Non-Mendelian Genetics I and II Notes PDF

Non-Mendelian Genetics I and II Dayna Wolff, PhD Department of Pathology and Laboratory Medicine [email protected] OBJECTIVES: After studying this unit you should be able to: 1. Describe the relationship between triple repeats and disease (normal, premutation, full mutation; know ranges for Fragile X,...

Non-Mendelian Genetics I and II Dayna Wolff, PhD Department of Pathology and Laboratory Medicine [email protected] OBJECTIVES: After studying this unit you should be able to: 1. Describe the relationship between triple repeats and disease (normal, premutation, full mutation; know ranges for Fragile X, Huntington, myotonic dystrophy) 2. Identify triplet repeat disorders and know key clinical features (Fragile X, Huntington, myotonic dystrophy) 3. Define genomic imprinting; biologic mechanism responsible for imprinting 4. Describe how imprinting explains Prader-Willi and Angelman syndromes; describe basic clinical features of these disorders 5. Identify 3 mechanisms that result in Prader-Willi and 4 for Angelman 6. Define X inactivation 7. Describe the relationship between skewed X inactivation and human disease 8. Describe mitochondrial inheritance and compare/contrast homoplasmy with heteroplasmy; specify two mitochondrial disorders 9. Explain the conceptual basis of analyzing genetic and environmental interaction in the causation of disease 10. Explain the principles of multifaction inheritance and the threshold model expectation 11. Calculate heritability 8/31/2022 Non-Mendelian Genetics Daynna Wolff [email protected] Objectives The student should be able to:         Describe the relationship between triple repeats and disease (normal, premutation, full mutation; know ranges for Fragile X, Huntington, myotonic dystrophy) Identify triplet repeat disorders and know key clinical features (Fragile X, Huntington, myotonic dystrophy) Define genomic imprinting; biologic mechanism responsible for imprinting Describe how imprinting explains Prader-Willi and Angelman syndromes; describe basic clinical features of these disorders Identify 3 mechanisms that result in Prader-Willi and 4 for Angelman Define X inactivation Describe the relationship between skewed X inactivation and human disease Describe mitochondrial inheritance and compare/contrast homoplasmy with heteroplasmy; specify two mitochondrial disorders 1 8/31/2022 What is non-Mendelian?  Does not fit classical patterns of inheritance – not simple single gene  Triplet repeat disorders  Genomic imprinting  Mosaicism  Mitochondrial inheritance  Skewed X inactivation Case report:  Trevor was born at term following an uneventful pregnancy. At birth, he was noted to be severely hypotonic; had difficulty breathing and was placed on a vent; had a poor suck and needed an NT tube placed for nutrition Diagnosis of myotonic dystrophy made shortly after birth; evaluation of family members revealed that the mother and grandmother also had MD Cataract surgery, myotonia Weak facial muscles, Cataract via slit lamp, myotonia Not variable expression of symptoms, but anticipation. Anticipation = increasing severity of disease in successive generations. 2 8/31/2022 Triplet Repeats Tandem repeats of a series of three nucleotides within the DNA sequence  Trinucleotide repeats are found within coding regions or within regulatory regions of genes  Too many copies of a trinucleotide repeat (expansion) can lead to disruption of protein function or gene expression and result in clinical disease  Example of Triple Repeat disorder Myotonic Dystrophy (DMPK1 gene)    Inheritance looks like AD, but there is anticipation Progressive muscle deterioration CTG repeat in 3’ UTR Normal = 5–34 repeats  Premutation = 35-49  Penetrance >50   Expansions occur mostly during maternal meiosis  expansion to congenital form occurs maternally 3 8/31/2022 Correlation of Phenotype and CTG Repeat Length in Myotonic Dystrophy Phenotype Clinical Signs CTG Repeat Size Age of Onset Average Age of