The Challenges of Genes, Gene Expression and Genomics

Transcription

1 The Challenges of Genes, Gene Expression and Genomics Scott A. Ness Molecular Genetics & Microbiology University of New Mexico HSC Albuquerque, NM

2 Genes and Gene Products Chromosome: Gene: Spliced mrna: Encoded Protein: Functional Activity: Enzymes, hormones, structural proteins, oncogenes, etc.

3 Chromosome: Genes and Gene Products Mutation Gene: Spliced mrna: Encoded Protein: Activated Oncogene Functional Activity: Enzymes, hormones, structural proteins, oncogenes, etc. e.g. p53, ras, myb

4 Results of the Human Genome Project Humans have at least 50,000 genes Genes encode functional RNAs, proteins Many genes encode multiple products At least 200,000 different gene products Genetic Differences = Diversity At least 1,000 allelic differences per person

5 Genomics I: Measuring Differences in Gene Expression Profiles Different cell types (e.g. liver vs. kidney, normal vs. tumor) express different genes Gene expression patterns can distinguish between different cell or tumor types (classification) Differences in gene expression can identify novel targets for drug development

6 Comparison of Gene Expression Profiles Cells or Tissue e.g. Normal vs. Tumor Purify RNAs, label with fluorescent tags Hybridize to microarray, detect fluorescence

7 Affymetrix GeneChip GeneChip Probe Array 1.28cm Human Genome Array > 50,000 genes > 1,200,000 features

8 Genomics Research at UNM SOM Human Genomics Cancer Biology Novel Targets, Diagnostic Tools Asthma, Diabetes, Drug Screening, Schizophrenia Epidemiology Risk Detection and Prediction Genomics in Animal Models Stroke, Neurological Studies, Toxicology Microbial Genomics DNA Repair and Mutagenesis Cell Cycle Control, Gene Regulation Biosensor, Antibiotic, Diagnostics Development Hantavirus Biology Host-Pathogen Interactions (Cystic Fibrosis)

9 Example: Lymphoma Gene Profiling - Willman Lab 392 Genes 142 Patients

10 Gene Expression in PKD Samples Under-expressed in disease samples

11 Gene Expression in PKD Samples Over-expressed in disease samples

12 Vertebrates Express Three Myb Transcription Factors c-myb A-Myb B-Myb Highly Conserved Central Trans- Negative DNA Binding Activation Domain Domain Regulatory Domain

13 Myb Proteins Affect Development B-Myb c-myb A-Myb blastocyst embryo adult offspring B-Myb knockout blocks cell proliferation c-myb knockout blocks definitive hematopoiesis A-Myb knockout affects testis, mammary gland development

14 Myb Proteins are Transcription Factors Target Genes Myb Proteins Regulate Differentiation Regulate Apoptosis Regulate Proliferation Myb Proteins Control Cell Fate by Regulating the Expression of Other Genes

15 c-myb Expression in Hematopoiesis Hematopoietic Stem Cell Myeloid/Erythroid Stem Cell Lymphoid Stem Cell c-myb CFU-E CFU-Meg CFU-Bas CFU-Eosin CFU-GM Pre-B Pre-T Erythrocyte Megakaryocyte Basophil Eosinophil Neutrophil Monocyte B-Cell T-Cell

16 c-myb Expression in Hematopoiesis Hematopoietic Stem Cell Myeloid/Erythroid Stem Cell Lymphoid Stem Cell v-myb CFU-E CFU-Meg CFU-Bas CFU-Eosin CFU-GM Pre-B Pre-T Erythrocyte Megakaryocyte Basophil Eosinophil Neutrophil Monocyte B-Cell T-Cell

17 v-myb Induces Myeloid Leukemias Normal Chicken Blood v-myb-induced Leukemia

18 Myb Protein Comparisons A-, B- and c-myb proteins have distinct expression patterns A-Myb: specialized epithelial, hematopoietic cells B-Myb: all dividing cells c-myb: immature hematopoietic, epithelial v-myb: oncogenic, induces leukemia Each protein has a unique biological activity All the Myb proteins have similar structures

19 Test the Activities of Myb Proteins on Endogenous Human Genes Myb Expression Vector Recombinant Adenoviruses Use Affymetrix GeneChips to measure changes in endogenous gene expression Human Cells

20 MCF-7: Mammary Epithelial Cells Estrogen-responsive mammary carcinoma cells Common model for estrogen-responsive breast cancer Express A-Myb, B-Myb and c-myb during cell cycle, in response to estrogen

21 Adenovirus Expression Vectors c-myb A-Myb B-Myb MybEng c-myb DNA Binding Domain Engrailed Repressor Domain

22 Filtering Microarray Data to Identify Myb Regulated Genes Affymetrix U95A, U95B, U95C, U95D, U95E arrays 60,000 genes 100 % Filter for genes expressed above background 18,063 genes 30 % Filter for genes induced or repressed >2.5X 215 genes 3.5 %

