored the use of various molecular profiling techniques for identification of site/tissue of origin of CUP. These techniques include gene expression profiling utilizing microarray, reverse transcriptase polymerase chain reaction, RNA-sequencing, somatic gene mutation profiling with next-generation DNA sequencing, and epigenomics including DNA methylation profiling. Despite the generally poor prognosis of CUP, a minority of patients can expect to benefit from targeted therapy despite being agnostic to the tissue of origin. Studies have explored the use of various molecular profiling techniques to predict prognostic and therapeutic biomarkers, with the goal of improving outcome for patients with CUP. However, discordant results between non-randomized and randomized clinical trials in evaluating tumor-type specific therapies raise uncertainties of the benefits of molecularly-predicted tissue of origin-based treatment in routine clinical use. Nevertheless, the current overall trend is in favor of using molecular tools to refine the diagnosis and clinical management of patients with CUP. More large-cohort, randomized prospective studies are needed to assess and validate the utility and feasibility of molecular profiling to uncover potentially targetable genetic alterations. These efforts will also yield further biological insights into the biology and pathogenesis of CUP (Graphical Abstract).

The spectrum of pathological diagnoses in non-sentinel axillary lymph node biopsy: A single institution's experience

Although axillary lymphadenopathy is a common clinical encounter, systemic evaluation of non-sentinel lymph node biopsy is sparse. We reviewed our institution's 15-year experience to delineate the spectrum of diagnoses in non-sentinel axillary lymph nodes. 1165 non-sentinel axillary lymph node biopsies were retrieved and the diagnosis and relevant clinical information was reviewed. This spectrum of diagnoses was further stratified by gender, age, and oncologic history. The spectrum of diagnoses included: breast carcinoma (27.6%), lymphoma (29.2%), melanoma (3.5%), other carcinoma (2.9%), sarcoma (0.4%), and benign changes (36.3%). The most common diagnoses in men were lymphoma (61.8%) and benign changes (23.6%); while in women they were benign change (41.2%), breast carcinoma (37.8%) and lymphoma (16.7%). Besides benign changes, lymphoma and breast carcinoma were most common in women younger and older than 30 years, respectively. In patients with a history of malignancy, the most common diagnoses were metastasis from the known tumor and benign change; while in patients with a negative oncologic history and female patients without a history of breast cancer, the diagnosis was generally either lymphoma or benign change. Anaplastic large cell lymphoma was rare but may be mistaken as metastatic carcinoma thus a high index of suspicion is warranted. Thus through retrospective review of a large cohort of non-sentinel axillary lymph node biopsies, we described the spectrum of pathological entities based on the gender, age, and clinical history, which could provide valuable information for further work-up of axillary lymph node biopsy.

The diagnostic challenges of patients with carcinoma of unknown primary

INTRODUCTION

Cancer of unknown primary (CUP) is a disease entity encompassing heterogeneous malignancies without a clinically-detectable anatomical primary. It is usually a poor prognosis malignancy with dismal prognosis where molecular and genetic testing were expected to be a major breakthrough.

AREAS COVERED

In this review, we provide an overview of the advances in the understanding of the carcinogenesis, biology, diagnosis and treatment of patients with CUP. This review focuses on the advantages and inconveniences of immunohistochemistry and CUP classifiers in assessing the progress in the management of CUP.

EXPERT OPINION

CUP classifiers were expected to gradually replace the classical multistep approach in identifying the culprit tumors to guide site-specific therapy. Immunohistochemistry staining led to the prediction of a single tissue of origin in 10.8-51%. CUP classifiers identified the primary site in 61-89% of these cases and were concordant with immunohistochemistry in 57.1-100%. Immunohistochemistry is cheap, fast and broadly available whereas CUP classifiers are less widely available and have not been validated in randomized control trials. The diagnostic recommendations consist of a standard pathology evaluation based on morphology and algorithmic immunohistochemistry assessment. Physicians should weigh in the input of the CUP classifier to the clinical picture and pathology investigations before performing additional investigations.

