Evaluation of the clonal origin of multiple primary melanomas using molecular profiling

Independent primary cutaneous and mammary apocrine carcinomas with neuroendocrine differentiation: Report of a case and literature review

Cutaneous apocrine carcinomas share common features with their counterparts in the breast; hence, metastatic mammary carcinoma must be excluded before such lesions can be designated primary cutaneous neoplasms. Primary tumors from either source rarely exhibit neuroendocrine differentiation. We report a case of a 72-year-old female with a painless 1.2-cm scalp nodule. An incisional biopsy revealed dermal involvement by an invasive apocrine carcinoma juxtaposed to a benign apocrine cystic lesion. Immunohistochemically, the carcinoma expressed neuroendocrine proteins including synaptophysin, chromogranin, and CD56. A primary cutaneous apocrine carcinoma with neuroendocrine differentiation was favored, but additional investigations to exclude breast origin were recommended. These revealed a 1.1-cm nodule in the right breast, which proved to be an invasive ductal carcinoma, morphologically and immunophenotypically similar to the scalp lesion. This confounded the case, yet factors militating against metastatic breast carcinoma to skin included (a) the small size of the mammary tumor, (b) absence of other metastatic disease, and (c) juxtaposition of the scalp carcinoma to a putative benign precursor. Molecular studies were undertaken to resolve the diagnostic quandary. Single nucleotide polymorphism microarray analysis revealed distinct patterns of chromosomal copy number alterations in the two tumors, supporting the concept of synchronous and unusual primary neoplasms.

Influence of germline genetic variants on dermoscopic features of melanoma

Nevus count is highly determined by inherited variants and has been associated with the origin of melanoma. De novo melanomas (DNMMs) are more prevalent in patients with a low nevus count and have distinctive dermoscopic features than nevus-associated melanomas. We evaluated the impact of nine single nucleotide polymorphisms (SNPs) of MTAP (rs10811629, rs2218220, rs7023329 and rs751173), PLA2G6 (rs132985 and rs2284063), IRF4 (rs12203592), and PAX3 (rs10180903 and rs7600206) genes associated with nevus count and melanoma susceptibility, and the MC1R variants on dermoscopic features of 371 melanomas from 310 patients. All MTAP variants associated with a low nevus count were associated with regression structures (peppering and mixed regression), blue-whitish veil, shiny white structures, and pigment network. SNPs of PLA2G6 (rs132985), PAX3 (rs7600206), and IRF4 (rs12203592) genes were also associated with either shiny white structures or mixed regression (all corrected p-values ≤ .06). Melanomas from red hair color MC1R variants carriers showed lower total dermoscopy score (p-value = .015) and less blotches than melanomas from non-carriers (p-value = .048). Our results provide evidence that germline variants protective for melanoma risk and/or associated with a low nevus count are associated with certain dermoscopic features, more characteristic of de novo and worse prognosis melanomas.

Clonal relationship of synchronous head and neck cancer and esophageal cancer assessed by single nucleotide polymorphism-based loss of heterozygosity analysis

Background

The prognoses of head and neck squamous cell carcinoma (HNSCC) and esophageal squamous cell carcinoma (ESCC) are poor, especially when both tumors occur at the same time. We examined the clonal relatedness of HNSCCs with synchronous ESCCs to confirm whether the second tumors were metastasis or separate second primary malignancies (SPMs) using loss of heterozygosity (LOH) analysis.

Methods

Twenty-one pairs of formalin-fixed paraffin-embedded tissue from HNSCC patients with synchronous esophageal cancer were analyzed by single nucleotide polymorphism (SNP) array using the Illumina HumanCytoSNP FFPE-12 BeadChip (San Diego, CA), which contains approximately 300,000 probes. LOH was identified using Nexus Copy Number software (El Segundo, CA).

Results

Comparing the LOH pattern between HNSCC and paired ESCC, we found that 20 out of 21 paired tissues had a high number of discordant LOHs (LOH identified solely in the primary HNSCC but not in synchronous ESCC at the same genomic location) and a low number of concordant LOHs (LOH at the same genomic location in both HNSCC and ESCC). Only one case fell into the undetermined category. Therefore, these 20 ESCCs were classified as SPMs or second field tumors (SFTs). Moreover, the HNSCC patients with molecularly confirmed esophageal SPM had significantly poorer survival than the other patients.