23 ... Selected Gene Tree: Combined 215 smooth Colored by: MCF7 expressed genes Default Interpretation Gene List: Combined 2.5X up or down (320) 215 Myb Regulated Genes in MCF-7 Each Myb Protein Regulates a Different Set of Genes Uninf Cont A-Myb B-Myb c-myb MybEng Genes Repressed by A-Myb Genes activated by c-myb Genes activated by A-Myb Genes activated by B-Myb

24 Comparison of Myb Gene Activation in MCF-7 A-Myb Activated (119) B-Myb Activated (100) c-myb Activated (43) Genes activated 2.5X in independent replicate assays. More than 12,000 genes tested on U95A GeneChips.

25 Activation of Hep27 and DSIPI Legend Hep27 DSIPI Uninf Control c-myb MybEng Amyb Bmyb Affymetrix GeneChip Data

26 Myb Binding Sites in the Hep27 and DSIPI Gene Promoters Hep27 Promoter NFIL6 Myb Ets Ets Myb DSIPI Promoter YY1 Myb YY1 SP1

27 Swap Domains Between c-myb and A-Myb Conserved Restriction Sites A-Myb CHA AHC c-myb DNA Binding Domain Transcriptional Activation Domain

28 Selected Gene Tree: AC 30 genes >2.5X >2500 A-Myb or c-myb PEARSON Colored by: AC Swap Comparison Default Interpretation Gene List: AC 2.5X up >2500 A-Myb or c-myb (30) _at Homo sapiens cdna FLJ _s_at HEP _at LCP _s_at H1FX _at PP _at KRT _s_at SSAT _at SERPINA _at STHM _x_at MGC2479, FLJ21046, dj _at HEM _at HEM _s_at ASS1, CTLN _at MEH, EPHX _s_at PBP _at IGFBP _s_at CLLP _x_at MT1H _x_at MT _x_at MT _x_at MT _x_at GSPT _x_at MT _s_at FLJ _at CSD, CDB1, CSD1, CSD2, _s_at Homo sapiens cdna FLJ _s_at DRAL, SLIM _s_at RAB _s_at DIP, GILZ, TSC-22R _at EPAS1 A-Myb and c-myb Specificity in Human Cells Ø A CHA AHC C Activated by A- Myb and c-myb Activated by the c-myb transactivation domain Specific for the A-Myb DNA binding domain

29 A-Myb and c-myb Deletions A-Myb AP AB AN c-myb CCA CB CN

30 Domains that Affect Gene Activation Required for Required for activation of activation of Hep27 TGFBI A AP AB AN C CA CB CN Must Must be be removed removed to activate to activate DSIPI TGFBI Northern Blots The ability to activate many genes is determined by the C-terminal domains of c-myb and A-Myb Hep27 TGFBI α-catenin DSIPI

31 Structure of the Human c-myb Gene 1A 8A 9A 9B 10A 13A DBD TAD NRD Alternative splicing can yield > 64 different c-myb mrnas Myb proteins with alternative C-termini are likely to have different specificities and to activate different genes

32 Alternative c-myb Gene Exons Expressed in Normal Cells Exons 8A, 9A, 9B, 10A and 13A are all detected

33 Alternative c-myb Gene Exons in Leukemia Samples Leukemias Express Additional c-myb Transcripts

34 c-myb Alternative Splice Products c-myb +Exon 8A +Exon 9A +Exon 9B +Exon 10A +Exon 13A Alternative C-termini = Alternative Activities

35 Compare the Effects of Myb Proteins in Different Cell Types Myb-Expressing Adenoviruses Do Myb proteins activate the same genes in different cell types?

36 75 Myb Regulated Genes in Lung Epithelial Cells A-Myb 31 genes B-Myb 28 genes c-myb 55 genes Genes activated 2.5X in independent replicate assays. More than 12,000 genes tested on U95A GeneChips.

37 339 Myb Regulated Genes in Lung Fibroblast Cells A-Myb 225 genes B-Myb 142 genes c-myb 170 genes Genes activated 2.5X in independent replicate assays. More than 12,000 genes tested on U95A GeneChips.

