FM2004 & PM2004: Genetics PDF

FM2004 & PM2004: Genetics The molecular and biochemical basis of genetic disease I Dr Collette Hand UCC Department of Pathology [email protected] February 2023 FM2004&PM2004 Dr Hand Textbooks R9 R10 Robbins & Cotran Pathologic Basis of Disease A2 Robbins & Cotran Atlas of Pathology U6 U7 Underwood Gener...

FM2004 & PM2004: Genetics The molecular and biochemical basis of genetic disease I Dr Collette Hand UCC Department of Pathology [email protected] February 2023 FM2004&PM2004 Dr Hand Textbooks R9 R10 Robbins & Cotran Pathologic Basis of Disease A2 Robbins & Cotran Atlas of Pathology U6 U7 Underwood General & Systemic Pathology RBP9 RBP10 Kumar, Abbas, Aster Robbins Basic Pathology W5 Young, Stewart, O’Dowd Wheater’s Basic Pathology FM2004&PM2004 Dr Hand Textbooks- Genetics Emery’s Thompson & Thompson Strachan & Read Elements of Genetics in Medicine Human Molecular Medical Genetics T&T7/ T&T8 Genetics 2 /3 / 4 E14/ E15 HMG2/3/4 ?Online FM2004&PM2004 Dr Hand Outline of these 2 lectures: Diseases due to mutations in different classes of proteins Lecture 1 – Enzymes Lecture 2 – Receptor proteins – Transport proteins – Structural proteins – Mitochondrial diseases – Expansion of Repeat Sequences FM2004&PM2004 Dr Hand Genetic Disease All diseases (except trauma) have some genetic component Increasing amount information Genes for ~ 2,000 diseases known > 3,000 single gene disorders for which gene is unidentified at present Representative disorders FM2004&PM2004 Dr Hand Effect of Mutation on Function - Loss of function - Gain of function - Novel property - Incorrect expression T&T7/T&T8 Fig 11.1 A general outline of the mechanisms by which disease-causing mutations produce disease. FM2004&PM2004 Dr Hand How can mutations disrupt the formation of a biologically active protein? Ideas? FM2004&PM2004 Dr Hand How can mutations disrupt the formation of a biologically active protein? Ans Steps at which mutations can disrupt the production of a normal protein FM2004&PM2004 Dr Hand Think about protein functions Proteins- what do they do? Ideas? FM2004&PM2004 Dr Hand T&T7 / T&T8: Fig 12.1 Examples of the classes of proteins associated with diseases with a strong genetic component (most are monogenic), and the part of the cell in which those proteins normally function. FM2004&PM2004 Dr Hand Protein functions Proteins- large array of functions – – – – – – Enzymes Structural Organelles Nuclear Cytoplasmic Cell surface Mutations in virtually every functional class of protein can lead to genetic disease Examples FM2004&PM2004 Dr Hand Site of expression & site of disease 1 Housekeeping proteins – ~90% mRNA in cell – present in virtually every cell – fundamental roles in the maintenance of cell structure and function Tissue-specific specialty proteins – produced in only one or a limited number of cell types – unique functions which contribute to the individuality of the cells in which they are expressed. FM2004&PM2004 Dr Hand Site of expression and site of disease 2 1. Mutation in tissue-specific protein most often produces disease restricted to that tissue 2. Mutation in house-keeping genes rarely cause pathological changes in every tissue – Genetic redundancy – Other genes with overlapping biological activities lessen the impact of loss of function Protein over-expressed and/or serves a specific function in that tissue eg Tay-Sachs disease, damage to neuronal cells only FM2004&PM2004 Dr Hand Genotype and Phenotype Genotype: the genetic constitution of an individual, either overall or at a specific locus Phenotype: the observable characteristics of a cell or organism Phenotypic variation may result from 3 types of genetic variation: 1. Allelic heterogeneity different mutations on the same gene – The existence of many different disease-causing alleles at a locus; genotype-phenotype correlation 2. Locus heterogeneity 3. Modifier genes – – mutations on differnt loci but causing the same phenotype Determination of the same phenotype by mutations at different loci A gene whose expression can influence a phenotype resulting from a mutation at another locus FM2004&PM2004 Dr Hand Diseases