Week 9 - Part A - Identically Different: Introducing Epigenetics PDF

1/26/2025 Week 9 – Part A Identically Different: Introducing Epigenetics Part of eBook Chapter 9 and Blackboard information Epigenetics Epigenetics = on top of genetics Chemical modifications of chromosomal DNA and/or histo...

1/26/2025 Week 9 – Part A Identically Different: Introducing Epigenetics Part of eBook Chapter 9 and Blackboard information Epigenetics Epigenetics = on top of genetics Chemical modifications of chromosomal DNA and/or histones that change the pattern of gene expression without altering the DNA sequence Refers to processes that instruct our cells how and when to read the DNA blueprint May be inherited or acquired 1  1/26/2025 What is the Epigenome? https://www.youtube.com/watch?v=bJoYbtqPcaA Epigenetics All cells contain the same genes, BUT Gene expression patterns are different in different cells 2  1/26/2025 Epigenetics Gene expression patterns need to change during the lifetime of an organism Some genes are switched off and others on Epigenome must be Reprogrammed Embryos form from the joining of two specialised cells – sperm and egg These contain their own epigenetic tags These needs to be stripped so embryonic cells can become anything Sometimes epigenetic tags escape this reprogramming and get passed on 3  1/26/2025 Epigenome must be Reprogrammed Sperm and eggs contain epigenetic tags from parents Erased shortly after fertilisation Embryonic cells can become anything Epigenome remembers The cells in an embryo can develop into anything Changes in gene expression are regulated and the cells remember 4  1/26/2025 Epigenome remembers Epigenetic memory is important, otherwise cells wouldn’t know where to go Once a cell has gone down a particular path, epigenetics prevents it from going backwards Cells continue to develop down a path to specialisation Epigenome remembers As cells grow and divide the epigenetic tags are copied in the daughter cells Function is maintained 5  1/26/2025 Epigenome is changeable Cells are constantly listening for signals to change what they are doing Signals come from inside the cell, from neighbouring cells or the environment At different times in life different signals play important roles At each stage different genes are switched on or off to respond to needs Epigenome is changeable Direct contact with other cells Factors released from other cells nearby, or from within the cell itself Hormonal signals Environmental factors 6  1/26/2025 Epigenome is changeable Environmental signals may be direct (diet) or indirect (stress) Proteins carry signals to the DNA Whenever a signal is received, proteins bring the message inside the cell Eventually a gene regulatory protein gets the message and influences the way the DNA is used 7  1/26/2025 Gene Regulatory Proteins Switch genes on or off themselves, OR Recruit enzymes to add or remove epigenetic tags Epigenetic Inheritance - Imprinting Some epigenetic tags can be passed down to the next generation – imprinting Depending on the gene, one parents’ copy is silenced This usually happens during gamete production Epigenetic tags stay put for life Specific genes are always silent in the egg or sperm 8  1/26/2025 Epigenetic Inheritance - Imprinting Epigenetic Inheritance - Imprinting Required for normal development Should have only one active gene, diseases can result if you have two active copies, or no active copies Prader-Willi Syndrome – learning Angelman Syndrome – learning difficulties, short stature, difficulties, speech problems, compulsive eating seizures, jerky movements, unusually happy 9  1/26/2025 Epigenetic Inheritance - Imprinting Only one active gene, no “back-up” Changes to active gene are more obvious than if there were two copies In humans IGF2 is imprinted Failure to imprint/activation leads to Beckwith- Wiedemann Syndrome = overgrowth Epigenetic Inheritance Some epigenetic tags seem to pass on to the next generation without imprinting They are hard to prove, as the epigenome is designed to change to given circumstances Epigenetic changes need to be seen through many generations 10  1/26/2025 Epigenetic Inheritance 3 generations are exposed to the same environmental influences in a pregnant woman Mother – 1st generation Foetus– 2nd generation Reproductive cells – 3rd generation The Dutch Hunger Winter November 1944 – May 1945 Limited food supply to western Netherlands Began eating grass and tulip bulbs >20,000 people died Single incident population effect Excellent record keeping and health care in the Netherlands provided a unique study