1. The Cancer genome atlas (TCGA) and the search for a CUP genetic/epigenetic signature
Manel Esteller, MD, PhD.
Director, Josep Carreras Leukaemia Research Institute (IJC)
Director, Cancer Epigenetics and Biology Program (PEBC)
ICREA Research Professor
Genetics Chairman, School of Medicine, University of Barcelona

2. 2 years 35 >150 47 TCGA CUP project Sept 2018– Sept 2020
participating institutions
>150
collaborators 47
paired CUP cases (N&T)
Goal
n=500
2 years
Sept 2018– Sept 2020
TCGA CUP project

3. Project budget Cost to NCI is approximately:
Tissue Acquisition: $500 per case, for a total of $250,000
Tissue Processing: $2000/per case, for a total cost of $1,000,000.
Tissue Characterization: $5000/case, for a total of 2,500,000
Total Investment: $3,750,000$

4. TCGA CUP project
Collate 500 paired CUP/normal samples with comprehensive clinical information to perform
a multi-omic characterization
Genomic
Epigenomic
Transcriptomic
Clinical
data
Genomic
Epi
genomic
Trans-
criptomic

5. Material Transfer and Data Use Agreements
Collaborators from America
*samples are submitted directly to NCH
MTA must be established between your institution and the Nationwide Children’s Hospital (NCH) at USA.
Collaborators outside America
The NCH does not require to sign a MTA with collaborator institutions that do not are sending samples directly to NCH. However, if your institution requires to establish an agreement or contract, our institution (IJC) will be glad to sign it.

6. TGCA CUPP collaborator institutions1 2 3 4 15

7. Are you interested in becoming part of this multicentric world-wide TCGA project, providing CUP samples?
Collaborator
Hospitals &
Institutions
around the world
Tumor
Clinical
data
Frozen tissue
(50 mg)
FFPE block
FFPE sections
(10-20 sections, 10 um) +
Normal
Frozen blood
(8-10 ml, EDTA tube)
FFPE block
(normal tissue)
FFPE sections
(10-20 sections, 10 um)
PROSPECTIVE
SAMPLES
PROSPECTIVE &
RETROSPECTIVE
SAMPLES (RS)
LAST OPTION
*express shipping
*risk of degradation

8. TGCA CUPP OUTCOME
Expand our knowledge about the molecular mechanisms governing CUP development.
Define the existence of different entities, now grouped as CUPs.
Identify potential therapeutic targets that can be translated to the clinical practice.

9. DNA extraction Bioinformatic >250 ng
Pre-anti-PD1 FFPE samples from NSCLC Fully clinically annotated
Genome-wide DNA methylation profile: Illumina 850k array
beadchip
Methylation level in each CpG explored
Duruisseaux et al., The Lancet Respiratory Medicine 2018

10. EPIMMUNE Positive NSCLC : Prediction of Response to Anti-PD1 Therapy
EPIMMUNE + (N=10)
EPIMMUNE + (N=10)
EPIMMUNE – (N=24)
EPIMMUNE – (N=24)
Log-rank; P < 10-3
HR (95%CI)= (0.017 – 0.373); P=0.001
Log-rank; P < 10-6
HR (95%CI)= (3.29x10-4 – ); P=0.007
At risk:
EPIMMUNE 10 7 5 4 + 24 1 -
At risk:
EPIMMUNE 10 8 7 + 24 11 5 - B
PD-L1 positive
CD8 high
Log-rank; P= 0.004
HR (95%CI)= (0.149 – 0.727); P=0.006
EPIMMUNE + (N=14)
Mutational Load
EPIMMUNE – (N=33)
At risk:
EPIMMUNE 14 6 + 33 2 -
Duruisseaux et al. The Lancet Respiratory Medicine 2018

11. EPIMMUNE-TCGA Positive NSCLC : Prediction of Response to Anti-PD1 TherapyB
NSCLC Discovery Cohort (N=34)
EPIMMUNE-TCGA signature
NSCLC Discovery Cohort (N=34)
EPIMMUNE-TCGA signature
TCGA NSCLC cohorts (N=582)
EPIMMUNE -TCGA signature
Log-rank; P< 10-5
HR (95%CI)= ( );P<0.001
Log-rank; P=0.019
HR (95%CI)= (0.100 – 0.863);P=0.026
EPIMMUNE – (N=22)
EPIMMUNE + (N=12)
Log-rank; P=0.927
HR (95%CI)= (0.587 – 1.665);P=0.967
EPIMMUNE + (N=12)
EPIMMUNE + (N=110)
EPIMMUNE – (N=22)
EPIMMUNE – (N=472)
At risk:
EPIMMUNE 12 10 7 5 4 + 22 1 -
At risk:
EPIMMUNE 12 10 9 7 6 + 22 11 -
At risk:
EPIMMUNE
110 74 71 70 +
472
300
282
280
279 -
Duruisseaux et al. The Lancet Respiratory Medicine 2018

12. DNA Methylation Profiling Could Predict Clinical Response to PD1 Blockade in CUP-NSCLC

13. BENEFITS FOR COLLABORATORS
Access to multi-omic data for CUP cases.
Authorship in top high-impact publications (i.e. Nature, Science, Cell…)