Conclusions

We propose the use of a genome-wide SNP array as a tool to differentiate metastatic tumors from SPM/SFT. The SNP array offers genome-wide LOH information that earlier microsatellite analysis studies lack. The ability to accurately identify SPM should contribute to a better treatment plan and follow-up care of these patients.

Targeted sequencing identifies the mutational signature of double primary and metastatic malignancies: a case report

BACKGROUND

The accurate identification of the tissue of origin is critical for optimal management of cancer patients particularly those who develop multiple malignancies; however, conventional diagnostic methods at times may fail to provide conclusive diagnosis of the origin of the malignancy. Herein, we describe the use of targeted sequencing in distinguishing the primary and metastatic tumors in a patient with metachronous malignancies in the lung, colon and kidney.

CASE PRESENTATION

In December 2016, a 55-year-old Chinese male was diagnosed with stage IB lung adenosquamous carcinoma and treated with left lower lobectomy and 4 cycles of platinum-based chemotherapy. After being disease-free for 3.5 months, three colonic polyps were discovered and were diagnosed as invasive adenocarcinoma after polypectomy. Within 5.4 months from the polypectomy, squamous cell renal carcinoma was identified and was managed by radical nephrectomy. Immunohistochemistry results were inconclusive on the origin of the kidney tumor. Hence, the three archived surgical tissue samples were sequenced using a targeted panel with 520 cancer-related genes. Analysis revealed similar mutational signature between the lung and kidney tumors and a distinct mutational profile for the colon tumor, suggesting that the lung and colon malignancies were primary tumors, while the kidney tumor originated from the lung, revealing a diagnosis of metastatic double primary cancer - lung carcinoma with renal cell metastasis and second primary colon carcinoma.

CONCLUSION

Mutational profiling using targeted sequencing is valuable not only for the detection of actionable mutations, but also in the identification of the origin of tumors. This diagnostic approach should be considered in similar scenarios.

Molecular Profiling of Multiple Primary Merkel Cell Carcinoma to Distinguish Genetically Distinct Tumors From Clonally Related Metastases

Importance

Merkel cell carcinoma (MCC) is an aggressive cutaneous neuroendocrine carcinoma. In rare cases, the development of an additional cutaneous MCC tumor is clinically consistent with a second primary MCC tumor rather than a cutaneous metastasis, which has important treatment and prognostic implications.

Objective

To evaluate genetic relatedness in 4 cases with the clinical diagnosis of multiple primary MCCs.

Design, Setting, and Participants

In this case series, 7 cases of clinically designated multiple primary MCC were identified; 4 cases met inclusion criteria for next-generation sequencing (NGS) analysis. Mutations, copy number alterations, and Merkel cell polyomavirus (MCPyV) sequence were analyzed and compared between clinically designated multiple primary tumors to characterize genetic relatedness and hence assess clonality. Patients with clinically designated multiple primary MCC were identified from the multidisciplinary MCC Program at the University of Michigan, a tertiary care center.

Main Outcomes and Measures

Four cases of clinically designated multiple primary MCC were characterized by tumor sequencing and targeted MCPyV sequencing to distinguish independent primary tumors from related metastases.

Results

Overall, 4 patients in their 70s or 80s were included and analyzed. Cases 1 and 4 were verified as genetically distinct primary tumors and did not harbor similar copy number alterations or demonstrate significant mutational overlap. Cases 2 and 3 were designated as clonally related based on overlapping copy number alterations. In clonally related tumors, chromosomal copy number changes were more reliable than mutations for demonstrating clonality. Regardless of clonality, we found that MCPyV status was concordant for all tumor pairs and MCPyV positive tumors harbored predominatly subclonal mutations.

Conclusions and Relevance

Our findings suggest that patients with MCC may develop a second genetically distinct primary tumor; in this case, the subsequent tumor is likely to develop through similar mechanisms of pathogenesis, either MCPyV-mediated or ultraviolet light-mediated. Next-generation sequencing analysis of chromosomal copy number changes and mutations is useful in distinguishing multiple primary MCCs from progression of MCC clinically resembling multiple primaries, allowing appropriate staging of the patient.

