Shape of the dose-response for Cancer Christophe Badie Cancer - PowerPoint PPT Presentation

INTEGRATED SYSTEMS LEVEL ANALYSIS OF MYELOID LEUKAEMOGENESIS AND EVALUATION OF THE MOLECULAR ALTERATIONS OF ANTIGENIC T-CELL RECEPTOR REPERTOIRE FOLLOWING X-IRRADIATION WP5 Shape of the dose-response for Cancer Christophe Badie Cancer Genetics and Cytogenetics group Radiation Effects Department Centre for Radiation, Chemical & Environmental Hazards Public Health England United Kingdom

Aims • I. To provide a first integrated systems level description of myeloid leukaemogenesis following x-irradiation • II. To evaluate radiation-induced molecular alterations of the TCR (antigenic T cell receptor) gene repertoire in low dose irradiated mice

X-rays induced AML M&M Primary rAML material (infiltrated spleen tissues) Global gene expression Affymetrix GeneChip arrays control cell population* *BM sorted non committed progenitor cells (Lin - ) Proteomic alterations Isotope Coded Protein Label (ICPL) digested and analysed by mass spectrometry rAML cell-lines* *Derived from the primary tumours studied independently

Transcriptomics Differential modulation between primary rAML and cell lines Lin- cells Cell-lines Primary

Proteomics Common proteins within primary rAML Proteins involved in translation (Ribosomal) Eukaryotic translation initiation factor 2 (eIF2) is central to the onset of protein synthesis Common proteins within rAML cell lines Proteins involved in glucose metabolism

P53 expression C MLP3 RF12 RF26 C MLP3 RF12 RF26 P53 P53 actin actin 0.4 p53 relative expression 0.3 0.2 * * * * 0.1 0.0 c MLP3 RF12 RF24 C MLP3 RF12 RF26 Cell lines Primary cells

C-myc expression C MLP3 RF12 RF26 C MLP3 RF12 RF26 c-myc C-myc actin actin * * * * * * C MLP3 RF12 RF26 C MLP3 RF12 RF26 Cell lines Primary cells

40s ribosomal subunit S16 expression Protein synthesis RPS16 RPS16 actin actin 0.4 RPS16 relative expression * 0.3 * 0.2 * * * 0.1 0.0 c MLP3 RF12 RF24 c MLP3 RF12 RF24 C MLP3 RF12 RF26 Cell lines Primary cells

Thrombospondin Angiogenesis(-) -Immune regulation - Apoptosis Thrombospondin Thrombospondin actin actin * * * * * C MLP3 RF12 RF26 C MLP3 RF12 RF26 Cell lines Primary cells

Primary vs. control - genes Differentially expressed genes Upregulated genes Downregulated genes

Primary vs. control - genes Number of common genes and Sørensen-Dice index for deregulated genes Number of common Sørensen-Dice similarity Compared samples deregulated genes index for genes MLP3 and RF12 and RF26 5521 0.5549 MLP3 and RF12 6657 0.6376 MLP3 and RF26 6399 0.6934 RF12 and RF26 7347 0.7218 Number of common genes and Sørensen- Number of common genes and Sørensen- Dice index for upregulated genes Dice index for downregulated genes # common Sørensen- # common Sørensen- Compared Compared downregulated Dice upregulated Dice samples samples genes index genes index MLP3 and RF12 MLP3 and RF12 2526 0.5860 2995 0.5114 and RF26 and RF26 MLP3 and RF12 2982 MLP3 and RF12 3675 0.6851 0.5826 MLP3 and RF26 3014 MLP3 and RF26 3385 0.6824 0.6750 RF12 and RF26 3214 RF12 and RF26 4133 0.7722 0.6614

Primary vs. control - proteins Differentially expressed proteins Upregulated proteins Downregulated proteins

Primary vs. control - proteins Number of common genes and Sørensen-Dice index for deregulated proteins Number of common Sørensen-Dice similarity Compared samples deregulated proteins index for proteins MLP3 and RF12 and RF26 3 0.0304 MLP3 and RF12 11 0.1134 MLP3 and RF26 4 0.0454 RF12 and RF26 85 0.7658 Number of common genes and Sørensen- Number of common genes and Sørensen- Dice index for upregulated proteins Dice index for downregulated proteins # common Sørensen- # common Sørensen- Compared Compared downregulated Dice upregulated Dice samples samples proteins index proteins index MLP3 and RF12 MLP3 and RF12 2 1 0.0162 0.0337 and RF26 and RF26 MLP3 and RF12 6 MLP3 and RF12 5 0.1000 0.0789 MLP3 and RF26 1 MLP3 and RF26 3 0.0182 0.0508 RF12 and RF26 44 RF12 and RF26 41 0.6286 0.7387

Cell line vs. control - genes Differentially expressed genes Upregulated genes Downregulated genes