Progress in refining the clinical management of cancer of unknown primary in the molecular era

Cancer of unknown primary (CUP) is an enigmatic disease entity encompassing heterogeneous malignancies without a detectable primary tumour, despite a thorough diagnostic workup. A minority of patients with CUP (15-20%) can be assigned a putative primary tissue of origin according to clinical and histopathological findings and typically have a more favourable prognosis with the use of corresponding tumour type-specific therapies. Thus, the majority of patients with CUP have disease that cannot be assigned to a culprit primary tumour, are treated with empirical chemotherapy and have a poor prognosis. In the molecular era, the use of (epi)genomic or transcriptomic CUP classifiers and DNA or RNA sequencing offers two, sometimes overlapping, therapeutic strategies: tumour type-specific therapy and biomarker-guided therapy. Published data reveal that the accuracy of site-of-origin predictions made using CUP classifiers ranges between 54% and 98% when compared with the assignment made according to the recommended clinicopathological criteria. These advances have led to promising results in non-randomized prospective studies evaluating the efficacy of tumour type-specific therapy; however, the favourable outcomes were not confirmed in randomized controlled studies comparing this approach with standard empirical chemotherapy. Currently, the evidence supporting the use of biomarker-guided therapies is limited to case reports and small case series. In this Review, we discuss the clinical management of CUP in the era of precision medicine. We focus on the advances in understanding the biology of CUP, the implications for the diagnosis and classification of CUP according to the tissue of origin and the shift away from empirical therapy towards tailored therapy.

Cancer of Unknown Primary Site: Real Entity or Misdiagnosed Disease?

Metastasis is a late event in the progression of any tumour. However, invasive cancers are occasionally detected in the form of metastatic lesions without a clearly detectable primary tumour. Cancer of unknown primary site (CUP) is defined as a confirmed metastatic tumour, with unknown primary tumour site, despite the standardized diagnostic approach that includes clinical history, routine laboratory tests, and complete physical examination. Due to the lack of basic research on its primary causes, CUP is appropriately termed an 'orphan' cancer. Nevertheless, CUP accounts for 2-5% of diagnosed malignancies. To date, it is unclear whether CUP is an entity with primary dormancy as its hallmark or an entity with genetic abnormalities that cause it to manifest as a primary metastatic disease. In this review, we discuss different aspects of CUP, including its current diagnostic methods, angiogenesis effectors, relationship with cancer stem cells and current treatments.

Genomic profiling in oncology clinical practice

The development of high-throughput technologies such as next-generation sequencing for DNA sequencing together with the decrease in their cost has led to the progressive introduction of genomic profiling in our daily practice in oncology. Nowadays, genomic profiling is part of genetic counseling, cancer diagnosis, molecular characterization, and as a biomarker of prognosis and response to treatment. Furthermore, germline or somatic genomic characterization of the tumor may provide new treatment opportunities for patients with cancer. In this review, we will summarize the clinical applications and limitations of genomic profiling in oncology clinical practice, focusing on next-generation sequencing.

A Review on Cancer of Unknown Primary Origin: The Role of Molecular Biomarkers in the Identification of Unknown Primary Origin

The primary site cannot be found after clinical and pathological evaluation, which are called cancers of unknown primary origin (CUP). CUPs may resemble a specific primary tumor site which shares common clinicopathological characteristics and prognosis. However, it may be present as a distinct disease entity with undifferentiated pathological features. More than 4% of patients are diagnosed as CUP. These patients were diagnosed as malignant tumors by cytology or pathology. And they were usually treated with empirical chemotherapy and associated with a poor prognosis. How to accurately diagnose and treat a cancer of unknown primary origin is a major clinical concern. To address this question, a complex assessment is carried out which includes a complete medical history of the patient, physical examination, complete blood count, urinalysis, serum chemistries, histologic evaluation, chest radiograph, computed tomography, magnetic resonance imaging, and immunohistochemistry (IHC) studies. Molecular diagnostic information reflects that CUP's molecular characteristics are similar to primary tumors with the development of genomics and the expansion of gene sequencing technology. Gene expression profiling is the most commonly used molecular diagnostic method for CUP. In this chapter, we summarize the current diagnostic methods and challenges of CUP, and the clinical value of the molecular-level tumor diagnostic technique.

