Lecture 9: The Molecular, Biochemical, and Cellular Basis of Genetic Disease PDF

1 Heterogeneities Heterogeneity Alleles Locus/Loci Phenotype Allelic Heterogeneity 2+ 1 1 >200 alleles β-globin β-Thalassemia Multiple alleles BRAC...

1 Heterogeneities Heterogeneity Alleles Locus/Loci Phenotype Allelic Heterogeneity 2+ 1 1 >200 alleles β-globin β-Thalassemia Multiple alleles BRACA1 Breast Cancer Locus Heterogeneity 2+ 1 Α-globin and β-globin Thalassemia BRCA1 and BRCA2 Breast Cancer Phenotypic Heterogeneity 1 2+ Sickle Cell Disease and β- β-globin Thalassemia Breast cancer and ovarian BRCA1 cancer  2 THE MOLECULAR, BIOCHEMICAL AND CELLULAR BASIS OF GENETIC DISEASE BMSC711: Medical Genetics Nicholette D. (Palmer) Allred, PhD [email protected] 3 4 5  6 Learning Objectives Examine the molecular and biochemical basis of genetic disease beyond hemoglobinopathies. Explore variants among classes of proteins. Illustrate disease mechanisms with well-known disorders.  7 Disease Due to Variants in Different Classes of Proteins To date, pathogenic variants in over 4500 genes have been associated with a clinical phenotype Thompson & Thompson, 2024 Expected to reach ~20K https://omim.org/statistics/geneMap  8 Protein Classes Housekeeping Proteins Specialty Proteins Present in virtually every Found in only one or a cell limited number of cell types Fundamental roles in Unique functions that structure and function contribute to individuality https://www.proteinatlas.org/  9 Disease Due to Variants in Different Classes of Proteins Diseases Involving Enzymes - Enzymopathies Defects Defects in in Receptor Receptor Proteins Proteins Transport Transport Defects Defects Disorders Disorders of of Structural Structural Proteins Proteins Neurodegenerative Disorders  10 Disease Due to Variants in Different Classes of Proteins Diseases Involving Enzymes - Enzymopathies PKU, Tay-Sachs Defects in Receptor Proteins Transport Defects Disorders of Structural Proteins Neurodegenerative Disorders  11 Disease Involving Enzymes Enzymopathies: Aminoacidopathies - Hyperphenylalaninemias tetrahydrobiopterin Phenylketonuria (PKU) Results from variation in PAH  negatively impacts degradation of phenylalanine 1 in 2900 individuals PAH is expressed in the liver; Accumulation damages developing CNS Discovered in 1934 – first genetic defect to cause intellectual disability Clinical Presentation – normal at birth, failure to obtain developmental milestones, microcephaly, hyperactivity, seizures and learning disabilities Phenylalanine is an essential amino acid present in, but not limited to, fish, pork, cheese and breast milk Management?  12 Disease Involving Enzymes Enzymopathies: Aminoacidopathies - Hyperphenylalaninemias Phenylketonuria (PKU) >1000 mutations in PAH tetrahydrobiopterin  13 Allelic Heterogeneity  14 Disease Involving Enzymes Enzymopathies: Aminoacidopathies - Hyperphenylalaninemias Allelic Heterogeneity (PAH mutations) 3370* mutations worldwide found among patients with hyperphenylalanine associated with PKU, variant PKU and non- PKU China, Korea, Japan Compound Heterozygotes *http://www.biopku.org/home/pah.asp  15 Disease Involving Enzymes Enzymopathies: Lysosomal Storage Diseases Lysosomes are membrane-bound organelles containing a variety of hydrolytic enzymes (degradation) Variants in hydrolases result in accumulation of substrates in the organelle More than 50 lysosomal hydrolase or lysosomal membrane transport deficiencies have been described Example. Tay-Sachs Disease  Neurologist 16 Ophthalmologist Disease Involving Enzymes Enzymopathies: Lysosomal Storage Diseases – Tay-Sachs Disease Neuronal