4 Molecular Classification of Lung Cancer 1 1. Jordan EJ et al. - - PDF document

SLIDE 1

The TRK to Tumor-Agnostic Care in Solid Tumors

A Pathology-Focused Guide to the Clinical Role of TRK Fusions in Personalizing Cancer Therapy

Anna F. Farago, MD, PhD, Assistant in Medicine Massachusetts General Hospital Assistant Professor of Medicine Harvard Medical School Boston, Massachusetts

Disclosures

This CME/MOC activity is jointly provided by Medical Learning Institute, Inc. and PVI, PeerView Institute for Medical Education. This activity is supported by an independent educational grant from Bayer and Loxo Oncology.

Anna F. Farago, MD, PhD, has a financial interest/relationship or affiliation in the form of: Consultant For: AbbVie Inc.; AstraZeneca; Bayer; Genentech, Inc.; Loxo Oncology; PharmaMar; Boehringer Ingelheim; Roche; and Bristol-Myers Squibb. Speakers Bureau participant with: Foundation Medicine, Inc. Anna F. Farago, MD, PhD, does intend to discuss any non-FDA-approved or investigational use of the following products/devices: entrectinib, repotrectinib; LOXO-195.

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1 2 3

SLIDE 2

Genotype-Directed Therapy1

• 1. Mitsudomi T et al. Nat Rev Clin Oncol. 2013;10:235-244.

Molecular Classification of Lung Cancer1

• 1. Jordan EJ et al. Cancer Discov. 2017;7:596-609.

Types of Somatic Genomic Alterations in Cancers

EGFR mutations KRAS mutations BRAF mutations HER2 amplification MET amplification BCR-ABL ALK fusions NTRK fusions Alteration Common Examples Point mutations, short insertions, or deletions (indels) Point mutations, short insertions, or deletions (indels) Copy number alterations Copy number alterations Gene fusions Gene fusions

4 5 6

SLIDE 3

NTRK and TRK Terminology

NTRK1 TRKA NTRK2 TRKB NTRK3 TRKC GENES: PROTEINS:

TRK Biology and Signaling in the Nervous System1

• 1. Cocco E et al. Nat Rev Clin Oncol. 2018;15:731-747.

Schematic of Gene Fusion Leading to Activation1,2

• 1. https://www.cancer.gov/news-events/cancer-currents-blog/2016/leukemia-infant-research-model. Accessed May 14, 2018.
• 2. Farago AF, Azzoli CG. Transl Lung Cancer Res. 2017;6:550-559.

7 8 9

SLIDE 4

Schematic of Gene Fusion Leading to Activation (Cont’d)1,2

• 1. https://www.cancer.gov/news-events/cancer-currents-blog/2016/leukemia-infant-research-model. Accessed May 14, 2018.
• 2. Farago AF, Azzoli CG. Transl Lung Cancer Res. 2017;6:550-559.

Schematic of Gene Fusion Leading to Activation (Cont’d)1,2

• 1. https://www.cancer.gov/news-events/cancer-currents-blog/2016/leukemia-infant-research-model. Accessed May 14, 2018.
• 2. Farago AF, Azzoli CG. Transl Lung Cancer Res. 2017;6:550-559.

TRK Fusion Cancers as an Example

• f Fusion-Driven Cancer Pathogenesis1,2

Allows kinase portions of the TRK proteins to autophosphorylate independent of any regulation1,2 Allows kinase portions of the TRK proteins to autophosphorylate independent of any regulation1,2 Oncogenic fusions

• f NTRK genes retain the

kinase domain of TRK but cause constitutive dimerization/activation Oncogenic fusions

• f NTRK genes retain the

kinase domain of TRK but cause constitutive dimerization/activation As a result, TRK fusion proteins are constitutively active due to ligand- independent activation and propagate a constant signal cascade that causes cells to overproliferate and survive1,2

Dimerization of Chimeric Protein Signal Cascade Cell Growth and Proliferation

• 1. Amatu A et al. ESMO Open. 2016;1:e000023. 2. Vaishnavi A et al. Cancer Discov. 2015;5:25-34.

10 11 12

SLIDE 5

Estimated Frequency of TRK Fusions Across Tumor Types

• 1. Argani P et al. Mod Path. 2000;13:29. 2. Rubin BP et al. Amer J Path. 1998;153:1451-1458. 3. Leeman-Neill RJ et al. Cancer. 2014;120:799-807.
• 4. Wu G et al. Nat Genet. 2014;46:444-450. 5. Wiesner T et al. Nat Commun. 2014;5:3116. 6. Morosini D et al. 2015 American Society of Clinical Oncology Annual

Meeting (ASCO 2015). Abstract 11020. 7. Brenca M et al. J Path. 2016;238:543-549. 8. Bishop JA et al. Hum Pathol. 2013;44:1982-1988. 9. Tognon C et al. Cancer

• Cell. 2002;2:367-376. 10. Bourgeois JM et al. Am J Surg Pathol. 2000;24:937-946.
• Congenital mesoblastic

nephroma1,2

• Recurrent papillary thyroid

cancer3

• Pontine glioma4
• Spitzoid melanoma5
• Pediatric and young adult soft

tissue sarcomas6

• Pan-negative gastrointestinal

stromal tumors (GIST)7

• Mammary analogue secretory

carcinoma (MASC) of the salivary gland8

• Secretory breast carcinoma9
• Infantile fibrosarcoma10

5%-25% ≥75%

CNS

• Astrocytoma1
• Low-grade glioma2
• Glioblastoma3

GI

• Colorectal cancer2,4
• Cholangiocarcinoma5
• Pancreatic cancer6

Head and neck

• Squamous cell carcinoma2

Lung

• Adenocarcinoma2,7
• Large cell neuroendocrine

carcinoma8 Other

• Acute myeloid leukemia9
• Breast-invasive carcinoma2
• Melanoma2
• Sarcoma2

≤5%

Estimated Frequency of TRK Fusions Across Tumor Types (Cont’d)

• 1. Jones DT et al. Nat Genet. 2013;45:927-934. 2. Stransky N et al. Nat Commun. 2014;5:4846. 3. Kim J et al. PLoS One. 2014;9:3. 4. DeBraud F et al. ASCO 2014.

