MRD in ALL (pa,ent specific Ig/TCR PCR) Molecular Biology and Cytometry Course Mol: 2011 Marleen Bakkus

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1 MRD in ALL (pa,ent specific Ig/TCR PCR) Molecular Biology and Cytometry Course Mol: 2011 Marleen Bakkus

2 Cellular origin of B/T- cell malignancies Myeloid stem cell B-lymphocytes Stem cell precursor cells lymphoid stem cell T-lymphocytes Bone marrow Thymus Blood Lymphnode Bone marrow

3 MRD in ALL genezing

4 Which genes for MRD? Immunoglobulin (Ig) T-cell receptor (TCR)

5 More diversity junc,onal regions VH3-21 DH3-3 JH4-1 Cµ Junctional region VH3-21(germline) insertion DH3-3 (germline) insertion JH4-1(germline) TGTATTACTGTGCGAGA! GTATTACGATTTTTGGAGTGGTTATTATACC! ACTACTTTGACTACT! TGTATTACTGT AGGC CGATTTTTGGAGTGGTTATTATA GTCCA TGACTACT! TGTATTACTGTGCG TATCCGGA TTACGATTTTTGGAGTGGTTATTATAC CGATCG CTTTGACTACT! TGTATTACTGTGC CCGGACTG TTTTGGAGTGGTTATTATACC GGT ACTACTTTGACTACT! TGTATTACTGTGCGAG CTGAGTC TATTACGATTTTTGGAGTGGTTAT CGTAGCGTA TTTGACTACT! TGTATTACTG ACATCGA CGATTTTTGGAGTGGTTATTATA CGTAG ACTTTGACTACT! TGTATTACTGTGCG CGT TACGATTTTTGGAGTGGTTATTAT GGCTAAGG TGACTACT! TGTATTACTGTGC TTTGGAGTGGTTAT CC ACTTTGACTACT! TGTATTACTGTGCGAGA GGCTAG ATTACGATTTTTGGAGTGGTTATACC GTCGA GACTACT! TGTATTACTGTG GTCCAG TATTACGATTTTTGGAGTG CCGTAG CTACTTTGACTACT! TGTATTA CCGGA CGATTTTTGGAGTGGTTATTATA C ACT!

6 Primary repertoire diversity of human Ig and TCR molecules TCRαβ TCRγδ IgH Igκ Igλ TCRα TCRβ TCRγ TCRδ Number of genes - V genes >100 >50 >40 >50 > D genes J genes Combina,on diversity >5x10 6 >5x10 6 >5000 Junc,onal region diversity ++ +/- +/ Es#ma#on of total primary receptor repertoire >10 12 >10 12 >10 12

7 Frequency of TCR and Ig in childhood ALL B- lineage ALL T- lineage ALL IgH >95% 20-25% (~DH- JH) Igκ Igλ ~65% (~Kde) 15-20% TCRβ ~35% ~90% TCRγ ~55% ~95% TCRδ ~40% ~55% Vδ2- Jα29 ~40-45% Ref.: J.J.M. van Dongen en V.H.J. van der Velden: Detection of minimal residual disease in ALL

8 Genomic DNA TCR Gamma V N J TCR delta V N D PCR VH-CDR3 V N-D-N J DIAGNOSIS 125 bp Sequencing of the N-region Clono (N)-specific oligonucleotidic (ASO) probe/primer MRD Allele-specific real-time PCR PCR Genomic DNA <0.1%

9 Target iden,fica,on Diagnosis: Bone marrow sample DNA extrac,on PCR for IGH IGK TCRG TCRD TCRB (only in T- ALL) Sil- Tal (only in T- ALL)

10 Sequence targets PAGE Purify clonal band Sequence with forward and reverse primers

11 Sequence analysis and ASO design ASO-primer 2 IGHV3-64*05 (-6) N1 IGHD2-2*01 (-5, -13) N2 ASO-primer 1 IGHJ1 (-0) hardcopy

12 ASO design OLIGO soeware Tm: C Avoid stretches of more than 3 G s and C s in the last 5 bases Avoid dimer forma,on

13 ASO- primers in RQ- PCR IgH TCRδ VH DH JH V δ 2 D δ 3 n=3 n=6 n=1 n=1 TCRγ Igκ V γ J γ Vκ Kde n=1 n=2 n=1 n=1 ASO junctional region Probe Consensus primer Ref: Verhagen et al., Leukemia 2000, Van der Velden et al. Leukemia 2002

