Molecular Biologygido.es/images/04_mesa1_biologia_molecular_dra_jantus.pdf · KRAS mutations: correlation with Histology Table 3 KRAS Non Smoker Former Smoker Current Smoker Total

Molecular Biology: diagnostic, prognostic and predictive biomarkers

Dra. Eloisa Jantus Lewintre

Laboratorio de Oncología Molecular Fundación para la investigación del Hospital General Universitario de Valencia

Modified from Wistuba et al, Nat Rev Clin Oncol 2011

Biomarkers for LUNG CANCER

BLOOD sample

Evo

lve

Locoregional

Mestastatic


SAMPLE/ MATRIX ISSUES

Tissue

TYPE OF BIOMARKER

WHEN?

Diagnostic

Prognostic

Predictive

Diagnosis

Response evaluation

Progression

CNB

Blood (Serum/Plasma)

BAL, Sputum

Place of sample ?

How many ?

What methodology should be used ?



Tissue

CNB

Blood

BAL, Sputum

Place of sample ? How many ?

Fresh/ frozen

FFPE

HETEROGENEITY



Tissue Fresh/ frozen

FFPE

Biobank


Types of tumor specimens in lung cancer

TUMOR CELLS ARE NEEDED !!



Blood

Biobannk


CTCs

Cell free DNA

MA

TRIX

Serum Plasma (EDTA)

Proteins

Metabolites


PLASMA TUMOR

T. Mok

PLASMA C3


TYPE OF BIOMARKER

Diagnostic

Prognostic

Predictive


P. Massion

RISK DIAGNOSTIC

RESPONSE

PROGNOSIS

Ajona, JNCI 2013


Complement system: Innate immunity


• Caucasic • Three discovery studies -> plasma patients with benign and stage IA lung cancer (n=147) • The classifier was validated on an independent set of plasma samples (n = 104) • The classifier proteins are modulated by transcription regulators (NF2L2, AHR, MYC, and FOS) associated with lung cancer, lung inflammation, and oxidative stress networks

Sozzi, G

JCO in press 2013

miRNA signature: 24 miRNAS

(high, intermediate, low)

Blood samples

Diagnostic value: NPV: 99%

Prognostic biomarker and Predictive of response


1000 controls

85 lung cancer

Superior diagnostic performance of LDCT if combined with miRNA tests


TYPE OF BIOMARKER

Diagnostic

Predictive

Prognostic

Ferté, C. et al. Nat. Rev. Clin. Oncol. 7, 367–380 (2010)

Ca de pulmón Biomarkers for LUNG CANCER


KRAS SCC ADC* Others Total p

WT 67 51 16 134

0.002 98.5% 79.7% 88.9% 89.3%

Mutated 1 13 2 16

1.5% 20.3% 11.1% 10.7%

Table 2 . KRAS mutations: correlation with Histology

KRAS Non Smoker

Former Smoker

Current Smoker

Total p

WT 13 54 67 134

0.007 Mutated

6 4 6 16

37.5% 25% 37.5% 100%

Table 3. KRAS mutations: correlation with Smoking Status


KRAS SCC ADC* Others Total p

WT 67 51 16 134

0.002 98.5% 79.7% 88.9% 89.3%

Mutated 1 13 2 16

1.5% 20.3% 11.1% 10.7%

Table 2 . KRAS mutations: correlation with Histology

KRAS Non Smoker

Former Smoker

Current Smoker

Total p

WT 13 54 67 134

0.007 Mutated

6 4 6 16

37.5% 25% 37.5% 100%

Table 3. KRAS mutations: correlation with Smoking Status

81.2

mese

s 23

mese

s


TYPE OF BIOMARKER

Diagnostic

Prognostic

Predictive

Ferté, C. et al. Nat. Rev. Clin. Oncol. 7, 367–380 (2010)

Ca de pulmón Biomarkers for LUNG CANCER

De-selection


ADC

Li et al, J Clin Oncol 2013

SCC


ADC

CUALES DEBEN SER

EVALUADOS COMO

BIOMARCADORES

PREDICTIVOS????


•EGFR

•ALK

•KRAS

•HER2

•BRAF

•ROS1

•RET

BRAF Sensitive to Vemurafenib / Dabrafenib/ MEK inh

RET Sensitive to RET kinase inh

mut and amplif



Drilon, 2013

Stahel, 2013


In total, 3 of 91 tumor samples which had no other sign of cancer-causing genetic abnormalities, had fusions involving NTRK1.

NGS, Foundation Medicine

Asian population!!


TYPE OF BIOMARKER

Diagnostic

Prognostic

Predictive What methodology

should be used ?


EGFR mutation testing methodology

Test sensitivity

Mutations detected


Peters et al., 2013 Lung Cancer

ALK

ALK fusion variants in NSCLC


FISH

IHC

RNAseq


Tissue should be priorized for EGFR and ALK testing.

EGFR and ALK results should be available within 2 weeks (10 working days)

•In resection specimens, testing is not recommended in lung cancer that lack morphological or IHC evidence of adenocarcinoma differentiation

•In limited specimens (biopsies, cytology), testing may be performed in SCC or small cell histology + clinical criteria

Lindenman, JTO 2013


BUT…..

MULTIPLEX ANALYSIS (NGS) are more informative ….

Same amount of sample

Biomarkers can be determined in BLOOD

samples



TYPE OF BIOMARKER

Diagnostic

Prognostic

Predictive What we should do after resistance to

targeted therapies?

REBIOPSIES


Consider liquid biopsies!!

P. Giannikopoulos, WCLC 2013

RESISTANCE TO EGFR TKI

P. Giannikopoulos, WCLC 2013

sample sample

N=16

AXL overexpression in 2

R. Thomas, WCLC 2013

HGF (circulating levels) in SCLC is prognostic may be predictive?

E. Arriola,2013


Rebiopsies … why?


Squamous cell carcinoma


Squamous cell carcinoma : FGFR

Squamous cell carcinoma: FGFR


Squamous cell carcinoma


Squamous cell carcinoma : HLA-A


BIOMARKERS TESTS

Li T, et al, J Clin Oncol 2013


Li T, et al, J Clin Oncol 2013



Biomarkers for LUNG CANCER Take a home message ...

Biomarkers for LUNG CANCER Biomarkers for LUNG CANCER Take a home message ...

3rd and 4th generation sequencing for mutation analysis

Validation of the new methodologies: standardization, CLIA

References laboratories: networks organized by contries

Transcriptomic

miRNAs

Epigenetics

Proteomics and Metabolomics

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Molecular Biologygido.es/images/04_mesa1_biologia_molecular_dra_jantus.pdf · KRAS mutations: correlation with Histology Table 3 KRAS Non Smoker Former Smoker Current Smoker Total