Abstract 2502. 5. Ross JS et al. Oncologist. 2014;19: 235-242. 6. Bailey P et al. Nature. 2016;531:47-52. 7. Vaishnavi A et al. Nat Med. 2013;19:1469-1472.

• 8. Fernandez-Cuesta L et al. 2014 American Association of Cancer Annual Meeting (AACR 2014). Abstract 1531. 9. Kralik JM et al. Diag Path. 2011;6:19.

Detection of TRK Fusions Detection of TRK Fusions 13 14 15

SLIDE 6

Methods for Detection of TRK Fusions1-4

Hechtman et al:

• TRK IHC assessed using pan-Trk

monoclonal antibody clone EPR17341 (Abcam)

• Tested on 23 available NTRK fusion cases

and 20 consecutive tumors without evidence of NTRK fusion

• IHC was concordant with Archer RNA

testing in 21 of 22 cases

• IHC sensitivity 95.2%, specificity 100%

IHC Advantages  Rapid results  Detects transcribed and translated events

• nly

 Low cost as single test Disadvantages − Depletion of tissue − Fusion partner and position unknown − Less well- validated currently

• 1. Jordan EJ et al. Cancer Discov. 2017;7:596-609. 2. Hyman DM et al. ASCO 2017. Abstract LBA2501. 3. Farago AF et al. J Thorac Oncol. 2015;10:1670-1674.
• 4. Hechtman JF et al. Am J Surg Pathol. 2017;41:1547-1551.

Methods for Detection of TRK Fusions (Cont’d)1-4

IHC FISH Advantages  Rapid results  Detects transcribed and translated events

• nly

 Low cost as single test  Rapid results Disadvantages − Depletion of tissue − Fusion partner and position unknown − Less well- validated currently − Depletion of tissue − Fusion partner and position unknown − Can be difficult to interpret

• 1. Jordan EJ et al. Cancer Discov. 2017;7:596-609. 2. Hyman DM et al. ASCO 2017. Abstract LBA2501. 3. Farago AF et al. J Thorac Oncol. 2015;10:1670-1674.
• 4. Hechtman JF et al. Am J Surg Pathol. 2017;41:1547-1551.

Examples of IHC and FISH1,2

Take-home point: Techniques with faster results, such as IHC/FISH, may be useful in cancers in which the likelihood of a TRK fusion is high

• 1. Hyman DM et al. ASCO 2017. Abstract LBA2501. 2. Farago AF et al. J Thorac Oncol. 2015;10:1670-1674.

16 17 18

SLIDE 7

Methods for Detection of TRK Fusions (Cont’d)1-4

IHC FISH NGS Advantages  Rapid results  Detects transcribed and translated events

• nly

 Low cost as single test  Rapid results  Potential for multiplexed testing  Less depletion

• f tissue

 Fusion partner and position are defined Disadvantages − Depletion of tissue − Fusion partner and position unknown − Less well- validated currently − Depletion of tissue − Fusion partner and position unknown − Can be difficult to interpret − Longer wait time for results − Cost

• 1. Jordan EJ et al. Cancer Discov. 2017;7:596-609. 2. Hyman DM et al. ASCO 2017. Abstract LBA2501. 3. Farago AF et al. J Thorac Oncol. 2015;10:1670-1674.
• 4. Hechtman JF et al. Am J Surg Pathol. 2017;41:1547-1551.

Next-Generation Sequencing1

• 1. Meyerson M, Getz G. Nat Rev Genet. 2010;11:685-696.

DNA- vs RNA-Based NGS Approaches1,2

DNA-based NGS RNA-based NGS  Potential for multiplexed assessment for multiple different fusion targets  Potential for multiplexed assessment for multiple different fusion targets

• Detected fusions may or may not be expressed

 Detection of expressed transcripts

• Requires tiling through intronic regions

 Read directly through expressed transcripts

• Fusion positions are inferred based on reads

through genomic DNA  Fusion positions are directly demonstrated

• 1. Meyerson M, Getz G. Nat Rev Genet. 2010;11:685-696. 2. Zheng Z et al. Nature Med. 2014;20:1479-1484.

