Yue Wei 1, Rui Chen 2, Carlos E. Bueso-Ramos 3, Hui Yang 1, and Guillermo Garcia-Manero 1

Transcription

1 Genome-wide CHIP-Seq Analysis of Histone Methylation Reveals Modulators of NF- B Signaling And the Histone Demethylase JMJD3 Implicated in Myelodysplastic Syndrome Yue Wei 1, Rui Chen 2, Carlos E. Bueso-Ramos 3, Hui Yang 1, and Guillermo Garcia-Manero 1 1. Department of Leukemia, MD Anderson Cancer Center, Houston, TX 2. Human Genome Center, Baylor College of Medicine, Houston, TX 3. Department of Hematopathology, MD Anderson Cancer Center, Houston, TX

2 CHIP-Seq in MDS: Hypothesis Histone H3 Khairul 2009 Analysis of activating histone modification (H3K4me3) can provide a stable view of gene activation in MDS This will allow identification of altered signaling modules and/ or related epigenetic regulators as new therapeutic and/or prognostic targets in this disease

3 Chromatin Immunoprecipitation (CHIP) CHIP-Seq: Methodology Direct Sequencing (Seq) Bioinformatics

4 CHIP-Seq Strategy PATIENT CHARACTERISTICS Dx IPSS CYTO MDS BM (N=5) Control BM (N=4) RAEB INT-2-5/5q- & -7/7q- CMML INT-2 DIP RAEB INT-1 DIP RAEB INT-1 MIS RAEB-T HR DIP CD34+ CD34- CD34+ CD34- Ch-IP with H3K4me3 Antibody Solexa Sequencing of H3K4me3 Rich Chromatin Fragments Bio-info analysis Gene promoters specifically bearing high levels of H3K4me3 in MDS (Potential aberrantly active genes in MDS) Validations (in a large cohort of patient samples)

5 H3K4me3 CHIP-Seq in MDS criteria for peak selection K4me3 signals: within 2kb to transcription starting site (TSS) of a known gene K4me3 up-regulation: MDS vs control > 3 fold p value < 10-6 chr19

6 Validation of Gene Expression in Primary MDS CD34+ Cells 350 Relative RNA level in CD34+ (MDS vs control) P< C5AR1 FPR1 FPR2 AQP9 PRX FYB C19ORF133 FCAR IL8RA N=57 (previously reported CD34+ samples) Heinrichs et al. Leukemia 2008

7 H3K4me3 CHIP-Seq identify NF- B Effectors in MDS CD34+ Cells NF- B Genes involved in NF- B activation (11/36) C5AR1, FPR1, FPR2, FYB, FCGR2A, MEFV, IL8-RB, TYROBP, PTAFR, BCL2A1, NCF2 phospho-nf B-p65 *

8 Summary of Part I Defect of Epigenetic Regulation? NF- B activators promoter H3K4me3 MDS CD34+ NF- B activators expression NF- B signaling

9 Histone Demethylase JMJD3 is aberrantly up-regulated in MDS CD34+ Cells Relative Expression in CD34+ (MDS v.s. ctrl) JARID1A in MDS CD34+ cells --- Medium correlation with CHIP-Seq identified genes --- Strong correlation with PTAFR and TYROBP (NF- B effectors) JARID1B JARID1C JARID1D JHDM1A JMJD2A JMJD2B JMJD2C UTX UTY P<0.01 AJmjc domain H3K27 demethylase A positive regulator of H3K4me3 A direct transcriptional target of NF- B JMJD3 JMJD1A JMJD1B H3K4me H3K36me H3K9/36me H3K27me H3K9me1/2

10 Hypothesis: Positive Signaling Circuitry Between JMJD3 And NF- B JMJD3 (positive regulator of H3K4me3) (NF- B target) NF- B activators promoter H3K4me3 MDS CD34+ NF- B activators expression NF- B signaling

11 JMJD3 positively regulates NF- B JMJD3 knock-down: --- NF- B effectors suppressed --- NF- B signal inhibited phospho-nf B-p65 C5AR1 FPR1 FPR2 FYB FCGR2A MEFV IL8RB TYROBP PTAFR BCL2A1 NCF2 PRX AQP9 JMJD3 JMJD3? NF- B activators promoter H3K4me3 JMJD3 overexpression: --- NF- B effectors up-reuglated --- promoter H3k4me3 increase MDS CD34+ NF- B activators expression NF- B signaling

12 NF- B effectors positively regulate JMJD3 Knock-down 4 NF- B effectors: --- JMJD3 expression suppressed --- Dissociation of NF- B from JMJD3 control sirna sirna targeting NF-kB effectors sirna targeting NF-kB effectors control sirna C5AR1 PTAFR FPR2 TYROBP JMJD3 JMJD3 NF- B activators promoter H3K4me3 MDS CD34+? NF- B activators expression NF- B signaling

13 Conclusion 1. CHIP-Seq is applied to a human disease, identifying unique H3K4me3 code in MDS 2. This analysis reveals effectors of NF- B and JMJD3 as important signal modulators in MDS CD34+ cells 3. Future plans systematic analysis of clinical implications of JMJD3 and NF- B effectors in large cohort/ subtypes of MDS Confirm the direct association between JMJD3 and CHIP-Seq detected gene promoters in MDS validation/ analysis of CHIP-Seq data in MDS CD34- cells

14 Acknowledgement University of Texas MD Anderson Cancer Center Baylor College of Medicine Human Genome Center Dr. R Chen Group Leukemia Department Dr. G Garcia-Manero Group Hematophathology Department Dr. C Bueso-Ramos Group Bioinformatics Department Dr. H Yao Dr. J Wang Lixia Diao Dr. M Zhang This project is supported by NIH and LLSA

15 JMJD3 is H3K27 histone demethylase Involved in Up-regulation of H3K4me3 JMJD3 is a Jmjc domain H3K27 demethylase JMJD3 physically integrates in MLL2 complex and positively regulates H3K4me3 JMJD3 is crucial in lineage determination and gene activation during inflammatory response JMJD3 is a direct transcriptional target of NF- B Lan et al Nature 2007 De Santa et al Cell 2007

16 CHIP-Seq in MDS: Introduction MDS consists of a group of hematopoietic stem cell disorders characterized by: Inefficient hematopoiesis Increase rate of transformation to AML At cellular and molecular level, MDS is characterized by: Frequent cytogenetic alterations Aberrant DNA methylation Low prevalence of genetic lesions Research in MDS at molecular level is limited by: Lack of MDS cell lines Paucity of animal models

17 H3K4me3 CHIP-Seq in Hela Cells Overall Signal Distribution Chip-Seq Overlapping Chip-Chip Chip-Seq Only Chip-Chip Only ,000-20,000-10, ,000 20,000 30,000 Base pairs from TSS Alignment with CHIP-chip 21q22.11 IgG control ChIP-Seq: H3K4me3 ChIP-chip: H3K4me3 Known Genes

18 Molecular Research of MDS Search for genetic/ epigenetic alterations has been less informative, although recent SNP arrays and analysis of aberrant CpG methylation in MDS may help to identify genetic/ epigenetic lesions. -- Diverse molecular backgrounds; -- Lack of cell lines and representative animal models;