Lecture 12 Introduction to Genetics PDF

Genetics – An Introduction Lecture prepared by Professor Matthew Campbell School of Genetics & Microbiology, TCD. delivered by Dr Laetitia Chauve Biology - A Global Approach (11th edition, Pearson) Campbell, Urry, Cain, Wasserman, Minorsky & Reece  Genetics, an in...

Genetics – An Introduction Lecture prepared by Professor Matthew Campbell School of Genetics & Microbiology, TCD. delivered by Dr Laetitia Chauve Biology - A Global Approach (11th edition, Pearson) Campbell, Urry, Cain, Wasserman, Minorsky & Reece  Genetics, an introduction Key concepts that will be covered today: 1- History 2- DNA, Genes, Chromosomes 3- the Central Dogma of Biology 4- Genomics 5- Genetic diseases A Whistle-Stop Tour of 150 years of Genetics – History 1860s Mendel published his research on inheritance of unit factors. Cytologists describe chromosomes & their behaviour during mitosis & meiosis. 1900s Rediscovery of Mendel’s work. Chromosomes behave like unit factors. The term “Gene” proposed to replace unit factors. Genetics becomes a discipline in itself. 1905 William Bateson first uses the term ‘genetics’ to describe the study of inheritance 1940s Confirmation that the genetic material is DNA not protein. 1950s Watson and Crick describe double-helical structure of DNA - Molecular Biology Era Begins 1960s Cracking the triplet ‘code’ and defining the pathway of information flow: ‘DNA makes RNA makes protein’  James Watson DNA structure 1953 Francis Crick Rosalind Franklin and “photo 51” 1970s Discovery of restriction enzymes: Recombinant DNA technology becomes possible. Expression of human growth hormone gene in E. coli; Discovery of split genes in eukaryotes - introns & exons; methods for sequencing DNA. 1980s Commercialization of Recombinant DNA technology. Methods for making transgenic plants & animals. 1990s Genome sequencing: Human, plant, drosophila, nematode, microbial genomes & many other genomes sequenced. 1998 1970s Discovery of restriction enzymes: Recombinant DNA technology becomes possible. Expression of human growth hormone gene in E. coli; Discovery of split genes in eukaryotes - introns & exons; methods for sequencing DNA. 1980s Commercialization of Recombinant DNA technology. Methods for making transgenic plants & animals. 1990s Genome sequencing: Human, plant, drosophila, nematode, microbial genomes & many other genomes sequenced. 2000s First complete human genome sequence 2003. Cost approx. $3 billion! 2000s Technology for expression profiling of the entire gene complement in a genome. 2000s RNA interference; genome editing; induced pluripotent stem (iPS) cells & many others - some of which we will cover during the lecture course 2018 Whole human genome sequence (WGS) costs less than $1,000! 2019 Era of genome editing and gene therapy takes off ! Life’s processes involve the Expression & Transmission of Genetic Information Within cells, structures Each chromosome called chromosomes contains one long DNA contain genetic material in molecule with hundreds or the form of DNA thousands of genes (deoxyribonucleic acid) Genes are the units of inheritance - they encode information for building the molecules synthesized within the cell The genetic information encoded by DNA directs the development of an organism and the maintenance of cells in the organism Nuclei containing DNA Sperm cell Egg cell Fertilized egg with DNA from both parents Embryo’s cells with copies of inherited DNA Offspring with traits inherited from both parents © 2018 Pearson Education Ltd. The molecular structure of DNA accounts for its ability to store information A Each DNA molecule Nucleus C is made up of two DNA long chains arranged Nucleotide T in a double helix A Cell T A Each chain is made up C of four kinds of C chemical building blocks called nucleotides and G abbreviated A, G, C, T T A G Adenine T Guanine Thymine A Cytosine (a) DNA double helix (b) Single strand of DNA 3 x 109 bp of DNA in the human genome – 3 billion bases. If there were 3,000 letters on a typed page that would be 1 million pages of text in our genomes – the same 1 million pages of text in every nucleus of every cell in the human body. Approx. 1 in 1,000 bases varies between individuals.  How much DNA do we have? Humans have 10-100 trillions of cells, each cell with approx. 2 meters of DNA packaged into the nucleus of the cell. If the DNA from every cell in your body was put end to end, it would reach to the moon and back… …over 800 times! The genome comes tightly packed into chromosomes (Baylin and Schuebel, Nature 2007) Human Karyotype Male Female Human Karyotype Traditional methods of identifying chromosomes involve staining with dyes that produced banding patterns. These chromosomes are stained with Giemsa (G-banded). Another form of staining is Q-banding. What is this karyotype representative of...Male or Female?  DNA Genes –> RNA Messages –> Proteins The Central Dogma For many genes, the sequence provides the blueprint for The Central Dogma making a protein. of Molecular Biology Protein-encoding transcription genes control protein production indirectly. DNA is transcribed into RNA, which is It turns out that only about 1% then translated into a of our genome codes for proteins. protein. Much of our genome makes Gene expression is RNA but does not code for protein – translation the process of termed non-coding RNAs.. converting information from gene to cellular product.  Who has Who has the the most mostgenes? genes? 