Agenda 8:30 AM. Jennifer L. Hunt

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1 Agenda Topic Introduction Terence J. Colgan Jennifer L. Hunt Time 8:30 AM Pre-analytic Variables in Molecular Testing Philip A. Branton 8:40 AM Carcinoma of Unknown Primary Site Is Gene Expression Profiling the Way to Go? Choosing the Right Molecular Test Lessons from Colorectal Carcinoma Break Genetic Profiling of Tumors for Systemic Therapy Standard of Care or Passing Fad? The Present and Future Avalanche of Molecular Testing Build it or Buy It? Closing Comments and Final Q&A Federico A. Monzon Alyssa M. Krasinskas Jorge Reis-Filho Jeffrey A. Kant Moderator and Faculty 9:10 AM 9:40 AM 10:10 AM 10:40 AM 11:10 AM 11:40 AM 1

2 Choosing the Right Molecular Test: Lessons from Colorectal Carcinoma Alyssa M. Krasinskas, MD University of Pittsburgh Medical Center Pittsburgh, PA 2

3 ONCE UPON A TIME * * 3

4 What is the question? The test we choose will depend on the question: Do we want to detect a hereditary cancer syndrome? Do we need help with a diagnosis? Do we want to predict prognosis? Do we want to predict response to therapy? (I have nothing to disclose) 4

5 5 Do we want to detect a hereditary cancer syndrome?

6 Do we want to detect a hereditary cancer syndrome? Colorectal cancer is the prototypic tumor for the use of molecular testing to detect a hereditary cancer syndrome, Lynch syndrome Hereditary cancer syndromes Hereditary Breast & Ovarian Cancer Syndrome Li-Fraumeni Syndrome Multiple Endocrine Neoplasias Cowden Syndrome Von Hippel-Lindau Disease Familial Adenomatous Polyposis (FAP) Pathologist: Minor role Pathologist: Limited role Lynch Syndrome (HNPCC) Pathologist: Significant role 6

7 Colorectal Cancer 85% 15% CIN (Chromosome instability) MSI (Microsatellite instability) 84% <1% <1% 2-5% 12% Sporadic FAP MUTYH Lynch Sporadic Acquired APC P53 DCC KRAS LOH AD Germline APC AR Germline Bi-allelic MUTYH AD Germline MMR genes: MSH2 MLH1 MSH6 PMS2 Epigenetic silencing: Hypermethylation of MLH1 BRAF mutations 7

8 Colorectal Cancer (CRC) 85% 15% CIN (Chromosome instability) Location: Left > Right Sided Tumor morphology: - Gland-forming - Luminal necrosis MSI (Microsatellite instability) Location: Right > Left Sided Tumor morphology: - intratumoral lymphocytes - Mucinous features - Crohn-like reaction - Medullary phenotype 8

9 Why do we need to be familiar with the these pathways? 85% 15% CIN (Chromosome instability) MSI (Microsatellite instability) 84% <1% 2-5% 12% <1% Sporadic FAP MUTYH Lynch Sporadic Acquired APC P53 DCC KRAS LOH AD Germline APC AR Germline Bi-allelic MUTYH To detect patients with Lynch syndrome AD Germline MMR genes: MSH2 MLH1 MSH6 PMS2 Epigenetic silencing: Hypermethylation of MLH1 BRAF mutations 9

10 Microsatellite Instability (MSI) Microsatellites: Short, repetitive DNA segments present throughout the human genome, 1 to several bases in length:..aaaaaaaaa n.. (mononucleotide)..cacacacaca n.. (dinucleotide)..catgcatgcatgcatg n Microsatellite instability: Faulty DNA mismatch repair results in microsatellites of different lengths 10

11 DNA Mismatch Repair Pathway MSH6 MSH2 Normal DNA repair X MSH6 MSH2 X Defective DNA repair MLH1 PMS2 MMR proteins detect defects in repetitive DNA sequences and excise the defect X MLH1 X PMS2 If any of the MMR proteins are defective, the defect is not corrected New DNA is synthesized Incorrect DNA of a different length is synthesized 11

12 Tools to detect MSI (and exclude sporadic tumors) Immunohistochemistry used to detect the 4 main mismatch repair proteins: MLH1, MSH2, MSH6 and PMS2 PCR Detects MSI Sequencing of the suspected gene Confirms the diagnosis of Lynch syndrome BRAF mutational analysis BRAF mutation = sporadic CRC MLH1 methylation assay MLH1 promoter hypermethylation = sporadic CRC 12