Complete response to crizotinib in a metastatic adenocarcinoma of unknown primary harboring MET amplification and NTRK1 co-occurring mutation

Carcinomas of unknown primary (CUPs) have poor prognosis due to the paucity of data on their clinical characteristics and laboratory features, and empirical chemotherapy still remains the critical management for this kind of disease. This study aimed to present the knowledge of treating an elderly man with metastatic adenocarcinoma of unknown primary and also with a history of long-term hypertension and renal cysts. He was identified to harbor mesenchymal-epithelial transition factor (MET) gene amplification and neurotrophic tyrosine receptor kinase 1 (NTRK1) gene co-occurring mutation by targeted next-generation sequencing analysis upon the progression of empirical chemotherapy. He was then treated with a standard dose of crizotinib (250 mg, twice daily), which exhibited a satisfactory complete response (CR) of the targeted lesions after 1 month of treatment. When the number of renal cysts increased and renal inadequacy occurred after treatment for 2 months, crizotinib was reduced to half-dose (250 mg, once daily), and still conferred maintenance of CR for another 6.5 months and good quality life of the patient. These results suggested that treatments based on driver genes rather than primary tumor types could be a promising manipulation for achieving better treatment outcome, and a half-dose of crizotinib might be both effective and tolerable for MET-overexpressed CUPs with underlying renal diseases.

Does Cancer of Unknown Primary (CUP) Truly Exist as a Distinct Cancer Entity?

Cancer of unknown primary (CUP) designates an enigmatic cancer entity with histologic confirmation of malignancy from a metastasis but no identifiable primary tumor in spite of a thorough diagnostic work-up. In this review, we discuss the validity of CUP as a distinct cancer entity as well as diagnostic pitfalls. As arguments against a distinct entity, the diagnosis of CUP is erroneous in some cases. Diagnostic pitfalls include incomplete diagnostics, uncertainty in classifying a lesion as either primary or metastasis and mistaking a relapse of an antecedent malignancy as CUP due to histologic and immunohistologic disparities. Given the high frequency of prior malignancies in CUP patients, relapse of an antecedent cancer should always be carefully excluded. Gene expression profiling-based classifier assays aim at aligning the molecular profile of CUP patients with established primary cancer patterns for highest congruency in order to identify the putative primary and treat accordingly. However, the spectrum of predicted putative primaries by molecular techniques is somewhat at odds with the primaries identified in autopsy series. Also, a first randomized clinical trial did not show superiority of primary-tailored therapy over unspecific platinum-based chemotherapy. CUP cases share an aggressive clinical course, atypical metastasis pattern, rapid progression of metastases, a generally poor response to chemotherapy and dismal outcome as distinct clinical features. Metastatic spread appears to take place in the early stages of tumor evolution, with CUP metastases subsequently undergoing genetic evolution toward a chromosomally highly complex and instable karyotype independent from the primary tumor. In clinical practice, the diagnosis of CUP is valid when no primary tumor is detectable. Treatment should ideally offer broad spectrum coverage across numerous malignancies and be well-established in CUP as is the case for carboplatin/paclitaxel and cisplatin / gemcitabine in particular, but it should also cover the most likely putative primary. The diligent diagnosis of CUP is warranted for clinical trials, making the eligibility process particularly laborious. In conclusion, we deem CUP a distinct cancer entity and the diagnosis accurate in most patient cases.

[Carcinoma with unknown primary site: Morphological diagnosis]

Carcinoma with unknown primary site (CUPs) is a group of malignant tumors, the first manifestation of which is metastatic dissemination. A primary tumor cannot be usually identified by a physical examination of patients with CUPs; a postmortem study plays a significant role in the diagnosis of the origin of metastasis. The paper gives the data available in the literature data on the postmortem diagnosis of CUPs and considers the morphological characteristics of metastases and the possibilities of immunohistochemical diagnosis and a molecular genetic method in the search for a primary focus.

Multi-Institutional, Prospective Clinical Utility Study Evaluating the Impact of the 92-Gene Assay (CancerTYPE ID) on Final Diagnosis and Treatment Planning in Patients With Metastatic Cancer With an Unknown or Unclear Diagnosis

Purpose

Metastatic cancers of unknown primary or with unclear diagnoses pose diagnostic and management challenges, often leading to poor outcomes. Studies of the 92-gene assay have demonstrated improved diagnostic accuracy compared with standard pathology techniques and improved survival in patients treated on the basis of assay results. The current study assessed the clinical impact of the 92-gene assay on diagnostic and treatment decisions for patients with unknown or uncertain diagnoses.

