Epigenetics and Human Disease

Transcription

1 Epigenetics and Human Disease May 28,

2 Angelman Syndrome & Prader-Willi Syndrome Sister Syndromes Angelman Syndrome ~1/20,000 births happy disposition smile often bouts of laughter minimal verbal skills balance problems and hand flapping (Marionette Syndrome or Puppet Children) seizures severe developmental delay microcephaly dysmorphic features Angelman Syndrome & Prader-Willi Syndrome Sister Syndromes Prader-Willi Syndrome ~1/10,000 births mild-moderate mental retardation sometimes unhappy disposition obsessive-compulsive behaviors infantile hypotonia (low muscle tone) obesity/hyperphasia developmental delay short stature hypogonadism/genital hypoplasia small hands/feet thin upper lip almond shaped eyes 2

3 Angelman Syndrome & Prader-Willi Syndrome Sister syndromes because they are caused by seemingly identical genetic abnormalities Deletion of chromosome 15q11-q13 or Uniparental disomy How can these abnormalities result in two very different phenotypes? Genomic Imprinting Disorders normal Uniparental disomy (UPD) can lead to human diseases. Maternal UPD Paternal UPD 1st evidence for role of epigenetics in disease. 3

4 Genomic Imprinting Disorders Angelman Syndrome & Prader-Willi Syndrome Maternal deletion Paternal UPD Imprint Angelman Syndrome Prader-Willi Syndrome Paternal deletion Maternal UPD Genomic Imprinting Disorders The individual silenced gene that contribute to each disease are known Classical forward genetics - identified the genes lost to cause the phenotype Reverse genetics how does disruption of these genes result in the phenotype 4

5 Obesity and hyperphagia (excessive hunger) in Prader-Willi Ghrelin (hunger hormone) Neuropeptide produced in the GI tract Fluctuates with stomach contents Increases hunger and prepares GI for food intake Patients display elevated ghrelin levels that drives the insatiable appetite and obesity. Links missing genes and elevated ghrelin levels remains unclear Genomic Imprinting Disorders Beckwith-Wiedemann Syndrome (BWS) - defects map to ~1-Mb H19-IGF2 region on chromosome 11 (with >12 imprinted genes) Silver-Russell Syndrome (SRS) ~10% result from mat UPD for chromosome 7 UPD reported for all human chromosomes except 3 & 19 Loss of imprinting can also lead to cancer. 5

6 Trans Effects: Disorders affecting chromatin Complex multisystem phenotypes result from mutations in proteins involved in chromatin structure and remodelling. misregulation of multiple genes? 6

7 Trans Effects: Rett Syndrome neurodevelopmental disorder causing mental retardation, hand-wringing, language regression... Like autistic spectrum disorders, Rett Syndrome manifests after a period of apparent normal development, disrupts social and language development. Rett Syndrome occurs almost exclusively in females and shows a spectrum of phenotypic variability... Why? The gene responsible for this syndrome is found on the X chromosome (i.e. X-linked), thus typically lethal in males. The phenotypic variability arises because of the random inactivation of one of the X chromosomes in each cell in females. Trans Effects: Rett Syndrome Random inactivation of the X chromosomes in females can lead to a spectrum of phenotypic variability. X x X x X x x X less severe X x X x x X x X X x x X x X x X more severe 7

8 Trans Effects: Rett Syndrome Mutation of the gene encoding a methyl-cpg binding domain (MBD) protein, MECP2, is the major cause of Rett Syndrome. MECP2 MBD binds to symmetrically methylated CpG TRD interacts with histone deacetylases (HDACs) Trans Effects: ICF Syndrome ICF is an autosomal recessive disorder. Which parent contributed the mutation to the afflicted offspring? Both the mother and father were carriers of the mutation and contributed it to the afflicted offspring. 8

9 Trans Effects: ICF Syndrome In 1999, three labs independently reported that ICF was due to mutations in the DNA methyltransferase, DNMT3B. DNMT3B is a de novo DNA methyltransferase and is known to localize to centromeric satellite sequences. DNMT3B also known to partner with a number of chromatin regulatory proteins. Trans Effects: 9

10 Cis Effects: Fragile X Syndrome - Most common inherited cause of intellectual disability - X-linked Phenotype: Mental retardation, affected males have connective tissue defects (eg. hyperextensible joints), large ears, long face, shyness, etc. Females typically less severe phenotype (severity correlated with degree of X-inactivation on abnormal chromosome). 10

11 Cis Effects: Fragile X Syndrome Named for constriction seen cytologically on the X chromosome (Xq27.3). This cytologically visible constriction occurs in the 5 UTR of the FMR1 gene. The disease is manifested due to a lack of expression of the FMR1 gene, which encodes an RNA-binding protein (FMRP) thought to play a role as a translational suppressor through an RNAi-like pathway. What causes the repression of FMR1 expression in affected individuals? Cis Effects: Fragile X Syndrome 5-54: normal phenotype - Methylation: no - Histone acetylation: yes - Transcription: yes : mostly normal (develop distinct neurodegenerative syndrome: tremors & ataxia) 200+: Pathologic - Methylation: yes - Histone acetylation: no - Transcription: no Conclusion: The primary cause of Fragile X Syndrome is genetic but it depends on epigenetic processes. 11

