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Molecular Tools in Care of Patients with Pigmented

Lesions

Tammie Ferringer, MD Geisinger Medical Center,

Danville, PA tferringer@geisinger.edu

Tammie Ferringer, MD

F003 Pigmented Lesions: Shedding Light on the Blackness

DISCLOSURES

Castle Biosciences: Consultant

DISCLOSURE OF RELATIONSHIPS WITH INDUSTRY

Scolyer RA. Mol Onc, 2011.

MAPK Pathway FISH

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

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.

Next Generation Sequencing

Sam Behjati, and Patrick S Tarpey Arch Dis

Child Educ Pract Ed doi:10.1136/archdischild-2013-304340

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Molecular Tools for Dummies

Basic foundation

How do I use it to:

Diagnose

Prognosticate

Treat

Follow-up

Molecular Tools for Dummies

Basic foundation

How do I use to:

Diagnose

Prognosticate

Treat

Follow-up

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.

Courtesy Aleodor Andea, MD

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….

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Wiesner T, et al. Pathology Feb 2016;48(2):113-131.

Molecular Tools for Dummies

Where did it come from?

How do I use to:

Diagnose

Prognosticate

Treat

Follow-up

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

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Fluorescence In Situ Hybridization

Correlation with histopathology

Can identify many types of chromosomal abnormalities

Gains

Losses

Translocations

Wippold F ,et al. AJNR Am J Neuroradiol 2007;28:406-410

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%

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

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GEP via Adhesive Skin Biopsy

JAAD. 2014;71:237-44.

GEP via Adhesive Skin Biopsy

With PLA score specificity increased to 77%

Size of lesion 4mm or larger

Can be difficult to acquire the mRNA

Which of the following have you requested/performed?

A. CGH

B. FISH

C. 23 gene expression profile (Mypath)

D. Adhesive skin “biopsy” (DermTechs PLA)

E. None of the above

Molecular Tools for Dummies

Basic foundation

How do I use to:

Diagnose

Prognosticate

Treat

Follow-up

Spitz nevus

Atypical Spitzoid Tumor with 6q23 del

Spitzoid MM with 6p25 or 11q13 gain Spitzoid MM

with homozygous loss of 9p21

Conventional MM

Am J Surg Pathol 2013;37:676-84.

eLife 2015;4:e09519 doi: 10.7554/eLife.09519

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Pouryazdanparast P, et al. Am J Surg Pathol 2012 Cooper C, Sorrell J, Gerami P. Adv Anat Pathol 2012;19:410-416.

What’s Wrong With What We Have?

Prognosis and GEP

Established use in uveal MM

31 gene assay in

cutaneous MM

Stage I and II

Combined AJCC and GEP

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.

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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

Molecular

Clinical Histopath

Diagnose and Manage

Molecular Tools for Dummies

Basic foundation

How do I use to:

Diagnose

Prognosticate

Treat

Follow-up

MM Therapies

Kinase Inhibitors

Immunostimulators

MM Therapies

Kinase Inhibitors

BRAF Inhibitors

Vemurafenib

Dabrafenib

MEK Inhibitors

Trametinib

Cobimetinib

Immunostimulators

Anti-CTLA4 Antibody

Ipilimumab

Anti-PD-1 Antibodies

Nivolumab

Pembrolizumab

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Predicting BRAF-I Response Test most recent specimen with sufficient tissue

Can screen with IHC

Sanger sequencing

Cobas 4800 BRAF V600 Mutation Test®

Pyrosequencing

THxIDTMBRAF kit

Use the drug if testing is positive

Test other metastases or use alternate test if negative

Am J Dermatopathol 2017;39:1-13.

What about Molecular Analysis and Immune Checkpoint Inhibitors?

Epitope presence doesn’t seem to predict response

Antigen load and HLA class I expression is associated with clinical response

Molecular Tools for Dummies

Basic foundation

How do I use to:

Diagnose

Prognosticate

Treat

Follow-up

Melanoma-Predisposing Mutations

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Familial Atypical Multiple Mole Melanoma Syndrome

CDKN2A 21 yo scalp cyst

BAPomas/Weisner’s nevus (MBAITs)

Wiesner T. Nat Genet, 2012.

Flesh colored dome shaped papules

Epithelioid cells

Dermal

May have common nevus component and frequent TILs

IHC loss of nuclear expression

BAP1 Weisner Nevus/BAPoma

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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

Soura E, et al. Hereditary melanoma: Update on syndromes and management. J Am Acad Dermatol 2016;74:412-416.

BCC

Breast

Ovarian

Pancreatic

Colon

Meningioma, paraganglioma, neuroendocrine

Hepatic cholangiocarcinoma

31%

22%

13%

67%

Molecular Analysis Implications for

Understanding the biology of tumors

Diagnosis/classification

Prognostication

Development of targeted therapy

Prediction of response to therapy

Determine susceptibility