Death Mutable normal (premutation) None 35-49 NA NA 50-~150 20-70 yrs normal life span ~100-~1,000 10-30 yrs 48-55 yrs Mild Classic Congenital •Cataracts •Mild myotonia •Diabetes mellitus •Weakness •Myotonia •Cataracts •Balding •Cardiac arrhythmia •Infantile hypotonia •Respiratory deficits •Intellectual disability >1,000 3 •Classic signs in adults Birth to 10 yrs 45 yrs 4 In: GeneReviews® [Internet]. Seattle (WA): University of Washington, Seattle; 1993; 1999 Sep 17 [updated 2021 Mar 25]. PMID: 20301344 Anticipation: not typical for Mendelian disorders    Observation of earlier disease onset and/or increased severity with successive generations Associated with trinucleotide repeat diseases Explained by trinucleotide repeat expansion in offspring 4 8/31/2022 striatal atrophy Trinucleotide Repeat Disease  Huntington Disease:  Progressive neuromuscular disease  CAG repeat in protein coding region (glutamine)  Expands preferentially through male meiosis  Inherited similar to AD  But there is an earlier onset of disease with each successive generation Reduced Penetrance 27 to 35 36 to 39 40 or > Late onset = 36-50 repeats Juvenile = >60 repeats Trinucleotide Repeat Disease  Fragile X syndrome:  Most common form of inherited mental impairment  CGG repeat in 5’ UTR; promotor  expands exclusively through female meiosis  Most like X-linked dominant inheritance 5 8/31/2022 Fragile X syndrome     Affects more males than females Clinical features include: mental impairment, coarse facial features, large ears, hypermobile joints and postpubertal macroorchidism in males So named due to the observation of a “fragile site” within the X chromosome when cells are cultured in folic acid deficient media Both males and females are affected, but females tend to be affected less often and to have milder presentation due to X inactivation Triplet Repeat The Fragile X gene (FMR1) contains a CGG repeat within the 5’ UTR/promotor region  Triplet repeat thresholds:   <50 CGG repeats = normal  50 – 200 repeats = pre-mutation  >200 repeats = abnormal (affected)  How does this triplet repeat expansion lead to disease? 6 8/31/2022 Fragile X Etiology    Expanded CGG repeats are a target for methylation Methylation of the FMR1 promotor region leads to silencing of FMR1 expression and manifestation of disease Molecular methods are now used to determine the number of CGG repeats and methylation status for diagnosis of Fragile X syndrome and detection of pre-mutation carriers Epigenetics Modification of chromatin  Methylation = gene control (on/off)  Examples of epigenetic control   Totipotent cell -> differentiation  Tissue-specific gene expression  X-inactivation  Imprinting 7 8/31/2022 Genomic Imprinting  Same genomic deletion, two different syndromes Prader-Willi Angelman How can this phenomenon be explained? Imprinting    Differential expression of genes depending on the parent from which they are inherited Only one copy of imprinted genes are active, either the maternal or paternal copy Loss of the single active copy of such genes leads to disease 8 8/31/2022 Imprinted Genes in the PWS/AS region PWS CEN ZNF127 NDN IC AS SNRPN IC IPW PAR-5 UBE3A PAR-1 GABRA5 P TEL GABRB3 GABRG3 Imprinting control region Expression Pat + + ++ +++ -* +++ + Mat - - +- -- + +++ + Adapted from Cassidy,S et al. 2000 AJMG 97:136-146 Regulation of Imprinting  A person with normal (maternal and paternal) chromosomes must pass on appropriately imprinted chromosomes to offspring  Imprinting is re-set during gametogenesis  Imprinting control region is “re-set” button Imprinting is REVERSIBLE: it must be reset during meiosis in the germ cells 9 8/31/2022 Mechanisms that lead to disease (5%) Etiology of PWS/AS  Mechanism of loss of gene expression: Deletion  Uniparental Disomy  Imprinting center  Single gene mutation  Other  PWS AS 70-75% 25% 1-5% <1% 70-75% 5% 1-5% 10% 10% Williams et al., AJMG 2001; 101:59-64 10 8/31/2022 Mechanism for Uniparental Disomy Trisomy Rescue Meiotic nondisjunction