13 Immunohistochemistry (IHC) MMR proteins are normally expressed Loss of one or more of the MMR proteins is a surrogate marker of MSI MLH1 MSH2 PMS2 MSH6 13

14 If use IHC 4 versus 2 antibody panel: Mutation IHC result MSH2 X MSH6 MSH2 X MSH6 MSH2 X MSH2 and MSH6 loss MSH6 X MSH6 MSH2 X MSH6 MSH2 MSH6 loss; MSH2 intact MLH1 X MLH1 PMS2 X MLH1 X PMS2 MLH1 and PMS2 loss PMS2 MLH1 X PMS2 MLH1 X PMS2 (Shia J, AJSP, 2009; 33(11): ) (Mojtahed A, et al. Mod Pathol. 2011;24(7):1004) PMS2 loss; MLH1 intact 14

15 Immunohistochemistry Defect (mutation/hypermethylation) in MLH1: MLH1 MSH2 PMS2 MSH6 In each panel: Tumor, right; Normal, left 15

16 Microsatellite Instability Testing Bethesda panel alone can have low sensitivity for MSI-H (partially due to the ineffectiveness of detecting MSH6 mutations) When mononucleotide markers are added, sensitivities reach 100% A penaplex assay of 5 mononucleotide repeats (NR-21, BAT-26, BAT-25, NR-24 and NR-22) detects MSH6 mutations (You JF, et al. Br J Cancer. 2010;103(12):1840) Mononucleotide marker CAT25 (Bianchi F, et al. J Mol Diagn. 2009, 11:248) (Deschoolmeester V, et al. J Mol Diagn. 2008,10:154) 16

17 Additional Molecular Testing MLH1 promoter hypermethylation MSI in sporadic colon cancer is most often due to MLH1 gene inactivation by promoter hypermethylation (epigenetic silencing) (84%) (Herman JG, et al. Proc Natl Acad Sci USA. 1998;95(12):6870) BRAF mutational analysis BRAF mutations (V600E) are present in ~70% of tumors with hypermethylation of the MLH1 promoter Not identified in cases with MLH1 mutations (Deng G, et al. Clin Cancer Res 2004, 10:191; Domingo E, et al. J Med Genet 2004, 41:664) These assays can help determine if a MSI-H and/or MLH1 deficient tumor is sporadic or inherited: 17 The presence of one or both = sporadic The absence of both = inherited

18 Who or When do we screen for Lynch Syndrome? The EGAPP Working Group recommends offering genetic testing for Lynch syndrome to individuals with newly diagnosed CRC to reduce morbidity and mortality in relatives. (Berg AO, Genetic Med 2009) 500 CRC; 3.6% patients had Lynch Syndrome, 50% were >50 years; Bethesda criteria would fail to identify 28% (Hample H, et al. J Clin Oncol. 2008;26(35):5783) 214 patient with CRC; 3.7% had Lynch Syndrome, 75% were >50 years and 50% were >60; revised Bethesda guidelines missed 25% (2 of 8) probands with Lynch syndrome (Julie C, et al. Am J Gastroenterol 2008;103(11):2825) 1117 CRC in patients years; 4.5% likely had Lynch Syndrome, 70% were >50 years; Lynch profile detected in 3% >61 years (van Lier MG, et al. J Pathol. 2011; ahead of print Nov 14) 18

19 Which methodology? If all or a subset of patients with CRC are screened for Lynch syndrome, what is the ideal methodology? MSI? IHC? Both? > Zhang L. J Mol Diagn 2008;10:301 and Shia J. J Mol Diagn 2008;10:293 Rigorous application of clinical and family histories on the clinical side and recognition of probable MSI-H cancers on the pathology side will increase the identification of Lynch syndrome patients Currently, the best strategy relies on individual institutional resources 19

20 20 Do we need help with a diagnosis?

21 Do we need help with a diagnosis? Molecular diagnostics is most helpful in sarcomas and RCC FISH translocations Sacrcomas RCC: Xp11 (TFE3) translocation RCC (Romeo S, et al. Curr Opin Oncol. 2011;23(4):37) Limited role of molecular pathology in colorectal cancer Rare poorly differentiated tumors lack CK20 and CDX2 expression These medullary carcinomas of the colon MSI pathway Assessment of MMR protein status can be helpful 21

22 Do we need help with a diagnosis? Medullary carcinoma MLH1 PMS2 CK20 MSH2 MSH6 22 CDX2

23 23 Do we want to predict prognosis?

