Carcinoma Of Unknown Primary Patients Research Articles

Retrospective analysis of clinical characteristics and outcomes of patients with carcinoma of unknown primary from three tertiary centers in Australia.

Carcinoma of unknown primary (CUP) remains an important tumor entity and a disproportionate cause of cancer mortality. Little is known about the contemporary clinical characteristics, treatment patterns, and outcomes of CUP patients based on updated international classification guidelines. We evaluated a contemporary CUP cohort to provide insight into current clinical practice and the impact of tissue of origin assignment, site-specific and empirical therapy in a real-world setting. We conducted a retrospective cohort study of CUP patients, as defined by the updated European Society of Medical Oncology (ESMO) 2023 guidelines, across three tertiary referral centers in Australia between 2015 and 2022. We analyzed clinical characteristics, treatment patterns, and survival outcomes using the Kaplan-Meier method and Cox regression proportional hazard model between favorable and unfavorable risk groups. We identified a total of 123 CUP patients (n = 86 unfavorable, n = 37 favorable risk as per the 2023 ESMO guidelines). Sixty-four patients (52%) were assigned a tissue of origin by the treating clinician. Median progression free survival (PFS) was 6.8 (95% confidence interval (CI) 5.1-12.1) months and overall survival (OS) 10.2 (95% CI 6.0-18.5) months. Unfavorable risk (hazard ratio [HR] 2.9, p = 0.006), poor performance status (HR 2.8, p < 0.001), and non-squamous histology (HR 2.5, p < 0.05) were associated with poor survival outcome. A total of 70 patients (57%) proceeded to systemic therapy. In patients with non-squamous histology and unfavorable risk, site-specific therapy compared to empirical chemotherapy did not improve outcome (median OS 8.2 vs. 11.8 months, p = 0.7). In this real-world cohort, CUP presentations were heterogenous. Overall survival and rates of systemic treatment were poor. Poor performance status and unfavorable risk were associated with worse survival. For most patients, site-specific therapy did not improve survival outcome. Improved and timely access to diagnostic tests and therapeutics for this group of patients is urgently required.

A cross-cohort computational framework to trace tumor tissue-of-origin based on RNA sequencing

Carcinoma of unknown primary (CUP) is a type of metastatic cancer with tissue-of-origin (TOO) unidentifiable by traditional methods. CUP patients typically have poor prognosis but therapy targeting the original cancer tissue can significantly improve patients’ prognosis. Thus, it’s critical to develop accurate computational methods to infer cancer TOO. While qPCR or microarray-based methods are effective in inferring TOO for most cancer types, the overall prediction accuracy is yet to be improved. In this study, we propose a cross-cohort computational framework to trace TOO of 32 cancer types based on RNA sequencing (RNA-seq). Specifically, we employed logistic regression models to select 80 genes for each cancer type to create a combined 1356-gene set, based on transcriptomic data from 9911 tissue samples covering the 32 cancer types with known TOO from the Cancer Genome Atlas (TCGA). The selected genes are enriched in both tissue-specific and tissue-general functions. The cross-validation accuracy of our framework reaches 97.50% across all cancer types. Furthermore, we tested the performance of our model on the TCGA metastatic dataset and International Cancer Genome Consortium (ICGC) dataset, achieving an accuracy of 91.09% and 82.67%, respectively, despite the differences in experiment procedures and pipelines. In conclusion, we developed an accurate yet robust computational framework for identifying TOO, which holds promise for clinical applications. Our code is available at http://github.com/wangbo00129/classifybysklearn.

Carcinoma of Unknown Primary (CUP) versus CUP Turned to Primary Carcinoma of the Head and Neck-An Analysis of Diagnostic Methods and the Impact of Primary Tumor on Clinical Outcome.

Background. The purpose of this study was to analyze the value of different diagnostic methods in detecting the primary site and the impact of primary tumors on the clinical outcome of carcinoma of unknown primary (CUP). Methods. In this multicenter, retrospective study, 124 patients with true CUP (n = 94) and CUP turned to primary carcinoma (n = 30) were included. Patients with evidence of primary site during the clinical examination were excluded a priori. The diagnostic procedure was comprised of imaging and invasive methods (fine-needle-aspiration, tonsillectomy and panendoscopy). All patients were treated with curative intent. Results. Despite extensive diagnostic workup, the primary site remained unknown in 75.8%. Invasive diagnostic methods showed higher primary detection rates than imaging modalities (15.1% vs. 7.8%). Tonsillectomy and panendoscopy revealed the primary tumor in 14.9% and 15.2% of patients, whereas the detection rates of CT, MRI and FDG-PET-CT were 10.1%, 4.8% and 6.5%, respectively. The occurrence of primary tumors led to a significantly deteriorating 5-year overall survival (p = 0.002) and emerged as survival prognosticator (HR = 2.764, p = 0.003). Conclusion. Clinical examination in combination with tonsillectomy and panendoscopy was superior to imaging alone in detecting the primary tumor. When the CUP of patients turned to a primary tumor, clinical outcome was significantly worse than in CUP patients.