Random loss of father’s chromosome during early cell divsions Normal disjunction Prader-Willi is a contiguous gene disorder Phenotype caused by loss of function of multiple imprinted genes in the region  Several candidate genes but the it is not fully understood what genes contribute to phenotype  11 8/31/2022 Another example of epigenetics: X-inactivation   Several males in this family were diagnosed with ornithine transcarbamylase deficiency (urea cycle disorder); three died in infancy; proband’s cousins are being treated, but have developmental delay Proband presents with severe attack of vomiting, lethargy and lack of appetite ? What is the apparent inheritance pattern? How could this female have an X-linked recessive disorder? X Inactivation in Females Lyon Hypothesis  One X chromosome in female mammals is inactivated to maintain dosage compensation random process occurs early in embryogenesis silences majority of genes on one X  Pseudoautosomal region remains active inactivation status is maintained in cell lineage 12 8/31/2022 Get out of slide show and double click here - > x_inactivation-lg.wmv X Chromosome Inactivation  Three Pseudoautosomal region – pairs with the Y chrom Remains active steps: initiation of process XIST gene XIST gene propagation of signal maintenance of inactivation 13 8/31/2022 Spread of X inactivation signal Genes Unmethylated And active Most genes Methylated And inactive XIST RNA Barr body Non-random X inactivation Most or all cells - either the paternal or maternal X inactive  Why?   Stochastic variation  Carrier of X-linked disease allele  Carrier of structurally abnormal X About 50:50 ratio Paternal/Maternal Skewed - 95% maternal active CompleteNon-random 100% maternal active Selection against Mutant cells 14 8/31/2022 Example of skewing of X inactivation “unfortunate Lyonization” X-linked Recessive Disorders in Females Non-random or extremely skewed X inactivation  45,X karyotype  Affected father and carrier mother (common disorder, like color blindness)  Any questions about X-inactivation before we move on? 15 8/31/2022 Consider this pedigree… What do you notice about who transmits the gene?  What is this inheritance pattern associated with?  Mitochondrial Inheritance  Mitochondria contain their own genome separate from nuclear DNA (mtDNA)  Many mitochondrial genes are involved in energy production (oxidative phos pathway) 16 8/31/2022 Mitochondrial Inheritance Sperm contain few mitochondria none of which are transmitted to offspring  Therefore, mitochondria and mitochondrial diseases are only inherited maternally  Mitochondria Inheritance Since mitochondria lack DNA repair mechanisms, the mutation rate of mtDNA is about 10-fold higher than nuclear DNA  Each cell contains a population of mtDNA molecules, therefore a mix of normal and abnormal (mutated) mtDNA may exist (heteroplasmy)  17 8/31/2022 Mitochondrial Inheritance Normal mitochondria Abnormal mitochondria 70% mutant mitochondria = ? severe symptoms 30% mutant mitochondria = ? mild symptoms Homoplasmic cell Heteroplasmic cells All normal mitochondria Some mutant and some normal mitochondria Adapted from www.mda.org Why is there variability in phenotype with mitochondrial disorders? www.mda.org 18 8/31/2022 Mitochondrial Inheritance Mitochondrial diseases often manifest when the proportion of mutant mtDNA reaches a threshold  Since mitochondria and mtDNA function largely in energy production, organs with high energy demand are most often affected  Common symptoms include: epilepsy, dementia, ataxia, vision loss, hearing loss, muscle weakness, heart failure  Mitochondrial myopathies MELAS: mitochondrial encephalomyopathy, lactic acidosis and stroke-like episodes: : childhood to early adulthood : recurrent stroke-like episodes in the brain, migraine-like headaches, vomiting and seizures, and can lead to permanent brain damage, general muscle weakness, exercise intolerance, hearing loss, diabetes and short stature. MERRF: myoclonus epilepsy with ragged red fibers: : late childhood to adolescence : myoclonus (muscle jerks), seizures, ataxia and muscle weakness, hearing impairment and short stature. 