USING SOMATIC MUTATION DATA TO TEST TUMORS FOR CLONAL RELATEDNESS

A major challenge for cancer pathologists is to determine whether a new tumor in a patient with cancer is a metastasis or an independent occurrence of the disease. In recent years numerous studies have evaluated pairs of tumor specimens to examine the similarity of the somatic characteristics of the tumors and to test for clonal relatedness. As the landscape of mutation testing has evolved a number of statistical methods for determining clonality have developed, notably for comparing losses of heterozygosity at candidate markers, and for comparing copy number profiles. Increasingly tumors are being evaluated for point mutations in panels of candidate genes using gene sequencing technologies. Comparison of the mutational profiles of pairs of tumors presents unusual methodological challenges: mutations at some loci are much more common than others; knowledge of the marginal mutation probabilities is scanty for most loci at which mutations might occur; the sample space of potential mutational profiles is vast. In this article we examine this problem and propose a test for clonal relatedness of a pair of tumors from a single patient. Using simulations, its properties are shown to be promising. The method is illustrated using several examples from the literature.

Incidence of New Primary Melanomas After Diagnosis of Stage III and IV Melanoma

Purpose

New primary melanomas (NPMs) have developed in some patients with metastatic melanoma treated with BRAF inhibitors. We sought to determine the background incidence of spontaneous NPMs after a diagnosis of American Joint Committee on Cancer/International Union Against Cancer stage III or IV melanoma in patients not treated with a BRAF inhibitor.

Patients and Methods

Patients diagnosed with stage III or IV melanoma at Melanoma Institute Australia between 1983 and 2008 were analyzed, and those who received a BRAF inhibitor were excluded.

Results

Two hundred twenty-nine (5%) of 4,215 patients with stage III melanoma and 43 (1%) of 3,563 patients with stage IV melanoma had at least one NPM after diagnosis of stage III or IV disease. The 6-month, 1-year, and 10-year cumulative incidence rates of developing an NPM after stage III melanoma were 1.2% (95% CI, 0.86% to 1.51%), 1.8% (95% CI, 1.44% to 2.26%), and 5.9% (95% CI, 5.08% to 6.74%), respectively. The 3-month, 6-month, and 1-year cumulative incidence rates of NPM after diagnosis of stage IV melanoma were 0.2% (95% CI, 0.07% to 0.36%), 0.3% (95% CI, 0.15% to 0.51%), and 0.4% (95% CI, 0.25% to 0.7%), respectively. In both patients with stage III and stage IV melanoma, male patients and patients with a prior history of multiple primaries had a higher incidence of NPM.

Conclusion

Patients with stage III and stage IV melanoma remain at risk for development of further primary melanomas, particularly if they have a history of multiple primary melanomas before stage III or IV disease. The incidence rates are lower than those reported in patients receiving BRAF inhibitors. However, the results must be compared with caution because dermatologic assessment is more frequent in BRAF inhibitor trials.

Integrative genomics with mediation analysis in a survival context

DNA copy number aberrations (DCNA) and subsequent altered gene expression profiles may have a major impact on tumor initiation, on development, and eventually on recurrence and cancer-specific mortality. However, most methods employed in integrative genomic analysis of the two biological levels, DNA and RNA, do not consider survival time. In the present note, we propose the adoption of a survival analysis-based framework for the integrative analysis of DCNA and mRNA levels to reveal their implication on patient clinical outcome with the prerequisite that the effect of DCNA on survival is mediated by mRNA levels. The specific aim of the paper is to offer a feasible framework to test the DCNA-mRNA-survival pathway. We provide statistical inference algorithms for mediation based on asymptotic results. Furthermore, we illustrate the applicability of the method in an integrative genomic analysis setting by using a breast cancer data set consisting of 141 invasive breast tumors. In addition, we provide implementation in R.

