6/22/2015. Original Paradigm. Correlating Histology and Molecular Findings in Melanocytic Neoplasms

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1 6 Correlating Histology and Molecular Findings in Melanocytic Neoplasms Pedram Gerami MD, Associate Professor of Dermatology and Pediatrics at Northwestern University Disclosures: I have been a consultant to Abbott Molecular, Neogenomics, Myriad Genomics, and Derm Tech Int. Clonal Chromosomal Aberrations Original Paradigm Melanoma Nevi 95% Only 20% of Spitz Nevi Common Gains 6p, 7q, 17q, Isolated Gain 20q, 4q,8q, in 11p 1q, 11q Common Deletions 9p, 10, 21q Melanoma Cohort 3 (n=169) Melanocytic nevi n Common Nevus 25 Dysplastic Nevus 42 Spitz Nevus 14 Nevus on Acral Skin 3 Blue Nevus 2 86 Sensitivity=86.7% Specificity=95.4% Melanomas n Head & Neck 30 Trunk 27 Extremity 23 Glabrous Skin

2 Slide 1 6 1)start by saying what you want to go over a)briefly review CGH and some of the early studies on melanoma b)review the original study and development of the FISH assay c)get into the newer FISH probes Pedram Gerami, 10/19/2011

3 Multi-center collaborative study on Spitz tumors involving Northwestern Univ, UCSF, Univ of Michigan, MD Anderson, Memorial Sloan Kettering and Sydney Melanoma Unit Study Design 1)Multi-center retrospective case controlled study 2)Inclusion criteria: Diagnosis of AST 5 years follow up no adverse event or tumor spread beyond a sentinel lymph node or less than 5 years of follow up if there was evidence of tumor spread beyond the sentinel lymph node 3)FISH evaluation with probes targeting 6p25, 6q23, Cep 6, 11q13, 9p21, and 8q24 was performed on all cases blinded to the clinical outcome Data Collection and Analysis The following data points were collected for each case: 1)Age 2)Sex 3)Anatomic site 4)Breslow depth 5)Mitotic count 6)Clark Level 7)Ulceration status 8)Presence or Absence of kamino bodies 9)Expansile nodular growth 10)Epidermal Consumption 11)Epithelioid versus spindle morphology 12)Complete clinical follow up including sentinel node status 13)FISH data Summary of clinical, histological, and molecular data by clinical stage Clinical N Avera Sex Average Ulceratio Average Average % Patients Average Stage ge n with Ratio Breslow Mitotic Clark FU Time Age (M:F:NA) Status (Y: Positive (months) (mm) Rate Level N) (Yrs) (/mm 2 ) FISH M: 31F: 2.3 7Y: 57N NA 6 1a 13 1b 45 1x M: 4 F: 1NA 3.2 4Y: 4N M: 1F 6.6 1Y: 2N *NA- not available Frequency of FISH results for good (1a,1b,1x) vs. bad (2,4) outcome Spitzoid patients Patient outcome FISH result Good (1a,1b,1x) Bad (2,4) Fisher s exact test 6P Positive Negative q Positive Negative P Cep 6 Positive Negative q Positive Negative P Positive 3 9 < Negative q Positive Negative FISH outcome FISH old probe set Positive < Negative 49 0 Positive Negative 49 5 FISH new probe set Cytogenetic risk Positive 9 11 < Negative 55 0 Low risk 55 0 < Intermediate 6 2 High risk 3 9 2

4 Comparison of the frequency of each chromosomal copy number aberration by outcome groups Group 1 vs. 2 and 4 Group 1 and 2 vs. 4 FISH (# of positives / Group Group Fisher Group Group Fisher # of negatives ) exact test exact 1a/1b/1x 2/4 1a/1b/1x 4 test /2 6P25 8/56 5/ /61 2/ q23 8/56 1/ /63 0/ P/Cep 6 2/62 1/ /70 1/ q13 8/56 5/ /61 2/ P21 3/61 9/2 < /63 3/ q24 1/63 1/ /71 1/ FISH + probe set 1 or 15/49 11/0 < /49 3/ * FISH + probe set 1 ** 15/49 6/ /53 2/ FISH + probe set 2 9/55 11/0 < /55 3/ *** Cytogenetic risk**** 55/6/3 0/2/9 < /8/9 0/0/ ( # of low/ # of intermediate/# of high) Multivariate Analysis Comparing Variables for Group 1 versus Group 2 through 4 Variable Estimate Odds Ratio 95% CI for OR p-value Mitotic F9P (+ vs. -) Footnote: backward elimination method was used to derive the final multivariable models < Multivariate Analysis Comparing Variables for Group 1 and 2 versus Group 4 Variable Estimate Odds Ratio 95% CI for OR p-value F9P (+ vs. -) Footnote: backward elimination method was used to derive the final multivariable models 3