Incidence of synchronous contralateral tonsillar malignancy in a known case of unilateral tonsillar carcinoma.

The literature is divided with regards to contralateral tonsillectomy in a known/suspected case of ipsilateral tonsillar malignancy. In this study, we evaluate the incidence of indolent synchronous contralateral tonsillar malignancy (SCTC) in patients with known ipsilateral tonsillar malignancy. All patients diagnosed with ipsilateral tonsillar carcinoma (TC) at a tertiary teaching center between January 2016 and December 2019 were screened. None of the patients were suspected to have bilateral TC. All patients underwent appropriate imaging in the form of Magnetic resonance imaging and computed tomography of head and neck region and then underwent bilateral tonsillectomy. The prevalence of bilateral tonsillar malignancy and the factors predicting them were analyzed. In all 59 patients were included in the study. The mean and median age of the patient population was 60.8 and 59years, respectively, with a male to female ratio of 3.2:1. The incidence of bilateral tonsillar malignancy in carcinoma of unknown primary (CUP) was 3/10 (33.3%). Among the remaining 49 patients, incidence of synchronous contralateral tonsillar carcinoma (SCTC) was 2/49 (4.08%). Overall, 5/59 (8.5%) patients had synchronous bilateral tonsillar malignancy. Furthermore, dysplasia was found in the contralateral tonsil in 4/10 (40%) CUP patients. Among the remaining 49 patients, dysplasia was seen in the contralateral tonsil in 20/49 (40.8%) patients. The absence of p16 expression predicted higher probability of SCTC. Factors like gender, T stage, nodal status or smoking did not predict SCTC. We recommend bilateral tonsillectomy in all patients with suspected or proven TC (unilateral or bilateral) and CUP as it helps identify indolent SCTC and it does not add any significant morbidity to the patients. III.

Local ablative treatment with surgery and/or radiotherapy in single-site and oligometastatic carcinoma of unknown primary

BackgroundSingle-site carcinoma of unknown primary (CUP) is recognised as a distinct favourable subtype in the European Society of Medical Oncology (ESMO) classification. There is broad consensus that these patients are candidates for local ablative treatment strategies with surgery and/or radiotherapy, but data on their outcomes are scarce. Patients and methodsIn this study, we have addressed the prospects of cure and prognostic factors in a retrospective cohort of 63 patients who were eligible for local treatment at our centre. ResultsMedian event-free (EFS) and overall survival (OS) were 15.6 months and 52.5 months, respectively. Of 61 patients who received local treatment, 20 (32.8%) remained event-free over a median follow-up of 28 months. Baseline clinical parameters including affected organ, number, volume and histology of metastases had no significant impact on prognosis, whereas deleterious TP53 mutations and DNA copy number loss emerged as independent adverse risk factors with respect to EFS. Surgical treatment was associated with improved OS as compared to radiation-based therapy. ConclusionOur study advocates to pursue localised treatment with surgery and/or radiotherapy whenever feasible and implies that genetic parameters might additionally determine the clinical course of single-site CUP patients.

Genomic alterations and possible druggable mutations in carcinoma of unknown primary (CUP)

Carcinoma of Unknown Primary (CUP) is a heterogeneous and metastatic disease where the primary site of origin is undetectable. Currently, chemotherapy is the only state-of-art treatment option for CUP patients. The molecular profiling of the tumour, particularly mutation detection, offers a new treatment approach for CUP in a personalized fashion using targeted agents. We analyzed the mutation and copy number alterations profile of 1709 CUP samples deposited in the AACR Project Genomics Evidence Neoplasia Information Exchange (GENIE) cohort and explored potentially druggable mutations. We identified 52 significant mutated genes (SMGs) among CUP samples, in which 13 (25%) of SMGs were potentially targetable with either drugs are approved for the know primary tumour or undergoing clinical trials. The most variants detected were TP53 (43%), KRAS (19.90%), KMT2D (12.60%), and CDKN2A (10.30%). Additionally, using pan-cancer analysis, we found similar variants of TERT promoter in CUP and NSCLC samples, suggesting that these mutations may serve as a diagnostic marker for identifying the primary tumour in CUP. Taken together, the mutation profiling analysis of the CUP tumours may open a new way of identifying druggable targets and consequently administrating appropriate treatment in a personalized manner.

Standardized Diagnostics Including PET-CT Imaging, Bilateral Tonsillectomy and Neck Dissection Followed by Risk-Adapted Post-Operative Treatment Favoring Radio-Chemotherapy Improve Survival of Neck Squamous Cell Carcinoma of Unknown Primary Patients.