Methods

Patients in this prospective, multi-institutional, decision-impact study included those for whom the 92-gene assay was ordered as part of routine care. Participating physicians completed electronic case report forms that contained standardized, specialty-specific questionnaires. Data collection included patient and tumor characteristics and clinical history. The key study objective of clinical impact was calculated on the basis of changes in final diagnosis and treatment after testing.

Results

Data collection included 444 patients, 107 physicians (73 oncologists and 34 pathologists), and 28 sites. Molecular diagnoses from 22 different tumor types and subtypes across all cases were provided in 95.5% of patients with a reportable result (n = 397). Physicians reported that the 92-gene assay was used broadly for diagnostic dilemmas that ranged from single suspected tumor type (29%) to a differential diagnosis of two or more suspected tumor types (30%) or cancers of unknown primary (41%). Integration of 92-gene assay results led to a change in the recommended treatment in 47% of patients.

Conclusion

Findings from this clinical utility study demonstrate that the 92-gene assay led to a change in treatment decisions in every other patient case. These data additionally define the role of this assay in clinical practice and strongly support the consideration of molecular tumor typing in the diagnosis and treatment planning of patients with metastatic cancer with unknown or uncertain diagnosis.

Molecular Diagnostics in Clinical Oncology

There are multiple applications of molecular tests in clinical oncology. Mutation analysis is now routinely utilized for the diagnosis of hereditary cancer syndromes. Healthy carriers of cancer-predisposing mutations benefit from tight medical surveillance and various preventive interventions. Cancers caused by germ-line mutations often require significant modification of the treatment strategy. Personalized selection of cancer drugs based on the presence of actionable mutations has become an integral part of cancer therapy. Molecular tests underlie the administration of EGFR, BRAF, ALK, ROS1, PARP inhibitors as well as the use of some other cytotoxic and targeted drugs. Tumors almost always shed their fragments (single cells or their clusters, DNA, RNA, proteins) into various body fluids. So-called liquid biopsy, i.e., the analysis of circulating DNA or some other tumor-derived molecules, holds a great promise for non-invasive monitoring of cancer disease, analysis of drug-sensitizing mutations and early cancer detection. Some tumor- or tissue-specific mutations and expression markers can be efficiently utilized for the diagnosis of cancers of unknown primary origin (CUPs). Systematic cataloging of tumor molecular portraits is likely to uncover a multitude of novel medically relevant DNA- and RNA-based markers.

Site-specific Chemotherapy Based on Predicted Primary Site by Pathological Profile for Carcinoma of Unknown Primary Site

AIMS

Although platinum-based combination chemotherapies are commonly used for unfavourable subsets of cancer of unknown primary (CUP), the prognosis remains poor. Several studies have suggested that gene expression profiling or immunohistochemistry was useful for the prediction of primary sites in CUP, and site-specific therapy based on predicted primary sites might improve overall outcomes. In Japan, to identify primary sites, immunohistochemical tests were commonly used for CUP in clinical practice. However, it is unclear whether site-specific therapy based on predicted primary sites by pathological examination contributes survival benefit for unfavourable CUP subsets.

PATIENTS AND METHODS

In this study, 122 patients with unfavourable subsets of CUP were retrospectively reviewed. Ninety patients assigned to cohort A after July 2012 had received chemotherapy according to predicted primary sites; 32 patients assigned to cohort B before June 2012 had received platinum-based empiric chemotherapy.

RESULTS

In cohort A, 56 patients (62.2%) with predicted primary sites by pathological examination received site-specific therapy; 34 patients (37.8%) with unpredictable primary sites received platinum-based empiric chemotherapy, the same as cohort B. The median overall survival was 20.3 months in patients with predictable primary sites in cohort A and 10.7 months in those of cohort B, with a significant difference between these cohorts (P = 0.03, adjusted hazard ratio = 0.57, 95% confidence interval 0.34-0.94).

CONCLUSION

Site-specific therapy based on predicted primary sites by pathological examination could improve prognosis in patients with an unfavourable subset of CUP.