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7 Recurring Themes Among ASTs With Ree Aggressive Clinical Course : 1)9 of 11 cases with disease progression beyond the sentinel had homozygous 9p21 deletions 2) 4 of 9 patients with ASTs with homozygous 9p21 deletion developed recurrent in transit metastasis in the skin in addition to sentinel and non-sentinel lymph node involvement all of whom are still alive. One patient with up to 8 years of follow up. 3)Distant metastasis and death from disease from ASTs uncommon but when it does happen most cases likely to have homozygous 9p21 deletion and likely to occur with a more protracted course compared to conventional melanomas 36 6

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9 Heirarchy of Risk for Distant Metastasis in Melanocytic Neoplasms with Spitzoid Morphology Conventional Melanoma Most taggressive Spitzoid Melanoma with Homozygous 9p21 Deletion Intermediate 43 ASTs with no evidence of copy number aberrations Low Risk ASTs with 6q23 Deletion Low Risk ASTs with 3p21 Deletion/BAPomas Low Risk ASTs with 11p gains Low Risk Clinical Follow up for atypical Spitz tumors with 6q23 deletions Case # Age Sex Sentinel node biopsy result Follow up time (mo) 1 17 F Positive M Not available, Doing well 3 with no evidence of disease on follow up 5 5 F Not done F Not available, Doing well 18 with no evidence of disease on follow up 8 7 M Not available, Doing well with no evidence of disease on follow up M Positive F Positive NA Not done F Positive NA Positive F Negative F Not done F Negative F Not available, Doing well 3 with no evidence of disease on follow up 21 4 F Negative M Positive M Negative M Negative 3 A B C D E F 8

10 8 year old male with non-changing pink papule 9

11 Chromosomal Aberrations New Paradigm Melanoma Common Gains 6p, 7q, 17q, 20q, 4q,8q, 1q, 11q Spitz tumors 95% Chimeric Fusion Proteins: Ros, AlK, NTRK1, BRAF, RET Isolated Gain in 11p, can havae gains in 7q Common Deletions 9p, 10, 21q 3p21, 6q23, heterozygous loss of 9p21 Change in diameter from 3 to 5 mm in 3 month period 10

12 Molecular Assays for Staging Melanoma MSLT-1: Twice as many node-negative patients died compared to node-positive Initial Report 2006 Final Report 2014 Sentinel node negative (83 events) Sentinel node positive (41 events) Where we started: Gene expression profiling in uveal melanoma 15-gene expression profile test Prospective clinical validation study 1 Strong separation of metastatic risk by class % metastasis free p< Months Class 1 (low risk) Class 2 (high risk) Adopted by >95% of ocular oncologists as standard of care Achieved a market penetration of 70% Transformed care by enabling personalized treatment planning 2 Morton, N Engl J Med, 2006; Morton, N Engl J Med, Onken, 2012, Ophthalmology 2 Aaberg, 2014, Clinical Ophthalmology 66 11