20 470 20 000 to 25 000 genes genes The same 3 billion base pairs of DNA are present in every cell of your body. Approx. 20,000 genes in 23 pairs of human chromosomes in 3 billion DNA base pairs.  Epigenetic regulation: controlling gene expression Genes make RNA which is translated into proteins, the building blocks required for each cell to function. Different cell types need different proteins to function. How does each cell function so differently? Not all genes are active in all cell types. (Baylin and Schuebel, Nature 2007)  Genomics: Large-Scale Analysis of DNA Sequences ◆ An organism’s genome is its entire “library” of genetic instructions ◆ Genomics is the study of sets of genes in one or more species ◆ Proteomics is the study of whole sets of proteins and their properties ◆ The entire set of proteins expressed by a given cell, tissue, or organ is called a proteome The genomics approach depends on: ◆ “High-throughput” technology, which yields enormous amounts of data ◆ Bioinformatics, which is the use of computational tools to process a large volume of data ◆ Interdisciplinary research teams Human Genome Sequencing Project: 3 billion nucleotides of DNA code in the human genome - 1st human complete genome sequence published in 2003  Human Genome Sequencing 1st human genome sequence – estimated cost $2-3 billion (2003) Whole human genome sequence (WGS) costs less than $1,000 – 2019! Over a million fold price drop! We are in an era of big data (Moore's law is the observation that the number of transistors in a dense integrated circuit doubles approx. every two years). Genes and Diseases…… Mutations in the DNA sequence can result in no protein or incorrect proteins being formed giving rise to genetic disorders. Mutations in a single gene that give rise to a disease are called single gene defects (or Mendelian disorders after Gregor Mendel) Inheritance patterns quantitative traits Identifying disease genes and associated mutations Moving towards rational therapies based on genetic cause  Achondroplasia Affects 1 in 15,000 to 1 in 40,000 newborns. Most cases are sporadic – parents are not affected, and these cases are caused by de novo (spontaneous, new) mutations in the germ line. However, an affected individual will transmit the condition as an autosomal dominant disease – 50% of offspring on average will pick up the gene. Features: Short stature (av. 4 feet 1 inch – 124 cm); average sized trunk; but arms and legs short; disproportionately large head with prominent forehead; spinal curvature which can cause back pain in older subjects; short fingers; normal intelligence. Gene: a dominant mutation within the FGFR3 gene (encodes fibroblast growth factor receptor 3). The growth factor receptor becomes hyperactive – the mutant protein dominates the normal allele, negatively affecting bone development. http://www.google.ie/images?hl=en&q=achondroplasia  Autosomal dominant Mendelian Disorders These are single gene defects - diseases due to a mutation in a single gene On average 50% of children are affected with the disease and 50% are unaffected gig.org.uk/education2.htm  Retinitis pigmentosa (recessive form) Consanguineous pedigree Retinitis pigmentosa (RP) is a group of inherited eye disorders that cause progressive degeneration of the retina, the light-sensitive tissue at the back of the eye.  Autosomal recessive Mendelian Disorders Single gene defects - diseases due to a mutation in a single gene On average 25% of children are normal, 50% are carriers, 25% are affected with the disease gig.org.uk/education2.htm An X linked recessive Gene Haemophilia  X-linked / Sex linked XY XX XY XX Mendelian disorders – single gene defects - diseases due to a mutation in a sinlge gene All female children from an affected male will be carriers of the disease On average 50% of male children from a carrier female will have the disease & 50% of female children will be carriers  X-linked health.allrefer.com/pictures-images/x-linked-recessive-genetic-defects.html Over 3,000 single gene disorders / Mendelian disorders in humans Disorder Frequency per1000 births Examples of autosomal dominant diseases: Familial combined hyperlipidaemia 5.0 Familial hypercholsterolaemia 2.0 Dominant otosclerosis 1.0 Adult polycystic kidney disease 0.8 Multiple exostoses 0.5 Huntington's disease 0.5 Neurofibromatosis0.4 Myotonic Dystrophy 0.2 Congenital spherocytosis 0.2 Polyposis coli 0.1 Over 3,000 single gene disorders / Mendelian disorders in humans Disorder Frequency per 1000 births Examples of autosomal recessive Over 3,000 single gene disorders / diseases: Mendelian disorders in humans Cystic fibrosis 0.4 Disorder Frequency per 1000 births alpha-1-antitrypsin deficiency 0.2 Examples of x-linked recessive diseases: Phenylketonuria 0.1 Congenital adrenal hyperplasia 0.1 Fragile X syndrome 0.5 Spinal muscular atrophy 0.1 Duchenne muscular dystrophy 0.3 Sickle cell anaemia 0.1 X-linked ichthyosis 0.2 beta-Thalassaemia 0.05 Haemophilia A 0.1 Becker muscular dystrophy 0.05 Haemophilia B 0.03  Gene-based medicines Knowledge of the genes causing genetic conditions enables the development of methods of intervention Dominant diseases: The strategy may require suppression of expression of the mutant gene (& thereby the mutant protein) Recessive diseases: The strategy involves supply of the wild type / normal copy of the gene to supply the wild type protein Gene Replacement - see video LCA (vision loss - RPE65 gene)  Drug development Using knowledge from the human genome project and tools such