Immunohistochemistry for Diagnosis of Metastatic Carcinomas of Unknown Primary Site

Immunohistochemistry has become an essential ancillary examination for the identification and classification of carcinomas of unknown primary site (CUPs). Over the last decade, the diagnostic accuracy of organ- or tumour-specific immunomarkers and the clinical validation of effective immunohistochemical panels has improved significantly. When dealing with small sample sizes, diagnostic accuracy is crucial, particularly in the current era of targeted molecular and immune-based therapies. Effective systematic use of appropriate immunohistochemical panels enables accurate classification of most of the undifferentiated carcinomas as well as careful preservation of tissues for potential molecular or other ancillary tests. This review discusses the algorithmic approach to the diagnosis of CUPs using CK7 and CK20 staining patterns. It outlines the most frequently used tissue-specific antibodies, provides some pitfalls essential in avoiding potential diagnostic errors and discusses the complementary tools, such as molecular tumour profiling and mutation-specific antibodies, for the improvement of diagnosis and prediction of the treatment response.

Novel putative drivers revealed by targeted exome sequencing of advanced solid tumors

Next generation sequencing (NGS) is becoming increasingly integrated into oncological practice and clinical research. NGS methods have also provided evidence for clonal evolution of cancers during disease progression and treatment. The number of variants associated with response to specific therapeutic agents keeps increasing. However, the identification of novel driver mutations as opposed to passenger (phenotypically silent or clinically irrelevant) mutations remains a major challenge. We conducted targeted exome sequencing of advanced solid tumors from 44 pre-treated patients with solid tumors including breast, colorectal and lung carcinomas, neuroendocrine tumors, sarcomas and others. We catalogued established driver mutations and putative new drivers as predicted by two distinct algorithms. The established drivers we detected were consistent with published observations. However, we also detected a significant number of mutations with driver potential never described before in each tumor type we studied. These putative drivers belong to key cell fate regulatory networks, including potentially druggable pathways. Should our observations be confirmed, they would support the hypothesis that new driver mutations are selected by treatment in clinically aggressive tumors, and indicate a need for longitudinal genomic testing of solid tumors to inform second line cancer treatment.

Cancer diagnostics: The journey from histomorphology to molecular profiling

Although histomorphology has made significant advances into the understanding of cancer etiology, classification and pathogenesis, it is sometimes complicated by morphologic ambiguities, and other shortcomings that necessitate the development of ancillary tests to complement its diagnostic value. A new approach to cancer patient management consists of targeting specific molecules or gene mutations in the cancer genome by inhibitory therapy. Molecular diagnostic tests and genomic profiling methods are increasingly being developed to identify tumor targeted molecular profile that is the basis of targeted therapy. Novel targeted therapy has revolutionized the treatment of gastrointestinal stromal tumor, renal cell carcinoma and other cancers that were previously difficult to treat with standard chemotherapy. In this review, we discuss the role of histomorphology in cancer diagnosis and management and the rising role of molecular profiling in targeted therapy. Molecular profiling in certain diagnostic and therapeutic difficulties may provide a practical and useful complement to histomorphology and opens new avenues for targeted therapy and alternative methods of cancer patient management.

SEOM clinical guideline on unknown primary cancer (2017)

Cancer of unknown primary site is a histologically confirmed cancer that manifests in advanced stage, with no identifiable primary site following standard diagnostic procedures. Patients are initially categorized based on the findings of the initial biopsy: adenocarcinoma, squamous-cell carcinoma, neuroendocrine carcinoma, and poorly differentiated carcinoma. Appropriate patient management requires understanding several clinical and pathological features that aid in identifying several subsets of patients with more responsive tumors.

