Personalized Genetics Understanding Your Genetic Test Results Tracey Evans, MD September 29, 2017
Genetics 101 Punnett Square Genetic Pedigree 2
Genetics 101 Punnett Square Genetic Pedigree 3
It s not about you! ( or your parents or your kids) It s about YOUR TUMOR Cells: they grow and divide, requires replicating the DNA Mutation: Change in the DNA that gets passed on to daughter cells on subsequent cell divisions (other DNA changes include translocations, insertions/deletions, copy number changes) 4
Germline vs Somatic Mutations 5
X-Men: Germline Mutations 6
Germline vs Somatic Mutations 7
Mutations that Lead to Cancer 8
Evolution of Tumors 9
Stuff that messes with your genes Inheritable conditions that can predispose to cancers More likely to mutate/change (MEN2) Less able to repair mutations/change that inevitably occur (BRCA mutations leading to breast and ovarian cancer) Mutagens Viruses (HPV) Toxic exposures (tobacco, asbestos, radon) Chemotherapy/ radiation Defective immune system Unable to take out cells that go bad (HIV, organ transplants) Bad luck/time: random mistakes during normal replication 10
Cancer: Disease of acquired genetic and molecular abnormalities 11 The Hallmarks of Cancer Mucous hyperplasia Mild dysplasia Severe dysplasia Invasive carcinoma 11
Developments in the Diagnostics and Treatment of Lung Cancer From Plönes T et al, J Pers Med 2016, 6 (1). 12
Molecular Events in Lung Cancer 13 Point mutation Single base pair mutation in the EGFR gene Translocations in chromosome 2p Amplification of EGFR Signaling pathway alterations Evasion of immune destruction Chromosome 7 13
Molecular Events in Lung Cancer Point mutation Single base pair mutation in the EGFR gene Translocations in chromosome 2p Amplification of EGFR Signaling pathway alterations Evasion of immune destruction Chromosome 7 14
Recommended approach to Metastatic Non-small Cell Lung Cancer Metastatic disease: requires systemic (all over the body) approach 15
Mutations in Lung Adenocarcinomas These actionable mutations are often called driver mutations These mutations happen early in the disease course and are the primary drivers of the cancer The cancers are addicted to the pathways for which they code Therefore, interfering with this pathway can be very effective 16
NO Overlap in Driver Mutations 17
For Example: the Epidermal Growth Factor Receptor EGFR Invasion P P Angiogenesis Metastasis Nucleus PI3K MAPK Gene activation Cell cycle progression Signaling cascades Proliferation Myc Fos Jun M G 1 G 2 S Survival Apoptosis MAPK = mitogen-activated protein kinase. Roskoski. Biochem Biophys Res Commun. 2004;319:1. Rowinsky. Annu Rev Med. 2004;55:433. 18
The EGFR story Initial drugs to block the EGFR pathway (contributing factor in many epithelial cancers) Gefitinib: pill, small molecules gets INSIDE the cell and blocks receptor Cetuximab: IV, Antibody, blocks binding of ligand to receptor from OUTSIDE the cell Initially apparent that gefitinib worked DRAMATICALLY well in SOME lung cancers (about 10%) Women Never, distant former, or light tobacco use Adenocarcinoma East Asian ethnicity Initial study comparing gefitinib to traditional, IV cytotoxic chemotherapy done in Japan Overall, gefitinib better at controlling cancer than IV chemo THE CLINICAL OBSERVATION THAT SOME PATIENTS DID REALLY WELL LED TO THE DISCOVERY OF EGFR MUTATIONS THAT STUCK THE RECEPTOR ON 19
FDA approved Initial Treatment Options for EGFR mutated Lung Cancer Primary side effects Rash Hair and nail changes Diarrhea Rare interstitial pneumonitis (potentially dangerous inflammation of the lungs) Gefitinib Additional facts Similar effectiveness Recommended starting dose may be higher than needed Expensive! Provided through specialty pharmacies Erlotinib Afatinib 20
Facts About EGFR Mutation Lung Cancer NOT caused by tobacco exposure ~10% of lung adenocarcinomas Not all EGFR mutations are the same Most common (deletion 19, exon 21L858R) almost always respond to initial therapy with the EGFR TKI S (tyrosine kinase inhibitors) Less common EGFR mutations (exon 18) have variable responses Some (exon 20 insertion) don t seem to respond at all Almost inevitably, the cancer at some point develops resistance to the EGFR TKI (meaning the drug stops working to completely control the cancer) Sometimes this resistance is only in one location that can be managed with a local treatment (radiation or surgery) and the drug successfully continued Even when the cancer is growing on the drug, it often grows faster if the drug is stopped and nothing else started (unique to targeted agents called flare ) 21