Isolated limb infusion as a model to test new agents to treat metastatic melanoma

The limb model of in-transit disease can expand our understanding of treating melanoma because of the ease of obtaining tissue biopsies for correlative studies and the availability of preclinical animal models that allow validation of novel therapeutic strategies. This review will focus on regional therapy for in-transit melanoma as a platform to investigate novel therapeutic approaches to improve regional disease control, and help us develop insights to more rationally design systemic therapy trials.

Distribution of MC1R variants among melanoma subtypes: p.R163Q is associated with lentigo maligna melanoma in a Mediterranean population

BACKGROUND

Cutaneous melanoma tumour is classified into clinicohistopathological subtypes that may be associated with different genetic and host factors. Variation in the MC1R gene is one of the main factors of risk variation in sporadic melanoma. The relationship between MC1R variants and the risk of developing a specific subtype of melanoma has not been previously explored.

OBJECTIVES

To analyse whether certain MC1R variants are associated with particular melanoma subtypes with specific clinicohistopathological features.

METHODS

An association study was performed between MC1R gene variants and clinicopathological subtypes of primary melanoma derived from 1679 patients.

RESULTS

We detected 53 MC1R variants (11 synonymous and 42 nonsynonymous). Recurrent nonsynonymous variants were p.V60L (30·0%), p.V92M (11·7%), p.D294H (9·4%), p.R151C (8·8%), p.R160W (6·2%), p.R163Q (4·2%) p.R142H (3·3%), p.I155T (3·8%), p.V122M (1·5%) and p.D84E (1·0%). Melanoma subtypes showed differences in the total number of MC1R variants (P = 0·028) and the number of red hair colour variants (P = 0·035). Furthermore, an association between p.R163Q and lentigo maligna melanoma was detected under a dominant model of heritance (odds ratio 2·16, 95% confidence interval 1·07-4·37; P = 0·044). No association was found between p.R163Q and Fitzpatrick skin phototype, eye colour or skin colour, indicating that the association was independent of the role of MC1R in pigmentation. No association was observed between MC1R polymorphisms and other melanoma subtypes.

CONCLUSIONS

Our findings suggest that certain MC1R variants could increase melanoma risk due to their impact on pathways other than pigmentation, and may therefore be linked to specific melanoma subtypes.

Testing clonality of three and more tumors using their loss of heterozygosity profiles

Cancer patients often develop multiple malignancies that may be either metastatic spread of a previous cancer (clonal tumors) or new primary cancers (independent tumors). If diagnosis cannot be easily made on the basis of the pathology review, the patterns of somatic mutations in the tumors can be compared. Previously we have developed statistical methods for testing clonality of two tumors using their loss of heterozygosity (LOH) profiles at several candidate markers. These methods can be applied to all possible pairs of tumors when multiple tumors are analyzed, but this strategy can lead to inconsistent results and loss of statistical power. In this work we will extend clonality tests to three and more malignancies from the same patient. A non-parametric test can be performed using any possible subset of tumors, with the subsequent adjustment for multiple testing. A parametric likelihood model is developed for 3 or 4 tumors, and it can be used to estimate the phylogenetic tree of tumors. The proposed tests are more powerful than combination of all possible pairwise tests.

Number of primary melanomas is an independent predictor of survival in patients with metastatic melanoma

BACKGROUND

A history of multiple primary melanomas (PMs) has been associated with improved survival in patients with early stage melanoma, but whether it also is correlated with survival in patients with metastatic melanoma is unknown. The authors sought to address the latter question in the current study.

METHODS

Patients with metastatic melanoma diagnosed at the Melanoma Institute Australia between 1983 and 2008 were identified. Overall survival (OS) was calculated from date of first distant metastasis. Survival analysis was performed using the Kaplan-Meier method, log-rank tests, and multivariate Cox proportional hazards models.

RESULTS

Of 2942 patients with metastatic melanoma, 2634 (89.5%) had 1 PM and 308 (10.5%) had >1 PM. Factors that were associated independently with shorter OS were site of metastasis, including the brain (hazard ratio [HR], 2.41; 95% confidence interval [CI], 2.07-2.81; P < .001) and non lung viscera (HR, 1.92; 95% CI, 1.67-2.22; P < .001, vs lymph node/subcutaneous/soft tissue), age >60 years (HR, 1.23; 95% CI, 1.12-1.36; P < .001), shorter disease-free interval from PM to first distant metastasis (≤ 12 months vs >36 months: HR, 1.62; 95% CI, 1.39-1.89; P < .001), and fewer PMs (1 vs >1; HR, 1.26; 95% CI, 1.08-1.47; P = .004).

