A Multicenter Study Directly Comparing the Diagnostic Accuracy of Gene Expression Profiling and Immunohistochemistry for Primary Site Identification in Metastatic Tumors

To the Editor It was with great interest that I read the article by Dumur and colleagues1 on their clinical verification of the only US Food and Drug Administration–approved microarray-based test for the diagnosis of poorly and undifferentiated tumors, the Pathwork Tissue of Origin (TOO) Test (Pathwork Diagnostics, Sunnyvale, CA). Briefly, the Pathwork TOO Test is one of several tests currently on the market (CancerTYPE ID, Biotheranostics, San Diego, CA, and miRview mets, Rosetta Genomics, Rehovot, Israel, being others) that attempt to correlate the RNA profile of a given undifferentiated tumor with its suspected tissue of origin (hence, the clever names) through complementary DNA microarray analysis and predetermined algorithms. Based on the findings in the study by Dumur et al,1 the Pathwork TOO test seems to perform glowingly, with a reported 97% concordance rate between the TOO result and final diagnosis, when immunohistochemical and radiologic studies are included. Yet, while most of the available data for these assays are and have been promising with regard to their ability to retrospectively correlate diagnoses with standard analytic methods, several important questions remain, including “When is it appropriate to use one of these tests?” and “Who decides when these tests should be ordered?” As these tests are relatively new to the market and the field of pathology in general, some basic questions are, of course, warranted, especially because they are rather costly, and, as yet, there have been no published prospective studies comparing ultimate outcomes of cases diagnosed with these new techniques vs cases undergoing standard immunohistochemical workups. A recent case seen in our group raises some of these questions and provides a real-life example of when requests for these assays could be made. The patient was a 69-year-old man who had an abdominal computed tomography (CT) scan following a 1-month …

Cutaneous melanomas (CMs) with similar clinical and histopathologic features can harbor differing capacities for metastasis. A validated gene expression profile (GEP) test offers prognostic information by classifying CMs as low risk (Class 1A/1B) or high risk (Class 2A/2B) for metastasis. The authors sought to perform an independent study of the predictive accuracy of the GEP test, to determine what clinical and histopathologic features predict high-risk classification, and to evaluate how intermediate classes (1B & 2A) performed clinically. Using our institution's prospectively collected melanoma registry, the authors identified patients who had been treated for CM within the last 5 years and undergone GEP testing. Clinical, histopathologic, and outcomes data were analyzed. A subcohort of patients with known metastatic disease were identified and tested. The GEP test accurately identified 77% of metastatic CMs as high risk (Class 2). The GEP had a negative predictive value of 99% for Class 1 CMs. Class 2 CMs were 22 times more likely to metastasize. The GEP test's performance in our independent cohort corresponded with previous industry-sponsored studies and proved to be a helpful clinical prognostic tool with the potential to direct patient care protocols.

534 Background: Gene expression profiling (GEP) testing is prognostic for distant recurrence risk in women with hormone receptor positive (HR+), human epidermal growth factor receptor-2 negative (HER2-), axillary lymph node negative (LN-) breast cancer (BC). The TAILORx trial generated prospective evidence demonstrating the 21-gene recurrence score (RS) is also predictive of chemotherapy (CT) benefit. The literature suggests that GEP testing reduces adjuvant CT prescription and is cost-effective. In the same era, the SOFT/TEXT trials demonstrated disease-free survival benefit for the addition of ovarian function suppression (OFS) to endocrine therapy in premenopausal women. Real-world uptake and impact of these advances in the management of HR+, HER2-, LN- BC in young women may be limited due to complex reasons. This retrospective study evaluated GEP and CT use post TAILORx and OFS use post SOFT/TEXT in women 40 years old or younger diagnosed with HR+, HER2-, LN BC from 2011 to 2020 in Alberta, Canada. Methods: Clinical variables were retrieved from the Alberta Health Services Cancer Care Breast Data Mart and through review of the electronic medical record. GEP testing and CT use were compared between 3 cohorts of women defined by diagnosis: pre RS funding/pre TAILORx (before April 2014), post RS funding/pre TAILORx (April 2014-May 2018), post TAILORx (June 2018 and beyond). OFS use was compared between 2 cohorts of women defined by diagnosis pre- and post SOFT/TEXT (May 2015). In subgroup analyses, we compared CT use by GEP status and RS category and OFS use by CT status. Results: Among the 291 women identified, GEP testing increased by 37% post GEP funding (pre 2% vs. post 39%; P = < .0001) and by additional 15% post TAILORx (pre 39% vs. post 54%; P < .0001) whereas overall CT use declined by 15% post GEP funding (pre 85% vs. post 70%; P = .01) and by additional 16% post TAILORx (pre 70% vs. post 54%; P = .01). Although not significant, OFS use increased by 8% post SOFT/TEXT (pre 13% vs. post 21%; P = .08). In subgroup analyses, post TAILORx was associated with a significant reduction in CT use of 19.5% in non-GEP tested women (pre 85% vs. post 65% P = .01) and non-significant increase in CT use of 6% in RS tested women (pre 40% vs. post 46%; P = .61) mainly driven by high mid range RS 21-25 and lower high range RS 26-30. There was no significant change in OFS use in non-CT treated women post SOFT/TEXT (Pre 5.3% vs. Post 8%, P = .68) whereas OFS use increased by 15% in women treated with CT post SOFT/TEXT (pre 15% vs. post 30%; P = .01). Conclusions: Public GEP funding and TAILORx led to widespread adoption of GEP and real-world decline in CT use in women 40 years of age or younger diagnosed with HR+, HER2-, LN- BC in Alberta. SOFT/TEXT led to real-world incline in OFS use in those treated with CT but adoption remained suboptimal.