24 Anatomic and morphologic predictors of prognosis Current predictor of survival: TNM (AJCC) cancer staging Pros: Easy to implement Cons: Outcomes vary within stage New prognostic model Outperforms the current AJCC system Incorporates: tumor- and patientrelated variables such as T stage, # + and - LNs, T grade, patient age, and sex Concordance index: 24» AJCC 7 th ed = 0.60 (95% CI, 0.59 to 0.61)» New model = 0.68 (95% CI, 0.67 to 0.68) (Weiser MR, et al. J Clin Oncol. 2011, Nov 14) Per AJCC 7 th ed. 24

25 Predicting prognosis: When to treat Stage I Surgery alone Observation Stage II ASCO: integrate clinical risk criteria* to select patients for adjuvant therapy 5 year survival: 72-83% Who to treat? Stage III Adjuvant chemotherapy 5 year survival: 44-83% Not all patients may need therapy Predictive biomarkers are needed 25 *High risk features: Histologic = LVI, margin involvement, PD, <13 LN, T4; or emergency presentation with obstruction/perforation)

26 Molecular predictors of prognosis MSI as a prognostic marker: 1,913 patients with stage II CRC (Quick and Simple and Reliable (QUASAR) trial : Hutchins G, et al. J Clin Oncol. 2011;29(10):1261) MMR-deficient tumors have a 50% lower risk of recurrence compared to MMR-proficient tumors Prognostic value of MMR was similar in the presence & absence of chemotherapy Our data strongly support calls for IHC assessment of MMR status to become routine clinical practice Good prognosis in other recent studies (Guastadisegni C, et al. Eur J Cancer. 2010;46(15):2788) (Salazar R, et al. J Clin Oncol. 2010;29:17) (Gray RG, et al. J Clin Oncol. 2011; Epub Nov 7) 26

27 Molecular predictors of prognosis ColoPrint (Agendia) 18 gene signature for colon cancer prognosis Predicts disease relapse in early stage CRC 206 samples from patients with stage I, II, and III CRC (Salazar R. J Clin Oncol. 2010;29:17) In stage II CRC: signature had an HR of 3.34 (P=.017) and was superior to ASCO criteria in assessing the risk of cancer recurrence without prescreening for MSI MSI-H tumors: good prognosis and identified by the gene classifier MSI-H tumors: mainly seen in stage II disease, many had a BRAF mutation, and most were classified as ColoPrint low risk (26 of 29 patients; 90%) 27

28 Molecular predictors of prognosis Oncotype Dx Colon (Genomic Health, Inc.) 13 cancer-related genes (7 recurrence genes, 6 treatment benefit genes) 1,436 patients with stage II CRC (QUASAR trial : Gray RG, et al. J Clin Oncol. 2011; Epub Nov 7) Surgery alone group: Gene profile Recurrence Score was highly associated with recurrence (HR 1.38; 95% CI, 1.11 to 1.74; P=.004) Histologic factors also predictive: T stage (HR, 1.94; P<.001) and MMR status (HR, 0.31; P<.001) Adjuvant fluoropyrimidine chemotherapy group: Treatment Score was not predictive of chemotherapy benefit 28 28

29 Molecular predictors of prognosis Limitations for molecular-only tests: ColoPrint uses fresh-frozen tissues Only limited publications so far (more needed) Emphasis on Stage II CRC Histopathology still important Promise: Oncotype Dx Colon will have the greatest clinical utility when used as a complement to T stage and MMR status, specifically for patients who have T3, MMR-proficient, stage II disease. (Gray RG, et al. J Clin Oncol. 2011; Epub Nov 7) 29 29

30 Predicting prognosis: When to treat Stage I Surgery alone Observation Stage II Observe or treat? Stage III Adjuvant chemotherapy 30? 30

31 31 Do we want to predict response to therapy?