13 Cellular functions represented in GEP signature Migration/chemotaxis/ metastasis Chemokine/secreted molecules Gap junction/cellular adhesion CXCL14 SPP1 CLCA2 S100A9 S100A8 CCL14 MGP SPP1 GJA1 DSC1 PPL Differentiation/ proliferation Cell surface receptors Structural proteins CRABP2 SPRRIB BTG1 TACST D2 CLCA2 ROBO1 MGP SPP1 CST6 Lymphocytic invasion LTA4H Angiogenesis regulator CXCL14 Transcription factor TRIM29 Extracellular functions KRT6B KRT14 67 Gerami, Clin Cancer Res 2013 Validation Study #1: Background demographics Characteristics Training Set (n = 164) Validation Set (n = 104) Age, median yrs (range) 61 (23-89) 58 (18-94) Follow-up, median yrs (range) 4.9 ( ) 5.7 ( ) AJCC Stage n (%) n (%) 0 15 (9%) 0 (0%) I 63 (38%) 56 (54%) II 67 (41%) 34 (33%) III 18 (11%) 12 (11%) IV 1 (1%) 2 (2%) Breslow Thickness Median mm (range) 1.86 ( ) 1.4 ( ) 1mm 46 (28%) 45 (43%) > 1mm 101 (62%) 58 (56%) Mitotic Index 1/mm 2 43 (26%) 29 (28%) > 1/mm 2 82 (50%) 53 (51%) Ulceration Absent 104 (63%) 65 (63%) Present 46 (28%) 28 (27%) Growth Pattern Superficial spreading 75 (46%) 56 (54%) Nodular 47 (29%) 25 (24%) Desmoplastic/lentigo maligna/ acral lentiginous 25 (15%) 10 (10%) Gerami, Clin Cancer Res 2015 Censor date: May GEP Accuracy: Disease-free survival prediction all cases n=164 Training Set n=104 p< yr DFS Class 1 = 91% Class 2 = 25% ROC = Accuracy = 83% Sensitivity = 85% Validation Set n=104 5 yr DFS Class 1 = 97% Class 2 = 31% ROC = Accuracy = 86% Sensitivity = 89% GEP is an independent predictor of metastasis for Stage I and II melanoma Cox regression analysis comparing GEP to commonly assessed predictive factors revealed: GEP is a stronger predictor of metastatic recurrence than AJCC stage in multivariate analysis: HR 95% CI p-value AJCC GEP test GEP is also independent of Breslow s thickness, ulceration, mitosis and age Gerami, Clin Cancer Res 2015 Censor Date: May, Gerami, Clin Cancer Res 2015 Censor date: May, Validation Study #2: Baseline Demographics (n=217) SLNB positive SLNB negative Characteristics (n=58) (n=159) Age, median years (range) 57 (23-94) 63 (31-89) Time to metastasis, median years (range) 1.0 (0-7.6) 1.8 (0-8.7) Follow-up in cases without metastatic event, median years (range) 2.5 ( ) 6.1 (0-13.7) Regional plus distant metastasis (n) Distant metastasis only (n) AJCC Stage (n) I n/a 46 II n/a 112 III 58 0 IV n/a 1 Breslow Thickness Median mm (range) 4.0 (0.8-16) 2.3 (0.4-14) < 1mm 4 27 > 1mm Mitotic Index (n) < 1/mm > 1/mm Ulceration (n) absent present Gerami, JAAD in press 2015 Censor date: May

14 SLNB Status Disease-Free, Distant Metastasis-free and Overall Survival SLNB OR GEP Prognostic Prediction DFS DMFS OS SLNB vs. GEP 1 st and 2 nd Validation Studies with SLNB procedure Patients with SLN Procedure (n=217) SLN Results GEP Results SLN positive = 58 SLN negative = 159 Class 2 = 141 Class 1 = 76 Met = 37 Met = 70 Met = 91 Met = 16 GEP Class Non = 21 Non = 89 Non = 50 Non = 60 PPV = 64% NPV = 56% PPV = 65% NPV = 79% DFS = Disease Free Survival; DMFS = Distant Metastasis-Free Survival; OS = Overall Survival Gerami, JAAD in press 2015 Censor date: May Disease-Free, Distant Metastasis-free and Overall Survival SLNB AND GEP Prognostic Prediction GEP Prognostic Data Improves Prediction Over SLNB Negative Status for Overall Survival DFS Class 1/SLN Class 1/SLN+ Class 2/SLN Class 2/SLN+ DMFS Class 1/SLN Class 1/SLN+ Class 2/SLN Class 2/SLN+ OS Class 1/SLN Class 1/SLN+ Class 2/SLN Class 2/SLN+ OS SLNB 100% 75% SLNB- 50% 25% SLNB+ n=217 p= % Time (years) SLNB- (n=159) SLNB+ (n=58) Events yr OS 71% 62% % su urviving % survival GEP in SLNB- Patients 100% 75% Class 1/ SLNB- 50% 25% Class 2/ SLNBn=159 p< % Time (years) Class 1/SLNB- (n=67) Class 2/SLNB- (n=92) Events yr OS 91% 55% DFS = Disease Free Survival; DMFS = Distant Metastasis-Free Survival; OS = Overall Survival Gerami, JAAD in press 2015 Censor date: May Gerami, JAAD in press 2015 Censor date: May JandJan 2003 DP

15 January 2013 Primary Dermal Cutaneous Metastasis 14

16 mrna Expression for Diagnosis of Melanocytic Neoplasms From Myriad Evaluated 859 total lesions by mrna expression profiling focusing on 23 genes Gene Signature 1) 13 immune related genes 2) 1 cell differentiation gene 3) 9 housekeeping genes Training set of 464 and Validation set of

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