Use of prognostic gene expression profile (GEP) testing in cutaneous melanoma (CM) is rising despite a lack of endorsement as standard of care. To develop guidelines within the national Melanoma Prevention Working Group (MPWG) on integration of GEP testing into the management of patients with CM, including (1) review of published data using GEP tests, (2) definition of acceptable performance criteria, (3) current recommendations for use of GEP testing in clinical practice, and (4) considerations for future studies. The MPWG members and other international melanoma specialists participated in 2 online surveys and then convened a summit meeting. Published data and meeting abstracts from 2015 to 2019 were reviewed. The MPWG members are optimistic about the future use of prognostic GEP testing to improve risk stratification and enhance clinical decision-making but acknowledge that current utility is limited by test performance in patients with stage I disease. Published studies of GEP testing have not evaluated results in the context of all relevant clinicopathologic factors or as predictors of regional nodal metastasis to replace sentinel lymph node biopsy (SLNB). The performance of GEP tests has generally been reported for small groups of patients representing particular tumor stages or in aggregate form, such that stage-specific performance cannot be ascertained, and without survival outcomes compared with data from the American Joint Committee on Cancer 8th edition melanoma staging system international database. There are significant challenges to performing clinical trials incorporating GEP testing with SLNB and adjuvant therapy. The MPWG members favor conducting retrospective studies that evaluate multiple GEP testing platforms on fully annotated archived samples before embarking on costly prospective studies and recommend avoiding routine use of GEP testing to direct patient management until prospective studies support their clinical utility. More evidence is needed to support using GEP testing to inform recommendations regarding SLNB, intensity of follow-up or imaging surveillance, and postoperative adjuvant therapy. The MPWG recommends further research to assess the validity and clinical applicability of existing and emerging GEP tests. Decisions on performing GEP testing and patient management based on these results should only be made in the context of discussion of testing limitations with the patient or within a multidisciplinary group.

Purpose of reviewThe role of Sentinel Lymph Node Biopsy (SLNB) is pivotal in the contemporary staging of cutaneous melanoma. In this review, we examine advanced molecular testing platforms like gene expression profiling (GEP) and immunohistochemistry (IHC) as tools for predicting the prognosis of sentinel lymph nodes. We compare these innovative approaches with traditional staging assessments. Additionally, we delve into the shared genetic and protein markers between GEP and IHC tests and their relevance to melanoma biology, exploring their prognostic and predictive characteristics. Finally, we assess alternative methods to potentially obviate the need for SLNB altogether. Recent findingsProgress in adjuvant melanoma therapy has diminished the necessity of Sentinel Lymph Node Biopsy (SLNB) while underscoring the importance of accurately identifying high-risk stage I and II melanoma patients who may benefit from additional anti-tumor interventions. The clinical application of testing through gene expression profiling (GEP) or immunohistochemistry (IHC) is gaining traction, with platforms such as DecisionDx, Merlin Assay (CP-GEP), MelaGenix GEP, and Immunoprint coming into play. Currently, extensive validation studies are in progress to incorporate routine molecular testing into clinical practice. However, due to significant methodological limitations, widespread clinical adoption of tissue-based molecular testing remains elusive at present. SummaryWhile various tissue-based molecular testing platforms have the potential to stratify the risk of sentinel lymph node positivity (SLNP), most suffer from significant methodological deficiencies, including limited sample size, lack of prospective validation, and limited correlation with established clinicopathological variables. Furthermore, the genes and proteins identified by individual gene expression profiling (GEP) or immunohistochemistry (IHC) tests exhibit minimal overlap, even when considering the most well-established melanoma mutations. However, there is hope that the ongoing prospective trial for the Merlin Assay may safely reduce the necessity for SLNB procedures if successful. Additionally, the MelaGenix GEP and Immunoprint tests could prove valuable in identifying high-risk stage I-II melanoma patients and potentially guiding their selection for adjuvant therapy, thus potentially reducing the need for SLNB. Due to the diverse study designs employed, effective comparisons between GEP or IHC tests are challenging, and to date, there is no study directly comparing the clinical utility of these respective GEP or IHC tests.

