Biopsia liquida

(1)

Biopsia Liquida

nel mondo reale Patrizio Giacomini

patrizio.giacomini@ifo.gov.it

(2)

Modulo dichiarazione conflitto di interessi

Tutti i rapporti finanziari intercorsi negli ultimi due anni devono essere dichiarati.

Non ho rapporti (finanziari o di altro tipo) con le Aziende del farmaco

Ho / ho avuto rapporti (finanziari o di altro tipo) con le Aziende del farmaco

Relationship Company/Organization

Grant supporting LiqHERcept/GIM21 Roche Pharmaceuticals Grant supporting anti HER2 antibody

development

Ibi Lorenzini

(3)

Invasive

Bias in tissue sampling Single time point

Analyte virtually unlimited

Many aberrations at once (large panels) high sensitivity

Minimally invasive No bias

Longitudinal

ctDNA degraded and scarce Limits in panel complexity low sensitivity

+ +

-

Tissue Biopsy & Liquid Biopsy: complementary

+

combining tissue biopsy,

liquid biopsy and re-biopsy

+

(4)

metastatico stadi precoci

localmente avanzato

Terapia medica pre-

sintomatico

DNA circolante tumorale (ctDNA): ‘azionabile’ a tutti gli stadi di malattia

esempi ricaduta

clinica Scopo del

ctDNA

stadi avanzati

CancerSEEK

Prevenzione primaria e secondaria, sorveglianza

intensificata

TRACERx

anticipazione del rischio di recidiva

F-One Liquid

sospensione di terapia inefficace

evoluzione e complessità della

malattia

Assegnazione terapia bersaglio

anche non-standard

chirurgia avviamento al

trattamento chirurgico

sorveglianza post- chirurgica; trattamenti

adiuvanti etc.

(5)

HER2 breast cancer

T-DM1

(6)

Allegretti, M. … and Fabi, A. 2019, in preparation

Cycle 1 T-DM1

Cycle 2 T-DM1

Cycle 3 T-DM1

Cycleⁿ T-DM1 relapse

Ado-Trastuzumab- emtansine (T-DM1)

Alessandra

Fabi Michelangelo Russillo

Edoardo Pescarmona Simonetta

Buglioni Francesco

Cognetti

Matteo

Allegretti Elena

Giordan i

Paolo Romania

LiqBreasTrack: tracking mutational trajectories in T-DM1- treated HER2 breast carcinoma patients by Liquid Biopsy

TTZ/PTZ

+ taxanes etc Time 0

baseline

(7)

NGS dPCR

LiqBreasTrack: monitoring by

NGS & dPCR

(8)

1. Lead time to progression (ctDNA PD vs. RECIST PD) 2. Recurrent mutational patterns on progression

LiqBreasTrack: primary aims

(9)

LiqBreasTrack:

HER2 amplification

NGS

dPCR

(10)

“My mom always said life was like a box of

chocolates. You never know what you're gonna get.”

(11)

Plasma (on T-DM1)

Pre-T-DM1 at progression

Tissues (pre T-DM1) Evaluation of HER2 status

dPCR assay: HER2/EFTUD

Progression

R= 0.99

R= 0.94

R= 1.17

R=2.28

R= 1.08

R= 1.12

R= 1.04

R= 1.46 pt#2

pt#4

pt#5

pt#6

pt#9

pt#15

pt#18 pt#17

Cutoff 1.15 Cutoff 2.00

Post T-DM1 Re-biopsy

R= 1.31

Yr 2018

R= 0.98

R= 1.04

R= 1.09

on treatment on treatment

on treatment

Monitoring T-DM1 treated patients by liquid biopsy - HER2 amplification

VIC

FAM

HER2

EFTUD

non-amplified

double positives

HER2/EFTUD ratio - R

R= 2.55

Yr 2015

R= 1.92

Yr 1995

R= 1.33

Yr 2000

R= 10.1 Yr 2001

R= 0.85

Yr 2012

R= 1.25

Yr 2006

R= 1.11

Yr 2012 R= 2.74

Yr 2015

R= 30.5 Yr 2016

R= 3.44 Yr 2017

Yr 2015

R= 1.27

Yr 2018

R= 0.61

Yr 2017

R= 0.59

Yr 2018 R= 5.00

Yr 2012

R= 9.50

(12)

LiqBreasTrack: other genomic

alterations (SNVs) in blood (and tissues)

NGS

dPCR

(13)

Blood drawings 0,0%

1,0%

2,0%

3,0%

4,0%

5,0%

6,0%

1 2 3 4 5 6 7 8 9

pt#1 age 54

0,0%

0,2%

0,4%

0,6%

0,8%

1,0%

1 2 3 4 5 6 7 8 9 10 11 12

pt#2 age 59

pt#7 age 52

0,0%

0,2%

0,4%

0,6%

0,8%

1,0%

1 2 3 4 5 6 7

Blood drawings Blood drawings

V A F

(blood)

0,00%

0,04%

0,08%

0,12%

0,16%

0,20%

1 2 3 4 5 6 7 8 9 10 11 12 13

Lead time:

0.9 months Lead time:

2.8 months

Lead time:

2.9 months Lead time:

2.1 months

ctDNA present at time 0, and slowly going up

ctDNA NOT present at time 0, but de novo appearing some

time after the beginning of treatment

intersecting ctDNA trajectories delayed ctDNA

appearance

NGS dPCR

resistance (primary) resistance

(acquired/adaptive)

sensitivity &

resistance (bi-clonal ear-

marking) sensitivity

(best responders)

LiqBreastTrack: recurrent ctDNA patterns

Blood drawings

PIK3CA p.H1047R TP53

p.R273H

ESR1 p.Y357C p.D538G pt#3

age 38

(14)

PIK3CA E545K

(NGS IRE Anat Patol)

tDNA (breast, 2015)

FoundationOne (Roche) report

Trastuzumab/Pertuzumab neoadjuvant

tDNA (ax lympho, 2016)

Lymph node resection

tDNA (skin, 2017)

LiqBreasTrack: ultra-fast ctDNA clearance

pt#6, age 47

0,0%

2,0%

4,0%

6,0%

8,0%

10,0%

1 2 3 4 5 6

Allele frequency

Blood drawings PIK3CA E545K

(15)

LiqBreasTrack: convergent Darwinian evolution leading to vulnerability

0,0%

2,0%

4,0%

6,0%

8,0%

10,0%

1 2 3 4 5 6 7 8

ESR1 p.Y537S ESR1 p.D538G ESR1 p.Y537N

VAF

Blood drawings

NGS data dPCR data CT scan

progression Baseline

T-DM1

ESR1 p.D538G VAF: 1.4%

ESR1 p.D538G VAF: 0.4%

ESR1 p.Y537S VAF: 0.05%

ESR1 p. Y537N

VAF: 0.0% ESR1 p. Y537N

VAF: 0.2%

ESR1 p.Y537S VAF: 8.8%

pt#6, age 47

(16)

www.oncokb.org

LiqBreastTrack: assigning NON-SOC therapy by ctDNA

Mut frequency 8.3% advanced BrCa

ESR1 p.Y537S

ESR1 p.D538G ESR1 p.Y537N

bioinformatician surgeon

biostatistician

Molecular Biologist medical

oncologist nurse

Pharmacologist – Hospital Pharmacist

IRE Molecular Tumor Board

hematologist

pathologist

(17)

June 2019

October 2019

LiqBreastTrack: response to NON-SOC therapy

(18)

LiqBreasTrack reveals new vulnerabilities not present in archival tumor tissues

ID

Tissue mutations

(number) Plasma mutations Clinical behaviour (imaging)

Plasma behaviour (ctDNA)

Actionable (OncoKB level ≤3)

Primary Metastasis T=0 Prog T=0 Prog

pt#1 - - PD

pt#2 12 1 PD

pt#3 - - PD

pt#4 - 43, 11, 7 PD

pt#5 4 64 NA SD NA

pt#6 1 1, 1, 1 PD

pt#7 - - PD

pt#9 2 - NA SD NA

pt#10 2 PD

pt#12 - - NA SD NA

pt#13 - - PD

pt#14 - 1 - SD not available yet -

pt#15 2 - - SD not available yet -

pt#16 - - - SD not available yet -

pt#17 - 0 - SD not available yet -

brain metastasis

Pts w/actionable SNVs on progression

5/8 (62.5%)

NA: Not Applicable

- Tumor vulnerabilities only seen in blood

- Tumor vulnerabilities not present at the beginning of T-DM1 treatment

(19)

https://www.oncotech.org/gim21

PI Città Centro

Chairman: F. Cognetti

Study coordinator: A. Fabi RM IRCSS Istituto Nazionale Tumori Regina Elena C. Tondini BG A.O. Papa Giovanni XXIII

L. Moscetti MO A.O.U. Modena

L. Del Mastro GE IRCSS A.O.U. San Martino IST P. Marchetti RM A.O.U. Sant’Andrea G. De Placido NA Università degli Studi

Federico II

Moving forward: from LiqBreasTrack to GIM21

(20)

LiqBreasTrack: preliminary conclusions

1. HER2 amplification may be a marginal cancer driver at the time of T-DM1 administration

2. Yet, T-DM1 is active on HER2 tumors that have lost HER2-amp (implications upon the industrial ADC pipeline)

3. Clinical response may be broken down into independent clonal trajectories

4. Resistant clones may be ear-marked and anticipate progression by 2-3 months on average

5. Target therapy may wipe off in DAYS a resistance selected through YEARS of ERBB2 blockade … Molecular cancer evolution under T-DM1 pressure occurs on a

strikingly short timescale, as short as a few days or weeks

6. … sometimes resulting in the disappearance of actionable alterations (you cannot treat something that is no longer there)…

7. … and sometimes resulting in de novo appearance (during T.DM1 treatment) of actionable aberrations that are not present in archival tumor DNA

8. Why basket trials do not work as one would expect?

9. Liquid biopsy and tissue biopsy in combination drive optimal therapeutic decisions 10.Liquid biopsy must go on beyond progression (additional lines of therapy)

11.Ethics, deontology, regulatory issues (and a personal perspective)

Alessandra Fabi

Matteo Allegretti