group 11  1/26/2025 The Dutch Hunger Winter First trimester malnutrition = normal birth weight Third trimester malnutrition = low birth weight Common sense really, as babies do most of their growing in the last few months before birth The Dutch Hunger Winter Small babies stayed small, lower obesity Despite plentiful food Babies from mothers malnourished in early pregnancy were more obese than normal Epigenetic tags laid down in the first trimester influence the rest of their lives Some effects can be seen in the grandchildren 12  1/26/2025 Nutrition and the Epigenome What you eat influences your epigenome Especially foods that help make epigenetic modifiers – acetyl and methyl groups Nutrient Food source Epigenetic role Resveratrol Red Wine Removes acetyl from histones (improved health in lab mice) Sulforaphane Broccoli Increased histone acetylation turning on anti-cancer genes Diallyl sulphide Garlic Increased histone acetylation turning on anti-cancer genes Vitamin B12 Meat, Shellfish, Milk Methionine synthesis Nutrition and the Epigenome Food your Mum ate during pregnancy can affect you for life Your infant diet can affect you for life Methyl-deficient diet in adults changes gene expression, but these affects can be reversed 13  1/26/2025 Nutrition and the Epigenome All mammals have a gene called Agouti Methylated agouti = normal, brown mice Unmethylated agouti = fat, yellow mice Nutrition and the Epigenome Pregnant yellow mice fed: 1. Normal mouse food - mostly yellow, unhealthy pups 2. A methyl-rich diet - mostly brown, healthy pups 14  1/26/2025 Nutrition and the Epigenome Queen bees are genetically identical to worker bees apart from their diet Worker bees are sterile Royal jelly makes the queen develop ovaries and a large abdomen for egg laying Also gain queenly attitude Epigenome and behaviour People who commit suicide have less active rRNA genes Child abuse can leave epigenetic marks REELIN gene is under-methylated in schizophrenics Epigenetic scan showed ~60 genes different between psychiatric patients and healthy controls – most genes involved in normal brain signalling 15  1/26/2025 Epigenome and behaviour - Lick your rats Some rats spend a lot of time grooming their pups --- relaxed adults Others ignore them --- anxious adults Experiments swapping mothers prove the results to be epigenetic Temperament can be changed by environment So what are these epigenetic controls? 1. DNA methylation 2. Histone modifications 3. Other chromatin re-modelling 4. Non-coding RNA 16  1/26/2025 DNA Methylation Involves the addition of a CH3 (methyl) group to DNA 5’ position of the carbon ring of cytosines Occurs at CpG islands Prevents transcription Two types – de novo and maintenance DNA Methyl Transferases (DNMTs) DNA Methylation 17  1/26/2025 DNA Methylation – Base Flipping DNMTs need access to the cytosine Base flipping is used Cytosine is rotated 180o DNA demethylation Passive – loss via replication Active – base excision repair or mismatch repair….still theory 18  1/26/2025 Histone Modifications Histone tails protrude from nucleosome They can be modified to alter expression Histone Modifications Methylation – Lys and Arg Acetylation – Lys Phosphorylation – Ser and Thr Ubiquitination – Lys 19  1/26/2025 Histone Methylation No singular effect Some methylation represses transcription and some promotes transcription Reversible modification Histone methyl transferases (HMTs) or, Protein Arginine methyltransferases (PRMTs) add methyl groups Histone demethylases (HDMs) remove methyl groups Histone Methylation Recruits regulatory proteins to bind to the methylated residues 20  1/26/2025 Acetylation Direct relationship with gene expression Acetylation of lysines switches genes ON Deacetylation turns them OFF Histone acetyltransferase (HAT) or histone deacetylase (HDAC) Acetylation Acetylation neutralises the positive charge on the histone tail Reduced affinity for DNA Reduced affinity for nearby nucleosomes More open DNA structure 21  1/26/2025 Other Chromatin Re-modelling ATP-dependent chromatin re-modelling Move, eject or restructure nucleosomes Requires energy input from ATP (adenosine triphosphate) Non-coding RNA - lncRNA Non-coding RNAs are transcribed from DNA, but do not make proteins Long ncRNAs, over 200nt Developmentally regulated, cell-specific Many different modes of action – complementary binding to DNA/RNA, structural reassembly of mRNA, chromatin modification, bind proteins, miRNA precursors 22  1/26/2025 Non-coding RNA - sncRNA Short ncRNA, 200 CGG repeats within the gene Causes methylation and turning