BackgroundAbout five to 10% of cancers in the head and neck region are neck squamous cell carcinoma of unknown primary (NSCCUP). Their diagnosis and treatment are challenging given the risk of missing occult tumors and potential relapse. Recently, we described human papillomavirus (HPV)-related NSCCUP-patients (NSCCUP-P) as a subgroup with superior survival. However, standardized diagnostic workup, novel diagnostic procedures, decision-making in the multidisciplinary tumor board (MDTB) and multimodal therapy including surgery and post-operative radio-chemotherapy (PORCT) may also improve survival.MethodsFor assessing the impact of standardized diagnostic processes simultaneously established with the MDTB on outcome, we split our sample of 115 NSCCUP-P into two cohorts treated with curative intent from 1988 to 2006 (cohort 1; n = 53) and 2007 to 2018 (cohort 2; n = 62). We compared diagnostic processes and utilized treatment modalities applying Chi-square tests, and outcome by Kaplan–Meier plots and Cox regression.ResultsIn cohort 2, the standardized processes (regular use of [18F]-FDG-PET-CT imaging followed by examination under anesthesia, EUA, bilateral tonsillectomy and neck dissection, ND, at least of the affected site) improved detection of primaries (P = 0.026) mostly located in the oropharynx (P = 0.001). From 66.0 to 87.1% increased ND frequency (P = 0.007) increased the detection of extracapsular extension of neck nodes (ECE+) forcing risk factor-adapted treatment by increased utilization of cisplatin-based PORCT that improved 5-years progression-free and overall survival from 60.4 and 45.3 to 67.7% (P = 0.411) and 66.1% (P = 0.025).ConclusionsStandardized diagnostic workup followed by ND and risk-factor adapted therapy improves survival of NSCCUP-P.

Evaluating DNA Methylation, Gene Expression, Somatic Mutation, and Their Combinations in Inferring Tumor Tissue-of-Origin

Carcinoma of unknown primary (CUP) is a type of metastatic cancer, the primary tumor site of which cannot be identified. CUP occupies approximately 5% of cancer incidences in the United States with usually unfavorable prognosis, making it a big threat to public health. Traditional methods to identify the tissue-of-origin (TOO) of CUP like immunohistochemistry can only deal with around 20% CUP patients. In recent years, more and more studies suggest that it is promising to solve the problem by integrating machine learning techniques with big biomedical data involving multiple types of biomarkers including epigenetic, genetic, and gene expression profiles, such as DNA methylation. Different biomarkers play different roles in cancer research; for example, genomic mutations in a patient’s tumor could lead to specific anticancer drugs for treatment; DNA methylation and copy number variation could reveal tumor tissue of origin and molecular classification. However, there is no systematic comparison on which biomarker is better at identifying the cancer type and site of origin. In addition, it might also be possible to further improve the inference accuracy by integrating multiple types of biomarkers. In this study, we used primary tumor data rather than metastatic tumor data. Although the use of primary tumors may lead to some biases in our classification model, their tumor-of-origins are known. In addition, previous studies have suggested that the CUP prediction model built from primary tumors could efficiently predict TOO of metastatic cancers (Lal et al., 2013; Brachtel et al., 2016). We systematically compared the performances of three types of biomarkers including DNA methylation, gene expression profile, and somatic mutation as well as their combinations in inferring the TOO of CUP patients. First, we downloaded the gene expression profile, somatic mutation and DNA methylation data of 7,224 tumor samples across 21 common cancer types from the cancer genome atlas (TCGA) and generated seven different feature matrices through various combinations. Second, we performed feature selection by the Pearson correlation method. The selected features for each matrix were used to build up an XGBoost multi-label classification model to infer cancer TOO, an algorithm proven to be effective in a few previous studies. The performance of each biomarker and combination was compared by the 10-fold cross-validation process. Our results showed that the TOO tracing accuracy using gene expression profile was the highest, followed by DNA methylation, while somatic mutation performed the worst. Meanwhile, we found that simply combining multiple biomarkers does not have much effect in improving prediction accuracy.

Extensive diagnostic work-up for patients with carcinoma of unknown primary.

Patients with carcinoma of unknown primary (CUP) present with metastatic disease without an identified primary tumour. The unknown site of origin makes the diagnostic work-up and treatment challenging. Since little information is available regarding diagnostic work-up and treatment in daily practice, we collected and analysed these in a patient cohort with regard to the recommendations of the national CUP guideline. Data of 161 patients diagnosed with CUP in 2014 or 2015 were extracted from the Netherlands Cancer Registry (NCR) and supplemented with diagnostic work-up information from patient files and analysed. Patients underwent an average of five imaging studies during the diagnostic phase (range 1-17). From the tests as recommended in the national guideline on CUP, a chest X-ray was most commonly performed (73%), whereas a PET-CT was done in one out of four patients (24%). Biopsies were taken in 86% of the study population, with Cytokeratin 7 being the most frequently tested histopathological marker (73%). Less than half of patients received therapy (42%). CUP patients undergo extensive diagnostic work-up. The performance status did not influence the extent of the diagnostic work-up in CUP patients, but it was an important factor for receiving treatment.