19 20 21

SLIDE 8

Example of Panel of Genes Tested Using an NGS-Based Approach1

Take-home point: NGS may be the most efficient method for capturing TRK fusions, particularly in settings where pretest probability is low (ie, lung cancer, CRC, or settings where other molecular aberrations may also be captured)

Current Gene List

Entire coding sequence (base substitutions, indels, copy number alterations) Select rearrangements ABL1 ABL2 ACVR1B AKT1 AKT2 AKT3 ALK AMER1(FAM123B ) APC ALK AR ARAF ARFRP1 ARID14 ARID1B ARID2 ASXL1 ATM ATR BCL2 ATRX AURKA AURKB AXIN1 AXL BAP1 BARD1 BCL2 BCL2L1 BCR BCL2L2 BCL6 BCOR BCORL1 BLM BRAF BRCA1 BRCA2 BRD4 BRAF BRIP1 BTG1 BTK C11orf30 (EMSY) CARD11 CBFB CBL CCND1 CCND2 BRAC1 CCND3 CCNE1 CD274 (PD-L1) CD79A CD79B CDC73 CDH1 CDK12 CDK4 BRCA2 CDK6 CDK8 CDKN1A CDKN1B CDKN2A CDKN2B CDKN2C CEBPA CHD2 BRD4 CHD4 CHEK1 CHEK2 CIC CREBBP CRKL CRLF2 CSF1R CTCF EGFR CTNNA1 CTNNB1 CUL3 CYLD DAXX DDR2 DICER1 DNMT3A DOT1L ETV1 EGFR EP300 EPHA3 EPHA5 EPHA7 EPHB1 ERBB2 ERBB3 ERBB4 ETV4 ERG ERRFI1 ESR1 EZH2 FAM46C FANCA FANCC FANCD2 FANCE ETV5 FANCF FANCG FANCL FAS FAT1 FBXW7 FGF10 FGF14 FGF19 ETV6 FGF23 FGF3 FGR4 FGF6 FGFR1 FGFR2 FGFR3 FGFR4 FH FGFR1 FLCN FLT1 FLT3 FLT4 FOXL2 FOXP1 FRS2 FUBP1 GABRA6 FGFR2 GATA1 GATA2 GATA3 GATA4 GATA6 GID4 (C17orf39) GLI1 GNA11 GNA13 FGFR3 GNAQ GNAS GPR124 GRIN2A GRM3 GSK3B H3F3A HGF HNF1A KIT HRAS HSD3B1 HSP90AA1 IDH1 IDH2 IGF1R IGF2 IKBKE IKZF1 MSH2 IL7R INHBA INPP4B IRF2 IRF4 IRS2 JAK1 JAK2 JAK3 MYB JUN KAT6A (MYST3) KDM5A KDM5C KDM6A KDR KEAP1 KEL KIT MYC KLHL6 KMT2A (MLL) KMT2C (MLL3) KMT2D (MLL2) KRAS LMO1 LRP1B LYN LZTR1 NOTCH2 MAGI2 MAP2K1 (MEK1) MAP2K2 (MEK2) MAP2K4 MAP3K1 MCL1 MDM2 MDM4 MED12 NTRK1 MEF2B MEN1 MET MITF MLH1 MPL MRE11A MSH2 MSH6 NTRK2 MTOR MUTYH MYC MYCL (MYCL1) MYCN MYD88 NF1 NF2 NFE2L2 PDGFRA NFKBIA NKX2-1 NOTCH1 NOTCH2 NOTCH3 NPM1 NRAS NSD1 NTRK1 RAF1 NTRK2 NTRK3 NUP93 PAK3 PALB2 PARK2 PAX5 PBRM1 PDCD1LG2 (PD-L2) RARA PDGFRA PDGFRB PDK1 PIK3C2B PIK3CA PIK3CB PIK3CG PIK3R1 PIK3R2 RET PLCG2 PMS2 POLD1 POLE PPP2R1A PRDM1 PREX2 PRKAR1A PRKCI ROS1 PRKDC PRSS8 PTCH1 PTEN PTPN11 QKI RAC1 RAD50 RAD51 TMPRSS2 RAF1 RANBP2 RARA RB1 RBM10 RET RICTOR RNF43 ROS1 RPTOR RUNX1 RUNX1T1 SDHA SDHB SDHC SDHD SETD2 SF3B1 SLIT2 SMAD2 SMAD3 SMAD4 SMARCA4 SMARCB1 SMO SNCAIP SOCS1 SOX10 SOX2 SOX9 SPEN SPOP SPTA1 SRC STAG2 STAT3 STAT4 STK11 SUFU SYK TAF1 TBX3 TERC TERT (Promoter only) TET2 TGFBR2 TNFAIP3 TNFRSF14 TOP1 TOP2A TP53 TSC1 TSC2 TSHR U2AF1 VEGFA VHL WISP3 WT1 XPO1 ZBTB2 ZNF217 ZNF703

• 1. Vaishnavi A et al. Cancer Discov. 2015;5:25-34.

Circulating Tumor Nucleic Acid for Identification of TRK Fusions?

 ctDNA testing can be used to assess the landscape of mutations in a tumor, and can be followed

• ver time.

✗ The sensitivity for detection of TRK fusions in ctDNA may be lower than in biopsies and may vary depending on the assay used. ✗ Commercial panels may not include all NTRK genes.

Case Study #1: TRK Fusions in Non-Small Cell Lung Cancer1,2

• 1. Farago AF et al. JCO Precision Oncology. 2018. 2. Jordan EJ et al. Cancer Discov. 2017;7:596-609.

22 23 24

SLIDE 9

MGH MSKCC Total Frequency, % (95% CI) NSCLC screened 1,804 3,068 4,872 — NTRK1 fusion 2 4 6 0.12 (0.05-0.27) NTRK2 fusion 1 1 0.02 (0.005-0.11) NTRK3 fusion 2 2 4 0.08 (0.02-0.21) All NTRK fusions 4 7 11 0.23 (0.11-0.40)

Case Study #1: TRK Fusions in Non-Small Cell Lung Cancer1

• 1. Farago AF et al. JCO Precision Oncology. 2018.