Guidelines for the management of patients with cancer of unknown primary (CUP), who have metastatic disease without an identified primary tumor site, have evolved. We sought to describe the diagnostic work-up and outcomes of patients with CUP in Canada over the last decade. We also sought to identify factors associated with improved prognosis in CUP, including primary tumor site identification, identification of "favorable subtypes," and concordance with published guidelines. With ethics board approval, patients with histologically confirmed CUP between 2012 and 2021 in 3 Canadian cancer centers were reviewed and clinicopathological variables retrospectively collected. The primary endpoint was to describe significant trends in CUP diagnosis and management over the decade using linear regression models. Univariable (UVA) and multivariable (MVA) logistic regression analyses identified variables correlated with primary site identification and overall survival (OS). Kaplan-Meier curves with the log-rank test were used to compare OS outcomes. In total, 907 patients were included, with a median follow-up of 5.1 months. There was an increase in both 5-year survival and identification of primary tumors over the decade. Diagnostic tests including next-generation sequencing were independently associated with primary site identification on UVA. However, primary site identification was not found to be predictive of survival; instead, patients with "favorable subtypes" of CUP had significantly longer OS. Survival in patients with CUP in Canada has been increasing over the last decade. Identifying the primary site does not influence survival, and efforts should be focused on discovering novel "favorable subtypes" which have superior outcomes.

Carcinoma of unknown primary (CUP) is a common and complex type of tumor in clinical practice, where the primary site cannot be determined through conventional diagnostic methods, posing significant challenges for clinical diagnosis and treatment. In recent years, advancements in gene expression profiling and genetic testing technologies have provided new perspectives for CUP research, driving progress in this field. By analyzing gene expression profiles, researchers can more effectively identify the tissue origin of tumors, thereby improving diagnostic accuracy. At the same time, the potential application of genetic testing is continuously being explored, offering new possibilities for personalized treatment. This article aims to discuss the latest advancements in the diagnosis of CUP, analyze the importance of gene expression profiling and genetic testing in tumor origin identification and their clinical applications, and summarize current research progress and future research directions, with the goal of providing a theoretical basis for the early diagnosis and treatment of CUP.

BackgroundAside from chemotherapy utilization, limited data are available on the relationship between gene expression profiling (GEP) testing and breast cancer care. We assessed the relationship between GEP testing and additional variables and the outcomes of endocrine therapy initiation, discontinuation and adherence, and breast imaging exams in women under age 65 years.MethodsData from five state cancer registries were linked with claims data and GEP results. We assessed variables associated with survivorship care outcomes in an incident cohort of 5014 commercially insured women under age 65 years, newly diagnosed with stage I or II hormone-receptor-positive, human epidermal growth factor receptor 2 (HER2) non-positive breast cancer from 2006 to 2010.ResultsAmong tested women, those with high Oncotype DX® Breast Recurrence Score® (RS) were significantly less likely to initiate endocrine therapy than women with low RS tumors (OR 0.40 (95% CI 0.20 to 0.81); P = 0.01). Among all test-eligible women, receipt of Oncotype DX testing was associated with a greater likelihood of endocrine therapy initiation (OR 2.48 (95% CI 2.03 to 3.04); P <0.0001). The odds of initiation were also significantly higher for tested vs. untested women among women who did not initiate chemotherapy within six months of diagnosis (OR 3.25 (95% CI 2.53 to 4.16)), with no effect in women who received chemotherapy. Discontinuation and adherence and breast imaging exams were unrelated to tested status or RS.ConclusionsLower endocrine therapy initiation rates among women with high RS tumors and among untested women not receiving chemotherapy are concerning, given its established efficacy. Additional research is needed to suggest mechanisms to close this gap.