off of FMR1 (CGG)n 28  1/26/2025 Rett Syndrome Severe genetic disorder of the nervous system Only seen in girls (1 in 15,000) Affects body movement, causes loss of speech and hand use, breathing difficulties, anxiety disorder Rett Syndrome Mutations in MeCP2 on Xq28 MeCP2 is expressed mostly in the brain MeCP2 protein binds the methyl groups on CpG islands upstream from genes MeCP2 fails to recognise methylated cytosines De-suppression An unusual epigenetic disease 29  1/26/2025 Rett Syndrome Possible mechanism – fails to turn off genes once methylated Normal Rett Syndrome Epigenetics and Cancer First human disease linked to epigenetics Diseased colorectal cancer tissue was less methylated than normal tissue CpG islands can also become excessively methylated in many cancers Genes control the cell cycle and help repair DNA Epigenetic changes can also make DNA unstable 30  1/26/2025 DNA methylation and Cancer Hypomethylation - gene overexpression Turn on genes that promote cell growth Increased chromosomal instability Telomerase – unlimited cell divisions Normal cell karyotype Cancer cell karyotype DNA methylation and Cancer Hypermethylation - gene silencing Turn off cell cycle checks, DNA repair genes 31  1/26/2025 Histone Modification and Cancer Specific acetylation and methylation patterns have been associated with cancer Deacetylation of histone 4, lysine 16 represses tumour suppressor genes Cancer in twins – a case study At 4yr 8m one identical twin was diagnosed with precursor B-cell lymphoblastic leukaemia Chemotherapy and bone marrow transplant from her sister controlled the disease At 25, same sister diagnosed with thyroid cancer Cured via thyroidectomy 32  1/26/2025 Cancer in twins – a case study At 29, same sister diagnosed with Type II Diabetes At 32, she gave birth to a healthy daughter At 34, both sisters examined, neither show signs of cancer Twin A Twin B Cancer in twins – a case study Methylation patterns were examined in fibroblasts of both sisters Examined the promoter of BRCA1 gene BRCA1 is a tumour-suppressor gene Healthy twin showed normal methylation Affected sister showed much greater methylation of BRCA1 Excessive methylation is typical for silenced genes 33  1/26/2025 Cancer in twins – a case study Each line is a sequenced DNA molecule, filled in circles show methylation. Arrows indicate hypermethylation of the BRCA1 promoter in the affected twin Epigenetic Therapy Turning genes on and off is easier than changing the DNA sequence Many drugs which inhibit methyltransferases or deacetylases have been approved for use Many other drugs are under development Treatment needs to be selective 34  1/26/2025 Week 9 – Part B Reproductive Technology, Genetic Testing and Gene Therapy based on eBook chapter 12 First Reproductive Technology Success First IVF baby born on the 25th of July, 1978 9 years of modifying techniques 80 failed attempts to collect and fertilise egg cells Egg and sperm combined in a sterile dish and incubated for 21 days before implantation Louise Brown later conceived naturally 35  1/26/2025 Normal Reproduction Successful reproduction requires: 1. Healthy gametes 2. A place for fertilisation to occur 3. Somewhere for the baby to develop 1. Eggs and Sperm 2. Fallopian tubes 3. Uterus Infertility is common Affects ~1 in 6 couples (~10-15%) Female infertility responsible ~40% Male infertility responsible ~40% ~20% of the time both or unknown Physical and psychological reasons can contribute 36  1/26/2025 Infertility is common Infertility increases with female age As does chance of chromosomal abnormality 1/3 of couples over 35 have trouble conceiving 100 100% 90 KEY 80 % likelihood of infertility 69% 70 60 % infertility 50 40 32% 30 20 15% 10 8% 3% 5% 0 20–24 25–29 30–34 35–39 40–44 45–49 50+ Age of female Chances of conception Never 100% each month Starts at ~25% each month and declines with age Infertility usually examined after 1 year, after 6 months if woman is >35 Per month chance of conception Age in years 37  1/26/2025 Two types of Infertility Primary Couples that have not had a child yet Secondary Couples that already have a child Causes of Female Infertility Ovaries No/damaged ovaries, Polycystic Ovarian Syndrome Hormones Low/no oestrogen Fallopian tube or Uterus Blockages, endometriosis 38  1/26/2025 Endometriosis Endometrium grows in abnormal locations (eg. outside of uterus, bowel, bladder, brain) Affects ~10% of menstruating women Pain, tiredness, bleeding, swelling Commonly associated with early puberty (25, already a mother, background check Newer Techniques – Multi-Parent