Concepts of Disease - Lecture 1 and 2 2024 PDF

Concepts of Disease Genetic Diseases: Lectures 1 and 2 Prof Deborah Mason  Learning outcomes 1. To understand how mutations cause pathology. 2. To be able to describe and discriminate between loss of function mutations, gain of function mutations, dominant negativ...

Concepts of Disease Genetic Diseases: Lectures 1 and 2 Prof Deborah Mason  Learning outcomes 1. To understand how mutations cause pathology. 2. To be able to describe and discriminate between loss of function mutations, gain of function mutations, dominant negative mutations and mutations that affect gene dosage. 3. To understand genetic pedigree analysis and terminology 4. To know and recognise the expected mendialian inheritance patterns in humans 5. To understand how autosomal dominant and autosomal recessive alleles are inherited 6. To know and understand how locus, allele and phenotype heterogeneity influence the phenotypes of single gene disorders Strachan Genetics and Genomics in Medicine Chapter 5 Single-Gene Disorders: Inheritance Patterns, Phenotype Variability, and Allele Frequecies 1. How do mutations cause pathology?  Molecular Pathology Molecular pathology – why a genetic change (mutation) results in a clinical phenotype Types of mutation – *deletions -1bp-Mbp’s – *insertions - 1bp-Mbp’s (including gene duplications) – single base substitutions missense = amino acid replaced with different amino acid nonsense = amino acid codon replaced with stop codon‡ *splice shifts = intron/exon splice sites lost or created * may alter reading frame = frameshift mutations ‡ ‡ may activate nonsense mediated mRNA decay  Effects of mutations in humans Gene Promotor exon intron Transcription Primary mRNA Mature AAAAAAAAA….A mRNA Translation Mutational heterogeneity Encodes protein Eg: Strachan & Read Table 9.5  2. Effects of different types of mutation – loss of function mutation – gain of function mutations – dominant negative mutations – mutations that affect gene dosage  Loss of function mutations – gene product has reduced or none of normal function any mutation that inactivates gene product will result in the same clinical symptoms – eg: Duchenne Muscular Dystrophy (DMD)  Duchenne muscular dystrophy: Loss of function  Clinical phenotype  progressive muscular weakness  death in 3rd decade  mostly males affected but occasionally females  occurs in families (1 in 3500 male births) Gower’s sign -patient that has  Treatment to use their hands and arms to  none "walk" up body from a squatting position due to lack of hip and  Inheritance thigh muscle strength.  X-linked recessive  Mutation  various  no detectable dystrophin expression  Gain of function mutations Gene product acquires new, abnormal function only the specific mutation that gives the product its new function will result in the clinical phenotype – eg: Huntington Disease Late onset, neurodegenerative, lethal disorder, dominant Strikes in midlife (30-50 years) Mutation occurs as expansion of an Death of medium spiny unstable CAG repeat within the coding neurons in striatum gene sequence for the protein huntingtin Motor, emotional & cognitive symptoms Death within 15-20 years  HD - trinucleotide repeat disease Eg. Expanded and unstable CAG repeat in exon 1 of the (huntingtin) HTT gene CAG(n) Exon 1 Normal alleles: 9-35 CAG repeats Affected alleles: 36-100 CAG repeats HD occurs when the number of repeats exceeds 35 the greater the number of repeats the earlier the age of onset the mutated allele is transcribed and translated encodes a polyglutamine tract in the protein causes the protein to aggregate causing neuronal cell death. protein aggregation - common in the pathology of CAG repeat diseases, Alzheimer disease, Parkinson disease and the prion diseases  Dominant Negative mutations Dominant-negative effect – mutant gene product not only loses its own function but also prevents other gene products from functioning correctly Common where mutation affects a multimeric protein encoded by more than 1 gene – eg: Osteogenesis Imperfecta mutations in Type I collagen have a dominant negative effect  Osteogenesis imperfecta (OI) Type I collagen is a major protein constituent of bone – exists as a triple helix (2 1 and 1 2 chains) – encoded by 2 different genes - COL1A1 & COL1A2 mutations in either COL1A1 or COL1A2 result in brittle bones Wide range of phenotypes  very mild to lethal o mild phenotype - the mutated alpha chain is excluded from Type I collagen o lethal phenotype - the mutated alpha chain is incorporated into Type I collagen  The effect of the mutation is enhanced due to the mutated chain interfering with the function of the normal alpha chains  Gene dosage effects Mutation varies level of gene product – effect depends upon gene and cell type eg: Downs Syndrome - extra (but normal) chromosome 21 – lethal phenotype associated with 50% increase in dosage of chromosome 21 OMIM (http://www.ncbi.nlm.nih.gov/omim) – Down syndrome (Down, 1866), a particular combination of phenotypic features that includes mental retardation and characteristic faces, is caused by trisomy 21 ( Lejeune et al., 1959), one of the most common chromosomal abnormalities in liveborn children. – Individuals with Down syndrome often have specific major congenital malformations such as those of the heart (30- 40% in some studies) and of the gastrointestinal tract.  