19 8/31/2022 Somatic Mosaicism: presence of different cell lines in one individual Chromosomal mosaicism Active X Chromosome mosaicism Mitichondrial mosaicism Consider this pedigree…  What is the inheritance pattern? Both children had Osteogenesis Imperfecta Type II Autosomal Dominant inheritance How can this be? 20 8/31/2022 Germline Mosaicism   More than one child with an autosomal dominant disorder – parent not affected Mosaicism in germ cells; no phenotype in parent but can pass along mutant gene How does mosaicism arise? 21 8/31/2022 Non-Mendelian Genetics Review  Non-Mendelian – does not follow Mendel’s rules of inheritance  Triplet repeat disorders: premutation carriers  Imprinting: differential gene expression based on parental origin  X inactivation: random inactivation of one X  Mitochondrial inheritance: maternal only inheritance  Mosaicism: multiple cell lines in same individual Multifactorial Inheritance Genetic Basis of Common Diseases Thompson and Thompson, 7th Edition, Chapter 8 Daynna Wolff 22 8/31/2022 Objectives A student will be able to:  Explain the conceptual basis of analyzing genetic and environmental interaction in the causation of disease  Explain the principles of multifactorial inheritance and the threshold model expectation  Calculate heritability Multifactorial Inheritance   Multifactorial inheritance means that the trait under consideration is caused by an interaction of gene(s) + environment Most physiological traits and most diseases are “multifactorial”       Birth defects Autism Cancer Mental illness Diabetes Alzheimer disease 23 8/31/2022 Complex phenotypes of multifactorial diseases  Qualitative  Disease is present or absent Breast cancer  Venous thrombosis  Cleft lip/cleft palate   Quantitative  Measurable physiological or biochemical quantities Height  Blood pressure  Historical Perspective  Francis Galton (Darwin’s cousin) study correlations between blood relatives for traits such as Intelligence  Height   Developed method for measuring “heritability” of traits 24 8/31/2022 Conceptual Basis of Heritability If a trait is “genetic” relatives should be more similar than non-relatives with respect to those traits  The degree of similarity should be proportional to the genes they have in common  Degrees of Relationship Relationship Proportion of genes shared 100% MZ twins First degree relatives: sibs, DZ twins, parents, children Second degree relatives: half-sibs, uncles, aunts, nephews, nieces Third degree relatives: first cousins, half nieces and half nephews 50% 25% 12.5% 25 8/31/2022 Heritability  For traits that are dichotomous we look for “concordance and discordance”  For traits that are continuously distributed on a Gaussian curve we measure the statistic – “correlation coefficient” and relative risk assessment Threshold Model Liability or predisposition to disease is due to additive effects of multiple predisposing genes and protective genes There is no single dominant gene Disease manifests when the liability exceeds a hypothetical “threshold” First proposed to explain the inheritance patterns of certain congenital malformations Applies to most common diseases as well 26 8/31/2022 The Threshold Model Liability (predisposition) is assumed to show a Gaussian distribution Disease manifests when liability exceeds a hypothetical threshold For some malformations and diseases males and females have different thresholds Threshold Model Expectations Higher the number of affected individuals in a family, greater is the liability and greater the recurrence risk. This is in contrast to Mendelian disorders where risk is the same - 50% or 25% - for each new “at-risk” pregnancy Cleft lip and cleft palate Cleft lip only 27 8/31/2022 Evidence from studies of Cleft Lip and Cleft Palate Incidence (%) General population One parent affected One sib affected One