Molecular Tools in Care of Patients with Pigmented Lesions Tammie Ferringer, MD Geisinger Medical Center, Danville, PA tferringer@geisinger.edu DISCLOSURE OF RELATIONSHIPS WITH INDUSTRY Tammie Ferringer, MD F003 Pigmented Lesions: Shedding Light on the Blackness DISCLOSURES Castle Biosciences: Consultant MAPK Pathway FISH Scolyer RA. Mol Onc, 2011. March J, Hand M, Truong A, Grossman D. Practical application of new technologies form melanoma diagnosis. Part II. Molecular approaches. J Am Acad Dermatol 2015;72:943-58. Wiesner T, et al. Genomic aberrations in spitzoid melanocytic tumours and their implication for diagnosis, prognosis and therapy. Pathology (Feb 2016) 48(2):113-131. CGH Next Generation Sequencing March J, Hand M, Truong A, Grossman D. Practical application of new technologies form melanoma diagnosis. Part II. Molecular approaches. J Am Acad Dermatol 2015;72:943-58. Wiesner T, et al. Genomic aberrations in spitzoid melanocytic tumours and their implication for diagnosis, prognosis and therapy. Pathology (Feb 2016) 48(2):113-131. Sam Behjati, and Patrick S Tarpey Arch Dis Child Educ Pract Ed doi:10.1136/archdischild- 2013-304340 1
Basic foundation How do I use it to: Basic foundation How do I use to: Molecular Alterations in Melanocytic Neoplasms Wiesner T, et al. Pathology. Feb 2016;48(2):113-131. Melis C, et al. Molecular genetic and immunotherapeutic targets in metastatic melanoma. Virchows Arch 2017. Where was Desmoplastic MM? Not your typical BRAF or NRAS mutations One of the most highly mutated cancers Potential improved response to immunostimulators NF1 and NFKBIE. Courtesy Aleodor Andea, MD 2
Wiesner T, et al. Pathology Feb 2016;48(2):113-131. Where did it come from? How do I use to: Why Bother? Comparative Genomic Hybridization Studies the entire genome for multiple copy number aberrations Good discovery tool CGH: Disadvantages Misses balanced translocations and inversions Not allow histologic correlation 30-50% of the specimen needs to be pure tumor cells Tumor cells can be microdissected from the specimen CGH: Disadvantages Microdissected Not microdissected 3
Fluorescence In Situ Hybridization Correlation with histopathology Can identify many types of chromosomal abnormalities Gains Losses Translocations FISH: Disadvantages Only looks at the loci probed Limited to small number of colors Less reliable in ambiguous tumors Frequency of FP and FN vary by subtype Sensitivity 80-90s%, specificity 90s% Wippold F,et al. AJNR Am J Neuroradiol 2007;28:406-410 Gene Expression Profiling Determine genes expressed Uses mrna 23 gene expression signature 2017;26(7):1107-13. 23 Gene Expression Profile in Diagnosis Excluding the indeterminate scores Specificity 96.2% Sensitivity 93.9% Size of lesion at least 0.5 x 0.1 mm with a minimum of 10% of cell of interest Can be difficult to acquire the mrna Not ideal for DM or metastases 4
GEP via Adhesive Skin Biopsy GEP via Adhesive Skin Biopsy JAAD. 2014;71:237-44. With PLA score specificity increased to 77% Size of lesion 4mm or larger Can be difficult to acquire the mrna A. CGH B. FISH Which of the following have you requested/performed? C. 23 gene expression profile (Mypath) D. Adhesive skin biopsy (DermTechs PLA) E. None of the above Basic foundation How do I use to: Am J Surg Pathol 2013;37:676-84. Atypical Spitzoid Tumor with 6q23 del Spitzoid MM with 6p25 or 11q13 gain Spitzoid MM with homozygous loss of 9p21 Conventional MM Spitz nevus elife 2015;4:e09519 doi: 10.7554/eLife.09519 5
What s Wrong With What We Have? Cooper C, Sorrell J, Gerami P. Adv Anat Pathol 2012;19:410-416. Pouryazdanparast P, et al. Am J Surg Pathol 2012 Prognosis and GEP Combined AJCC and GEP Established use in uveal MM 31 gene assay in cutaneous MM Stage I and II Combined SLNB and GEP Improves prognostic accuracy of metastatic risk in GEP class 1 New Classification? Wiesner T, et al. Pathology Feb 2016;48(2):113-131. 6
Am J Surg Pathol 2017;41:491-498. FISH of this lesion from a 5yo showed a homozygous 9p21 deletion. After excision you.. A. Reassure the family B. Plan follow-up starting at 18 years of age C. Plan follow-up in 4 months D. Order a PET scan Clinical Molecular Histopath Basic foundation How do I use to: Diagnose and Manage BRAF Inhibitors Kinase Inhibitors Kinase Inhibitors Vemurafenib Dabrafenib MEK Inhibitors MM Therapies MM Therapies Trametinib Cobimetinib Anti-CTLA4 Antibody Immunostimulators Immunostimulators Ipilimumab Anti-PD-1 Antibodies Nivolumab Pembrolizumab 7
Predicting BRAF-I Response Test most recent specimen with sufficient tissue Can screen with IHC Sanger sequencing Cobas 4800 BRAF V600 Mutation Test Pyrosequencing THxID TM BRAF kit Use the drug if testing is positive Test other metastases or use alternate test if negative What about Molecular Analysis and Immune Checkpoint Inhibitors? Am J Dermatopathol 2017;39:1-13. Epitope presence doesn t seem to predict response Antigen load and HLA class I expression is associated with clinical response Basic foundation How do I use to: Melanoma-Predisposing Mutations 8
Familial Atypical Multiple Mole Melanoma Syndrome CDKN2A 21 yo scalp cyst BAPomas/Weisner s nevus (MBAITs) Flesh colored dome shaped papules Epithelioid cells Dermal May have common nevus component and frequent TILs IHC loss of nuclear expression Wiesner T. Nat Genet, 2012. BAP1 Weisner Nevus/BAPoma 9
Which of the following has an established association with the BAP1 tumor syndrome? A. Acute myeloid leukemia B. Cervical cancer C. Mesothelioma D. Myelodysplastic syndrome E. Prostate cancer BAP1 Tumor Syndrome 13% 67% 31% 22% BCC Breast Ovarian Pancreatic Colon Meningioma, paraganglioma, neuroendocrine Hepatic cholangiocarcinoma Soura E, et al. Hereditary melanoma: Update on syndromes and management. J Am Acad Dermatol 2016;74:412-416. Implications for Molecular Analysis Understanding the biology of tumors Diagnosis/classification Prognostication Development of targeted therapy Prediction of response to therapy Determine susceptibility 10