12 Epigenetics and Cancer Malignant Neoplasia (harmful new growth) Should cancer be classified by tissue type or causitive mutations? Leukemia Acute or Chronic Lymphoid or Myeloid» B cell or T cell Pre-B or Pro-B o Translocation (1:19, 9:22, etc) C-Kit (receptor tyrosine kinase) mutations are causitive in AML, GIST and melanoma Cancer is incredibly diverse. What characteristic are shared by all cancers? 23 Epigenetics and Cancer Cancer results from the semi-heritable deregulation of genes that normally control the hallmarks of cancer Gene disregulation is typically divided into activated oncogenes (dominant) and silenced tumor suppressors (recessive) 12

13 The interplay between genetics and epigenetics is complex and multifaceted 26 13

14 Gene expression changes are often mediated by mutation of chromatin modifiers M: Missense F: Frameshift N: Nonsense S: Splice site T: Translocation D: Duplication PTD: Partial Tandem Duplication Chromosomal translocations are a hallmark of childhood acute leukemias Look, AT. Science MLL translocations (chromosome 11) are the defining mutation of a therapeutic subtype (poor prognosis) MLL (mixed-lineage leukemia) methylates H3K4. K4 methylation is associated with active transcription. >50 fusion partners have been identified in MLL translocations. All result in disruption of AT-hook and KMTase domain Models of MLL-translocated ALL have been elusive and the role in mutant MLL in leukemogenesis remain largely unclear 14

15 Gene expression changes are often mediated by mutation of chromatin modifiers DNA methylation can lead to cancer in various ways Global hypomethylation hallmark of human cancer and may lead to genomic instability (deletions/inversions/duplications/translocations) - Heterochromatin is typically refractory to Double-strand breaks and less sensitive to DNA damage 15

16 DNA methylation can lead to cancer in various ways Presence of a methyl group on the C favors formation of carcinogenic adducts on adjacent G (eg. benzo(a) pyrene in smoke). DNA methylation can lead to cancer in various ways Methyl groups change the absorption spectrum of C (moving it into range of sunlight) leading to pyrimidine dimers in skin. 16

17 DNA methylation can lead to cancer in various ways Methylation is inherently mutagenic due to the spontaneous deamination of cytosines. Why m C and not Cs? Spontaneous deamination of cytosines vs. methylated cytosines cytosine uracil methylated cytosine thymine (not repaired as efficiently) The most common single nucleotide mutation found in the genome and accounts for the paucity of the CpG dinucleotide in vertebrate genomes - so TpG overrepresented. Remember that DNA methylation is found predominantly (if not exclusively) at CpGs in vertebrates. The CpG dinucleotide occurs in roughly the expected frequency at regions called CpG islands, which are found in the promoter regions of many genes. CpG islands are thought to retain their expected frequency of CpGs because they are typically not methylated. >50% of p53 mutations occur at methylated CpG sites 17

18 DNA methylation can lead to cancer in various ways Hypermethylation of the CpG islands associated with tumor suppressor genes is typical. Leading to the transcriptional silencing. 18

19 Hypermethylation induced silencing of key tumor suppressors p16, associated with failure of cells to reach mortality checkpoint leading to progressive abnormalities MLH1 (mismatch repair) gene (multiple genetic alterations) Rb retinoblastoma protein (cell cycle regulator) gene - interacts with many chromatin remodellers. E-cadherin (metastasis suppressor - promotes cell-cell adhesion) Chfr (checkpoint regulating - chromosomal instability) O6-MGMT (DNA repair - alkylation damage leads to G->A) GST-Pi (DNA repair - oxidative damage at adenines) SFRPs (secreted frizzled related protein - affects Wnt signalling HIC-1 (hypermethylated in cancer) (Zn-finger repressor) Epigenetic therapy Mesothelioma BEFORE SAHA mass compresses lung (black) AFTER 4mo. SAHA treatment Shrinkage of tumor; lung expands 19

20 Can the environment influence the epigenome? Evidence for epigenetic-environment interactions Control Hypertension Hypertensive Mother = Hypertensive F1 Hypertensive Parent = Hypertensive F2 No differences Can the environment influence the epigenome? Evidence for epigenetic-environment interactions Diet of pregnant mother mouse (e.g. folate, vitb12) affects DNA methylation of agouti gene in offspring affecting coat color, as well as obesity thus susceptibility to diabetes and cancer. *Pregnant women take supplementary folic acid for proper fetal neural tube development. Similarly, men with uremia have reduced DNA methylation that can be reversed with dietary folate. Uremia: A toxic condition resulting from kidney disease in which there is retention in the bloodstream of waste products normally excreted in the urine. 20

21 A way to think about interactions among genetic, epigenetic and environmental factors 21

22 The mechanism of silencing is unknown but once methylation established, it plays dominant role? Cis Effects: FSHD (Facioscapulohumeral Dystrophy) An autosomal dominant muscular dystrophy characterized by wasting of muscles of face, upper arm, shoulder, etc. Major locus maps to heteorchromatic subtelomeric region of 4q35 near D4Z4, an array of 3.3 kb GC-rich units. Normally units; 1-10 units on FSHD chromosomes Contraction of repeats is necessary for FSDH WHY? Best guess: 27bp sequence in D4Z4 binds D4Z4- repressing complex (DRC) and this is required to increased expression of genes in the region, including FRG1&2 and adenine nucleotide tranporter-1 (ANT1). 22