Age at diagnosis, median (range) 47.6 (25.3-86.0) Gender, n (%) Male Female 6 (55) 5 (45) Smoking history in pack years, n (%) 0-5 5-20 >20 8 (73) 0 (0) 3 (27) Pack years, median (range) 0 (0-58) Stage at diagnosis (AJCC 7th edition), n (%) I II III IV 0 (0) 2 (18) 1 (9) 8 (73) Histology (local assessment) Adenocarcinoma Squamous cell carcinoma Neuroendocrine carcinoma 9 (82) 1 (9) 1 (9) Sites of metastasis, n Lymph nodes Bone Pleura or malignant effusion Lung Liver Brain Adrenal Skin/soft tissue Pericardium Trachea 8 6 5 5 4 4 2 1 1 1

Case Study #1: TRK Fusions in Non-Small Cell Lung Cancer1

• 1. Farago AF et al. JCO Precision Oncology. 2018.

Case Study #1: TRK Fusions in Non-Small Cell Lung Cancer1

• 1. Farago AF et al. JCO Precision Oncology. 2018.

25 26 27

SLIDE 10

Case Study #1: TRK Fusions in Non-Small Cell Lung Cancer1

• 1. Farago AF et al. JCO Precision Oncology. 2018.

GIST? Undifferentiated sarcoma Case Study #2: Undifferentiated Sarcoma Strong TRK expression by IHC Case Study #2: Undifferentiated Sarcoma

28 29 30

SLIDE 11

Genomic alterations identified: TPM3–NTRK1 fusion PTEN truncation exon 5

Case Study #2: Undifferentiated Sarcoma TRK Inhibitor (Larotrectinib) in Undifferentiated Sarcoma (Not GIST) With NTRK1 Gene Fusion

Baseline a Cycle 4 a

a Patient treated prior to FDA approval in November 2018.

Confirmed objective response (partial remission) after 2 cycles of larotrectinib

• NTRK gene fusions act as oncogenic drivers

– Point mutations and amplification are not clear oncogenic drivers and do not predict TRK-inhibitor sensitivity based on currently available data

• Look carefully at the NTRK gene alteration

– Oncogenic NTRK fusions involve a 5’ partner and a 3’ NTRK gene that contains the TRK kinase domain

• A multiplexed testing approach using next-generation sequencing is an

efficient approach for identifying TRK fusions if the pretest probability is low – IHC or FISH may be faster and preferred if the likelihood of a TRK fusion is high

• In common cancer types, there is no defining clinical or pathologic feature
• f TRK fusion cancers

– All solid tumors without another known oncogenic driver should be screened

Biomarkers: Take-Home Points

31 32 33

SLIDE 12

TRK Inhibitors in the Clinic TRK Inhibitors in the Clinic

The Spectrum of TRK Inhibitors in Cancer1

• 1. Cocco E et al. Nat Rev Clin Oncol. 2018;15:731-747.

TRK Inhibitors: Current Status of Selected Agents

Larotrectinib FDA-approved

Treatment of adult and pediatric patients with solid tumors that:

• Have an NTRK gene fusion without a

known acquired resistance mutation, are metastatic or where surgical resection is likely to result in severe morbidity, and

• Have no satisfactory alternative

treatments or that have progressed following treatment.

Entrectinib

• Phase 2/3 testing
• FDA Breakthrough Status

Repotrectinib

• Phase 1 testing

LOXO-195

• Phase 1 testing

34 35 36

SLIDE 13

• Larotrectinib is a highly potent and

selective small-molecule inhibitor of TRKA, TRKB, and TRKC (IC50 5-11 nM in cellular assays)

• Prolonged responses in adult patients

with TRK fusions (recommended phase 2 dose in adults is 100 mg BID)

• Promising tolerability profile
• Liquid formulation for pediatric patients

Larotrectinib Is the First Selective Pan-TRK Inhibitor in Development1

TRKA/B/C

• 1. Drilon A et al. New Engl J Med. 2018;378:731-739.
• TRK fusion status determined by

local CLIA (or similarly accredited) laboratories

• Primary endpoint for the

combined analysis: – Overall response rate according to independent review

• Secondary endpoints:

– Duration of response – PFS – Safety

• Dosing

– Single-agent larotrectinib, administered predominately at 100 mg BID continuously – Treatment beyond progression permitted if patient continuing to benefit

The Larotrectinib Development Program Spans Several Trials1

Adult phase 1

• Aged ≥18 y
• Advanced solid tumors

SCOUT: Pediatric phase 1/2

• Aged ≤21 y
• Advanced solid tumors

NAVIGATE: Adult/adolescent phase 2 basket trial

• Aged ≥12 y
• Advanced solid tumors
• TRK fusion positive

N = 55 TRK fusion patients n = 8 n = 12 n = 35

• 1. Drilon A et al. New Engl J Med. 2018;378:731-739.

17 Unique Cancer Types Were Treated With Larotrectinib1,a

a Percentages may not total 100 because of rounding.

• 1. Drilon A et al. New Engl J Med. 2018;378:731-739.

37 38 39

SLIDE 14

Larotrectinib Has Tumor-Agnostic Activity in NTRK Gene Fusion-Positive Cancers (Cont’d)1

Response Investigator Assessment (N = 55) Central Assessment (N = 55) Percenta ORR, % (95% CI)b 80 (67-90) 75 (61-85) Best response Partial response 64c 62 Complete response 16 13 Stable disease 9 13 Progressive disease 11 9 Could not be evaluated 4

a Percentages may not total 100 because of rounding. b The best overall response was derived from the responses as assessed at specified time points according to RECIST

v1.1. c Data include one patient who had a partial response that was pending confirmation at the time of the database lock. The response was subsequently confirmed and the patient’s treatment and response are ongoing.