CONCLUSIONS

A history of multiple PM was an independent predictor of improved survival for patients with metastatic melanoma. The results indicate that a history of multiple PMs should be incorporated into multivariate analyses of prognostic factors and treatment outcomes.

Clinicopathologic features of incident and subsequent tumors in patients with multiple primary cutaneous melanomas

BACKGROUND

0.6-12.7% of patients with primary cutaneous melanoma will develop additional melanomas. Pathologic features of tumors in patients with multiple primary cutaneous melanomas have not been well described. In this large, international, multicenter, case-control study, we compared the clinicopathologic features of a subsequent melanoma with the preceding (usually the first) melanoma in patients with multiple primary cutaneous melanomas, and with those of melanomas in patients with single primary cutaneous melanomas.

METHODS

Multiple primary melanoma (cases) and single primary invasive melanoma (controls) patients from the Genes, Environment and Melanoma (GEM) study were included if their tumors were available for pathologic review and confirmed as melanoma. Clinicopathologic characteristics of invasive subsequent and first melanomas in cases and invasive single melanomas in controls were compared.

RESULTS

A total of 473 pairs comprising a subsequent and a first melanoma and 1,989 single melanomas were reviewed. Forward stepwise regression modeling in 395 pairs with complete data showed that, compared with first melanomas, subsequent melanomas were more commonly contiguous with a dysplastic nevus, more prevalent on the head/neck and legs than other sites, and thinner. Compared with single primary melanomas, subsequent melanomas were more likely to be associated with a contiguous dysplastic nevus, more prevalent on the head/neck and legs, and thinner. The same differences were observed when subsequent melanomas were compared with single melanomas. First melanomas were more likely than single melanomas to have associated solar elastosis and no observed mitoses.

CONCLUSIONS

Thinner subsequent than first melanomas suggest earlier diagnosis, perhaps due to closer clinical scrutiny. The association of subsequent melanomas with dysplastic nevi is consistent with the latter being risk factors or risk markers for melanoma.

Histologically ambiguous ("borderline") primary cutaneous melanocytic tumors: approaches to patient management including the roles of molecular testing and sentinel lymph node biopsy

It is well recognized that the pathologic diagnosis of melanocytic tumors can sometimes be difficult. For some atypical melanocytic tumors that do not display clear-cut features of malignancy, it may be difficult or impossible to exclude a diagnosis of melanoma; this includes those showing some resemblance to Spitz nevi, blue nevi, deep penetrating nevi, and possible nevoid melanomas. When there is uncertainty about whether a primary melanocytic tumor is a nevus or a melanoma, we recommend that a second opinion be sought from one or more experienced colleagues. If diagnostic uncertainty persists, the evidence for or against the various differential diagnostic considerations should be presented in the pathology report and a "most likely" or "favored" diagnosis given. Molecular testing of the primary tumor by using techniques such as comparative genomic hybridization or fluorescence in situ hybridization may assist in establishing a diagnosis of melanoma if multiple chromosomal aberrations are identified. However, these tests require further independent validation and are not widely available at present. Complete excision of the lesion is probably mandatory, but plans for further management should be formulated on a case-by-case basis. While the safest course of action will usually be to manage the tumor as if it were a melanoma (taking into account the tumor's thickness and other prognostic variables), this may not always be appropriate, particularly if it is located in a cosmetically sensitive site such as the face. In some cases, it may be appropriate for the surgical oncologist to convey the diagnostic uncertainty to patients and to present them with management choices so that they can decide whether they wish to be managed aggressively (as for a melanoma) or conservatively. While a sentinel lymph node biopsy may be recommended on the basis of the primary tumor characteristics, the clinical significance of lymph node involvement for these tumors is not yet clear, and it may not have the same prognostic implications as nodal involvement from an unequivocal "conventional" melanoma.