Diagnosis and management of metastatic neoplasms with unknown primary

In cancer of unknown primary (CUP), metastases are clinically and histologically confirmed, but the primary tumor site remains elusive after extensive work-up. CUPs make up for 2-3% of all epithelial malignancies. The two prevailing histologies are adenocarcinomas and undifferentiated carcinomas, whereas squamous cell carcinomas, neuroendocrine carcinomas and rare histologies account for the remaining 10%. The diagnostic work-up in CUP relies strongly on a detailed immunohistological (IHC) analysis in order to characterize the tumor type, nowadays aided by molecular techniques. Diagnostics also include a thorough clinical examination, a basic lab draw with the most relevant tumor markers, and cross sectional imaging. Additional PET-CT is recommended in cervical lymph nodes suggestive of head and neck cancer and in limited metastases potentially treatable in curative intent. As for treatment, it is paramount to identify patients who fall into one of the six well defined "favorable" subset categories, namely extragonadal germ cell tumors, adenocarcinoma with isolated unilateral axillary lymph nodes in female patients, squamous cell carcinoma with neck lymph nodes, squamous cell carcinoma with inguinal lymph nodes, serous papillary peritoneal carcinomatosis in females and blastic bone metastasis in males with elevated PSA. These subsets are distinct both regarding the required treatment and the comparably favorable prognosis. Within the remaining "unfavorable" group, patients of colon and renal cancer type should be identified based on IHC and clinical picture, since the prognosis of these patients seems to improve with the use of therapy tailored to the presumed primary as well. For the few patients with limited metastases it should be assessed whether they are candidates for surgery, radiotherapy or surgery followed by irradiation in curative intent. The remaining majority of patients are treated with empiric palliative chemotherapy, typically a platinum - paclitaxel combination, though the level of evidence for this therapy recommendation is low. Gemcitabine alone or in combination can be used as an alternative. Decoding of the molecular profiles in CUP offers the prospect of targeted therapy with novel agents. However, there appears to be no uniform molecular pattern for CUP, and the observed molecular diversity thus poses a challenge to respective clinical trials.

MET Activation and Physical Dynamics of the Metastatic Process: The Paradigm of Cancers of Unknown Primary Origin

The molecular and cellular mechanisms which drive metastatic spread are the topic of constant debate and scientific research due to the potential implications for cancer patients' prognosis. In addition to genetics and environmental factors, mechanics of single cells and physical interaction with the surrounding environment play relevant role in defining invasive phenotype. Reconstructing the physical properties of metastatic clones may help to clarify still open issues in disease progression as well as to lead to new diagnostic and therapeutic approaches. In this perspective cancer of unknown primary origin (CUP) identify the ideal model to study physical interactions and forces involved in the metastatic process. We have previously demonstrated that MET oncogene is mutated with unexpected high frequency in CUPs. We here analyze and discuss how the MET activation by somatic mutation may affect physical properties in giving rise to such a highly malignant syndrome, as that defined by CUP.

Neck lymph node metastases from unknown primary

Metastatic cervical carcinoma from unknown primary is a metastatic disease in the lymph nodes of the neck without any evidence of a primary tumour after appropriate investigation. The condition is rare and definite evidence is lacking for both diagnosis and treatment. In this review of the literature, we tried to draw some clinical indications based on the few available studies. We ultimately came to the following conclusions: (1) a thorough and accurate diagnostic work-up should be systematically offered. It includes accurate inspection with fibroscopy, CT or MRI, fine needle aspiration, panendoscopy and positron emission tomography, (2) Patients with low-volume neck disease, N1 and N2a stage and without extracapsular extension on histopathological examination should receive single modality treatment. Radiotherapy and surgery may be similarly effective but, if possible, surgery (excisional biopsy, neck dissection and tonsillectomy) should be favoured because it consents a more precise staging, (3) patients with more advanced conditions require combined treatment in the form of either resection followed by adjuvant radiation (±chemotherapy) or primary chemoradiation (±post-therapy neck dissection).

Lung Adenocarcinoma with Anaplastic Lymphoma Kinase (ALK) Rearrangement Presenting as Carcinoma of Unknown Primary Site: Recognition and Treatment Implications

Background

Molecular cancer classifier assays are being used with increasing frequency to predict tissue of origin and direct site-specific therapy for patients with carcinoma of unknown primary site (CUP).

Objective

We postulated some CUP patients predicted to have non-small-cell lung cancer (NSCLC) by molecular cancer classifier assay may have anaplastic lymphoma kinase (ALK) rearranged tumors, and benefit from treatment with ALK inhibitors.