sib and one parent affected Both parents affected One sib and both parents affected 0.1 3.0 3.0 11.0 34.0 40.0 Threshold Model Expectations More severe defect suggests higher liability and higher recurrence risk For example bilateral cleft palate is more severe defect than a unilateral cleft 28 8/31/2022 Effect of Severity on Recurrence Risk Risk to siblings (%) Bilateral cleft lip + cleft palate 5.7 Unilateral cleft lip + cleft 4.2 palate Unilateral cleft lip 2.5 Threshold Model Expectations For sex-influenced traits: proband of the less commonly affected sex indicates that the parents have accumulated greater liability (predisposing genes) therefore, a higher recurrence risk is predicted for future offspring 29 8/31/2022 Congenital Pyloric Stenosis: An example of sex-influenced trait  Associated with hypertrophy of the pyloric sphincter. Infants present with projectile vomiting at about six weeks of age  Overall incidence 3 per 1,000 live births Males 1 in 200; Females 1 in 1,000  Males are 5 times more likely to have this condition than females The Threshold Model - pyloric stenosis Liability (predisposition) shows a Gaussian distribution Lower threshold in males 30 8/31/2022 Recurrence Risk (%) for Congenital Pyloric Stenosis Carter, C.O. Br.Med.Bull 32:21-26,1976 Note the differences between populations: gene frequencies and environmental factors influence risk, in addition to sex of proband Male Probands London Female Probands Belfast London Belfast Affected 3.8 Brothers 9.6 9.2 12.5 Affected 2.7 Sisters 3.0 3.8 3.8 Threshold Model Expectations Recurrence risk drops off precipitously for relatives beyond the first degree indicating absence of a single major gene influence In contrast, for dominant and recessive Mendelian traits, risk is precisely defined by the segregation of the disease allele 31 8/31/2022 Recurrence Risk and Degree of Relationship Condition Degree of relationship 1st 2nd 3rd Incidence Cleft lip/palate Club foot Cong. hip dysplasia Infantile autism 4.0 2.5 5.0 4.5 0.7 0.5 0.6 0.1 0.3 0.2 0.4 0.05 0.1 0.1 0.2 0.04 Twin Studies  Monozygotic twins share 100% of their genes, expect 100% concordance if a trait is determined exclusively by genes  Dizygotic twins share 50% of their genes, expect 50% concordance  Any deviation from these expectations are “non-genetic” or environmental influences 32 8/31/2022 Estimating Heritability (h2) For purely genetic traits heritability is 1.0 h2 = 2(CMZ - CDZ) = 1.0 CMZ = concordance rate for MZ twins = 1.0 CDZ = concordance rate for DZ twins = 0.5 Heritability of Some Traits h2 = 2(CMZ - CDZ) Condition Alcoholism BMI Height IQ MZ 0.60 0.95 0.94 0.76 DZ heritability h2 0.30 0.60 0.53 0.84 0.44 1.0 0.51 0.50 33 8/31/2022 Heterogeneity of the Phenotype Affects Heritability Estimates Condition MZ DZ h2 Diabetes Type I 0.35-0.50 0.05-0.10 0.6-0.8 Type II 0.70-0.90 0.25- 0.40 0.9-1.0 Clinical Features of Diabetes Types I & II Feature Type I Age of onset (years) Usually <40 Insulin production None Insulin resistance No Autoimmunity Yes Obesity Not common MZ-twin concordance 0.35- 0.50 Sibling recurrence risk 1% - 6.0 % Type II Usually >40 Partial Yes No Common 0.90 10% - 15% 34 8/31/2022 Limitations of Twin Studies MZ and DZ twins may be reared differently MZ twins share their environment more than DZ twins Solution: Compare MZ twins reared together to those reared apart to mitigate “shared environment bias” Epidemiologic Evidence for Genetic vs. Environmental Influences Ethnicity/race Stronger genetic component e.g. Diabetes in Pima Indians Socio-economic status Environmental exposures, nutritional factors e.g. NTDs Clustering within families Cleft Palate Gender differences e.g. Congenital Hip Dysplasia Congenital pyloric stenosis 35 8/31/2022 Questions? Please feel free to email questions to me directly and I will do my best to answer in a timely fashion.  Also, you can call my office at 843-7923574.  If you are struggling with concepts, we can set up a time to meet in my office.  36