Making Sense of Novel Prognostics: NOTCH1, SF3B1

Jennifer R Brown, MD PhDDirector, CLL Center

Dana-Farber Cancer Institute

October 24, 2014

What is High Risk CLL?

• Historically defined solely by clinical features:– Stage, lymphocyte doubling time, b2m– Therapy resistance

• Biologic prognostic factors are increasingly important:

• IGHV, FISH, somatic mutation profile

Immunoglobulin VH Gene Mutation

Years from DiagnosisBlood 94: 1840, 1999

Med Surv 9 yrs

Med Surv>24 yrs

Overall Survival by FISH

100

80

60

40

20

00 12 24 36 48 60 72 84 96 120 144 168

Pa

tie

nts

su

rviv

ing

(%

)

Months

17p-11q-12q trisomyNormal13q deletion assole abnormality

NEJM 2000;343:1910

Del 17p: 32 m

Del 11q: 79 m

IGHV Mutation and Cytogenetics: Independent Predictors

Blood 100: 1410, 2002

Insights from Sequencing: NOTCH Mutations

NOTCH1: recurrent mutation (2 bp deletion; P2515fs)

-Fabbri et al:

-15.1% overall, assoc with UM IGHV and TP53 disruption

-21% in chemorefractory

-31% in Richter’s transformation

-predictor poor OS in MVA

-Puente et al:

-12.2% overall, assoc with UM IGHV, ZAP70, CD38

-23% in RT; poor OS 21% at 10 yrs Fabbri et al. J Exp Med. 2011 Jul 4;208(7):1389-401.

Puente et al. Nature. 2011 Jun 5;475(7354):101-5.

NOTCH Mutations: Short TFS and Higher Risk RT

Blood 119: 521, 2012

Mutation Discovery Through Sequencing a Large Initial Sample Set

• Increases detection of the full range of mutated genes

• Enables reconstruction of gene pathways underlying disease pathogenesis

• Reveals associations between genetic events and clinically important disease features

NEJM 365:2497, 2011

Sequencing CLL Reveals 9 Significantly Mutated Genes

Recently associatedEstablished

Novel

0 4 8 12 16

MAPK1

DDX3X

ZMYM3

NOTCH1

FBXW7

ATM

MYD88

SF3B1

TP53

Sig

nif

ican

tly

mu

tate

d g

enes

# mutations / 91 CLLs

NEJM 365:2497, 2011

SF3B1 Mutated in 15% of CLLs

SF3B1 chromosome 2 q33.1

1 2222 PP2A repeats

R62

5LN

6 26H

K70

0 E (7

)G

740E

K74

1NG

742D

(2

)

Q90

3R

1 1304 aa

• At the catalytic core of U2 snRNP

• 14 mutations in 14 CLL patients in a restricted region of the C-terminal domain

- K700E was recurrent

• Mutations in SF3B1 also seen in myelodysplasia

Yoshida et al, Nature 2011; Papaemmanuil et al, NEJM 2011

The Significantly Mutated Genes Associate with Known Prognostic

Markers

P<0.001

P=0.004

P=0.009

P=0.009

P=0.001

del(13q)

Trisomy 12

del(11q)

del(17p)

TP53

SF3B1

MYD88

NOTCH1

FISH Cytogenetic Features

Significantly mutated genes

IGHV mutational Status

1 91

MAPK1

FBXW7

ATM

DDX3X

ZMYM3

RNA processing

Notch1 signaling

Inflammatory pathway

Cell cycle or DNA damage

NEJM 365:2497, 2011

SF3B1 Mutation Independently Predicts Poor Prognosis

Months from diagnosis to first therapyNEJM 365:2497, 2011

SF3B1 Mutations Confer Poor Prognosis

Rossi et al Blood 2011;118:6904-8

BIRC3 Mutation Associated with Poor OS

Blood 119:2854

Fre

qu

enc

y o

f C

E (

%)

N=202 casesN=469 samplesMedian interval between sampling: 62 months

Inclusion criteria:• >2 years of follow-up • >2 sequential samples collected at the following time points:

a. Diagnosisb. Progression requiring treatment in progressive

casesc. Last follow-up in non-progressive/untreated cases

New NOTCH1, SF3B1 and BIRC3 Lesions are Developed During the CLL Clinical Course

N=3618%

N=136%

N=94%

N=105%

N=105% N=8

4%

N=105%

N=52%

N=63%

N=52%

N=42% N=1

0.5% N=0 N=0

High risk clonal evolution(TP53, NOTCH1, SF3B1, BIRC3)