Methods

We retrospectively reviewed CUP patients who had the 92-gene molecular cancer classifier assay (CancerTYPE ID; bioTheranostics, Inc.) performed on tumor biopsies to identify patients predicted to have NSCLC. Beginning in 2011, we have tested these patients for ALK rearrangements and epidermal growth factor receptor (EGFR) activating mutations, based on the proven therapeutic value of these targets in NSCLC. We identified CUP patients with predicted NSCLC who were subsequently found to have ALK rearrangements.

Results

NSCLC was predicted by the molecular cancer classifier assay in 37 of 310 CUP patients. Twenty-one of these patients were tested for ALK rearrangements, and four had an EML4-ALK fusion gene detected. The diagnosis of lung cancer was strongly suggested in only one patient prior to molecular testing. One patient received ALK inhibitor treatment and has had prolonged benefit.

Conclusions

We report on patients with lung adenocarcinoma and ALK rearrangements originally diagnosed as CUP who were identified using a molecular cancer classifier assay. Although ALK inhibitors treatment experience is limited, this newly identifiable group of lung cancer patients should be considered for therapy according to guidelines for stage IV ALK-positive NSCLC.

Poorly differentiated neoplasms of unknown primary site: diagnostic usefulness of a molecular cancer classifier assay

PURPOSE

Definition of the lineage of poorly differentiated neoplasms (PDNs) presenting as cancer of unknown primary site (CUP) is important since many of these tumors are treatment-sensitive. Gene expression profiling and a molecular cancer classifier assay (MCCA) may provide a new method of diagnosis when standard pathologic evaluation and immunohistochemical (IHC) staining is unsuccessful.

PATIENTS AND METHODS

Thirty of 751 CUP patients (4%) seen from 2000-2012 had PDNs without a definitive lineage diagnosed by histology or IHC (median 18 stains, range 9-46). Biopsies from these 30 patients had MCCA (92-gene reverse transcriptase-polymerase chain reaction mRNA) performed. Additional IHC, gene sequencing, fluorescent in situ hybridization for specific genetic alterations, and repeat biopsies were performed to support MCCA diagnoses, and clinical features correlated. Seven patients had MCCA performed initially and received site-specific therapy.

RESULTS

Lineage diagnoses were made by MCCA in 25 of 30 (83 %) patients, including ten carcinomas (three germ cell, two neuroendocrine, five others), eight sarcomas [three peritoneal mesotheliomas, one primitive neuroectodermal tumor (PNET), four others], five melanomas, and two lymphomas. Additional IHC and genetic testing [BRAF, i(12)p] supported the MCCA diagnoses in 11 of 16 tumors. All seven patients (two germ cell, two neuroendocrine, two mesothelioma, one lymphoma) responded to site-specific therapy based on the MCCA diagnosis, and remain alive (five progression-free) from 25+ to 72+ months.

CONCLUSION

The MCCA provided a specific lineage diagnosis and tissue of origin in most patients with PDNs unclassifiable by standard pathologic evaluation. Earlier use of MCCA will expedite diagnosis and direct appropriate first-line therapy, which is potentially curative for several of these tumor types.

Practical Applications in Immunohistochemistry: Carcinomas of Unknown Primary Site

CONTEXT

-Identification of the site of origin of carcinoma of unknown primary using immunohistochemistry is a frequent requirement of anatomic pathologists. Diagnostic accuracy is crucial, particularly in the current era of targeted therapies and smaller sample sizes.

OBJECTIVES

-To provide practical guidance and suggestions for classifying carcinoma of unknown primary using both proven and new antibodies, as well as targeting panels based on integration of morphologic and clinical features.

DATA SOURCES

-Literature review, the authors' practice experience, and authors' research.

CONCLUSIONS

-With well-performed and interpreted immunohistochemistry panels, anatomic pathologists can successfully identify the site of origin of carcinoma of unknown primary. It is crucial to understand not only the diagnostic uses of the many available antibodies but also the potential limits and pitfalls.