Utility of circulating cell-free DNA (cfDNA) analysis in patients with carcinoma of unknown primary (CUP) in identifying alterations with strong evidence for response or resistance to targeted therapy.

105 Background: CUP is a rare, heterogeneous group of cancers with an overall poor prognosis; the standard treatment remains chemotherapy. The OncoKB database is a curated list of somatic molecular alterations. Alterations with the highest classification must be an FDA-recognized biomarker associated with response to an FDA-approved drug (Level 1), be recommended by major guidelines or expert panels as predictive of response to an FDA-approved drug (Level 2) or be predictive of resistance to an FDA-approved drug (R1). We explored the landscape of alterations classified as Level 1, 2 or R1 based on the OncoKB scale in a large cohort of CUP patients tested via a well-validated cfDNA assay. Methods: We queried consecutive samples from advanced cancer patients with a listed diagnosis of CUP who underwent testing via a commercially available liquid biopsy assay (Guardant360) between November 2016 and November 2019. The cfDNA assay included targeted next-generation sequencing of 73- to 74-genes specifically curated to include genes with potential targeted therapy options. Alterations were classified based on their ranking in the OncoKB database as of January 2020. Results: In total we identified 2,022 samples with a diagnosis of CUP, and 90.0% of these samples had &gt;1 cfDNA alteration detected. The median age of patients was 68 years and 51% were female. Overall, 20.7% of patients had a Level 1 alteration, 9.5% had a Level 2 alteration, and 23.9% had an R1 alteration (select alterations outlined in Table). Conclusions: cfDNA analysis of patients with advanced CUP identified a significant number of patients with alterations associated with strong evidence for either response or resistance to treatment based on the OncoKB classification schema. While many of these alterations are associated with approvals in specific cancer types, the identification of these alterations suggests many CUP patients may have targeted therapy options. We will present case examples illustrating patient outcomes from CUP patients who received targeting therapy based on cfDNA results. [Table: see text]

Incidence of mutated DNA damage response pathway and clinically actionable alterations in Chinese patients with unknown primary tumor revealed by comprehensive genomic profiling.

e13523 Background: Carcinoma of unknown primary(CUP) is a clinically aggressive disorder with early tumor dissemination. Without drugs specifically approved for CUP, the outcome of standard chemotherapy is generally poor. Identifying molecular traits of CUP can be beneficial not only for better therapy approach but also potentially for all patients with metastatic dissemination. Methods: From January 2015 to July 2019, 36 unique cases were diagnosed as CUP. DNA was extracted with formalin-fixed paraffin-embedded specimens(FFPEs) or plasma samples and sequenced with 400+ gene panels. Results: In this cohort, identified sites of tumor dissemination included lymph node(36%), bone(19%), liver(8%), lung(5%), gut(5%). More than half of patients were male(65%) with a median age of 62 years old(range:42-82). 83% of CUP patients harboured at least one altered DNA damage repair(DDR) gene including TP53(74%), ATM(19%), ARID1A(11%), ATR(11%). Patients with altered homologous recombination repair (HRR) pathway(42%) showed significantly increased tumor mutational burden(TMB) compared to patients with intact HRR(p = 0.025). MYC gene displayed the most copy number variation (gain, 22%) followed by CDKN2A(loss, 15%) and ZNF217(gain, 15%). Clinically actionable mutations were identified in ten patients including KRAS G12C(3), PIK3CA E545K(2), PIK3CA E542K(1), BRAF V600L(1), EGFR L861Q(1), EML4- ALK(1), ALK L1196M(1). One SCC patient with lymph node metastasis had a PIK3CA mutation E545K and a resistant ALK mutation L1196M without prior ALK TKI treatment, suggesting this patient might benefit from PI3K inhibitors. Unfortunately, He progressed on paclitaxel and cisplatin and died in 2019. The other ADC patient with lymph node metastasis achieved SD on pemetrexed disodium and oxaliplatin. He harboured a KRAS G12C mutation (allele frequency 77.75%), indicating target therapy with KRAS inhibitor might be a better treatment option. Conclusions: Majority of CUP patients showed impaired DDR pathway. TMB of CUP patients with altered HRR pathway is significantly higher than ones with intact HRR. Comprehensive genomic profiling revealed the potentiality of target therapy in CUP patients with clinically actionable mutations.