As acute cellular cardiac allograft rejection is a systemic process affecting the entire organism, we hypothesized that scores of a peripheral blood mononuclear cell gene expression profiling (GEP) test developed and validated to rule out International Society of Heart and Lung Transplantation (ISHLT) grade > or = 3A/2R acute cellular cardiac allograft rejection also reflects biologically plausible changes of the routinely assessed clinical parameters. We retrospectively analyzed 76 patients who underwent GEP testing, at the time of their routine clinical follow-up in our Institution between February 1, 2006 and January 31, 2007. Data were analyzed with t-test, nonparametric tests, bivariate Spearman's correlation, and multivariate linear regression modeling. More activated GEP-score correlated with longer corrected QT (QTc)-interval (r = 0.377, p = 0.001, n = 63), longer QRS duration (r = 0.231, p = 0.03, n = 66), higher heart rate (r = 0.221, p = 0.037, n = 66), higher serum creatinine (r = 0.26, p = 0.01, n = 75), higher gamma-glutamyl transferase (GGT) GGT (r = 0.266, p = 0.037, n = 46), lower pulmonary artery oxygen saturation (r = -0.313, p = 0.003, n = 76), lower platelet count (r = -0.372, p = 0.001, n = 74), lower monocyte count (r = -0.208, p = 0.040, n = 72), and lower high-density lipoprotein (HDL) HDL level (r = -0.242, p = 0.041, n = 53). Multivariate analysis showed a significant amount of variance in the GEP score independently explained by the variability of QTc-interval (beta = 1.998, p = 0.001) and platelet count (beta = -1.540, p = 0.017). Post hoc analysis of the 11 individual GEP-classifier genes showed WDRA40 (p = 0.02) and ras homolog gene family, member U (RHOU) RHOU (p = 0.01) independently related to mixed venous O(2)Sat%. A GEP test developed and validated to detect the absence of cardiac rejection correlates with electrocardiographic and hemodynamic cardiac parameters as well as renal, hepatic, bone marrow, and lipid metabolism parameters suggesting a complex relationship between rejection, leukocytes, and organ function within the continuum between alloimmunological quiescence and rejection.

10584 Background: Expected survival is an important factor in treatment selection and patient decision making. Gene expression profiling for tissue of origin (GEP TOO) can be used to classify metastatic and poorly-differentiated tumors according to the most likely primary site for difficult-to-diagnose tumors. The Pathwork Tissue of Origin Test, (Redwood City, CA) generates Similarity Scores (SS), one for each of the 15 tissues on the Tissue of Origin Test Panel and sum to 100. The highest SS has been validated as the most likely tissue of origin in a large validation study (Pillai et al. 2010). This abstract reports the relationship between the highest SS for a sample and patient survival. Methods: Two cohorts were analyzed in IRB-approved studies. Cohort 1 consisted of 45 patients with carcinoma of unknown primary treated empirically with therapy for carcinoma of unknown primary with known outcome data including survival. Cohort 2 consisted of 107 patients receiving the TOO test in routine clinical practice and included in a decision impact registry study. The relationship between the highest SS generated by the TOO test was examined using parametric (Gamma) and non-parametric (Cox Proportional Hazards) regression models with covariates of age, gender and median survival of the cancer type indicated. Logrank tests were performed to compare survival in patients with SS above or below 50 in each cohort. Results: The highest SS generated by the TOO Test was strongly and positively correlated with patient survival in both Cohort 1 (p = 0.0093, Cox PH) and in Cohort 2 (p=0.0045, Gamma). In Cohort 1, survival for patients with a SS &lt; 50 was 5.9 mos and for patients with a SS ≥ 50 was 9.7 mos (p=0.03, logrank). In Cohort 2, survival for patients with a SS &lt; 50 was 10.6 mos and 22.6 mos for patients with a SS ≥ 50 (p=0.0073, logrank). Conclusions: The Similarity Scores generated by GEP TOO Test have been validated as an aid to diagnosis for difficult-to-diagnose malignancies. Two independent studies of this GEP TOO Test demonstrated a strong positive relationship between the highest SS and survival. This has the potential to expand the clinical utility of this test beyond diagnosis to include prognosis. Further studies to examine this question are underway.