a viral vectors and cell and animal models, the development of therapies for many human genetic disorders becomes a realistic aspiration. Knowledge of the underlying genetic basis of a condition enables the development of designer therapies targeted towards the cause of the disease, as opposed to the somewhat random approach (serendipity) at times used to develop drugs in the past. Inherited Retinal Disorders Leber Congenital Amaurosis (LCA) – an autosomal recessive eye disorder. The RPE65 gene is one of the causes of LCA and also some other types of recessive eye disease. The RPE65 gene encodes an important enzyme involved in regenerating light sensitive molecules in the retina. Gene Medicines In Action for a Recessive Eye Disorder – RPE65 Let’s look at a very short video of a gene medicine at work in the eye..... one of the first ever patients treated with this gene medicine in the world by Professors Jean Bennett, Albert McGuire & Kathy High in the University of Pennslyvania and now being developed by Spark Therapeutics Inc (Philadelphia). FDA approved - Dec 2017.  LCA/RPE65 – Gene Therapy Video Leber’s Congenital Amaurosis (LCA) is a recessive genetic eye disorder where often children early in life have significant visual loss. It is recessive & so in principle delivery of the normal (wild type) gene should provide benefit. There are some human clinical trials for LCA. Here is a video from a University of Pennsylvania trial (Prof Jean Bennett, Albert Maguire, Kathy High & colleagues), now being developed by Spark Therapeutics (Philadelphia). Patients in the U Penn/Spark trials have been evaluated in Phase I/II & III trials. The therapy, Luxturna, provided benefit & as of December 2017 has been approved by the US regulatory body, the FDA. In this video the patient is injected in one eye with a virus (AAV) that carries the normal gene (RPE65 gene). The other eye is untreated. Knowledge of the cause of a genetic disease together with a method to get the normal gene into the target cell type represents a powerful therapeutic approach for many genetic disorders. To gain an understanding of a gene therapy like Luxturna, some background information about genetics is required, which will be presented over the course of the next few lectures. Genetics has many applications – here are just a few examples relating to human health 1. Production of safer vaccines: recombinant single subunit vaccines e.g. hepatitis B vaccine 2. Production of recombinant human “therapeutic” proteins e.g. insulin, growth hormone, clot dissolving proteins 3. Inherited disorders can be diagnosed prenatally 4. Prenatal genotyping – in vitro fertilisation & pre implantation diagnosis 5. Pharmacogenomics: using genomics to genotype populations & individuals for alleles that determine responsiveness to drug therapies. ….and many others Let’s quickly look at 2 examples…  Individualisation of medicines - Pharmacogenomics Research is on-going into understanding differences in drug response that exist between patients – Pharmacogenomics. What genes influence drug response? In liver & intestine a large number of genes are expressed into drug metabolising enzymes (DMEs). Allelic variants of the genes encoding DMEs exist in human populations resulting in heritable differences in DMEs between people. These genetic variants are in part responsible for the differences between people in response to drugs including chemotherapeutics, immuno-suppressants, anti-depressants, pain killers etc. For example, TPMT is a DME that is involved in the metabolism of chemotherapeutic drugs. 1 in 300 people are deficient in this enzyme (homozygous mutant) due to mutations in the gene encoding the enzyme. 1 in 10 people have lower levels of the enzyme (heterozygotes). Homozygotes can experience extreme toxicity to chemotherapeutic drugs which can at times be fatal. Adverse drug responses account for approx. 100,000 deaths per year in the US alone. Pharmcogenomics should enable the identification of such people prior to adminstering a drug thereby prevention such adverse events.  CYP2D6 and Codeine The prodrug codeine is metabolised to the active drug morphine by an enzyme termed CYP2D6 (involving O-demethylation of codeine into morphine). The metabolism of codeine to morphine is undertaken almost exclusively by CYP2D6. Codeine has a 200x lower affinity for mu opioid receptors than morphine. Plasma morphine concentrations in patients after codeine administration is influenced by genotype at CYP2D6 (with almost no morphine present in some poor metabolisers). CYP2D6 poor metabolisers encode either dysfunctional or partially inactive CYP2D6 enzyme due to variants in the CYP2D6 gene - approximately 10% of Caucasians. In such individuals, codeine may be an ineffective analgesic as the active drug is not formed or is formed at low levels. For patients reporting lack of pain relief from analgesics based on codeine, in many cases it may be that CYP2D6 genotype is responsible. Codeine is an active ingredient in a lot of non-prescription analgesic medications, e.g. Solpadeine etc Biological Information: Genetics, Heredity and DNA Lectures 2-5 Key concepts that will be covered: * Introduction to genetics: history, overview, applications * Mendelian genetics * Linkage and recombination * Identification of DNA as the hereditary material * Quantitative genetics * DNA, structure and function * DNA – mutation, recombination and repair * The central dogma MCQ evaluation Laetitia Chauve [email protected]