38 Myb Activities are Context-Specific MCF-7 A-Myb LE MCF-7 B-Myb LE MCF-7 c-myb LE LF LF LF Almost no overlap in Myb activated genes in different cell types

39 Unique Activities in Each Cell Type MCF genes LE 75 genes Three Myb proteins, three cell types, little overlap amongst activated genes LF 339 genes

40 MSI1 Gene Activation 7 Legend 6 A-Myb B-Myb c-myb Fold Activation MCF-7 Lung Epith Lung Fibro

41 TGFBI Gene Activation 4.5 Legend A-Myb B-Myb c-myb Fold Activation MCF-7 Lung Epith Lung Fibro

42 HSPA6 Gene Activation 90 Legend A-Myb B-Myb c-myb Fold Activation MCF-7 Lung Epith Lung Fibro

43 IL8 Gene Activation 60 Legend 50 A-Myb B-Myb c-myb Fold Activation MCF-7 Lung Epith Lung Fibro

44 B-Myb Gene Activation Legend A-Myb B-Myb c-myb Fold Activation MCF-7 Lung Epith Lung Fibro

45 Mechanisms that Could Alter the Specificity of Myb Proteins Tissue-Specific Combinatorial Interactions Different cell types have different cooperating factors Myb proteins cooperate with other transcription factors Unique domains in Myb protein interact with different factors A Myb B X C Myb X

46 Mechanisms that Could Alter the Specificity of Myb Proteins Tissue-Specific Combinatorial Interactions Different cell types have different cooperating factors Myb proteins cooperate with other transcription factors Unique domains in Myb protein interact with different factors Context-Specific Post-Translational Modifications Myb proteins are modified at numerous sites Different cell types have different modifying enzymes Modifications may alter Myb activity or promote specific interactions

47 Myb Proteins are Subject to Multiple Modifications c-myb A-Myb B-Myb X X X X X X X X X X Myb proteins are modified by X*-ylation Do Differences in Modifications Alter Interactions with Cellular Co-Factors? X* Insert your favorite modification here

48 Multiple Modifications of c-myb CKII Pim-1 CDK6 MAPK c-myb p300/cbp

49 Context-Specific Modifications A Gene 1 Myb B Gene 1 Gene 2 Gene 2 Myb

50 Mutations Unmask the Oncogenic Potential of c-myb c-myb v-myb N-Terminal Deletion Point Mutations Contribute to Transforming Activity C-Terminal Deletion Removes Negative Regulatory Domain AMV v-myb is a mutated, oncogenic version of c-myb

51 The v-myb Mutations Could Deregulate c-myb Repressed c-myb v-myb + C-Terminal Deletion Removes Negative Regulatory Domain

52 Structures of A-Myb, c-myb and v-myb A-Myb CHA AHC c-myb MutMyb v-myb AMV v-myb is a mutated, oncogenic version of c-myb

53 Test the Activities of Myb Proteins on Endogenous Human Genes Myb Expression Vector Recombinant Adenoviruses Use Affymetrix GeneChips to measure changes in endogenous gene expression Human Cells

54 Selected Gene Tree: ACV36 std Colored by: ACV Myb U133A Feb 03 Default Interpretation Gene List: ACV 36 genes up 2.5X >2500 in A,C,v or MutMyb (36) _at Homo sapiens cdna FLJ _s_at HEP _at PP _at KRT _at SERPINA _at STHM _s_at SSAT _s_at H1FX _x_at MGC2479, FLJ21046, dj _at HEM _at HEM _s_at ASS1, CTLN _at MEH, EPHX _s_at FLJ _s_at PBP _at IGFBP _x_at MT1H _x_at MT _x_at MT _x_at MT _at CSD, CDB1, CSD1, CSD2, C _x_at MT _x_at GSPT _s_at DRAL, SLIM _s_at DIP, GILZ, TSC-22R _s_at RAB _s_at Homo sapiens cdna FLJ _at EPAS _s_at CLLP _s_at EHM _at MEMD, CD _at LCP _at KIAA _s_at _s_at _s_at HSP105A, KIAA0201, NY-CO- Comparing A-Myb, c-myb, v-myb Ø A CHA AHC C Mut V The DBD mutations do not affect some genes The v-myb DBD mutations affect a subset of the c-myb regulated genes The activity of v-myb is the most unique Some genes are preferentially activated by MutMyb or v-myb

55 Unique Specificity of v-myb Con C Mut V A AHC CHA Minor differences in Myb proteins cause dramatic changes in gene expression DSIPI TGFBI Hep27 actin Northern Blot

56 The v-myb Protein Has a Unique Transcriptional Activity c-myb MutMyb v-myb The mutations in v-myb make it qualitatively different from c-myb

57 Ness Lab: Adenoviruses, Genomics: Hematopoiesis, Lentiviruses: My Backyard John Rushton Wanli Lei Fan Liu Lisa Davis John O Rourke Pim-1 Activity: Louise Winn (Queen s U., Kingston) Collaborators: Achim Leutz, Berlin Kathy Weston, London Anton Berns, Netherlands Tim Bender, Virginia Scott A. Ness Molecular Genetics & Microbiology University of New Mexico HSC Albuquerque, NM USA