• 1. Drilon A et al. New Engl J Med. 2018;378:731-739.

Larotrectinib Has Tumor-Agnostic Activity in NTRK Gene Fusion-Positive Cancers1

a One patient not shown here. Patient experienced clinical deterioration and no post-baseline tumor measurements were recorded. b Patient had TRK solvent-front resistance mutation (NTRK3-G623R) at baseline due to prior therapy. c Pathologic CR.

• 1. Drilon A et al. New Engl J Med. 2018;378:731-739.

c

Soft tissue sarcoma

93.2 b a

NEJM population1 NEJM population1 Update ESMO2 Update ESMO2

Larotrectinib in Patients With TRK Fusion Cancer: Supplementary Dataset1,2

• 1. Drilon A et al. New Engl J Med. 2018;378:731-739. 2. Lanssen U et al. European Society for Medical Oncology 2018 Congress (ESMO 2018). Abstract 409O.

Adult Phase 1

• Age ≥18 years
• Advanced solid tumors

Adult Phase 1

• Age ≥18 years
• Advanced solid tumors

SCOUT: Pediatric Phase 1/2

• Age ≤21 years
• Advanced solid tumors

SCOUT: Pediatric Phase 1/2

• Age ≤21 years
• Advanced solid tumors

NAVIGATE: Adult/Adolescent Phase 2 Basket Trial

• Age ≥ 2 years
• Advanced solid tumors
• TRK fusion cancer

NAVIGATE: Adult/Adolescent Phase 2 Basket Trial

• Age ≥ 2 years
• Advanced solid tumors
• TRK fusion cancer

n = 8 n = 12 n = 35 Primary n = 55 n = 2 n = 25 n = 40 Supplementary n = 67 122 patients with TRK fusion cancer 122 patients with TRK fusion cancer

• TRK fusion status

determined by local CLIA (or similarly accredited) laboratories

• Primary endpoint

− Best ORR (RECIST 1.1)

• Secondary endpoints

─ Duration of response ─ PFS ─ Safety

• Dosing

─ Single-agent larotrectinib administered predominantly at 100 mg BID continuously ─ Treatment beyond progression permitted if patient continuing to benefit

40 41 42

SLIDE 15

Diversity of TRK Fusion Cancers Treated With Larotrectinib1,2

Primary Dataset (n = 55) Supplementary Dataset (n = 67)

Subtypes of STS

• 1. Drilon A et al. New Engl J Med. 2018;378:731-739. 2. Lanssen U et al. ESMO 2018. Abstract 409O.

Supplementary Dataset: Larotrectinib Efficacy Consistent With Primary Dataset1

• 1. Lanssen U et al. ESMO 2018. Abstract 409O.

Primary (n = 55) Supplementary (n = 54) ORR, % (95% CI) 80 (67-90) 81 (69-91) Best response, % PR CR 62 18 65 17

Investigator response assessments, as of July 30, 2018

Integrated Dataset: Larotrectinib Is Efficacious Regardless of Tumor Type1

• 1. Lanssen U et al. ESMO 2018. Abstract 409O.

Integrated (n = 109) ORR, % (95% CI) 81 (72-88) Best response, % PR CR 63 17

Investigator response assessments, as of July 30, 2018

43 44 45

SLIDE 16

Integrated Dataset: Larotrectinib Is Efficacious Regardless of Age1

• 1. Lanssen U et al. ESMO 2018. Abstract 409O.

Investigator response assessments, as of July 30, 2018

Integrated (n = 109) ORR, % (95% CI) 81 (72-88) Best response, % PR CR 63 17

Responses to Larotrectinib in TRK Fusion-Positive Cancers Are Durable: Integrated Dataset1

• 1. Lanssen U et al. ESMO 2018. Abstract 409O.

Primary Dataset Supplementary Dataset

Kaplan–Meier Landmark Analysis July 17, 2017 July 30, 2017 6 mo, % 83 88 12 mo,% 71 75

Sustained Responses With Larotrectinib (DOR)1

• 1. Lanssen U et al. ESMO 2018. Abstract 409O.

46 47 48

SLIDE 17

Larotrectinib activity in brain metastases

Presented By Alexander Drilon at 2019 ASCO Annual Meeting

Larotrectinib activity in brain metastases

Presented By Alexander Drilon at 2019 ASCO Annual Meeting

Larotrectinib activity in primary CNS tumors

Presented By Alexander Drilon at 2019 ASCO Annual Meeting

49 50 51

SLIDE 18

Response to Larotrectinib Was Brisk and Dramatic in Several Cases1

Baseline Day 6 Day 20

• 14-year-old female with ETV6-NTRK3 secretory breast carcinoma and

prior therapy: 4 lines of chemotherapy and repeated resections

• Treated with larotrectinib under expanded access
• 1. Shukla N et al. JCO Precision Oncol. 2017.

60-Year-Old Woman With Widely Metastatic, Refractory MPNST and TPM4-NTRK3 Fusion1,2

Enrolled in Phase 2 trial of Larotrectinib

• 1. RC Doebele et al. Cancer Discovery. 2015;5:1049-1057. 2. Gounder MM et al. ASCO 2017. Abstract 11001.