Therapy for advanced melanoma has transformed during the past decade, but early detection and prognostic assessment of cutaneous melanoma (CM) remain paramount goals. Best practices for screening and use of pigmented lesion evaluation tools and gene expression profile (GEP) testing in CM remain to be defined. To provide consensus recommendations on optimal screening practices and prebiopsy diagnostic, postbiopsy diagnostic, and prognostic assessment of CM. Case scenarios were interrogated using a modified Delphi consensus method. Melanoma panelists (n = 60) were invited to vote on hypothetical scenarios via an emailed survey (n = 42), which was followed by a consensus conference (n = 51) that reviewed the literature and the rationale for survey answers. Panelists participated in a follow-up survey for final recommendations on the scenarios (n = 45). The panelists reached consensus (≥70% agreement) in supporting a risk-stratified approach to melanoma screening in clinical settings and public screening events, screening personnel recommendations (self/partner, primary care provider, general dermatologist, and pigmented lesion expert), screening intervals, and acceptable appointment wait times. Participants also reached consensus that visual and dermoscopic examination are sufficient for evaluation and follow-up of melanocytic skin lesions deemed innocuous. The panelists reached consensus on interpreting reflectance confocal microscopy and some but not all results from epidermal tape stripping, but they did not reach consensus on use of certain pigmented lesion evaluation tools, such as electrical impedance spectroscopy. Regarding GEP scores, the panelists reached consensus that a low-risk prognostic GEP score should not outweigh concerning histologic features when selecting patients to undergo sentinel lymph node biopsy but did not reach consensus on imaging recommendations in the setting of a high-risk prognostic GEP score and low-risk histology and/or negative nodal status. For this consensus statement, panelists reached consensus on aspects of a risk-stratified approach to melanoma screening and follow-up as well as use of visual examination and dermoscopy. These findings support a practical approach to diagnosing and evaluating CM. Panelists did not reach consensus on a clearly defined role for GEP testing in clinical decision-making, citing the need for additional studies to establish the clinical use of existing GEP assays.

Donor-derived cell free DNA (dd-cfDNA) and gene expression profiling (GEP) offer noninvasive alternatives to rejection surveillance after heart transplantation; however, there is little evidence on the paired use of GEP and dd-cfDNA for rejection surveillance. A single center, retrospective analysis of adult heart transplant recipients. A GEP cohort, transplanted from January 1, 2015 through December 31, 2017 and eligible for rejection surveillance with GEP was compared to a paired testing cohort, transplanted July 1, 2018 through June 30, 2020, with surveillance from both dd-cfDNA and GEP. The primary outcomes were survival and rejection-free survival at 1year post-transplant. In total 159 patients were included, 95 in the GEP and 64 in the paired testing group. There were no differences in baseline characteristics, except for less use of induction in the paired testing group (65.6%) compared to the GEP group (98.9%), P<.01. At 1-year, there were no differences between the paired testing and GEP groups in survival (98.4% vs. 94.7%, P=.23) or rejection-free survival (81.3% vs. 73.7% P=.28). Compared to post-transplant rejection surveillance with GEP alone, pairing dd-cfDNA and GEP testing was associated with similar survival and rejection-free survival at 1year while requiring significantly fewer biopsies.

Uveal Melanoma Tumor Size Correlated with Gene Expression Profiling: the Md Anderson Experience

Hypertrophic osteopathy (HO) is a paraneoplastic syndrome, and the most notable cause in dogs is pulmonary metastatic osteosarcoma (OSA). Although many molecular factors in canine OSA have been shown in metastasis, little is known about the gene expression profile of HO secondary to metastatic OSA. Therefore, the purpose of this study was to compare the gene expression profiles between primary and metastatic OSA lesions from the same dog and to look for gene expression changes that can elucidate the molecular mechanism of metastases and HO. Tumoral samples were obtained from a 2-year-old, intact male, Labrador retriever. At the first visit, the patient presented with an appendicular OSA as the primary lesion. About 10 months later, the dog developed HO due to a single pulmonary metastasis. Using these primary and metastatic samples from the same dog, as well as normal canine osteoblasts, we investigated the gene expression profiling using the NanoString nCounter® Canine IO panel. A total of 180 differentially expressed genes were identified between malignant OSA cells and non-malignant canine osteoblasts. Furthermore, 5 genes (CCL17, VEGFC, C3, C4BPA, and FOS) were differentially expressed in comparison between primary and metastatic OSA samples. CCL17 and VEGFC were upregulated in the primary lesion compared to the metastatic lesion, while C3, C4BPA, and FOS were downregulated in the primary lesion relative to the metastatic lesion. Given that the metastatic lesion was relevant to the development of HO, the different gene expression profiles may be relevant to understanding the pathophysiology of HO.

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