24% at 10 years

Blood 2013;121(8):1403–1412

16 previously reported CLL driversWang et al., NEJM, 2011Quesada et al., Nat Gen, 2011Fabbri et al., JEM, 2011Brown et al., Clin Can Res, 2011Edelmann et al., Blood 2012

25 Recurrent Drivers in CLL

(n=160 Patients)

82/160 WES used in Wang et al. NEJM 2011

* 9 novel putative CLL drivers identified

Landau et al Cell 2013

NOTCH1 Mutation Status: High Risk Patient Characteristics

All WES NOTCH1 wt NOTCH1 p.P2514fs deletion# of patients 160 145 (91%) 15 (9%)Median age at diagnosis 54 53 58Male 99 (62%) 90 (62%) 9 (60%)Ever treated 33 (21%) 28 (19%) 5 (33%)IGHV unmut 60 (38%) 47 (32%) 13 (87%)Zap70 + 56 (35%) 50 (49%) 6 (40%)

Cytogenetics (Döhner hierarchy):17p- 18 (11%) 13 (9%) 5 (33%)11q- 25 (16%) 24 (17%) 1 (7%)Trisomy 12 16 (10%) 13 (9%) 3 (20%)normal 16 (10%) 14 (10%) 2 (13%)13q- 68 (43%) 64 (44%) 4 (27%)

Number affected

% of affected samples that are clonal

100

0

* Higher rate of clonal

frequencies, q<0.1

Inferring Earlier and Later Drivers in CLL

Landau et al Cell 2013;152:714–726

Biology of High Risk CLL • Clinical significance of del17p/TP53 mutation >

del11q > UM IGHV is well established

• Genomic complexity (FISH, karyotype or CN) associates with prognosis and appears quite adverse– but has not been routinely studied – Not analyzed in multivariable analyses

• Sequencing data suggest SF3B1, NOTCH1 and subclonal driver mutations associate with poor prognosis– Increasing data on TP53, SF3B1 and NOTCH1

in clinical cohorts

Recurrent Mutations Refine Prognosis

Balakas et al. Leukemia 2014: 1-8.

Balakas et al. Leukemia 2014: 1-8.

Recurrent Mutations Refine Prognosis

Recurrent Mutations Correlated to Cytogenetics

Jeromin et al. Leukemia 2014: 108-117

Balakas et al. Leukemia 2014: 1-8.

Recurrent Mutations Refine Prognosis

del13q14Normal/+12

NOTCH1 M/SF3B1 M/del11q22-q23TP53 DIS/BIRC3 DIS

del13q14Normal/+12

NOTCH1 M/SF3B1 M/del11q22-q23TP53 DIS/BIRC3 DIS

OS Treatment

Integrated Mutational and Cytogenetic Model for CLL Prognostication

N % 10-years OS155 26% 69%228 39% 57%99 17% 37%

101 17% 29%

p<0.0001 p<0.0001

N % Treated at 10 years155 26% 41%228 39% 50%99 17% 83%

101 17% 100%

Rossi et al. Blood 2013;121(8):1403

80%

14%6%

del13q14

NOTCH1 M/SF3B1 M

TP53 M/BIRC3 DIS

81%

14%5%

Normal

NOTCH1 M/SF3B1 M

TP53 M/BIRC3 DIS

70%

23%

7%

+12

NOTCH1 M/SF3B1 M

TP53 M/BIRC3 DIS

+12 by FISH

By Integrating Mutations, ~20% Low Cytogenetic Risk CLL are Reclassified into

High Risk Subgroups

del13q14 only by FISH Normal by FISH

Rossi et al

What About After Therapy?

CLL8 Study Design

817 patients with untreated, active CLL and good physical fitness (CIRS ≤

6, creatinine clearance ≥ 70

mL/min)

R

FCR

FC

6 courses

Follow up

C1 C2 C3 C4 C5 C6

Median observation time 5.9 years

Demographics similar between two treatment arms

Hallek M, et al: Lancet. 376:1164, 2010

CLL8: Addition of Rituximab to FC

CLL8: Addition of Rituximab to Fludarabine and Cyclophosphamide

CLL8: Survival after FCR by FISH

17p deletion

Lancet 2010: 376: 1164

+12q

13q-single

11q-

Not 17p-/11q-/+12q/13q-

17p-

MDACC: TTF after FCR Based on FISH (2004-2010)

0 12 24 36 48 60 72Months

0.0

0.2

0.4

0.6

0.8

1.0

Pts. Failed FISH 36 23 17p- 75 30 11q- 67 18 Trisomy 12 100 18 13q- 70 19 Negative

Pro

port

ion

Courtesy of M Keating

0 12 24 36 48 60 72 84

Months

0.0

0.2

0.4

0.6

0.8

1.0

Pts. Relapsed Status FISH 79 5 Mutated 54 20 Unmutated 11q- 104 20 Unmutated Other