A strategy for distinguishing optimal cancer subtypes

Much attention is directed currently to identifying subtypes of cancers that are genetically and clinically distinct. The expectation is that subtyping on the basis of somatic genomic characteristics will supplant traditional pathological subtypes with respect to relevance for targeted therapies and clinical course. Less attention has been paid to the goal of validating subtypes on the basis of the distinctiveness of their etiologies. In this article it is shown that studies of individuals with double primary malignancies provide uniquely valuable information for establishing the etiologic distinctiveness of candidate tumor subtypes. Studies of double primaries have the potential to definitively rank candidate taxonomic systems with respect to their etiological relevance by determining which subtypes are most highly correlated in the double primaries. The concept is illustrated with data from studies of the concordance of estrogen and progestin status in bilateral breast cancers, where it is shown that double primaries are much more likely to be concordant with respect to estrogen receptor (ER) status than for PR status. The high concordance of ER status is consistent with a growing literature demonstrating the etiologic distinctiveness of ER+ and ER- tumors.

Evaluating cancer epidemiologic risk factors using multiple primary malignancies

BACKGROUND

Several authors have proposed the use of patients with double primary malignancies affecting the same or contralateral organ as a genetically enriched resource of cases for epidemiologic case-control studies in cancer. Such an approach is based on the assumption that the factors that increase the risk of a second primary are the same ones which influence the risk of a first primary. The advantages for statistical power are premised on the assumption that relative risks in survivors of a first primary cancer are similar to relative risks in the unaffected population. We explore these assumptions theoretically and empirically using published data from breast cancer studies involving bilateral breast cancer.

METHODS

We conducted a literature review to identify case-control studies of variants in 4 genes known to affect breast cancer risk: CHEK2*1100delC; multiple variants in BRCA1 and BRCA2; and FGFR2 rs2981582. Summary odds ratios were obtained for each of 3 study designs: a conventional case-control design, the design comparing bilateral cases with unilateral controls, and the design comparing bilateral cases with population controls.

RESULTS

The data show strong patterns of steadily increasing prevalence of risk factors from healthy controls to primary cases to bilateral cases, as expected. Relative risks in survivors of unilateral breast cancer are either the same as in the general population, or modestly attenuated.

CONCLUSIONS

Patients with double primary malignancies are a very important underused resource for cancer epidemiologic investigation. Such patients are especially useful for broad genome-wide discovery studies, and for studies of rare, strong risk factors such as high penetrance genes.

Testing clonal relatedness of tumors using array comparative genomic hybridization: a statistical challenge

In recent years several investigative groups have sought to use array technologies that characterize somatic alterations in tumors, such as array comparative genomic hybridization (ACGH), to classify pairs of tumors from the same patients as either independent primary cancers or metastases. A wide variety of strategies have been proposed. Several groups have endeavored to use hierarchical clustering for this purpose. This technique was popularized in genomics as a means of finding clusters of patients with similar gene expression patterns with a view to finding subcategories of tumors with distinct clinical characteristics. Unfortunately, this method is not well suited to the problem of classifying individual pairs of tumors as either clonal or independent. In this article we show why hierarchical clustering is unsuitable for this purpose, and why this method has the paradoxical property of producing a declining probability that clonal tumor pairs will be correctly identified as more information is accrued (i.e., more patients). We discuss alternative strategies that have been proposed, which are based on more conventional conceptual formulations for statistical testing and diagnosis, and point to the remaining challenges in constructing valid and robust techniques for this problem.

[What's new in dermatological research?]

Fundamental research in Dermatology has been once more very active during the past year and more specifically focused on immunological grounds of inflammatory diseases, the identification of risk loci associated with psoriasis and tumors, cutaneous lymphomas and on the genodermatosis where large international collaborative studies provided with a molecular understanding of an increasing amount of conditions especially affecting pigmentation and differentiation. In silico investigations become increasingly prominent especially with the rising power of new actor, China, the demographical and resulting epidemiological weight of which can hardly be challenged. Some of these fundamental breakthroughs might result in practical interventions although in an undefined future.