TRANSCRIPTION FACTORS in ONCOGENESIS

Transcription

1 TRANSCRIPTION FACTORS in ONCOGENESIS

2 TRANSCRIPTION

3 Basal transcription TAF TBP TATAA IIA RNA Polimerasi IIB IIF IIE IIH Transcription factors Gene-specific Tissue-specific Time-specific

4 Enhancer TAF RNA POLY II TBP IIA TATAA IIE IIF IIH IIB

5 TAF REPRESSOR TBP TATAA IIA RNA Polimerasi IIB IIF IIE IIH

6 IIH TAF IIA IIF IIE IIB REPRESSOR TATAA TBP

7 Transcription factor N DBD TAD/RD C DNA Binding Domain Transactivation Domain/ Repressor Domain

8 Transcription factors 1 Basic domains 1.1 Basic leucine zipper factors (bzip) 1.2 Basic helix-loop-helix factors (bhlh) 1.3 Basic helix-span-helix factors (bhsh) 2 Zinc-coordinating DNA-binding domains 2.1 Nuclear receptors with C4 zinc fingers 2.2 Other C4 zinc finger-type factors 2.3 C2H2 zinc finger factors 2.5 DM-type intertwined zinc finger factors 2.6 CXXC zinc finger factors 2.7 C2HC 2.8 C3H zinc finger factors 2.9 C2CH THAP-type zinc finger factors 3 Helix-turn-helix domains 3.1 Homeo domain factors 3.2 Paired box factors 3.3 Fork head / winged helix factors 3.4 Heat shock factors 3.5 Tryptophan cluster factors 3.6 TEA domain factors 3.7 ARID 4 Other all-alpha-helical DNA-binding domains 4.1 High-mobility group (HMG) domain factors 4.2 Heteromeric CCAAT-binding factors 5 alpha-helices exposed by beta-structures 5.1 MADS box factors 5.3 SAND domain factors 6 Immunoglobulin fold 6.1 Rel homology region (RHR) factors 6.2 STAT domain factors 6.3 p53 domain factors 6.4 Runt domain factors 6.5 T-Box factors 6.6 NDT80 domain factors 6.7 Grainyhead 7 beta-hairpin exposed by an alpha/beta-scaffold 7.1 SMAD/NF-1 DNA-binding domain factors 7.2 GCM domain factors 8 beta-sheet binding to DNA 8.1 TATA-binding proteins 8.2 A.T hook factors 9 beta-barrel DNA-binding domains 9.1 Cold-shock domain factors 0 Yet undefined DNA-binding domains

9 Transcription factors

10 Chromatine ImmunoPrecipitation (ChIP) ChIP-Seq

11 ChIP-Seq

12 ChIP-Seq

13 ChIP-Seq

14 TF binding site databases Name ChIPBase ChEA CistromeMap Factorbook hmchip HOCOMOCO JASPAR SwissRegulon Description ChIPBase a database for Transcription factor-binding sites, motifs (~1290 transcription factors) and decoding the transcriptional regulation of LncRNAs, mirnas and protein-coding genes from ~10,200 curated peak datasets derived from ChIP-seq methods in 10 species transcription factor regulation inferred from integrating genome-wide ChIP-X experiments. a knowledgebase and web server for ChIP-Seq and DNase-Seq studies in mouse and human. a Wiki-based database for transcription factor-binding data generated by the ENCODE consortium. a database and web server for exploring publicly available human and mouse ChIP-seq and ChIP-chip data. a comprehensive collection of human transcription factor binding sites models. The JASPAR CORE database contains a curated, non-redundant set of profiles, derived from published collections of experimentally defined transcription factor binding sites for eukaryotes. a database of genome-wide annotations of regulatory sites.

15 FACTORBOOK

16 FACTORBOOK

17 FACTORBOOK

18 TFBIND

19 High probability (94%) LYF1 binds our sequence at nucleotide 17 on bottom strand (-) TFBIND

20 TFBIND

21 ENCODE PROJECT DATABASE

22 HOW ARE TFs GOING MAD?

23 Viral oncogenes 1970s Oncogene Disease Gene Human disease v-myb myeloblastosis (avian) c-myb T-cell leukemia v-myc myelocytomatosis (avian) c-myc Burkitt's lymphoma v-fos fbj osteosarcoma (murine) c-fos Breast Ca. v-jun 'ju-nana' sarcoma (avian) c-jun Breast Ca. v-ets erythroblastosis [E26] (avian) ets1/erg PCa/AML/Sarcoma

24 Retroviral-mediated transduction Hijack Host DNA

25 MECHANISMS OF ONCOGENIC TRANSFORMATION GENETIC DEFECT GENE AMPLIFICATION CHROMOSOMAL REARRANGEMENT GENE OVEREXPRESSION GENE FUSION MUTATION OVEREXPRESSION