Why to the EGFR targeted drugs stop working? New molecular changes: Determined by REBIOPSY (or blood or urine te 22
Osimertinib Approved for use in T790M positive EGFR mutated non-small cell lung cancer Gets into blood-brain barrier better than other EGFR TKI s Inhibits the common EGFR mutations even WITHOUT T790 mutation Less wild type EGFR activity (does not affect normal, nonmutated EGFR as much) Less rash, diarrhea Recently shown to be better in terms of cancer control compared to Gefitinib or Erlotinib when patients treated with this initially (FLAURA) Not yet FDA approved in this setting 23
Alk Positive Lung Cancer 3-7% of lung adenocarcinomas More common in never/minimal/distant smokers Not caused by tobacco exposure Treatment with targeted approach leads to better cancer control than traditional IV chemotherapy Alectinib recently shown better at controlling cancer longer than first approved drug crizotinib (Alex) No real consistent side effect profile across class 24
Alk positive lung cancer: Resistance Many are NOT due to known mutations And yet, the mutations that CAN occur respond to different drugs.. 25
.and the rest! 26
.and the rest! ROS-1 translocation: 1-2%, crizotinib RET translocation: 1-2%, crizotinib, cabozantonib BRAF V600E: 1-3%, dabrafenib and trametinib MET exon 14 skipping: 4%, crizotinib Her2: 2-4%, ado-trastuzumab emtansine, IV KRAS?: NO approved or known effective treatment yet PD-L1? Not a genetic marker, MORE ABOUT THIS LATER! STAY TUNED FOR MORE! 27
What do we test to figure out tumor genetic profile? Tissue: Gold standard Need ENOUGH to do all the tests Biopsy or resection Bone biopsies not always eligible for testing Cytology: Fine needle biopsy, cells from fluid (pleural effusion) Blood!: Testing circulating DNA within plasma In the Lung Cancer Mutation Consortium study (14 U.S. academic centers), only 66% of enrolled patients could have their specimens tested for all 10 genes Commercially available test for 70 point mutations, 18 amplifications, 6 fusions, 3 internal deletions Quantitative Urine Least invasive of all! Urine primary route of elimination for circulating DNA and remains stable up to 2 weeks. Commercially available test evaluates for EGFR, KRAS, BRAF 28
How is the testing done? Next-generation sequencing (NGS), multiplex testing: optimal Massively parallel sequencing Get all you need at once, may require more tissue Generally requires sample be 30% 40% tumor cells Does not cover translocations CPD (Center for Personalized Diagnostics) at Penn Targets 153 genes TAKES 3-4 WEEKS Sequential sequencing: PCR-based approaches, one gene at a time Less tissue initially than next gen, may be faster for initial test More likely to run out of tissue, takes longer overall FISH (fluorescence in situ hybridization) Used for translocations Antibodies for immunohistochemistry Requires less tissue, fastest Variable accuracy At Penn, used as initial screen for Alk, ROS1, and used for PD-L1 29
When to Rebiopsy or Re-do Molecular Testing When you have reason no to trust your result Small sample, clinical scenario does not make sense, could not run all desired testing When there is a treatment for particular mode of resistance EGFR and small cell transformation/t790 Some Alk mutations in Alk translocated cancers When NOT Hoping a new driver mutation will pop up 30
Your CPD Report.. 31
Blood-based Molecular Test Report 32
Another commercially available report. 33
Next Steps Studies incorporating targeted therapies in early stage lung cancer After surgery in patients with appropriate mutations/translocations With radiation in patients getting chemoradiation for stage III disease Looking for actionable gene mutations in squamous cell Getting more reliable results with smaller samples and with non-invasive samples Figuring out something for KRAS 34
A Case About Why this is Important 66 yo developed cough late 11/14, fainting episode 12/14 Found to have lung adenocarcinoma with fluid surrounding heart. 2 small brain mets diagnosis. Tobacco: 1ppd 15 yrs quit 1988 CPD at Penn reported 2/21/15 deletion of 3 nucleotides in the intron of MET involving the canonical splice donor site Chemotherapy through 6/23/15, brain radiation 6/15 ASCO: Response to crizotinib with mutations that cause MET exon 14 skipping Sudden shortness of breath 9/15 with new, large pleural effusion requiring drainage Crizotinib on 9/18/15 Able to attend daughter s wedding 5/16 9/18/15 10/30/15 35
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