involving Enzymes 1 Enzymes: biological catalysts that mediate conversion of a substrate to a product ≥ 5000 genes that encode enzymes – -> many human enzyme defects: enzymopathies FM2004&PM2004 Dr Hand Diseases involving Enzymes 2 Aminoacidopathies – Hyperphenylalaninemias Lysosomal storage disease – Tay Sachs Disease – Mucopolysaccharidoses Abnormal post-translational modification – Loss: I-cell disease Impaired binding or metabolism of cofactors – Homocystinuria Mutation of enzyme inhibitor – Alpha1 antitrypsin deficiency FM2004&PM2004 Dr Hand Hyperphenylalaninemias An aminoacidopathy Increased level phenylalanine in blood – Phenylalanine hydroxylase (PAH) deficiency – PAH: phe->tyr – Phenylketonuria T&T7/ T&T8: Fig 12.2 Loss of function of mutations – PAH gene (> 95% cases) – genes required for synthesis / utilisation of cofactor tetrahydrobiopterin (BH4) FM2004&PM2004 Dr Hand Phenylketonuria 1 Classical inborn error of metabolism 1/3,000 births Autosomal recessive First recognised genetic cause of mental retardation Inability to degrade phenylalanine, increase conc. in body fluids Damages developing CNS – seizures, low IQ Newborn screening: blood phe:tyr ratio Early treatment (< 4 weeks) is effective Low-phenylalanine diet in childhood, pregnancy – Recommend low-phe diet for life FM2004&PM2004 Dr Hand Phenylketonuria 2 dont need to know detail Allelic & locus heterogeneity PAH – > 400 mutations – 7 mutations -> 2/3 known European mutations – 6 (other) mutations -> 80% known Asian mutations – Other mutations are individually rare Compound heterozygotes are common T&T7:Fig 12.3, T&T8:Fig 12.4 The nature and identity of PAH mutations in populations of European and Asian descent FM2004&PM2004 Dr Hand Lysosomal Storage Diseases 1 Lysosomes – Membrane bound organelles – Hydrolytic enzymes – Degradation of biological macromolecules Genetic defects of these hydrolases – -> accumulation of substrates – -> cellular dysfunction – -> cell death FM2004&PM2004 Dr Hand Lysosomal Storage Diseases 2 Accumulation -> unrelenting progression – Uniform clinical feature of these diseases Substrate storage manifests in affected tissues / organs – In brain -> neurodegeneration Clinical phenotypes aid diagnosis – specific disease / class of disease > 50 lysosomal hydrolase or lysosomal membrane hydorlases are mutated so dont break down substrate transport deficiencies – Autosomal recessive mutated mem. trasnport deficiencies -> dont let in substate to be broken down Emerging enzyme replacement therapies FM2004&PM2004 Dr Hand Tay-Sachs Disease 1 GM2 is made in brain A GM2 gangliosidose disease – Inability to degrade GM2 ganglioside – Clinically indistinguishable- differ in enzyme affected Deficiency of Hexosaminidase A (Hex A) – Ubiquitously expressed – Clinical impact in brain Predominant site GM2 ganglioside synthesis FM2004&PM2004 Dr Hand Tay-Sachs Disease: genes T&T7:Fig 12.4 T&T8:Fig 12.5 The three-gene system required for hexosaminidase A activity and the diseases that result from defects in each of the genes FM2004&PM2004 Dr Hand Tay-Sachs Disease 2 Progressive neurological deterioration from 3-6 months until death at 2-4 years – Neuronal death observed in cherry spots in retina 3 mutations = 99% Ashkenazi Jewish alleles – 100 x incidence 1 in 27 Ashkenazi Jews is a carrier of a TaySachs mutation FM2004&PM2004 Dr Hand Tay-Sachs Disease: mutations T&T7 T&T7: Fig 12.5, T&T8: Fig 12.6 Four-base insertion (TATC) in the hexosaminidase A gene in Tay-Sachs disease, leading to a frameshift mutation. FM2004&PM2004 Dr Hand Mucopolysaccharidoses 1 Diseases in which mucopolysaccharides accumulate in lysosomes – mucopolysaccharide / glycosaminoglycan – = polysaccharide chains synthesised by connective tissue – long disaccharide repeat units nature of repeat unit distinguishes types Heterogeneous group, > 12 disorders Deficiency of enzyme required for degradation Undegraded mucopolysaccharides in urine – Detected by screening tests FM2004&PM2004 Dr Hand Hurler syndrome coarse facial features skeletal abnormalities short stature mental retardation some success with enzyme replacement therapy T&T7: F12.6 A child with Hurler