32 Lessons learned from CRC: The EGFR KRAS story EGFR Ras Raf MEK MAPK 32 Cell survival Angiogenesis Invasion Metastasis Proliferation 32

33 Lessons learned from CRC: The EGFR KRAS story Monoclonal antibodies Cetuximab Panitumumab EGFR Ras Raf MEK MAPK EGFR X Ras Raf MEK MAPK EGFR Kinase Inhibitors Erlotinib Gefitinib 33 Cell survival Angiogenesis Invasion Metastasis Proliferation 33 33

34 EGFR Testing 34 34

35 EGFR Testing: IHC IHC results response to therapy 35 35

36 EGFR (IHC) KRAS (mutational analysis) Raf EGFR Ras MEK MAPK Cell survival Angiogenesis Invasion Metastasis Proliferation Even with receptor expression and blockade, KRAS or BRAF mutations = constitutive Activation of the EGFR cascade 36

37 The EGFR KRAS story Today ASCO Provisional Clinical Opinion: Based on systematic reviews of the relevant literature, all patients with metastatic colorectal carcinoma who are candidates for anti-egfr antibody therapy should have their tumor tested for KRAS mutations in a CLIA-accredited laboratory. If a KRAS mutation in codon 12 or 13 is detected, then patients with metastatic colorectal carcinoma should not receive anti-egfr antibody therapy as part of their treatment. (Allegra CJ, et al. J Clin Oncol. 2009;27(12):2091) 37 37

38 EGFR (IHC) KRAS (mutations) BRAF other Ligand EGFR PTEN PI3K P P Grb2 SOS Ras Dysregulation of other genes/ proteins can impact the EGFR pathway AKT MAPK Raf MEK Cell survival Angiogenesis Invasion Metastasis Proliferation 38

39 The EGFR KRAS BRAF story Tomorrow KRAS mutational analysis of codons 61 and 146? BRAF mutational analysis if KRAS wild type? PIK3CA (PI3K) mutational analysis if KRAS wt? PTEN LOH (or PTEN IHC) if KRAS wt? 39 39

40 Other molecular predictors of response to therapy MSI as a predictive marker: (Guastadisegni C, et al. Eur J Cancer. 2010;46(15):2788) Meta-analysis of CRC survival data (31 studies, >12,000 patients) In a subset of patients treated with 5-FU-based chemotherapy, significantly improved prognosis was found for MSS tumors (OR = 0.52, 95%CI , p<0.0001) No clear conclusion was reached for MSI tumors (due to high inter-study heterogeneity, other factors involved) Oncotype Dx Colon Neither the Treatment Score, pathologic features or molecular markers (such as MSI) were associated with treatment efficacy (Gray RG, et al. J Clin Oncol. 2011; Epub Nov 7) 40 40

41 Pearls of Pathology CRC is a disease that bridges the divide between molecular and surgical pathology The test we choose will depend on the question: Do we want to detect a hereditary cancer syndrome? While surgical pathology can play a role, it is recommended that molecular testing (MSI or IHC) be performed on all newly diagnosed CRC Do we need help with a diagnosis? Surgical pathology is the main player in CRC, but IHC staining for the MMR proteins can help 41

42 Pearls of Pathology Do we want to predict prognosis? Surgical pathology currently plays and will continue to play a key role in determining prognosis in CRC Additional information is needed to accurately predict prognosis in many patients Patients with Stage II disease treat or don t treat? Patients wit Stage III disease do we need to teat all? Assessment of MSI (MMR proteins) appears to play a major role (another reason to test all CRC for MSI) Will OncotypeDx Colon, ColoPrint or other gene assays be clinically useful? 42

43 Pearls of Pathology Do we want to predict response to therapy? Surgical pathology has a limited role Predicting response to anti-egfr therapy: Molecular testing to detect alterations in the EGFR pathway are both currently utilized (KRAS and BRAF mutational analysis) and on the horizon (PI3KCA mutations, loss of PTEN function) Other molecular tests currently have a limited role MSS / MMR protein-proficient tumors may have a survival benefit when treated with 5 FU-based therapy Gene profile assays will likely help in the future 43

44 SUMMARY: Evolution of CRC reporting CAP cancer protocols developed Erbitux approved by FDA for IHCproven EGFR+ CRC ASCO states that all patients with metastatic CRC should have their tumor tested for KRAS mutations Past Future 44 ASC CoC mandated use of the data elements in all SP reports on cancer specimens EGAPP Working Group recommends offering genetic testing for Lynch syndrome to individuals with newly diagnosed CRC?

