Faculty Bibliography

In the recent decade, cutting edge molecular and proteomic analysis platforms revolutionized biomarkers discovery in cancers. Melanoma is the prototype with over 51,100 biomarkers discovered and investigated thus far. These biomarkers include tissue based tumor cell and tumor microenvironment biomarkers and circulating biomarkers including tumor DNA (cf-DNA), mir-RNA, proteins and metabolites. These biomarkers provide invaluable information for diagnosis, prognosis and play an important role in prediction of treatment response. In this review, we summarize the most recent discoveries in each of these biomarker categories. We will discuss the challenges in their implementation and standardization and conclude with some perspectives in melanoma biomarker research.

Angiogenesis, the formation of new blood vessels from existing blood vessels, is a complex and highly regulated process that plays a role in a wide variety of physiological and pathological processes. In malignancy, angiogenesis is essential for neoplastic cells to acquire the nutrients and oxygen critical for their continued proliferation. Angiogenesis requires a sequence of well-coordinated events mediated by a number of tightly regulated interactions between pro-angiogenic factors and their corresponding receptors expressed on various vascular components (e.g., endothelial cells and pericytes) and stromal components forming the extracellular matrix. In this review, we discuss the functional roles of key growth factors and cytokines known to promote angiogenesis in cutaneous melanoma and key factors implicated in the extracellular matrix remodeling that acts synergistically with angiogenesis to promote tumor progression in melanoma, incorporating some of the most up-to-date basic science knowledge from recently published in vivo and in vitro experimental studies.

Multifocal breast cancer (MFBC), ductal type, has been hypothesized to arise by one of two mechanisms: either through intramammary/intralymphatic spread from a single index tumor (MBC-1), or as multiple independent tumors with each focus carrying its corresponding ductal carcinoma in-situ (MBC-2). In order to improve our understanding of MFBC pathogenesis, we employed laser capture microdissection coupled with whole-exome sequencing to study clonal origin in MFBC. We selected three cases of MBC-1 (C1 to C3) and MBC-2 (C4 to C6) and analyzed three foci from each case. MBC-1 cases were histologically similar and showed a strong predilection for satellite foci, vascular invasion and nodal metastasis when compared to MBC-2. Our bioinformatics approach provided strong evidence for clonal relationships in MBC-1, as demonstrated by distinct clusters of genes conserved across all tumor foci. Conversely, no gene clusters were shared across all the foci in MBC-2, suggesting multiple independent tumors. These findings provide further support for the two distinct pathogenetic mechanisms in MFBC.

PURPOSE/OBJECTIVE:While multimodal chemotherapy has improved outcomes for patients with osteosarcoma (OS), the prognosis for patients who present with metastatic and/or recurrent disease remains poor. In this study, we sought to define how often clinical genomic sequencing of OS samples could identify potentially actionable alterations. EXPERIMENTAL DESIGN/METHODS:We analyzed genomic data from 71 OS samples from 66 pediatric and adult patients sequenced using MSK-IMPACT, a hybridization capture-based large panel NGS assay. Potentially actionable genetic events were categorized according to the OncoKB precision oncology knowledge base, of which Levels 1-3 were considered clinically actionable. RESULTS:We found at least one potentially actionable alteration in 14/66 patients (21%), including amplification of CDK4 (n=9, 14%: Level 2B) and/or MDM2 (n=9, 14%: Level 3B), and somatic truncating mutations/deletions in BRCA2 (n=3, 5%: Level 2B) and PTCH1 (n=1, Level 3B). Additionally, we observed mutually exclusive patterns of alterations suggesting distinct biological subsets defined by gains at 4q12 and 6p12-21. Specifically, potentially targetable gene amplifications at 4q12 involving KIT, KDR and PDGFRA were identified in 13 of 66 patients (20%), which showed strong PDGFRA expression by immunohistochemistry. In another largely non-overlapping subset of 14 patients (24%) with gains at 6p12-21, VEGFA amplification was identified. CONCLUSIONS:We found potentially clinically actionable alterations in approximately 21% of OS patients. Additionally, at least 40% of patients have tumors harboring PDGFRA or VEGFA amplification, representing candidate subsets for clinical evaluation of additional therapeutic options. We propose a new genomically-based algorithm for directing OS patients to clinical trial options.

We present the case of a 22-year-old woman who developed increasing headaches, nausea, and vomiting. Imaging identified a 3 × 3 cm heterogeneously enhancing cystic mass in the posterior III ventricular/pineal region. Pathology review of the initial lesion revealed a highly malignant spindle cell neoplasm composed of round to mostly oval elongated cells with relatively small amounts of cytoplasm arranged in sheets and fascicles with focal storiform pattern. Whole genome methylation analysis through unsupervised clustering with data generated from other primary intracranial tumors and peripheral sarcomas was performed at the German Cancer Research Center (DKFZ) and classified the tumor with the group of alveolar rhabdomyosarcomas (ARMS). Further RNA sequencing revealed an in frame PAX3 (EX 7)-NCOA2 (EX12) fusion confirming the diagnosis. This is the first evidence of occurrence of PAX3-NCOA2 in primary CNS ARMS.