Post-Resection Study Baseline Study Cycle 2 Day 1 Study Cycle 5 Day 1

Larotrectinib Is Active Against Intracranial Disease1

Early Radiographic and Clinical Response in GBM With an ETV6-NTRK3 Gene Fusion2

• 3-year-old female diagnosed at

5 months of age; failed treatment with multiple surgical resections, intensive chemotherapy, and focal radiation

• Completed 2 cycles of

larotrectinib and ongoing

• Significant improvement in

milestones within 2 weeks of commencing treatment

Baseline After 2 cycles

• 1. Turpin B et al. 2017 American Association for Cancer Research Pediatric Cancer Conference. 2. Images courtesy of Dr. David Ziegler; Sydney Children’s hospital;

manuscript in submission.

52 53 54

SLIDE 19

Potential Role for Larotrectinib in the Neoadjuvant Setting in IFS?1-3

• 2-year-old girl with IFS, ETV6-

NTRK3

• 2 cycles of vincristine/actinomycin-D/

cyclophosphamide  progression  amputation was the only alternative

• 4 cycles larotrectinib  PR 

referred for surgery

• >98% necrosis and negative

margins (R0 resection)

• No functional deficit post-surgery
• Off larotrectinib x8 months and no

evidence of disease Baseline Start of Cycle 3

• 1. Images courtesy of Dr. Leo Mascarenhas. 2. DuBois S et al. Connective Tissue Oncology Society 2017 Annual Meeting. Abstract 2762187.
• 3. DuBois S et al. Cancer. 2018;124:4241-4247.

Adverse Events With Larotrectinib: ≥15% in Safety Database (n = 207)1

• 1. Lanssen U et al. ESMO 2018. Abstract 409O.
• 11 (9%) of 122 patients with TRK fusion cancer required dose reductions; all maintained tumor regression on reduced dose
• 1 (<1%) of 122 patients with TRK fusion cancer discontinued larotrectinib due to an adverse event

Treatment-Emergent AEs, % Grade 1 Grade 2 Grade 3 Grade 4 Total Fatigue 18 15 3

• 36

Dizziness 25 3 1

• 29

Nausea 24 3 1

• 29

Constipation 22 5 <1

• 27

Anemia 10 7 10

• 27

ALT increased 17 5 3 <1 26 AST increased 18 5 3

• 26

Cough 23 3 <1

• 26

Diarrhea 16 6 1

• 23

Vomiting 17 6 <1

• 23

Pyrexia 12 5 <1 <1 18 Dyspnea 10 6 2

• 18

Headache 13 4

• 16

Myalgia 12 3 1

• 16

Peripheral edema 12 4

• 15

Treatment-Related AEs, % Grade 3 Grade 4 Total <1

• 18

<1

• 21

1

• 15
• 12

2

• 11

2 <1 21 1

• 19
• 1
• 5
• 10
• 1
• 1
• 4

<1

• 7
• 7
• Larotrectinib is active in NTRK gene fusion positive cancers

across multiple tumor types – Durable responses – Active regardless of age (adult and pediatric patients) – Clinical potential as an adjuvant/neoadjuvant option

• FDA approved in November 2018 for use in adult and

pediatric patients with NTRK gene fusion positive tumors

Larotrectinib in TRK Fusion Cancers: Summary

55 56 57

SLIDE 20

• Orally administered inhibitor of TRKA/B/C, ROS1, and ALK

Entrectinib: Pan-TRK/ROS1/ALK Inhibitor1

Chemical Structure

• f Entrectinib

X-ray Crystallography Model of Entrectinib Binding in the Kinase Pocket of TRKA Signaling Pathways of TRK and TRK Fusions Biochemical Activity of Entrectinib Target TRKA TRKB TRKC ROS1 ALK IC50 (nM) 1.7 0.1 0.1 0.2 1.6

• 1. Wei G et al. 2016 EORTC-NCI-AACR Molecular Targets and Cancer Therapeutics Symposium. Abstract 78.

Entrectinib Development Program: Combined Phase 1 Studies1

ALKA-372-001 (N = 54)

• Dosing: Intermittent and

continuous

• NTRK/ROS1/ALK alterations
• Italy

─ FIH study: Nerviano Medical Sciences in October 2012 → Ignyta assumed responsibility in November 2013 STARTRK-1 (N = 65)

• Dosing: Continuous
• NTRK/ROS1/ALK alterations
• US, EU, and Asia

─ Ignyta initiated in July 2014

• RP2D: 600 mg PO once daily, continuous
• Total clinical experience (n = 119 patients)

─ Updated safety and efficacy data ─ Data cut-off: March 7, 2016

• 1. Drilon A et al. Cancer Discov. 2017;7:400-409.

Entrectinib Is an Active Drug in NTRK Gene Fusion-Positive Cancers1

• 1. Drilon A et al. Cancer Discov. 2017;7:400-409.

Best Response in TKI Treatment-Naïve NTRK-Rearranged Tumors (n = 4)

• Response achieved in 100% of

tumors ─Rapid (within 1 month of treatment) and prolonged (~1 year, ongoing) responses were observed

• Response achieved in a variety of

histologies and fusion types ─CRC: NTRK1-LMNA ─Astrocytoma: NTRK1-BCAN ─NSCLC: NTRK1-SQSTM1 ─MASC: NTRK3-ETV6

0%

• 100%
• 90%
• 80%
• 70%
• 60%
• 50%
• 20%
• 40%
• 30%
• 10%

RECIST V1.1 3D volumetric assessment (Courtesy of P Brastianos, MD, MGH) SD by RECIST V1.1 Tumor Reduction, % CRC Astrocytoma NSCLC MASC

58 59 60

SLIDE 21

Baseline Characteristics: Adult Patients in Entrectinib Trial With NTRK Gene Fusion-Positive Solid Tumors1

• 1. Demetri GD et al. ESMO 2018. Abstract LBA17.