45 References 1. Allegra CJ, Jessup JM, Somerfield MR, et al. American Society of Clinical Oncology provisional clinical opinion: testing for KRAS gene mutations in patients with metastatic colorectal carcinoma to predict response to anti-epidermal growth factor receptor monoclonal antibody therapy. J Clin Oncol 2009;27: Berg AO. Recommendations from the EGAPP Working Group: genetic testing strategies in newly diagnosed individuals with colorectal cancer aimed at reducing morbidity and mortality from Lynch syndrome in relatives. Genet Med 2009;11: Bianchi F, Galizia E, Catalani R, et al. CAT25 is a mononucleotide marker to identify HNPCC patients. J Mol Diagn 2009;11: Deng G, Bell I, Crawley S, et al. BRAF mutation is frequently present in sporadic colorectal cancer with methylated hmlh1, but not in hereditary nonpolyposis colorectal cancer. Clin Cancer Res 2004;10: Deschoolmeester V, Baay M, Wuyts W, et al. Detection of microsatellite instability in colorectal cancer using an alternative multiplex assay of quasi-monomorphic mononucleotide markers. J Mol Diagn 2008;10:

46 References 6. Domingo E, Laiho P, Ollikainen M, et al. BRAF screening as a low-cost effective strategy for simplifying HNPCC genetic testing. J Med Genet 2004;41: Gray RG, Quirke P, Handley K, et al. Validation Study of a Quantitative Multigene Reverse Transcriptase-Polymerase Chain Reaction Assay for Assessment of Recurrence Risk in Patients With Stage II Colon Cancer. J Clin Oncol Guastadisegni C, Colafranceschi M, Ottini L, Dogliotti E. Microsatellite instability as a marker of prognosis and response to therapy: a meta-analysis of colorectal cancer survival data. Eur J Cancer 2010;46: Hampel H, Frankel WL, Martin E, et al. Feasibility of screening for Lynch syndrome among patients with colorectal cancer. J Clin Oncol 2008;26: Herman JG, Umar A, Polyak K, et al. Incidence and functional consequences of hmlh1 promoter hypermethylation in colorectal carcinoma. Proc Natl Acad Sci U S A 1998;95: Hutchins G, Southward K, Handley K, et al. Value of mismatch repair, KRAS, and BRAF mutations in predicting recurrence and benefits from chemotherapy in colorectal cancer. J Clin Oncol 2011;29:

47 References 12. Julie C, Tresallet C, Brouquet A, et al. Identification in daily practice of patients with Lynch syndrome (hereditary nonpolyposis colorectal cancer): revised Bethesda guidelines-based approach versus molecular screening. Am J Gastroenterol 2008;103: ; quiz Mojtahed A, Schrijver I, Ford JM, et al. A two-antibody mismatch repair protein immunohistochemistry screening approach for colorectal carcinomas, skin sebaceous tumors, and gynecologic tract carcinomas. Mod Pathol 2011;24: Romeo S, Dei Tos AP. Clinical application of molecular pathology in sarcomas. Curr Opin Oncol 2011;23: Salazar R, Roepman P, Capella G, et al. Gene expression signature to improve prognosis prediction of stage II and III colorectal cancer. J Clin Oncol 2011;29: Shia J. Immunohistochemistry versus microsatellite instability testing for screening colorectal cancer patients at risk for hereditary nonpolyposis colorectal cancer syndrome. Part I. The utility of immunohistochemistry. J Mol Diagn 2008;10:

48 References 17. Shia J, Tang LH, Vakiani E, et al. Immunohistochemistry as first-line screening for detecting colorectal cancer patients at risk for hereditary nonpolyposis colorectal cancer syndrome: a 2-antibody panel may be as predictive as a 4-antibody panel. Am J Surg Pathol 2009;33: van Lier MG, Leenen CH, Wagner A, et al. Yield of routine molecular analyses in colorectal cancer patients </= 70 years to detect underlying Lynch syndrome. J Pathol Weiser MR, Gonen M, Chou JF, et al. Predicting Survival After Curative Colectomy for Cancer: Individualizing Colon Cancer Staging. J Clin Oncol You JF, Buhard O, Ligtenberg MJ, et al. Tumours with loss of MSH6 expression are MSI- H when screened with a pentaplex of five mononucleotide repeats. Br J Cancer 2010;103: Zhang L. Immunohistochemistry versus microsatellite instability testing for screening colorectal cancer patients at risk for hereditary nonpolyposis colorectal cancer syndrome. Part II. The utility of microsatellite instability testing. J Mol Diagn 2008;10:

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