Mechanism for targeting CDK4, BTK and PI3K in Mantle Cell Lymphoma. Selina Chen-Kiang, Ph.D. Weill Cornell Medicine

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1 Mechanism for targeting CDK4, BTK and PI3K in Mantle Cell Lymphoma Selina Chen-Kiang, Ph.D. Weill Cornell Medicine

2 Goal To develop mechanism-based therapy in mantle cell lymphoma Effective, tolerable, durable Mechanism of resistance Biomarkers

3 Bench to Bedside and Back Approach Basic science Preclinical studies Clinical relevance Hypothesis-driven combination therapy Longitudinal genomics and IHC RNA and exome-sequencing Single cell RNA-seq ATAC (Assay for Transposase-Accesible Chromatin)-seq Cell free DNA analysis Candidate driver genes bioinformatics Mechanism--loss and gain of function studies Back to bedside!!

4 The Cell Cycle Positive Negative Go M G2 S G1 Cyclin D + CDK4/6 ps-rb-e2f Cyclin E + CDK2 p16 p15 p18 p19 p21 p27 p57 mid-g1 checkpoint pst-rb E2F release CDK: Cyclin-Dependent Kinase p18 INK4c (CDKN2C)

5 CDK4 and CDK6-Specific Inhibitor PD (palbociclib, Ibrance) LEE011 (ribociclib) LY (abemaciclib)

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7 Targeting CDK4/CDK6 in lymphoma and myeloma CDK4/6 Inhibitor Partner agent (low dose, selective ) Weill Cornell Mantle cell lymphoma Multiple Myeloma Mantle cell lymphoma Phase I palbocilib Phase I/II palbociclib-bortezomib-dex Phase I palbociclib-bortezomib In progress Mantle cell lymphoma Phase I palbociclib-ibrutinib Multiple myeloma Phase I palbociclib-lenalidomide-dex 3/2017 Mantle cell lymphoma Phase II palbociclib-ibrutinib

8 Mantle Cell Lymphoma (MCL) Non-Hodgkin s lymphoma (6%) with an overall poor prognosis. Incurable due to the eventual development of drug Resistance. Constitutive cyclin D1 expression due to chromosomal t(11;14) translocation and mutations. Overexpression of CDK4.

9 Bench to Bedside and Back Approach Basic science Preclinical studies Clinical relevance Hypothesis-driven combination therapy Longitudinal genomics and IHC RNA and exome-sequencing Single cell RNA-seq ATAC (Assay for Transposase-Accesible Chromatin)-seq Cell free DNA analysis Candidate driver genes bioinformatics Mechanism--loss and gain of function studies Back to bedside!!

10 Prolonged Early G1 Arrest (pg1) Hypothesis Asynchronous pg1 Cyclin D M G2 G1 CDK4 Rb S M G2 S Cyclin D CDK4 G1 Rb palbociclib 12 hr M G2 S G1 Rb 24 hr M G2 S M G2 S G1 G1 Rb Rb M G2 S Cyclin D CDK4 G1 Rb Imbalance in Gene expression Huang et al., 2012, Blood

11 Prolonged Early G1 Arrest (pg1) Hypothesis Asynchronous pg1 pg1s M G2 S Cyclin D CDK4 G1 Rb M G2 S Cyclin D CDK4 G1 Rb palbociclib 12 hr M G2 S G1 Rb Bortezomib 24 hr M G2 S M G2 S G1 G1 Rb Rb M G2 S Cyclin D CDK4 G1 Rb palbociclib M G2 S Cyclin D CDK4 G1 Imbalance in Gene expression pg1-s: Release from pg1

12 Phase I study of palbociclib + bortezomib in patients with recurrent MCL Martin, Di Liberto, Chiron, Ely, Mason, Leonard, unpublished

13 Bench to Bedside and Back Approach Basic science Preclinical studies Clinical relevance Hypothesis-driven combination therapy Longitudinal genomics and IHC RNA and exome-sequencing Single cell RNA-seq ATAC (Assay for Transposase-Accesible Chromatin)-seq Cell free DNA analysis Candidate driver genes bioinformatics Mechanism--loss and gain of function studies Back to bedside!!

14 Discovering driver genes that mediate targeting CDK4/6 in lymphoma therapy Martin, Di Liberto, Chiron, Ely, Mason, Leonard, unpublished

15 Inhibition of CDK4/6 induces early G1 arrest in all MCL cells in vivo initially Early G1 Late G1-S G2-M R: complete and partial response NR: progression disease Di Liberto, Chiron, Mason, Martin, Leonard, Ely, unpublished

16 Inhibition of CDK4/6 induces reversible early G1 arrest in all MCL cells initially. Can we identify driver genes in pg1(day 8) that discriminate sensitivity from resistance to targeting CDK4 in combination with bortezomib? Di Liberto, Chiron, Mason, Martin, Leonard, Ely, unpublished

17 Phase I study of palbociclib + bortezomib (Palbz) in patients with recurrent MCL Martin, Di Liberto, Leonard, et al, unpublished

18 Bench to Bedside and Back Approach Basic science Preclinical studies Clinical relevance Hypothesis-driven combination therapy Longitudinal genomics and IHC RNA and exome-sequencing Single cell RNA-seq ATAC (Assay for Transposase-Accesible Chromatin)-seq Cell free DNA analysis Candidate driver genes bioinformatics Mechanism--loss and gain of function studies Back to bedside!!