Baseline characteristics NTRK+ Patients (n = 54) Age, y Median (range) 57.5 (21–83) Sex, % Female Male 59.3 40.7 Race, % White Asian 79.6 13.0 ECOG PS, % 1 2 42.6 46.3 11.1 Prior lines of systemic therapy, % 1 ≥2 37.0 20.4 42.6 CNS mets at baseline, % 22.2

Sarcoma 24% NSCLC 19% MASC 13% Breast 11% Thyroid 9% CRC 7% Pancreatic 6% Neuroendocrine 6% Gynecological 4% Cholangiocarcinoma 2%

Entrectinib Activity in NTRK Fusion-Positive Solid Tumors: Individual Patient Responses by Tumor Type1

• 1. Demetri GD et al. ESMO 2018. Abstract LBA17.

NTRK+ Patients (n = 54) ORR (95% CI) 57.4% (43.2-70.8) SD 9 (16.7) PD 4 (7.4) Non-CR/PD missing or unevaluable 10 (18.5)

• 1. Demetri GD et al. ESMO 2018. Abstract LBA17.

Entrectinib Activity in NTRK Fusion-Positive Solid Tumors: Individual Responses by CNS Mets Status1

CNS Mets at Baseline (n = 12) No CNS Mets at Baseline (n = 42) ORR (95% CI) 50.0% (21.1-78.9) 59.5% (43.3-74.4)

61 62 63

SLIDE 22

Entrectinib Activity in NTRK Fusion-Positive Solid Tumors: Intracranial ORR in Patients With CNS Mets1

• 1. Demetri GD et al. ESMO 2018. Abstract LBA17.

Patients With CNS Mets at Baseline (n = 11) per BICR Intracranial ORR, n (%) (95% CI) 6 (54.5) (23.4-83.3) CR 3 (27.3) PR 3 (27.3) SD 1 (9.1) PD 1 (9.1) Non CR/PD, missing or unevaluable 3 (27.3) Intracranial median DOR, mo (95% CI) NE (5.0-NE) Intracranial median PFS, mo (95% CI) 14.3 (5.1-NE)

Entrectinib activity in patients with CNS metastases

Figure 1. Waterfall plot of change in tumor size (NTRK+ solid tumor)

*Best change at any single timepoint. SLD, sum of longest diameter. 60 20

• 100

Best % change from baseline in SLD CNS mets at baseline No CNS mets at baseline

• 80
• 60
• 40
• 20

40 Best percent change from baseline in tumor size*

Table 4. Intracranial efficacy in patients with baseline CNS disease*,†

NTRK+ solid tumors (n=11) ROS1+ NSCLC (n=20) ORR, % (95% CI) 54.5 (23.4–83.3) 55.0 (31.5–76.9) Median DoR, months (95% CI) NE (5.0–NE) 12.9 (5.6–NE) Median PFS, months (95% CI) 14.3 (5.1–NE) 7.7 (3.8–19.3) *CNS disease at baseline determined by investigator; †Includes patients with both measurable and non-measurable CNS lesions at baseline. Presented by Siena et al., ASCO Annual Meeting 2019

Entrectinib: Safety Overview1

• 1. Demetri GD et al. ESMO 2018. Abstract LBA17.

Overall safety population (N = 355)

• Most adverse events were

grades 1/2 and reversible

• Treatment-related AEs

leading to − Dose reduction: 27.3% − Dose interruption: 25.4% − Discontinuation from treatment: 3.9%

• No grade 5 treatment-related

events Treatment-related AEs in the NTRK fusion–positive safety population are consistent with the overall safety population Treatment-Related AEs Reported in ≥10% of Patients NTRK Fusion-Positive Safety Population (n = 68) Overall safety population (N = 355) Patients, n (%) Grades 1/2 Grade 3 Grades 1/2 Grade 3 Dysgeusia 32 (47.1) 146 (41.1) 1 (0.3) Constipation 19 (27.9) 83 (23.4) 1 (0.3) Fatigue 19 (27.9) 5 (7.4) 89 (25.1) 10 (2.8) Diarrhoea 18 (26.5) 1 (1.5) 76 (21.4) 5 (1.4) Oedema peripheral 16 (23.5) 1 (1.5) 49 (13.8) 1 (0.3) Dizziness 16 (23.5) 1 (1.5) 88 (24.8) 2 (0.6) Blood creatinine increase 12 (17.6) 1 (1.5) 52 (14.6) 2 (0.6) Paraesthesia 11 (16.2) 67 (18.9) Nausea 10 (14.7) 74 (20.8) Vomiting 9 (13.2) 48 (13.5) Arthralgia 8 (11.8) 42 (11.8) 2 (0.6) Myalgia 8 (11.8) 52 (14.6) 2 (0.6) Weight increased 8 (11.8) 7 (10.3) 51 (14.4) 18 (5.1) AST increase 7 (10.3) 35 (9.9) 3 (0.8) Muscular Weakness 6 (8.8) 1 (1.5) 22 (6.2) 3 (0.8) Anaemia 5 (7.4) 8 (11.8) 27 (7.6) 16 (4.5)

64 65 66

SLIDE 23

Entrectinib1

• 1. Demetri GD et al. ESMO 2018. Abstract LBA17.
• Entrectinib treatment resulted in clinically meaningful, deep, and

durable systemic responses (ORR 57.4%) in NTRK fusion–positive adult patients with solid tumors − Across 10 tumor types, including at least 19 distinct histopathologies − In patients with and without CNS metastases

• Clinically meaningful and durable CNS antitumor activity was

demonstrated in patients with baseline CNS metastases, with intracranial responses (54.5%) similar to systemic responses

• Entrectinib was tolerable with a manageable safety profile

− Most AEs were managed with dose interruption/reduction, and the discontinuation rate was low

Acquired Resistance Acquired Resistance

On-Target Acquired Resistance to First-Generation TRK Inhibitors1

• 1. Drilon A et al. Cancer Discov. 2017;7:400-409.