syndrome, showing the typical coarse facial features. At 5 years of age, he is only as tall as a typical 3-year-old. FM2004&PM2004 Dr Hand Post-translational modification How do proteins get to their correct location in the cell? Some information in primary amino acid sequence Post-translational modification – Hydrolases: glycoproteins with phosphorylated mannose residues – Mannose 6-phosphate required for recognition by cells / lysosomes FM2004&PM2004 Dr Hand I-cell disease -> Defect in the enzyme that transfers phosphate group to mannose residues -> Hydrolases are not correctly directed to lysosomes but released in body fluids; cell levels reduced Abnormal lysosomes, inclusions (I-cell) in cytoplasm Autosomal recessive disorder Severe disorder, facial features, skeletal changes, growth and mental retardation, death by 5-7 years FM2004&PM2004 Dr Hand Impaired binding or metabolism of cofactors some need cofactor Some proteins are only active once bound to cofactors Mutations that interfere with cofactor binding, synthesis, transport, removal Increase in cofactor concentration can restore activity – eg water soluble vitamin Homocystinuria – Impaired cofactor binding – Homocysteine is an intermediary in methionine-> cysteine pathway only 2 sulphur containing aa FM2004&PM2004 Dr Hand Homocystinuria: genes T&T8: Fig 12.8 Genetic defects in pathways that impinge on cystathionine synthase, or in the enzyme itself, that cause homocystinuria. FM2004&PM2004 Dr Hand Homocystinuria: clinical Autosomal recessive Cystathionine β-synthase (CBS) deficiency Pyridoxal (Vit B6) is CSB co-factor – -> can treat with large amounts of pyridoxal Accumulation of homocysteine (aminoacidopathy) Lens dislocation – primary symptom 80% cases Mental retardation – 1/3 cases normal IQ Osteoporosis Long bones & vascular abnormalities: MI, stroke, pulmonary embolism – may be confused with Marfan syndrome: AD connective tissue disorder FM2004&PM2004 Dr Hand Mutation of enzyme inhibitor NB Alpha1 antitrypsin (α1AT) deficiency Affects 1/5000 people, 2% are carriers Substantial risk of – chronic obstructive lung disease (emphysema) – cirrhosis of liver α1AT - family of protease inhibitors – serine protease inhibitors or serpins α1AT inhibits many proteases, principle role is to bind and inhibit elastase FM2004&PM2004 Dr Hand Alpha1 antitrypsin deficiency Many α1AT alleles (> 120) Three common alleles: M, S, Z (Z= Glu342Lys) – Enzyme activity: MM= 100%; SS = 50-60%; ZZ = 10-15% LIVER – α1AT gene expressed principally in liver – 17% Z/Z individuals neonatal jaundice 20% of these -> cirrhosis – Mutant allele aggregates, become trapped in hepatocyte ER -> NOVEL PROPERTY LUNG – α1AT deficiency -> Gradual destruction of pulmonary elastic tissue by elastase Block of hepatic release ZZ reduced ability to inhibit elastase Protein replacement treatment FM2004&PM2004 Dr Hand Alpha1 antitrypsin T&T7/ T&T8: Fig 12.9 The effect of smoking on the survival of patients with alpha1-antitrypsin deficiency T&T7 / T&T8 : Fig 12.10 A posteroanterior chest radiograph of an individual carrying two Z alleles of the alpha1AT gene, showing the hyperinflation and basal hyperlucency characteristic of emphysema. FM2004&PM2004 Dr Hand Enzymopathies- general concepts 1 T&T7: Fig 12.8; T&T8: Fig 12.3 A model metabolic pathway showing that the potential effects of an enzyme deficiency 1) accumulation of the substrate (S) or derivatives of it (S1, S2, S3) and 2) deficiency of the product (P) or compounds made from it (P1, P2). FM2004&PM2004 Dr Hand Enzymopathies- general concepts 2 Almost always recessive – Heterozygotes ~50% activity- enough to prevent disease Substrate accumulation or product deficiency Diffusible vs macromolecular substrates – Diffuse: distributed – Macromolecule: accumulates with cell / organelle Loss of multiple enzyme activities Phenotypic homology – Clinical features may be shared by diseases of other enzymes that function in the same area of metabolism FM2004&PM2004 Dr Hand Outlines of classes Enzymes NEXT CLASS Receptor proteins Transport proteins Structural proteins Mitochondrial diseases Expansion of Repeat Sequences FM2004&PM2004 Dr Hand