Learning Outcome 3. To understand genetic pedigree analysis and terminology  Single Gene Disorders Rare, but important contributors to disease Follow defined patterns of inheritance Phenotype –describes observable characteristics – disease phenotype is associated with a single gene disorders – Tends to be called trait when not disease associated (e.g. blue eyes/blood group etc) Genetic variation is the primary influence on phenotype Factors such as environment also contribute  Electronic resources for human single gene disorders General information can be obtained from: – Genecards (http://www.genecards.org) Gene centered database 50,000 entries mostly relating to human genes Biological data on individual genes – GenereviewsTM (http://www.ncbi.nlm.nih.gov/books/ NBK1116/) Series of clinically and genetically orientated reviews of single gene disorders Reviews are assigned a PubMed identifier (PMID), e.g Huntington disease is at PMID 20301 482 – OMIM (http://www.ncbi.nlm.nih.gov/omim) Online Mendelian Inheritance in Man database – Most comprehensive source of of information on human mendelian pheontypes and underlying genes – Includes historical context  Genetic terminology Locus – Individual genes or DNA in our nuclear DNA have a chromosomal location that defines its position E.g. ABO blood group locus is called D3S1 563 (a polymorphic DNA marker on chromosome 3) Allele – An individual copy of a gene that is present at a locus on a single chromosome – Humans are diploid, therefore have 2 alleles for each chromosomal locus, one inherited from mother (maternal allele) and the other from father (paternal allele) Genotype – Combination of alleles that a person possesses at a locus Homozygous if both alleles the same Heterozygous if alleles are different Hemizygous – Humans are diploid for autosomes and X chromosome in females, but the sex chromosomes, X and Y are very different in structure and gene content Females have 2 alleles for X chromosome, can be homozygote or heterozygote for any locus on X chromosome Males have only one allele for X and one allele for Y chromosomes, therefore are hemizygous Pedigree Analysis – The genetic basis of a disorder can be established by assessing a family pedigree – Representation of a family tree that uses standard symbols to depict biological characteristics Pedigree Terminology – please learn in your own time = one or more recent ancestors = Brother/sister Pedigree Terminology Generations are labeled with roman numerals, lowest at the top of the page Individuals within each generation are numbered from left to right Extended families covering many generations are called kindreds The family member through which the family is first brought to the attention of clinicians is called the proband and may be marked with an arrow  Learning Outcomes 4. To know and recognise the expected mendialian inheritance patterns in humans 5. To understand how autosomal dominant and autosomal recessive alleles are inherited  Mendelian Inheritance in Humans Mendelian characters determined by chromosomal loci – on autosomes (chromosomes 1-22) – or on a sex chromosome ( X or Y) Females are diploid for all loci – 23 pairs of homologous chromosomes Males are – Diploid for autosomes – Hemizygous for X and Y Mendelian inheritance patterns – Autosomal dominant – Autosomal recessive – X-linked dominant – X-linked recessive – Y-linked  Autosomal dominant inheritance Rare – Affected individuals nearly always heterozygous – Very occasionally affected homozygotes may be born to 2 affected heterozygote parents Usually have the same phenotype (diseased) as the heterozygote Homozygotes may have: – more severe phenotype » E.g. achondroplasia (homozygous lethal) – Earlier age of onset » E.g. familial hypocholesterolemia Autosomal dominant Phenotype manifests in male and female heterozygotes Disease locus in one autosome Both sexes equally likely to transmit and inherit the disorder Affected individuals have a 50% chance of of having offspring with the disease Achondroplasia - autosomal dominant DISEASE CHARACTERISTICS: – disproportionate small stature. – short arms and legs, a large head, and characteristic facial features – most common cause of small stature – achondroplasia (ACH) is caused by heterozygous mutation in the fibroblast growth factor receptor-3 gene (FGFR3; 134934) on chromosome 4p16.3. DIAGNOSIS/TESTING: – characteristic clinical and radiographic findings usually sufficient – If diagnostic uncertainty, molecular genetic testing to detect a mutation in FGFR3. detects mutations in 99% of affected individuals.  