Concepts of Disease (BI2332) Epigenetics Lectures 4 PDF

BI2332: Concepts of Disease Module co-ordinator: Dr Prytherch Epigenetics and underlying principles Professor Ros John Head of Biomedicine Division Human Epigenetics lecture 4 Genomic Imprinting  Benign ovar...

BI2332: Concepts of Disease Module co-ordinator: Dr Prytherch Epigenetics and underlying principles Professor Ros John Head of Biomedicine Division Human Epigenetics lecture 4 Genomic Imprinting  Benign ovarian teratoma A germ cell tumor Rare Teratoma consists of tissues derived from all the three germ layers Can have hair, sebaceous glands, skin and teeth. Most ovarian teratomas are benign Most have two maternal genomes  Hydatidiform mole A gestational trophoblastic disorder Rare About one in every 1,200 pregnant women Disorganised mass of placental tissue without a fetus Most molar pregnancies are benign Most have two paternal genomes. In mammals, you cannot have normal development without two parental genomes Why?  Genomic Imprinting Me M Me P Biallelic Maternally expressed Paternally expressed: e.g. Cdkn1c e.g. Peg3 Two copies Two copies Both expressed One expressed Imprinted genes 0.4% of mammalian genes  Me M Normal cell P Me M Me Teratoma M Ovarian teratoma has two maternal genomes Loss of expression of normally paternally expressed genes Gain in expression of normally maternally expressed genes  Me M Normal cell P P Mole P Hydatidiform mole has two paternal genomes Gain in expression of normally paternally expressed genes Loss of expression of normally maternally expressed genes Genomic imprinting is an epigenetic process unique to mammals (and some flowering plants) Genomic imprinting explains why mammals cannot develop parthenogenetically  The imprinting cycle Establishment of maternal imprints in growing oocyte (postnatal) KDM1A/B remove H3K4me2/3; transcription through ICs; SETD2 adds H3K36me3; DNMT3A & DNMT3L methylate ICs Haploid Diploid female gamete primordial oocyte germ cell Diploid zygote Oogenesis Establishment of paternal imprints in Gametic imprint spermatogonia (prenatal-postnatal) gDMR Fertilisation NSD1 adds H3K36me2; DNMT3A & DNMT3L or DNMT3B & piRNAs methylate ICs Spermatogenesis Haploid male gamete Maintenance of gDMRs Sperm ZFP57 & ZFP445 bind methylated IC , Global demethylation and erasure of recruit TRIM28 & SETDB1 to add parental imprints in developing germline H3K9me3; recruit maintenance DNA Post-implantation methylase DNMT1 & UHRF1; LncRNAs and (E6.5-E11.5) Blastocyst embryo and histone modifications ”spread” imprint Passive genome-wide demethylation placenta (DNA replication) in PGCs followed by active demethylation (TET1). Maintenance and spreading of imprints DNMT1 maintains DNA methylation at ICs; Histone modifications continue Primordial ”spreading”; Somatic DMRs established germ cells (PGCs)  Genomic Imprinting disorders Beckwith Weidemann Syndrome (BWS) Silver Russell Syndrome (SRS) Prader-Willi Syndrome Angelman Syndrome  Human chromosome 11p15 Human chromosome 11p15 contains several imprinted genes Some are expressed only from maternal allele (red) Some are expressed only from paternal allele (blue) Some are non-coding RNAs = H19 and Lit1 Me M CDKN1C H19 Me P LIT1 IGF2 White box = not expressed, black box = biallelically expressed  Differentially methylated regions (DMRs) Human chromosome 11p15 contains two DMRs H19DMR is methylated in sperm H19DMR controls imprinted expression of IGF2 and H19 KvDMR1 is methylated in oocytes KvDMR1 controls imprinted expression of CDKN1C and several additional maternally expressed genes KvDMR1 H19DMR Me M CDKN1C H19 Me P LIT1 IGF2  Insulin-like growth factor 2 Paternally expressed gene IGF2 encodes insulin-like growth factor 2 IGF2 is a growth factor which promotes cell division and growth  Cyclin-dependent kinase inhibitor 1c Maternally expressed gene CDKN1C encodes cyclin-dependent kinase inhibitor 1c CDKN1C is a cell cycle inhibitor which inhibits cell division and growth Beckwith Weidemann Syndrome Fetal overgrowth syndrome Identical twins – genetically indistinguishable  Beckwith Weidemann Syndrome OMIM 130650 Affects 1 in 13,700 Babies in the 95th weight percentile at birth Macroglossia (large tongue) Omphalocoele (abdominal wall defects) Predisposition to Wilms' tumour Cleft palate Placentomegaly (large placenta) Neonatal hypoglycaemia (low blood sugar)  Some BWS patients have paternal disomy of human chr. 11p15 Two paternal copies IGF2 Me P IGF2 Me P 0 x CDKN1C 2 X IGF2 Not enough Too much CDKN1C IGF2  Many other genetic and epigenetic alterations reported in BWS patients. Point Translocations Loss of methylation Hypermethylation at H19 Mutation >1% 60% and/or excess IGF2 5% 20% KvDMR H19DMR Me M CDKN1C H19 Me P IGF2 Most common epigenetic alterations is loss of DNA methylation at KvDMR1 M H19 LIT1 Me P LIT1 IGF2 Loss of DNA methylation DNA sequence not mutated Associated with loss of expression of CDKN1C Beckwith Weidemann Syndrome (BWS) Too much IGF2 and/or Too little CDKN1C  Silver Russell Syndrome A fetal growth restriction disorder Identical twins – genetically indistinguishable  Silver Russell Syndrome OMIM 180860 Affects 1 in 100,000 