Granulocyte colony-stimulating factor-producing carcinoma of unknown primary site

Granulocyte colony-stimulating factor (G-CSF)-producing nonhematopoietic malignancies have been reported in various organs and are associated with a poor clinical outcome. Moreover, carcinoma of unknown primary site (CUP) is an uncommon malignancy that occurs in about 2-6% of cancer patients. CUP also has a poor prognosis due to its missing profile. Since both G-CSF-producing carcinoma and CUP are rare, G-CSF-producing CUP (GCSF-CUP) is considered to have an even poorer prognosis and is seldom encountered. Herein, we report the case of a GCSF-CUP patient. A 75-year-old man was admitted to our hospital complaining of cervical lymphadenopathy. Multiple bulky lymph nodes without a primary site were revealed by image analysis. His complete blood count showed leukocytosis, and his blood chemistry panel indicated highly elevated levels of G-CSF. Although the patient was treated with combination chemotherapy of carboplatin, paclitaxel, bevacizumab and erlotinib, he died of intestinal perforation due to tumor invasion 23 days after the start of the therapy. An autopsy confirmed that the tumor was positive for anti-G-CSF antibody, but the primary site was still not detected.

Development and validation of a microRNA based diagnostic assay for primary tumor site classification of liver core biopsies

Identification of the primary tumor site in patients with metastatic cancer is clinically important, but remains a challenge. Hence, efforts have been made towards establishing new diagnostic tools. Molecular profiling is a promising diagnostic approach, but tissue heterogeneity and inadequacy may negatively affect the accuracy and usability of molecular classifiers. We have developed and validated a microRNA-based classifier, which predicts the primary tumor site of liver biopsies, containing a limited number of tumor cells. Concurrently we explored the influence of surrounding normal tissue on classification. MicroRNA profiling was performed using quantitative Real-Time PCR on formalin-fixed paraffin-embedded samples. 278 primary tumors and liver metastases, representing nine primary tumor classes, as well as normal liver samples were used as a training set. A statistical model was applied to adjust for normal liver tissue contamination. Performance was estimated by cross-validation, followed by independent validation on 55 liver core biopsies with a tumor content as low as 10%. A microRNA classifier developed, using the statistical contamination model, showed an overall classification accuracy of 74.5% upon independent validation. Two-thirds of the samples were classified with high-confidence, with an accuracy of 92% on high-confidence predictions. A classifier trained without adjusting for liver tissue contamination, showed a classification accuracy of 38.2%. Our results indicate that surrounding normal tissue from the biopsy site may critically influence molecular classification. A significant improvement in classification accuracy was obtained when the influence of normal tissue was limited by application of a statistical contamination model.

Mutational profiling of the RAS, PI3K, MET and b-catenin pathways in cancer of unknown primary: a retrospective study of the Hellenic Cooperative Oncology Group

Cancer of unknown primary origin (CUP) had a poor prognosis, determined by clinico-histological characteristics, partly due to the lack of insights on its biology. We screened tumour DNA from 87 patients with CUP for CTNNB1 (coding exons 2,3,4,5), MET (coding exon 18), PIK3CA (coding exons 9,20), KRAS (coding exons 1,2), BRAF (coding exon 15) gene mutations by using dd-sequencing and evaluated their impact on prognosis. Mutated gene incidences in the 87 CUP cases were: KRAS 11 (12.6 %), BRAF 5 (5.7 %), PIK3CA 8 (9 %), MET 6 (6.7 %) and CTNNB1 18 (20.7 %). Several mutations in the KRAS gene were not the commonly encountered mutations in other solid tumours. Activating mutations were observed in 10.2 % in KRAS, 4.5 % in BRAF, 6.6 % in PIK3CA, 4.5 % in MET, and 19.5 % in CTNNB1. Activating mutations in PIK3CA coding exon 9 were inversely correlated with MET coding exon 18 activating mutations (p = 0.036). MET activating mutations were prognostic for poor Progression-Free Survival (median PFS 5 vs 9 months, p = 0.009) and Overall Survival (median OS 7 vs 20 months, p = 0.005). The complex profile of either CTNNB1 or MET mutations also had an adverse prognostic significance (median OS 11 vs 21 months, p = 0.015). No other gene mutation exhibited prognostic significance. In multivariate analysis, poor performance status, male gender, visceral disease and adenocarcinoma histology, but not gene mutations, were independently associated with poor patient outcome. CTNNB1 gene mutations are frequent, and along with MET mutations have an adverse prognostic effect in patients with CUP.