14 Temperature gradient 60 C 63 C 65 C Vg9 Patient 10-2 Healthy controls

15 Temperature gradient 60 C 63 C 65 C IgH VH2

16 Quan,fica,on of FU samples qaso-pcr FU1 FU2 Quantitative range: 10-4 Sensitivity: 10-5 FU3 FU2 FU1 FU1: 0,04% FU2: positive, not-quantifiable FU3: negative

17 Control gene Albumin Standard: commercial DNA

18 Ref: VHJ van der Velden, 2007, Leukemia

19 European Study Group on MRD detec,on in ALL (ESG- MRD- ALL; 32 laboratories in 17 countries) DCLSG Interfant ALL9 99 MRC- ALL 97/99 UKALL-R3 COALL FRALLE 2000 EORTC- CLG BFM- AIEOP ALL-2000 ESG MRD ALL NOPHO ALL-2000 R e l a p s e d A L L A L L - R E Z B F M 2002 adult ALL GMALL 06/99 adult ALL LALA 2000 (pre-)bmt ALL adult ALL UKALL XII adult ALL PETHEMA/ GETH Europe Stockholm Israel Singapore Glasgow Leeds Sheffield Kiel London Amsterdam Hamburg Bristol Lille Paris Rotterdam Brussel Copenhague Hannover Berlin Frankfurt Heidelberg Zurich Prague Vienna Petach Tikwa Australia Singapore Padova Monza Salamanca Sydney

20 EORTC- CLG (France, Belgium) EFS % MRD < MRD > 10-2 VHR Overall Logrank test: p< (years) O N Number of patients at risk : MRD < 10-2 MRD > 10-2 Cavé et al., NEJM 1998

21 EORTC- CLG MRD VLR R Ia-D Ia-P + R Ib no aspa Ib aspa interval IIa 4/8 maintenance If 10-2 vhr AR low R IA D IA P + R IB no aspa IBaspa interval IIA 4/8 R maintenance maintenance + pulse If 10-2 vhr AR high R IA D IA P + R IB no aspa IB aspa interval IIA 4/8 R mt mt+pulse If 10-2 vhr R1 R2 R3 R1 R2 R3 VHR R IA D IB vanda 3xHD MTX maintenance IA P BMT-MSD * W

22 Avoiding AlloSCT 3 y QR: , sensitivity:

23 Earlier predic,on of relapse QR: , sensitivity

24 Why qaso- PCR More sensi,ve than genescan Later,mepoints can be tested Beter predic,on of relapse Preven,on of over treatment Very standardised, possibility to compare with other ALL trials

25 Future Pa,ents will be stra,fied according to their early molecular response to treatment in future clinical protocols. The good responders might be cured using a less aggressive chemotherapeu,c regimen, avoiding side effects and therapy related long term toxici,es. In contrast, poor responders will need more intensive but also more toxic approaches including allogeneic stem cell transplanta,on.

26 Antwerpen, Koningin Paola Kinderziekenhuis (Dr. P. Maes) Brussel, UZ Brussel (Dr. J. Otten, Dr. A. van Damme/Dr. J. van der Werff ten Bosch) Brussel, HUDE Reine Fabiola (Dr. A. Ferster) Brussel, UCL Saint Luc (Dr. C. Vermylen) Gent, UZ Gent (Dr. Y. Benoit) Leuven, Gasthuisberg Leuven (Dr. A. Uyttenbroeck) Luik, Hopital Citadelle Liege (Dr. M-F. Dresse/ Dr. C. Hoyoux) Montegnee, C.H. St. Joseph Esperance (Dr. P.Philippet/ Dr. N. Francotte)

27 Molecular- Hematology lab

Minimal residual disease in childhood ALL (patient specific Ig/TCR PCR) Molecular Biology and Cytometry Course Mol: 2013 Marleen Bakkus

Minimal residual disease in childhood ALL (patient specific Ig/TCR PCR) Molecular Biology and Cytometry Course Mol: 2013 Marleen Bakkus Survival of childhood cancer patients Major challenges Treatments