Babies IVF to overcome known mitochondrial disorders Mother’s chromosomes, donor’s mitochondria Two main methods: Maternal spindle transfer (MST) Pronuclear transfer (PNT) Tightly regulated in the UK and USA, illegal in Australia 46  1/26/2025 Newer Techniques – Multi-Parent Babies Maternal spindle transfer Pronuclear transfer Material is swapped between Material is swapped between mother and donor egg prior to mother and donor egg after fertilisation fertilisation Risks of using ART Ovarian Hyperstimulation Syndrome Risk of low birth weight Increased risk of multiple births and premature birth with IVF Increased premature births Single baby Low birth weight Chromosomal abnormalities Ectopic pregnancy Twins Male infertility Triplets or more 25 50 75 100 KEY Low birth weight Preterm birth 47  1/26/2025 Genetic Testing and Genetic Screening Pre-conception, pregnancy and post-birth Genetic Testing Voluntary Identify disease gene carriers Genetic Screening May be legally required Populations where there is a high risk of disease Types of Tests Used Newborn screening tests Done in all hospitals in Australia 48-72 hours post birth Heel prick and blood collection Cystic fibrosis, hypothyroidism, phenylketonuria Follow-up tests are done if needed 48  1/26/2025 Types of Tests Used Carrier testing Done on families or ethnic groups with disease history Detect carriers and determine risk of passing on the disorder (25% for AR) May assist in the decision to have children Types of Tests Used Prenatal testing Testing done on the foetus >200 diseases can be tested for Family history or mother’s age suggestive Ultrasound, Amniocentesis, Chorionic Villus Sampling 49  1/26/2025 Types of Tests Used Prenatal testing Pre-implantation Genetic Diagnosis (PGD) Test embryos at 6-8 cells post fertilisation Remove a single cell, extract DNA, PCR Family history or positive carrier screening result Autosomal recessive or X-linked Medical sex selection Types of Tests Used Prenatal testing Polar body biopsy Test eggs before fertilisation Remove polar body and examine by PCR Determine which X-chromosome is in the egg cell X-linked recessive diseases 50  1/26/2025 Ethics of Pre-natal Genetic Diagnosis Saviour babies for already affected children Prevention of diseases with less than 100% risk Selecting babies to have disabilities to conform with family Maguire Family Children Gene Therapy Recombinant-DNA methods to correct individual mutated genes Normal gene inserted and functional protein produced Chemical, physical, viral methods 51  1/26/2025 Gene Therapy Viral vectors most common Limited viral genes  no disease Human gene inserted  functional protein Viral DNA inserts into human chromosomes after infection and becomes part of the genome Normal protein should be produced Viral Vectors for Gene Therapy 52  1/26/2025 Gene Therapy – what can go wrong There are risks associated with viral vectors: Unwanted Immune Reactions – Immune system recognizes the viruses as foreign and attacks them Targeting the wrong cells – healthy cells may be damaged, and illness, disease or cancer may result Infection – viruses may be able to cause disease themselves Tumour formation – disruption of genes leading to proliferation Gene Therapy Issues & Successes Limited success so far 1999 – one patient died as a result of an immune reaction to the vector 2000 – two children developed leukaemia from treatment Successful treatment of blindness 53  1/26/2025 Gene Therapy Issues & Successes Improvements in technology have lead to more successes and more diseases being treated Ethical Issues of Gene Therapy Patients are volunteers Strict guidelines and monitoring Somatic Gene Therapy – body cells Germ-line Gene Therapy – sperm and egg cells targets for gene transfer Enhancement Gene Therapy – using genes to enhance specific traits 54  1/26/2025 Genetic Counselling Explain to families about and the risks of certain diseases Communicates to the family: 1. Medical facts 2. Contribution of heredity 3. Alternatives 4. Services No direction provided, just facts Genetic Counselling Recommended for: Women >35 Couples with an already affected child Couples with ethnic bias to disease Related couples Individuals with work-related exposure Women with >2 miscarriages or infant deaths Parents of a newborn diagnosed by routine screening People concerned about birth defects or inherited disorders Women with medical tests that show increased risk 55  1/26/2025 Genetic Counselling How is it done? 1. Detailed family medical history 2. Prenatal screening or testing 3. Risk-assessment 56