2037P - A challenging task – Identifying carcinoma of unknown primary (CUP) patients according to ESMO guidelines: The CUPISCO trial experience

BackgroundThe CUPISCO trial (NCT03498521) is an ongoing, phase II, randomised, multicentre study comparing molecularly-guided therapy with standard platinum-based chemotherapy in newly diagnosed poor-risk CUP patients. MethodsEligible patients have poor-risk adeno- or undifferentiated CUP as defined by ESMO 2015 guidelines and tissue for molecular sequencing. Local sites initiate the screening process with potentially eligible patients. Patients then undergo central Eligibility Review (ER), a cooperative effort between a central pathology laboratory, external referent oncologists and each site’s investigator and pathology laboratory to confirm the diagnosis. Patients with favourable prognostic subsets or with a strong suspicion of an existing primary site of origin based on immunohistochemistry (IHC) signature and clinical picture are excluded. ResultsAs of 19 March 2019, 157 patients had been screened, of whom 91 (58%) failed screening. Three patients were successfully re-screened. Of the 88 patients who permanently failed screening, 23 were due to technical reasons (e.g. insufficient quality/quantity of tissue for sequencing), 20 for failure to meet inclusion/exclusion criteria not directly related to CUP diagnosis, and 14 for other reasons (e.g. declining health status). A set of 31 patients were not enrolled because the CUP diagnosis could not be confirmed at the IHC level, 19 of those after ER review. Central IHC review results included pathological signatures more typical of specific primary tumours (e.g. prostate cancer or melanoma), or marker combinations typically positive in favourable CUP subsets or rare tumour entities. ConclusionsExperience with the CUPISCO study has highlighted challenges with standardised screening and diagnostic processes in an international clinical trial and the difficulties inherent in accurate diagnosis of poor-risk CUP. Confirming a CUP diagnosis for a clinical trial with multiple review checkpoints can result in many reasons for screen failures. By sharing this experience, we aim to foster understanding and to improve diagnostic algorithms for CUP. Clinical trial identificationNCT03498521. Editorial acknowledgementMedical writing assistance was provided by Ian Leighton, PhD, Nspm Ltd, Meggen, Switzerland, and supported by F. Hoffmann-La Roche Ltd, Basel, Switzerland. Legal entity responsible for the studyF. Hoffmann-La Roche Ltd. FundingF. Hoffmann-La Roche Ltd. DisclosureC. Pauli: Honoraria (self), Research grant / Funding (institution), Travel / Accommodation / Expenses: Roche. T. Bochtler: Honoraria (self), Research grant / Funding (institution), Travel / Accommodation / Expenses: Roche. L. Mileshkin: Travel / Accommodation / Expenses: Roche; Travel / Accommodation / Expenses: Beigene. G. Baciarello: Advisory / Consultancy, Travel / Accommodation / Expenses: Amgen; Advisory / Consultancy, Travel / Accommodation / Expenses: Janssen Oncology; Advisory / Consultancy, Travel / Accommodation / Expenses: Sanofi; Advisory / Consultancy, Travel / Accommodation / Expenses: Astellas-Pharma; Advisory / Consultancy: Roche; Travel / Accommodation / Expenses: AstraZeneca; Travel / Accommodation / Expenses: Ipsen. F. Losa: Advisory / Consultancy, Speaker Bureau / Expert testimony, Research grant / Funding (institution), Travel / Accommodation / Expenses: Roche; Advisory / Consultancy, Research grant / Funding (institution): Amgen; Advisory / Consultancy, Research grant / Funding (institution), Travel / Accommodation / Expenses: Merck; Advisory / Consultancy, Speaker Bureau / Expert testimony: Sanofi; Advisory / Consultancy: Servier. J.S. Ross: Shareholder / Stockholder / Stock options, Full / Part-time employment: Foundation Medicine Inc. S. Yalcin: Honoraria (self): Roche; Honoraria (self): Sanofi; Honoraria (self): Amgen; Honoraria (self): Novartis; Honoraria (self): Lilly; Honoraria (self): MSD; Honoraria (self): Merck Serono. A. Beringer: Full / Part-time employment: F. Hoffmann-La Roche Ltd.. S. Foser: Full / Part-time employment: F. Hoffmann-La Roche Ltd. J. Scarato: Full / Part-time employment: F. Hoffmann-La Roche Ltd.. M. Mueller-Ohldach: Full / Part-time employment: Hoffmann-La Roche Ltd. H. Moch: Honoraria (self), Research grant / Funding (institution), Travel / Accommodation / Expenses: Roche. A. Krämer: Honoraria (self), Research grant / Funding (institution), Travel / Accommodation / Expenses: Roche. All other authors have declared no conflicts of interest.