TRKA G595R Larotrectinib Tumor Type Fusion Resistance Mutation Colorectal TPM3- NTRK1 TRKA G595R Colorectal LMNA- NTRK1 TRKA G595R NSCLC TPR-NTRK1 TRKA G595R Sarcoma TPM3- NTRK1 TRKA G595R IFS ETV6- NTRK3 TRKC G623R Cholangiocarcino ma LMNA- NTRK1 TRKA F589L + GNAS Q227H

• TRK solvent-front mutations detected in

5 of 6 patients with acquired resistance

67 68 69

SLIDE 24

TRK Inhibitors Have Different Levels of Activity Against Emergent Mutations1

• 1. Cocco E et al. Nat Rev Clin Oncol. 2018;15:731-747.

LOXO-195 Is a Next-Generation Agent That Addresses On-Target Resistance1

Larotrectinib

• 1. Drilon A et al. Cancer Discov. 2017;7:400-409.

LOXO-195 Is a Next-Generation Agent That Addresses On-Target Resistance1

TRKA G595R Larotrectinib LOXO-195 Tumor Type Fusion Resistance Mutation Colorectal TPM3- NTRK1 TRKA G595R Colorectal LMNA- NTRK1 TRKA G595R NSCLC TPR- NTRK1 TRKA G595R Sarcoma TPM3- NTRK1 TRKA G595R IFS ETV6- NTRK3 TRKC G623R Cholangiocarci noma LMNA- NTRK1 TRKA F589L + GNAS Q227H LOXO-195 Treatment

• TRK solvent-front mutations detected in 5 of 6

patients with acquired resistance

• First 2 patients successfully treated with LOXO-195
• 1. Drilon A et al. Cancer Discov. 2017;7:400-409.

70 71 72

SLIDE 25

LOXO-195 Is in Phase 1/2 Clinical Trial Testing

Phase 1: Dose escalation Phase 2

• Patients aged 1 month and older
• Advanced TRK-fusion solid tumor
• Progressed on prior TRK inhibitor therapy or patient was

intolerant to any prior kinase inhibitor with anti-TRK activity

• Advanced TRK-fusion

solid tumor that has progressed on a prior TRK inhibitor

• Advanced TRK-fusion

solid tumor where patient was intolerant to a prior TRK inhibitor MTD/recommended phase 2 dose

• Age 12+
• Age <12

Parallel enrollment for age <12 treated at cleared dose levels for age 12+ Starting dose Age 12+

LOXO-195 (BAY2731954) Phase I and Expanded Access Experience

Presented by David Hyman, AACR Annual Meeting 2019 Presented by David Hyman, AACR Annual Meeting 2019

LOXO-195 (BAY2731954) Phase I and Expanded Access Experience

73 74 75

SLIDE 26

Presented by David Hyman, AACR Annual Meeting 2019

LOXO-195 (BAY2731954) Phase I and Expanded Access Experience

Presented by David Hyman, AACR Annual Meeting 2019

LOXO-195 (BAY2731954) Phase I and Expanded Access Experience Sequential TRK-Inhibitor Use Can Prolong Disease Control1,2

TRK-inhibitor (larotrectinib

• r entrectinib) response

TRK-inhibitor treatment post-progression LOXO-195 1 2 3 Tissue and/or liquid biopsy Excision, ablation, radiation

• 1. Drilon A et al. Cancer Discov. 2017;7:400-409. 2. Blake J et al. Eu J Cancer. 2016;69(suppl 1):S144-S145.

76 77 78

SLIDE 27

Repotrectinib: Designed to bind within the ATP-binding boundary with high affinity and to target wild type and mutant kinase Potently inhibited wild type and mutant TRKs in vitro and in vivo, especially the solvent- front mutations that render common resistances to TRK inhibitors Phase 1/2 clinical trial is

• ngoing for TPX-0005 for

cancer patients with solid tumors harboring ALK, ROS1, or NTRK fusion genes (NCT03093116)

Repotrectinib (TPX-0005): Potent TRK Inhibitor May Overcome Resistance Mutations1

• 1. Cui JJ et al. EORTC-NCI-AACR Molecular Targets and Cancer Therapeutics Symposium 2017. Abstract B184.

Efficacy of TPX-0005 against wild type and mutant fusion TRKs in xenograft tumor models

The anti-tumor efficacy in the NIH3T3 LMNA-TRKA wild type xenograft model The anti-tumor efficacy in the NIH3T3 LMNA-TRKA G595R xenograft model The effect of TPX-0005 on the growth of NIH3T3 LMNA-TRKA G667C tumors

• NTRK gene fusions occur across cancer types and can be detected by

NGS-based platforms, IHC and FISH

• TRK fusion proteins act as oncogenic drivers, and predict sensitivity to

TRK inhibitors TRK inhibitors:

• Larotrectinib is FDA-approved for NTRK fusion cancers
• Entrectinib: FDA Breakthrough status
• Next-generation TRK inhibitors to overcome acquired resistance

mutations are in clinical development

Summary

Audience Q&A

79 80 81

SLIDE 28

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