26 MECHANISMS OF ONCOGENIC TRANSFORMATION FUNCTIONAL EFFECT HYPER-ACTIVATION HYPER-REPRESSION ACTIVATOR REPRESSOR SHIFT DNA BINDING SITE DOMINANT NEGATIVE ALTERED SUBCELLULAR LOCALIZATION

27

28

29 ON Differentiation Stemness Cell Nov 3;127(3):

30 Colon carcinoma β-catenin mutation APC mutation Cell Nov 3;127(3):

31 - Differentiation - Proliferation - Survival Nature Reviews Immunology 8, (May 2008)

32 T-cell acute linfoblastic leukemia HD domain mutation Nonsense mutation Nature Reviews Immunology 8, (May 2008)

33 Myc:Max:Mad network Myc over-expressed in 50% human tumors Adapted from : Amati, B., S. R. Frank, et al. (2001). "Function of the c-myc oncoprotein in chromatin remodeling and transcription." Biochim Biophys Acta 1471(3): M

34 c-myc target genes cyclin A, p53, Gadd45, Cdc25 The Encyclopedia of Cancer, 2002

35 c-myc driven oncogenesis ON ON Adapted from: Shachaf CM et al. Nature, 2004, 431(7012):1112-7

36 c-myc amplification Melanoma normal tumor chr. 8 myc

37 8 14 IgH/myc translocation Burkitt s Lymphoma

38 RUNX1-CBFb complex RUNX1

39 RUNX1/RUNX1T1 Acute myeloid leukemia Chr.21 RUNX1 Chr.8 RUNX1T1 RUNX1/RUNX1T1 most common chromosomal translocation in acute myeloid leukemia (AML)

40 RUNX1/RUNX1T1 co-activators RUNX1 RUNX1/RUNX1T1 co-repressors TAD RD DBD DBD

41 RARa CoR CoR RARa RA RXRa

42 PML/RARa Acute promyelocytic leukemia CoR CoR PML PML RA RARa RA RA RA RA RARa CoR CoR

43 PLZF/RARa Acute promyelocytic leukemia CoR CoR CoR CoR PLZF RA RARa RA RA RA RA PLZF RARa CoR CoR CoR CoR

44 HOW CAN WE FIGHT BACK?

45 TARGETING block expression block activity Antisense RNAi Peptides Small-molecules

46 ANTISENSE AAAAA

47 PML/RARa Acute promyelocytic leukemia CoR CoR RARa PML

48 PML/RARa - Antisense PML/RARa Control Gambacorti-Passerini C, Mologni L, et al., Blood, 1996

49 PML/RARa Adapted from: Mologni L, et al., Cancer Res, 2001

50 ANTISENSE PRO Specific Versatile Simple design Cheap CON Degradation (PO) Immune response (PS) Cell penetration (PNA)

51 RNA INTERFERENCE (RNAi) small interfering RNA

52 short-hairpin RNA sirna shrna

53 Colon carcinoma β-catenin mutation APC mutation Cell Nov 3;127(3):

54 b-catenin RNAi Van de Wetering et al., EMBO Rep., 2003

55 b-catenin RNAi Colon carcinoma b-catenin actin 100,000 -DOX 50, DOX Mologni et al., Cancer Res., 2010

56 RNAi PRO Potent Specific Versatile Simple design CON Delivery Degradation Inflammatory response

57 PEPTIDES

58 PEPTIDES

59 Peptide BPI Diffuse large B cell lymphoma N-CoR BCL-6 Differentiation

60 Peptide BPI N-CoR CD80 TAT--Gly-Arg-Ser-Ile-His-Glu-Pro-Arg BCL Polo JM et al., Nat. Med., 2004

61 PEPTIDES PRO Specific Versatile Simple design CON Unstable Degradation Immune response Cell penetration

62 Peptidomimetic RI-BPI TAT D-Arg-Pro-Glu-His-Ile-Ser-Arg-Gly degradation Cerchietti et al., Blood, 2009

63 STAPLED PEPTIDES Advantages Stability Helicity Affinity Cell penetration

64 Notch1 stapled peptide T-LLA Moellering et al., Nature, 2009

65 Notch1 stapled peptide control non-staple -secretase inhibitor staple Moellering et al., Nature, 2009

66 SMALL-MOLECULE INHIBITORS

67 BRD4-NUT translocation in squamous carcinoma

68 Bromodomain Inhibitors Target genes Target genes

69 Bromodomain Inhibitors

70 Le Pourcelet, et al., Cancer Cell, 2004

71 b-catenin activity PKF PKF Le Pourcelet, et al., Cancer Cell, 2004

72 MUTANT B-CAT NORMAL B-CAT Le Pourcelet, et al., Cancer Cell, 2004

73 SMALL-MOLECULE INHIBITORS PRO Cell penetration No immune response Drug-like CON Specificity/Tox PK Difficult to design

74