Achondroplasia GENETIC COUNSELING: – autosomal dominant – 80% of individuals with achondroplasia have parents with average stature and have achondroplasia as the result of a de novo gene mutation.. An individual with achondroplasia who has a reproductive partner with average stature has a 50% risk in each pregnancy of having a child with achondroplasia. When both parents have achondroplasia: – 25% risk of having offspring with average stature – 50% risk of having achondroplasia – 25% risk of having homozygous achondroplasia (a lethal condition)  Familial hypercholesterolemia (FHC) Autosomal dominant (OMIM 143890) elevation of serum cholesterol bound to low density lipoprotein (LDL), promotes deposition of cholesterol in the skin, tendons, and coronary arteries. 2 clinical forms (heterozygous and homozygous): Homozygous more severe clinically -earlier presentation, usually in the first 2 decades of life the aortic root is prone to develop atherosclerotic plaque at an early age. The ranges of serum cholesterol and LDL-cholesterol (mg per dl), are: 250-450 and 200-400 in heterozygotes, >500 and >450 in homozygous Cholesterol deposition in patients heterozygous for familial hypercholesterolemia (a, b) Tendon xanthomata, and (c) corneal arcus (lipid infiltration of the corneal stroma). Fig. Disease box 11 ©Scion Publishing Ltd, Photos courtesy of Dr Paul Durrington, National  FHC: OMIM 143890 – please check website ‘Text’ section summarises clinical features, pathogenesis, diagnosis, treatment etc… E.g Diagnosis (1985-2005) Humphries et al. (1985) found a RFLP of the LDL receptor gene using the restriction enzyme PvuII. About 30% of persons are heterozygous for the polymorphism which is, therefore, useful in family studies and early diagnosis of FHC. Schuster et al. (1989) also used RFLPs of the LDLR gene in the diagnosis of FH. Bhatnagar et al. (2000) reported a case-finding experience in the UK among relatives of patients with familial hypercholesterolemia by a nurse-led genetic register. By performing cholesterol tests on 200 relatives, 121 new patients with familial hypercholesterolemia were discovered. The newly diagnosed patients were younger than the probands and were generally detected before they had clinically overt atherosclerosis. A case was made for organizing a genetic register approach, linking lipid clinics nationally. Umans-Eckenhausen et al. (2001) found that in the Netherlands targeted family screening with DNA analysis proved to be highly effective in identifying patients with hypercholesterolemia. Most of the identified patients sought treatment and were successfully started on cholesterol- lowering treatment to lower the risk of premature cardiovascular disease. Newson and Humphries (2005) discussed cascade testing in familial hypercholesterolemia. They questioned whether and how family members should be contacted for testing. The implications of the test results for life planning, employment, or ability to obtain life insurance are concerns. The pros and cons of cascade testing were reviewed by de Wert (2005).  Learning outcomes 1. To understand how mutations cause pathology. 2. To be able to describe and discriminate between loss of function mutations, gain of function mutations, dominant negative mutations and mutations that affect gene dosage. 3. To understand genetic pedigree analysis and terminology 4. To know and recognise the expected mendialian inheritance patterns in humans 5. To understand how autosomal dominant and autosomal recessive alleles are inherited - Autosomal Dominant (achondroplasia & FHC) 6. To know and understand how locus, allele and phenotype heterogeneity influence the phenotypes of single gene disorders Strachan Genetics and Genomics in Medicine Chapter 5 Single-Gene Disorders: Inheritance Patterns, Phenotype Variability, and Allele Frequecies Autosomal dominant Phenotype manifests in male and female heterozygotes Disease locus in one autosome Both sexes equally likely to transmit and inherit the disorder Affected individuals have a 50% chance of of having offspring with the disease  Autosomal Recessive A person affected by an autosomal recessive disease can be of either sex and is usually born to unaffected heterozygote parents (both carriers), e.g. Sickle Cell disease, cystic fibrosis. Affected individuals carry 2 mutant alleles, one from each parent The parents to children in generation IV are carriers with one normal allele (N) and one mutant allele (M) If they are not related, they may have different mutant alleles (pink v red) and affected children are called compound heterozygotes The pedigree does not tell us who