MDACC: TTP for FCR Responders by IGHV and 11q

Pro

port

ion

Incidence of Genetic Lesions

CLL8: CLL3X:* CLL2H:# 1st Line High-Risk F-refractory

(FC vs. FCR) (Allo-SCT) (Alemtuzumab)n=635 n=80 n=97

TP53mut 11.5 30.0 37.4

NOTCH1mut 10.0 13.8 13.4

SF3B1mut 18.4 26.3 17.5

IGHV UM 63.0 95.6 76.3

17p- 8.2 18.1 30.1

11q- 24.6 36.1 19.4

*Dreger et al. abstract 966, Tue 8:45, #Schnaiter et al. abstract 710, Mo 4:45

Cox regression including: FC, FCR, age, sex, stage, ECOG, B-symptoms, WBC, TK, β2MG, 11q-, +12, 13q-, 17p-, IGHV, TP53, NOTCH1, SF3B1

CLL8 Multivariable Analysis: PFS

PFS: HR p-value

FCR 0.510 <.001

TK>10 1.367 0.019

IGHV UM 1.727 <.001

11q- 1.536 <.001

17p- 2.949 <.001

TP53mut 2.113 <.001

SF3B1mut 1.348 0.024

OS: HR p-value

FCR 0.652 0.006

Age>65 y. 1.467 0.018

ECOG>0 1.609 0.002

ß2MG>3.5 1.493 0.014

TK>10 1.961 0.003

IGHV U 2.125 <.001

17p- 3.175 <.001

TP53mut 2.852 <.001

CLL8 Multivariable Analysis: OS

CLL8: Impact of TP53 Mutation on OS

FCRFC

TP53: wild type mutated

Therapy:

Cox regression including: FC, FCR, TP53, NOTCH1, SF3B1, and treatment interaction

CLL8 Multivariable Analysis: Predictive Factors

PFS: HR p-value

FCR 0.544 <.001

TP53mut 3.607 <.001

SF3B1mut 1.355 0.012

NOTCH1mut 1.652 0.022Interaction

OS: HR p-value

FCR 0.654 0.002

TP53mut 4.470 <.001

NOTCH1mut 1.331 0.344Interaction

CLL8: NOTCH1 as Predictive Marker

FCRFC

NOTCH1: wild type mutated

Therapy:

Mutation Frequency in Fludarabine Refractory CLL

Rossi et al. Blood 2013;121:1403

TP53, SF3B1, and NOTCH1 Mutations and Outcome of Allotransplantation

Dreger et al. Blood 2013: 121 (16); 3284-3286

Summary

• SF3B1 mutation: associated with 11q deletion, UM IGHV, and shorter TTFT and PFS, ?OS

• NOTCH1 mutation: associated with trisomy 12, UM IGHV, shorter TTFT and Richter’s transformation– ? No benefit of anti-CD20 antibody

• Genomic complexity is adverse but requires further analysis in large trials

Summary

• Deletion of 17p or TP53 mutation predict highest risk CLL, followed by 11q deletion (NOTCH1, SF3B1) and Unmutated IGHV– Early data suggest high response but

shorter PFS with 17p or 11q deletion even with BCR pathway inhibitors

– No good data with BCR inhibitors for NOTCH1, SF3B1

• AlloSCT may overcome poor prognosis of these somatic mutations

What is Actionable?

• 17p / TP53: prognosis; therapy selection (TP53 independent: BCR, ?SCT)

• 11q: prognosis; FC-based CIT

• Mutated IGHV (esp trisomy 12): FCR

• SF3B1, NOTCH1, BIRC3: prognosis

Acknowledgments

DFCI BiostatisticsDonna NeubergLillian WernerHaesook Kim Kristen Stevenson

Brown Lab, DFCIBethany TesarStacey FernandesSasha VartanovReina ImprogoJosephine Klitgaard

NIH, NHGRICLL Research Consortium

Okonow-Lipton FundMelton Fund Rosenbach Fund

Lymphoma Program, DFCIArnold S FreedmanDavid C FisherAnn S LaCasceEric Jacobsen Philippe ArmandMatthew Davids

Clinical ResearchKaren FrancoeurKaren CampbellShannon MililloHazel Reynolds

Center for CancerGenome Discovery, DFCIMegan HannaLaura Macconaill

Wu Lab, DFCICatherine WuDan-Avi LandauLili WangYouzhong Wan

Broad Institute Eric LanderGaddy GetzCarrie SougnezNir HacohenStacey GabrielMike LawrencePetar StojanovAndrey SivachenkoKristian CibulskisDavid Deluca