Glioblastoma (GBM), representing WHO grade IV astrocytoma, is a relatively common primary brain tumor in adults with an exceptionally dismal prognosis. With an incidence rate of over 10 000 cases in the United States annually, the median survival rate ranges from 10-15 months in IDH1/2-wildtype tumors and 24-31 months in IDH1/2-mutant tumors, with further variation depending on factors such as age, MGMT methylation status, and treatment regimen. We present a cohort of 4 patients, aged 37-60 at initial diagnosis, with IDH1-mutant GBMs that were associated with unusually long survival intervals after the initial diagnosis, currently ranging from 90 to 154 months (all still alive). We applied genome-wide profiling with a methylation array (Illumina EPIC Array 850k) and a next-generation sequencing panel to screen for genetic and epigenetic alterations in these tumors. All 4 tumors demonstrated methylation patterns and genomic alterations consistent with GBM. Three out of four cases showed focal amplification of the CCND2 gene or gain of the region on 12p that included CCND2, suggesting that this may be a favorable prognostic factor in GBM. As this study has a limited sample size, further evaluation of patients with similar favorable outcome is warranted to validate these findings.

BACKGROUND:The role of the mammalian target of rapamycin (mTOR) in hair follicle tumorigenesis is unclear. mTOR controls cell growth and can be activated through ribosomal S6 kinase. Herein, we sought to evaluate the expression of phospho-S6 in six different benign and malignant follicular tumor types. METHODS:test (p<0.05). RESULTS:All malignant neoplasms in our series [8/8 (100%) cases of tricholemmal carcinoma, 1/1 (100%) trichoblastic carcinoma and 1/1 (100%) malignant proliferating tricholemmal tumor] demonstrated a strong and diffuse pattern of staining with phospho-S6 involving 70-90% of tumor cells. By contrast, a minority of benign tumors were positive for phospho-S6 and most stained in a patchy pattern including 12/17 (71%) fibrofolliculomas, 9/20 (45%) trichoepitheliomas and 1/10 (10%) tricholemmomas, involving 30-50%, 5-20%, and 40-50% of tumor cells, respectively. Most pilomatricomas [17/19 (89%)] exhibited a stronger, but distinctive staining pattern, staining mostly the basaloid cells with a multifocal distribution, involving 70-90% of tumor cell. CONCLUSIONS:Phospho-S6 is differentially expressed among benign and malignant hair follicle tumors (p = 0.0044). While malignant tumors show diffuse expression, only a small subset of benign neoplasms were positive, primarily in a patchy distribution.

BACKGROUND AND IMPORTANCE/BACKGROUND:Liposclerosing myxofibrous tumors (LSMFTs) are rare benign fibro-osseous tumors most frequently occurring in the proximal femur. We report the first case of this rare tumor occurring within the calvarium. CLINICAL PRESENTATION/METHODS:Our patient presented with a 2-yr history of enlarging, painless, fixed mass over the left forehead. She underwent surgical resection and the mass was histologically confirmed to be a LSMFT. CONCLUSION/CONCLUSIONS:LSMFT is a rare tumor that should remain on the differential for lesions of the calvarium. When diagnosed, this lesion can be removed with the goal of gross total resection and excellent cosmesis can be achieved.

Superficial/cutaneous malignant peripheral nerve sheath tumor is a rare soft tissue neoplasm that shares morphological, immunohistochemical, and molecular features with spindle/desmoplastic melanoma. We aimed to identify a methylome signature to distinguish these two entities. We analyzed 15 cases of spindle/desmoplastic melanoma and 15 cases of cutaneous malignant peripheral nerve sheath tumor in 23 men and 7 women. DNA from formalin-fixed, paraffin-embedded tissues was extracted and processed using the Illumina Infinium Methylation EPIC array interrogating 866,562 CpG sites. Using a home-grown informatics pipeline, we identified differentially methylated positions between the two entities. Functional network analysis for enrichment signatures was performed using DAVID tools. Identified differentially methylated positions were compared with the Cancer Genome Atlas's cutaneous melanoma dataset and a recently published malignant peripheral nerve sheath tumor dataset to assess the specificity of the identified signature. Unsupervised hierarchical clustering showed different patterns of methylation in cutaneous malignant peripheral nerve sheath tumor and spindle/desmoplastic melanoma. Two probes, cg20783223 and cg13332552, colocalized in the promoter region of BCAT1 and miR-2504. Pathway analysis highlighted enrichment in a subset of genes involved in breast and gastric cancer centered on BCAT1 and downstream activated genes in the mTOR pathway. Our study identifies BCAT1 as a novel methylome signature distinguishing spindle/desmoplastic melanoma from cutaneous malignant peripheral nerve sheath tumor.