carried the mutant alleles in generations I and II For subsequent children  Autosomal Recessive A person affected by an autosomal recessive disease can be of either sex and is usually born to unaffected heterozygote parents (both carriers), e.g. Sickle Cell disease, cystic fibrosis. Affected individuals carry 2 mutant alleles, one from each parent This pedigree differs as there is relatedness (consanguinity) III-2 and III-3 are first cousins, and must both be carriers as the have produced affected offspring Since they are related, it is likely that the mutant allele is the same and the affected individuals in generation IV are true homozygotes We can also conclude that the mutant allele must also have been inherited by II-2 and II-4 We cannot determine whether I-1 or I-2 was the original carrier for this family  Cystic Autosomal recessive inheritance Loss of function Fibrosis Gene: cystic fibrosis transmembrane conductance regulator (CFTR) protein - regulates the flow of salt and fluids in and out of the cells characterized by the buildup of thick, sticky mucus symptoms include progressive damage to the respiratory system and chronic digestive system problems. Mucus clogs the airways, leading to severe breathing problems and bacterial infections in the lungs, causing chronic coughing, wheezing, and inflammation. Mucus buildup and infections cause permanent lung damage, including the formation of scar tissue (fibrosis) and cysts in the lungs. Mucus buildup in the pancreas reduces the production of insulin leading to diabetes and prevents digestive enzymes from reaching the intestines leading to malnutrition. used to be a fatal disease of childhood. improved treatments mean that many people with https://ghr.nlm.nih.gov/condition/cystic-fibrosis cystic fibrosis now live well into adulthood.  X-linked inheritance in man Females have 2X chromosomes and males 1X and 1Y Generally, more than 1 copy of any chromosome has severe consequences due to gene dosage effects, e.g. Trisomy 21 causes Downs syndrome, loss of any chromosome is lethal Mechanisms to compensate for extra X chromosome in females – X inactivation (will be covered later) X-linked recessive inheritance – Affected individuals usually male and born to unaffected parents, inheriting the mutation from their mother – No father to son transmission of mutation X-linked dominant inheritance – Affected individuals either male or female, but more females affected – Usually one parent is affected – No father to son transmission of mutation  X-linked recessive inheritance Affected males in generations III and IV have inherited the mutation from female carrier in generation I (I-2) Mutant allele is inherited from mother. If the offspring is female, the risk of being affected is zero, although she has a ½ chance of being a carrier. If the offspring is male, the risk of being affected is ½ Mutant allele is inherited from father. If the offspring is female, the risk of being affected is zero, although she will be a carrier. If the offspring is male, the risk of being affected is zero, as he inherits his X from  X-linked dominant inheritance Each child of an affected parent has a ½ chance of being affected. An affected mother has 50% chance of transmitting the mutation to a male or female child. This is not the case for an affected father as he cannot transmit his X to a son, so all sons will be unaffected. However, his daughters have to inherit his X chrom and therefore inherit the disease. Mutant allele is inherited from mother. If the offspring is female, the Mutant allele is inherited from father. risk of being affected is ½. If the offspring is female, the risk of being If the offspring is male, the risk affected is 100% as she has to inherit the of being affected is ½. mutated X from her father. If the offspring is male, the risk of being affected is zero, as he inherits his X from mother.  Learning Outcome 6. To know and understand how locus, allele and phenotype heterogeneity influence the phenotypes of single gene disorders  Heterogeneity and Variable expression There are other modes of inheritance Pseudo-autosomal and Y-linked Mitochondrial There are uncertainties in mode of inheritance small pedigrees new mutations and mosaicism Heterogeneity in relating phenotypes to underlying mutations – Locus Heterogeneity – Mutational heterogeneity  Locus heterogeneity Clinical phenotype – result of the failure of a pathway involving many genes a defect in any of these genes may result in a similar clinical outcome This means that parents apparently carrying the same recessive disorder may not have affected offspring CARTILAGE A B C D E collagen proteoglycans COMP F G  Locus Heterogeneity: As underlying genes for ‘single gene’ disorders become known, it is clear that many show locus heterogeneity: – Autosomal recessive deafness – Usher syndrome (autosomal