Cell line vs. control - genes Number of common genes and Sørensen-Dice index for deregulated genes Number of common Sørensen-Dice similarity Compared samples deregulated genes index for genes MLP3 and RF12 and RF26 5220 0.5870 MLP3 and RF12 0.7391 6590 MLP3 and RF26 0.7059 6338 RF12 and RF26 0.7123 6255 Number of common genes and Sørensen- Number of common genes and Sørensen- Dice index for upregulated genes Dice index for downregulated genes # common Sørensen- # common Sørensen- Compared Compared upregulated Dice downregulated Dice samples samples genes index genes index MLP3 and RF12 MLP3 and RF12 2713 0.5392 2507 0.5988 and RF26 and RF26 MLP3 and RF12 3476 MLP3 and RF12 3114 0.7047 0.7427 MLP3 and RF26 3408 MLP3 and RF26 2930 0.6566 0.7050 RF12 and RF26 3270 0.6576 RF12 and RF26 2985 0.7087

Cell line vs. control - proteins Differentially expressed proteins Upregulated proteins Downregulated proteins

Cell line vs. control - proteins Number of common genes and Sørensen-Dice index for deregulated proteins Number of common Sørensen-Dice similarity Compared samples deregulated proteins index for proteins MLP3 and RF12 and RF26 55 0.4508 MLP3 and RF12 0.6056 76 MLP3 and RF26 0.5830 65 RF12 and RF26 0.5814 75 Number of common genes and Sørensen- Number of common genes and Sørensen- Dice index for upregulated proteins Dice index for downregulated proteins # common Sørensen- # common Sørensen- Compared Compared downregulated Dice upregulated Dice samples samples proteins index proteins index MLP3 and RF12 MLP3 and RF12 27 0.4197 28 0.4667 and RF26 and RF26 MLP3 and RF12 37 0.5920 MLP3 and RF12 39 0.6047 MLP3 and RF26 33 0.5690 MLP3 and RF26 32 0.5664 RF12 and RF26 43 0.5931 RF12 and RF26 32 0.5424

Primary vs. cell line - genes Differentially expressed genes Upregulated genes Downregulated genes

Primary vs. cell line - genes Number of common genes and Sørensen-Dice index for deregulated genes Number of common Sørensen-Dice similarity Compared samples deregulated genes index for genes MLP3 and RF12 and RF26 5034 0.4141 0.5766 MLP3 and RF12 7096 0.5960 MLP3 and RF26 6720 0.6659 RF12 and RF26 8582 Number of common genes and Sørensen- Number of common genes and Sørensen- Dice index for upregulated genes Dice index for downregulated genes # common Sørensen- # common Sørensen- Compared Compared upregulated Dice downregulated Dice samples samples genes index genes index MLP3 and RF12 MLP3 and RF12 2007 0.4205 3027 0.3629 and RF26 and RF26 MLP3 and RF12 2584 MLP3 and RF12 4512 0.5724 0.5337 MLP3 and RF26 2854 MLP3 and RF26 3866 0.5774 0.5219 RF12 and RF26 3053 RF12 and RF26 5529 0.6279 0.6037

Primary vs. cell line - proteins Differentially expressed proteins Upregulated proteins Downregulated proteins

Primary vs. cell line - proteins Number of common genes and Sørensen-Dice index for deregulated proteins Number of common Sørensen-Dice similarity Compared samples deregulated proteins index for proteins MLP3 and RF12 and RF26 40 0.2532 0.4125 MLP3 and RF12 66 0.3599 MLP3 and RF26 52 0.7316 RF12 and RF26 124 Number of common genes and Sørensen- Number of common genes and Sørensen- Dice index for upregulated proteins Dice index for downregulated proteins # common Sørensen- # common Sørensen- Compared Compared upregulated Dice downregulated Dice samples samples proteins index proteins index MLP3 and RF12 MLP3 and RF12 18 0.2000 22 0.2558 and RF26 and RF26 MLP3 and RF12 28 0.3256 MLP3 and RF12 38 0.4000 MLP3 and RF26 29 0.3580 MLP3 and RF26 23 0.2857 RF12 and RF26 68 0.6602 RF12 and RF26 56 0.6788

17 Genes/Proteins

I. Conclusions • Significant similarity in dysregulated pathways identified with transcriptomics and proteomics • Primary tumour materials should be used for identification of key drivers of leukaemogenesis as use of in vitro cultured materials could be misleading • Demonstrate the power of this approach to identify genes and pathways associated with radiation-induced leukaemia

II. Analysis of TCR repertoires following acute low dose exposure What are the effects of low dose exposure on immune cells development? Analysis of T lymphocyte diversity Innate Adaptive Immunity Immunity Dranoff, Nature Reviews Cancer,2004 Gitlin AD and Nussenzweig MC Nature 2015

Selections of T cell repertoire Each lymphocyte express a unique antigenic receptor The theoritical abTCR: more than 10 14 different possibilities Can radiation exposure perturb the system and increase genetic instability in lymphocytes? Attaf M. et al. CEI 2015

V(D)J recombination: T cell receptor genes Keener AB. Nature Med. 2015 Attaf M. et al. CEI 2015