Genomic profiling for unfavorable carcinoma of unknown primary patients.

e13140 Background: Cancer of unknown primary site (CUP) is the seventh prevalent cancer around the world. Whether most CUP patients share a distinct molecular genome-phenotype is unclear. Methods: A total of 179 unfavorable CUP patients were retrospectively enrolled from Taipei Veterans General Hospital between Jan 2000 and Dec 2009. 33 qualified FFPE samples were sequenced by 275 target gene panel (QIAseq Human Comprehensive Cancer Panel [DHS-3501Z], QIAGEN). Identified significant variants were enriched by using DAVID software (https://david.ncifcrf.gov/). Results: Among 33 patients’ samples, total 6816 variants, including SNP and INDEL from both germline SNPs and somatic mutations were enrolled. After clustering, 112 variants which accounted for 1.64% were selected. Somatic and germline variants were 63.4% (71/112) and 36.6% (41/112), respectively. Profiles between these two groups were different after enrichment that pathway in cancer (fold enrichment [FE] = 6.64, P = 7.03E-09) is most important for somatic mutation and lysine degradation (FE = 25.6, P = 3.78E-04) for germline SNPs (Table). Conclusions: This genomic profile provides new insight into unfavorable CUP patients. Further studies between genotypes vs. phenotypes and drug targets vs. genotypes are warranted.[Table: see text]

Application of 18F-FDG PET/CT and other conventional imaging technologies in carcinoma of unknown primary site

Carcinoma of unknown primary (CUP) is a diagnostic and therapeutic challenge in oncology. The early and correct detection of the primary tumors of CUP is very important to its diagnosis, treatment, therapeutic response evaluation and prognosis prediction. This review summarizes the implications and development of the imaging technologies, especially 18F-FDG PET/CT scan, in the diagnosis, treatment and prognosis prediction of CUP patients. Key words: Neoplasms, unknown primary; Positron-emission tomography; Tomography, X-ray computed; Deoxyglucose; Trends

Gene expression profiling identifies responsive patients with cancer of unknown primary treated with carboplatin, paclitaxel, and everolimus: NCCTG N0871 (alliance)

Carboplatin (C) and paclitaxel (P) are standard treatments for carcinoma of unknown primary (CUP). Everolimus, an mTOR inhibitor, exhibits activity in diverse cancer types. We did a phase II trial combining everolimus with CP for CUP. We also evaluated whether a gene expression profiling (GEP) test that predicts tissue of origin (TOO) could identify responsive patients. A tumor biopsy was required for central confirmation of CUP and GEP. Patients with metastatic, untreated CUP received everolimus (30 mg weekly) with P (200 mg/m(2)) and C (area under the curve 6) every 3 weeks. The primary end point was response rate (RR), with 22% needed for success. The GEP test categorized patients into two groups: those having a TOO where CP is versus is not considered standard therapy. Of 45 assessable patients, the RR was 36% (95% confidence interval 22% to 51%), which met criteria for success. Grade ≥3 toxicities were predominantly hematologic (80%). Adequate tissue for GEP was available in 38 patients and predicted 10 different TOOs. Patients with a TOO where platinum/taxane is a standard (n = 19) tended to have higher RR (53% versus 26%) and significantly longer PFS (6.4 versus 3.5 months) and OS (17.8 versus 8.3 months, P = 0.005), compared with patients (n = 19) with a TOO where platinum/taxane is not standard. Everolimus combined with CP demonstrated promising antitumor activity and an acceptable side-effect profile. A tumor biomarker identifying TOO may be useful to select CUP patients for specific antitumor regimens. NCT00936702.

A multiplexed marker-based algorithm for diagnosis of carcinoma of unknown primary using circulating tumor cells.

Real-time, single-cell multiplex immunophenotyping of circulating tumor cells (CTCs) is hypothesized to inform diagnosis of tissue of origin in patients with carcinoma of unknown primary (CUP). In 20 to 50% of CUP patients, the primary site remains unidentified, presenting a challenge for clinicians in diagnosis and treatment. We developed a post-CellSearch CTC assay using multiplexed Q-dot or DyLight conjugated antibodies with the goal of detecting multiple markers in single cells within a CTC population. We adapted our approach to size-based CTC enrichment protocols for capturing CTCs and subsequent immunofluorescence (IF) using a minimal set of markers to predict the primary sites for common metastatic tumors. The carcinomas are characterized with cytokeratin 7 (CK7), cytokeratin 20 (CK20), thyroid transcription factor 1 (TTF-1), estrogen receptor (ER) or prostate-specific antigen (PSA. IF has been optimized in cultured tumor cells with individual antibodies, then with conjugated antibodies to form a multiplex antibody set. With IF, we evaluated antibodies specific to these 5 markers in lung, breast, colorectal, and prostate cancer cell lines and blood from metastatic prostate and breast cancer patients. This advanced technology provides a noninvasive, diagnostic blood test as an adjunct to routine tissue biopsy. Its further implementation requires prospective clinical testing.

The use of gene expression profiling and mutation analysis increases the cost of care for patients with carcinoma of unknown primary; does it also improve survival?