recessive forms) Profound hearing loss, vestibular dysfunction, retinitis pigmentosa Caused by mutations at any one of 11 loci – Bardet-Biedl syndrome (PMID 20301537) (autosomal recessive inheritance) Night blindness, tunnel vision, learning disabilities, kidney disease, extra toes/fingers, obesity, gonad abnormalities Caused in mutations in any of at least 15 genes – All regulate cilia function  Locus heterogeneity: deafness Father: Deafness is autosomal homozygous recessive for mutation at DEAF1 Parents are each Homozygous for normal deaf allele at DEAF2 No offspring are deaf! Mother: homozygous for normal 2 different allele at DEAF1 autosomal Homozygous recessive locifor mutant causing allele at DEAF2 deafness, called DEAF1 and DEAF2 Offspring: ALL UNAFFECTED as heterozygous at both N= normal allele What would happen if both parents had loci D= mutant (deaf) different mutations in DEAF1? The normal alleles compensate at each All offspring would be deaf locus,  Locus Heterogeneity: Bardet-Biedl Syndrome Bardet-Biedl syndrome (PMID 20301537) (autosomal recessive inheritance) - Night blindness, tunnel vision, learning disabilities, kidney disease, extra toes/fingers, obesity, gonad Percentages indicate proportion of mutant alleles attributable to the abnormalities indicatedCaused gene lociin mutations in any of at least 15 genes - All regulate cilia function 7 genes account for ¾ of the mutations  Mutational Heterogeneity Molecular pathology – why a genetic change (mutation) results in a clinical phenotype Types of mutation – *deletions -1bp-Mbp’s – *insertions - 1bp-Mbp’s (including gene duplications) – single base substitutions missense = amino acid replaced with different amino acid nonsense = amino acid codon replaced with stop codon‡ *splice shifts = intron/exon splice sites lost or created * may alter reading frame = frameshift mutations ‡ ‡ may activate nonsense mediated mRNA decay  Effects of mutations Gene Promotor exon intron Transcription Primary mRNA Mature AAAAAAAAA….A mRNA Translation Mutational heterogeneity Encodes protein Eg: Strachan & Read Table 9.5  Duchenne muscular dystrophy:understanding the molecular basis of human genetic disorders  Clinical phenotype  60-65% patients have deletions » progressive muscular weakness  5-15% duplications » death in 3rd decade  20-35% small mutations, intron deletions, » mostly males affected but occasionally exon insertions of repetitive sequences females Generally  Frameshift deletions in dystrophin cause  Genetics DMD » X-linked disorder » no detectable dystrophin expression - » mendelian inheritance severe clinical symptoms » Recessive  Frame neutral deletions in dystrophin cause » Gene product = DYSTROPHIN BMD » Mutations cause – expression of a lower mwt form of – Duchenne (severe) dystrophin - – Beckers (mild) less severe symptoms  Penetrance Penetrance – Of a single gene disorder is the probability that a person with the mutant allele will express the disease phenotype – Dominant conditions – show in heterozygotes, therefore by definition, show 100% penetrance Not always the case as sometimes a person with the mutation does not show the disease = non penetrance Non penetrance – due to other effects (epigenetic, other genes, environmental) modifying the expression of the phenotype Late onset disorders Probability that an individual with – Age-related penetrance HD allele will develop symptoms means that the disease phenotype does not show by a certain age until later in life – disease first manifests in adult – Due to accumulation of harmful products, gradual process of cell death e.g. Huntington Disease The CAG repeat encodes a polyglutamine tract in the protein. polyglutamine tract causes the protein to aggregate Neuronal cell death.  Variable Expressivity Some Mendelian disorders, usually dominant, show variable expression in different family members Non-penetrance – The extreme endpoint of variable expressivity Variable expressivity – Due to the influences of other genes, epigenetics, environment Tuberous Sclerosis Family (AD disorder caused by mutation in eith TSC1 or TSC2 – together make a tumor suppressor protein causing benign tumours in multiple organs)  Learning outcomes 1. To understand how mutations cause pathology. 2. To be able to describe and discriminate between loss of function mutations, gain of function mutations, dominant negative mutations and mutations that affect gene dosage. 3. To understand genetic pedigree analysis and terminology 4. To know and recognise the expected mendialian inheritance patterns in humans 5. To understand how autosomal dominant and autosomal recessive alleles are inherited 6. To know and understand how locus, allele and phenotype heterogeneity influence the phenotypes of single gene disorders Chapter 5 Single-Gene Disorders: Inheritance Patterns, Phenotype Variability, and Allele Frequecies