Low birth weight – below 5th percentile Poor postnatal growth Classic facial phenotype Asymmetry Lack of subcutaneous fat Night sweats  Some SRS patients have maternal disomy of human chr. 11p15 Two maternal copies Me M CDKN1C H19 Me M CDKN1C H19 2 x CDKN1C 0 X IGF2 Too much Not enough CDKN1C IGF2 Note: Other mutations in SRS at 11p15 and maternal uniparental disomy for chromosome 7 (mUPD(7)) occurs in up to 10% of SRS Silver Russel Syndrome (SRS) Too little IGF2 and/or Too much CDKN1C  Mode of inheritance Most imprinting disorders result from de novo (new) mutations Some are genetic mutations which can be inherited ex. CDKN1C point mutations in BWS and microduplications in SRS These have distinct pedigrees  Mode of inheritance A*A acts as an autosomal dominant mutation after maternal transmission A*A AA AA A*A AA* AA AA* AA Acts like a recessive or AA A*A “silent” mutation after paternal transmission Sex specific transmission and but not sex-specific inheritance  Pattern of inheritance for dominant X-linked disorder XY *XX *XX XY XX *XY XX XY XY *XX *XX Sex specific transmission and inheritance  Pattern of inheritance for recessive X-linked disorder XY *XX *XX XY XX *XY XX XY XY *XX *XX Sex specific transmission and inheritance Angelmann Syndrome and Prader Willi Syndrome are also reciprocal imprinting disorders Genomic imprinting disorders: Involve genetic and epigenetic mutations Can involve several genes Not simply loss of gene expression Dominant inheritance but can appear recessive Can skip generations Depend on parent-of-origin Cancer Generally cancer is thought of as a genetic disease initiated by alterations in genes, such as oncogenes and tumor suppressors, that regulate cell proliferation and survival. But genomic hypomethylation and site specific hypermethylation is a widely observed as an early step in human tumorigenesis Melanoma nucleus can be reprogrammed to make ES cells which make ‘normal’ mice Developmental origins of disease Non-communicable diseases (NCDs) related to metabolic, cardiovascular and mental function (e.g., heart disease, obesity, type 2 diabetes and depression) represent leading causes of illness and death globally (World Health Organization) Diseases are more prevalent in people exposed to adversity in early life Adversity Low birth Neurodevelopmental (diet, stress, weight disorders obesity, smoking) (ADHD) impact fetus and placenta 1 in 14 Mental health disorders live (Depression, anxiety, Schizophrenia) births Metabolic syndrome (type 2 diabetes, obesity) Cardiovascular disease Adversity “programs” ill health The Dutch famine of 1944–1945 (Hongerwinter) German occupied Netherlands Winter of 1944–1945 German blockade cut off food and fuel shipments causing widespread starvation At least 22,000 deaths occurred due to the famine Pregnant women survived on between 400 and 800 calories/day (2,400 calories per day during the third trimester). Schizophrenia in the 1944-1946 Dutch birth cohorts Exposed Cases occurring at age 24- 4 3.5 48 years, per 1,000 survivors to age 18 3 2.5 2 1.5 1 0.5 0 Jan-June July-Dec Jan-Oct 14th Oct 15th - Jan-June July-Dec 1944 1944 1945 Dec 31st 1946 1946 1945 Environmental programming  Identical mice? These mice are identical genetically but have a range of coat colours from pure yellow to agouti They were born from the same mother so why are they different? Epigenetic inheritance at the agouti locus in the mouse Nature Genetics 23, 314 - 318 (1999)  Agouti gene Normally only active for a short time Insertion of Intracisternal A particle (IAP) murine retrotransposon Avy mutation Constituitive expression from IAP promoter acetylation Me Me Me Me Me Silenced by DNA methylation at IAP element Paternal Maternal Transgenerational  Agouti viable yellow (Avy) mice Maternal diet can alter epigenetic marks Blewitt. M and Whitelaw, E. The use of mouse models to study epigenetics. Cold Spring Harbour Perspect in Biol 1;5(11):a017939 (2013)  Exposure to maternal smoking in pregnancy association with altered DNA methylation in adult children Wiklund, P., Karhunen, V., Richmond, R.C. et al. DNA methylation links prenatal smoking exposure to later life health outcomes in offspring. Clin Epigenet 11, 97 (2019).  Epidrugs Histone deactylases (HDACs) remove acetyl groups from chromatin DNA methylation inhibitors remove DNA methylation Can these enzymes be used as drugs to reactivate silent genes in vivo? The DNMT inhibitor azacitidine (Vidaza; Celgene) is already approved by the European Medicines Agency for the treatment of the rare blood cancer myelodysplastic syndrome Learning outcomes/Summary Both loss of DNA methylation and inappropriate addition of DNA methylation can cause epigenetic disease Epigenetic diseases cannot be detected by DNA sequencing X-inactivation and Genomic imprinting are classic examples of epigenetic processes X-inactivation and Genomic imprinting disorders have characteristic pedigree patterns distinct from classic Mendelian inheritance Cancer, aging and behaviour are all influenced by epigenetics Epigenetic marks can be influenced by environmental factors such as diet Epigenetic diseases may be reversed using epidrugs