Carcinoma of unknown primary (CUP) signifies metastatic disease in the absence of a detectable primary site after adequate diagnostic evaluation [1]. The diagnosis carries a poor prognosis, with median survival of just 1 year when treated with cytotoxic agents in contemporary studies [2]. Until recently, the standard approach to CUP patients was to use first line treatment with a cytotoxic drug combination selected based upon the cancer’s histopathologic and immunohistochemical similarity to known primary site cancers [3,4]. Yet, in recent years, advances in genetic and personalized medicine have led to two principal areas of investigation, and departures from the historical treatment approach. Specifically, gene expression profiling can now suggest a tissue of origin (TOO) in previously indeterminate cases, and drug-able mutational analysis

Abstract 1600: A multiplexed marker-based algorithm for diagnosis of carcinoma of unknown primary using circulating tumor cells

Abstract Abstract: Real-time, single-cell multiplex immunophenotyping of circulating tumor cells (CTCs) is hypothesized to inform diagnosis of tissue of origin in patients with carcinoma of unknown primary (CUP). In 20 to 50% of CUP patients, the primary site remains unidentified, presenting a challenge for clinicians in diagnosis and treatment. Invasive tissue biopsy is the gold standard for diagnosis but improved methodology is needed. We developed a post-CellSearch CTC assay using multiplexed Q-dot or DyLight conjugated antibodies with the goal of detecting multiple markers in single cells within a CTC population. We adapted our approach to size-based CTC enrichment protocols for capturing CTCs and subsequent immunofluorescence (IF) using a minimal set of markers to predict the primary sites for common metastatic tumors. The carcinomas are diagnosed with cytokeratin 7 (CK7), cytokeratin 20 (CK20), thyroid transcription factor 1 (TTF-1), estrogen receptor (ER) or prostate-specific antigen (PSA) as the minimal set of informative markers. IF has been optimized in cultured tumor cells with individual antibodies, then with conjugated antibodies to form a multiplex antibody set. With IF, we evaluated antibodies specific to these 5 markers in lung, breast, colorectal, and prostate cancer cell lines and blood samples from metastatic prostate and breast cancer patients. Our technological advance provides a noninvasive, inexpensive, diagnostic blood test as an adjunct to routine tissue biopsy. Its further implementation requires prospective clinical testing. Citation Format: Elizabeth M. Matthew, Lanlan Zhou, Namrata Vijayvergia, David T. Dicker, Karen S. Gustafson, Harry S. Cooper, Eric A. Ross, Bora Lim, Ramdane Harouaka, Si-Yang Zheng, Nicholas E. Lamparella, Joseph J. Drabick, Cristina I. Truica, Zhaohai Yang, Wafik S. El-Deiry. A multiplexed marker-based algorithm for diagnosis of carcinoma of unknown primary using circulating tumor cells. [abstract]. In: Proceedings of the 106th Annual Meeting of the American Association for Cancer Research; 2015 Apr 18-22; Philadelphia, PA. Philadelphia (PA): AACR; Cancer Res 2015;75(15 Suppl):Abstract nr 1600. doi:10.1158/1538-7445.AM2015-1600

Abstract 604: Impaired cell cycle arrest with concurrent epigenetic deregulation identified through next generation sequencing in patients with advanced carcinoma of unknown primary: Implications for personalized medicine

Abstract Background: Patients with advanced carcinoma of unknown primary (CUP) have limited effective therapeutic options given the challenges of phenotypic and genotypic diversity. To identify future novel therapeutic strategies we conduct an ongoing exploratory analysis of next-generation sequencing (NGS) of relapsed, refractory CUP. Methods: We identified CUP patients referred to our phase I clinic with adequate FFPE sections from archival tissue for a targeted CLIA-certified NGS assay (Foundation One, MA). Over 2000 exons of 186 cancer-related genes plus over 30 introns from 14 genes often rearranged in cancer were fully sequenced for point mutations, insertions/deletions, copy number alterations (CNAs) and select gene fusions. Results: Of 19 patients seen (10 male, 9 female; median age at diagnosis 49 years), 17 demonstrated genomic alterations (median 3 aberrations/tumor, range 0 - 10); two patients had no reportable genomic alterations. Of the 71 detected aberrations, 17 (24%) have been implicated in impaired cell cycle regulation and arrest; specifically in genes which encode the cyclin-dependent kinases (CDK12 Q570*, CDKN2A/B loss, CDKN2A p16INK4a loss and p14ARF exon 2-3 loss) or their associated proteins including amplification of CCND1 and CCNE1 (n = 3). Of these 8 patients with impaired cell cycle regulation, 5 (63%) demonstrated concurrent mutations associated with epigenetic deregulation and impaired DNA methylation, most commonly ARID1A Y1211fs*5 and S1929fs*25, which encodes the AT-rich interactive domain-containing protein 1A, Arid1a, a member of the SWI/SNF chromatin remodeling complex); other mutations observed are CREBBP S893L (encoding a ubiquitously expressed transcriptional coregulatory protein controlling chromatin remodeling via its histone acetyltransferase activity); MLL2 R4904* (encoding an H3K4-specific histone methyltransferase) and KDM6A S466* (encoding the histone H3 lysine 27 demethylase UTX). Overall 5 of 19 (26%) patients with advanced relapsed CUP demonstrated a profile of aberrations that concurrently impact cell cycle arrest and epigenetic regulation. Conclusion: Through NGS-based molecular profiling, we can a subset of patients with advanced carcinoma of unknown primary with coexisting mutations leading to impaired cell cycle arrest and epigenetic deregulation, highlighting a therapeutic combination with a cell cycle inhibitor (such as Cdk4/6 inhibitors currently in clinical trial) and histone deacetylase inhibitors. Note: This abstract was not presented at the meeting. Citation Format: Ishwaria M. Subbiah, Gauri Varadhachary, Apostolia M. Tsimberidou, Jennifer J. Wheler, Vivek Subbiah, Filip Janku, Sinchita Roy Chowdhuri, Ralph Zinner, David S. Hong. Impaired cell cycle arrest with concurrent epigenetic deregulation identified through next generation sequencing in patients with advanced carcinoma of unknown primary: Implications for personalized medicine. [abstract]. In: Proceedings of the 106th Annual Meeting of the American Association for Cancer Research; 2015 Apr 18-22; Philadelphia, PA. Philadelphia (PA): AACR; Cancer Res 2015;75(15 Suppl):Abstract nr 604. doi:10.1158/1538-7445.AM2015-604