19 Opposite regulation of genes in pg1 (d8/d1) in responding vs non-responding patients d 1 M G2 S Cyclin D CDK4 G1 Rb D 8 M G2 S Cyclin D CDK4 G1 Rb Metabolism Redox homeostasis PI3K activation Imbalance in Gene expression Di Liberto, Martin, Huang, et al, unpublished

20 pg1 reprogramming of MCL cells by CDK4 inhibition Palbociclib CDK4/6 pg1 PIK3IP1 PI3K Metabolism Oxidative stress Cell death Chiron, Di Liberto, Martin et al, Cancer Discovery, 2014

21 Bench to Bedside and Back Approach Basic science Preclinical studies Clinical relevance Hypothesis-driven combination therapy Longitudinal genomics and IHC RNA and exome-sequencing Single cell RNA-seq ATAC (Assay for Transposase-Accesible Chromatin)-seq Cell free DNA analysis Candidate driver genes bioinformatics Mechanism--loss and gain of function studies Back to bedside!!

22 Overriding ibrutinib resistance By targeting CDK4/6 in Combination therapy

23 Targeting Bruton Tyrosine Kinase (BTK) by Ibrutinib in MCL BCR Lyn p Syk p p Lyn p Syk p PIP3 BTK p PLCg2 PKCb NFkB PI3K Ibrutinib p p Proliferation Survival Akt BTK is required for survival of lymphoma cells; Targeting BTK with Ibrutinib is highly effective in MCL 1 ; However, relapse is virtually universal-- aggressive proliferation and poor prognosis 2 1. Wang et al. N Engl J Med Martin et al. Blood 2016.

24 Ibrutinib resistance is concurrent with PI3K activation BCR Growth factors Lyn p Syk p p Lyn p Syk p PIP3 BTK PI3K p PLCg2 Ibrutinib PKCb NFkB p p Akt Proliferation Survival Chiron, Di Liberto, Martin et al, Cancer Discovery, 2014

25 Prolonged CDK4 inhibition reprograms MCL cells for ibruitinib killing by inhibiting both BTK and AKT Chiron, Di Liberto, Martin et al, Cancer Discovery, 2014

26 Phase I clinical trial of palbociclib + Ibrutinib in recurrent MCL Abstract #150 Martin et al. A Phase I Trial of Ibrutinib Plus PD (Palbociclib) in Patients with Previously Treated Mantle Cell Lymphoma

27 Phase I clinical trial of palbociclib + Ibrutinib in recurrent MCL Palbociclib + Ibrutinib Ibrutinib Palbociclib Overall response 64% 68% 18% Complete response 43% 21% 5% Partial response 21% 47% Durable only one CR patient progressed Well tolerated Clinical Trial is planned for early 2017 Phase II

28 Concurrent loss of Rb and p16 and CDK4 amplification in resistance to palbociclib-ibrutinib therapy Copy number variation (CNV) of MCL cells Frequent monoallelic deletion of Rb1 (9/15), CDKN2A/B (7/15), ATM (7/15) and TP53 (4/15), and amplification of CDK4 (6/15) and PIK3CA/B (6/15) CR and PR despite these CNVs or aggressive proliferation (KI67>50%) CR and PR despite concurrent CDK4 amplification and CDKN2A/B deletion PD was associated with concurrent CDK4 amplification and Rb deletion in 4/5 patients, and additional CDKN2A/B, ATM or BIRC3 deletion in 3/5 patients. Di Liberto, Huang, Martin, Elemento, unpublished

29 Inhibition of CDK4 reprograms MCL cells for vulnerability to BTK or PI3K inhibition BTK inhibitor Palbociclib CDK4/6 PI3K inhibitor BTK PIK3IP1 pg1 PIK3IP1 PI3K NFkB NFkB Metabolism Oxidative stress Cell death

30 Promises and Challenges in targeting CDK4/6 Mechanism of therapeutic targeting of CDK4/6 Chromatin remodeling Reprogramming of gene expression Cancer cell metabolism Mechanism-based combination therapy Selection of partners - cell cycle specificity Node of integration Sequence, toxicity Mechanism of resistance Tumor intrinsic and extrinsic Identification of biomarkers longitudinal integrative WES/WTS scrna-seq, ATAC-seq, ctdna analysis Disease specificity

31 Acknowledgements Maurizio Di Liberto Xiangao Huang David Chiron David Jayabalan Pooja Khanna Priya Vijay Selina Chen-Kiang Peter Martin Kristi Blum (OSU) John Leonard Kami Maddocks (OSU) Scott Ely Nancy Bartlett (Wash U) Steven Park (UNC) Patients Lewis Cantley Costas Lyssiotis Chris Mason Olivier Elemento Ken Eng NIH/NCI V Foundation Lymphoma Research Foundation Leukemia and Lymphoma Society Starr Cancer Consortium

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