Abstract 4700: One size does not fit all: Fingerprinting advanced carcinoma of unknown primary through comprehensive profiling identifies aberrant activation of the PI3K and MAPK signaling cascades in concert with impaired cell cycle arrest

Abstract Background: Carcinoma of unknown primary (CUP) represents a heterogeneous group of cancers without an identifiable primary disease site where staining for a vast array of immunohistochemical markers is undertaken to identify tumor lineage. Given rapid advances in characterizing cancer genomes, we sought to describe the molecular profiles of patients with advanced CUP treated with novel targeted therapies on phase I clinical trials to identify pathways of interest to drive future therapeutic strategies. Methods: Of patients with advanced malignancies seen in the Phase I clinic, we identified 16 CUP patients on whom adequate tissue was available to perform next-generation sequencing (NGS) from FFPE sections using a targeted NGS assay in a CLIA laboratory (Foundation One, MA). Over 2000 exons of 186 cancer-related genes plus over 30 introns from 14 genes often rearranged in cancer were fully sequenced for point mutations, insertions/deletions, copy number alterations (CNAs) and select gene fusions. Results: Of 16 tumor specimen, 14 demonstrated genomic alterations with a median of 4 aberrations within each specimen (range 0 - 10, total of 69 alterations); two patients did not demonstrate any tested changes. All patients with detected mutations possessed an exclusive unique molecular profile of aberrations with no two patients demonstrating an identical panel of mutations. A total of 69 alterations were identified of which 18 (26%) led to aberrant cell signaling within the PI3K/AKT/MTOR (including 4 with PIK3CA mutations) or the MAPK signaling cascades, primarily KRAS mutations in 3 patients. Also noted were 13 (19%) alterations impairing cell cycle arrest most commonly affecting cyclin dependent kinases, 10 (14%) impacting epigenetic regulation and DNA methylation, 10 (14%) affecting known tumor suppressor genes including TP53 in 8 patients, and 10 (14%) unique alternations in transcriptional regulators. Conclusion: With thorough molecular profiling, we can identify the unique fingerprint of potential actionable aberrations in a subset of advanced CUP patients. Herein we identified activation of the PI3K/AKT/MTOR and RAS/RAF/MEK signaling pathways combined with impaired cell cycle arrest in 8 of 16 (50%) tested patients, suggesting that a combination of PI3K and MAPK cascade inhibitors in combination with a cell cycle inhibitor may be of therapeutic value to these patients. Further matching patients to these actionable aberrations is underway, thereby translating these therapeutic targets to the bedside with the development of novel targeted therapies. Note: This abstract was not presented at the meeting. Citation Format: Ishwaria M. Subbiah, Gauri Varadhachary, Apostolia M. Tsimberidou, Jennifer J. Wheler, Vivek Subbiah, Filip Janku, Sinchita Roy Chowdhury, Ralph Zinner, Funda Meric-Bernstam, David S. Hong. One size does not fit all: Fingerprinting advanced carcinoma of unknown primary through comprehensive profiling identifies aberrant activation of the PI3K and MAPK signaling cascades in concert with impaired cell cycle arrest. [abstract]. In: Proceedings of the 105th Annual Meeting of the American Association for Cancer Research; 2014 Apr 5-9; San Diego, CA. Philadelphia (PA): AACR; Cancer Res 2014;74(19 Suppl):Abstract nr 4700. doi:10.1158/1538-7445.AM2014-4700