cytoplasmic membrane Glycolipid https://www.frontiersin.org/articles/10.3389/fphys.2018.01663/full  17 Disease Involving Enzymes Enzymopathies: Lysosomal Storage Diseases – Tay-Sachs Disease Pseudodeficiency Alleles – A clinically benign allele that has a reduction in functional activity detected by in vitro assays but that has sufficient activity in vivo to prevent insufficiency Hex A Pseudodeficiency Alleles Individuals have a low level of hex A activity (in leukocytes, about 20% that of controls) that is still adequate to prevent the accumulation of the GM2 ganglioside substrate in the brain Impact on screening Complicate prenatal diagnosis because a pseudodeficient fetus may be incorrectly diagnosed as affected Indicates that comparable alleles may exist at other loci and may cause confounding  18 Disease Due to Mutations in Different Classes of Proteins Diseases Involving Enzymes Defects in Receptor Proteins Familial Hypercholesterolemia Transport Defects Disorders of Structural Proteins  19 Receptor Proteins Familial Hypercholesterolemia – LDL receptor Familial Hypercholesterolemia Group of metabolic disorders, i.e. hyperlipoproteinemias Characterized by elevated levels of plasma lipids (cholesterol, triglycerides, or both) carried by apolipoprotein B (apoB)-containing lipoproteins Abnormalities in 4 genes lead to familial hypercholesterolemia Typical LDL Pattern of Effect of Disease- Cholesterol Level Mutant Gene Product Inheritance Causing Mutations (Normal Adults: ≈120 mg/dL) Heterozygotes: 350 mg/dL LDL receptor Autosomal dominant Loss of function Homozygotes: 700 mg/dL Heterozygotes: 270 mg/dL Apoprotein B-100 Autosomal dominant* Loss of function Homozygotes: Increased LDL in the circulation leads to premature atherosclerosis 320 mg/dL and increased Autosomal ARH adaptor protein risk for recessive heart attack Lossand † stroke of function Homozygotes: 470 mg/dL J Heterozygotes: Am Coll Cardiol. 2014 May 20;63(19):1935-47. PCSK9 protease Autosomal dominant Gain of function  20 Defects in Receptor Proteins Familial Hypercholesterolemia: Mutations that alter function of the LDLR Over 1100 mutations have been identified in LDLR Chr. 19  21 Defects in Receptor Proteins Familial Hypercholesterolemia: Mutations that alter function of the LDLR Most Common Null Alleles Improper Folding Internalization  22 Defects in Receptor Proteins Familial Hypercholesterolemia: A Genetic Hyperlipidemia Familial Hypercholesterolemia resulting from LDLR mutations is an autosomal semidominant trait Both homozygous and heterozygous phenotypes Gene dosage – earlier manifestation and severity Homozygotes – significant CAD Obligate Heterozygotes – one of the most common single gene disorder, i.e. 2 per 1000  23 Defects in Receptor Proteins The PCSK9 Protease, a Potential Drug Target for Lowering LDL Cholesterol Proprotein Convertase Subtilisin/Kexin Type 9 (PCSK9) targets the LDLR for lysosomal degradation Gain-of-function Variants Cause autosomal dominant familial hypercholesterolemia (rare) Increase in PCSK9 activity  reduced levels of LDLR  increased levels of LDL in circulation  increased risk for CHD Loss-of-function Variants Decrease in PCSK9 activity  increased levels of LDLR  decreased levels of LDL in circulation  decreased risk for CHD Absence of PCSK9 has no adverse clinical consequences  24 Defects in Receptor Proteins The PCSK9 Protease, a Potential Drug Target for Lowering LDL Cholesterol Some PCSK9 variants protect against CHD LDL Cholesterol Sequence Level Impact on Incidence of Population Frequency Variant (Normal ≤ Coronary Heart Disease ≈100 mg/dL) Rare genetic compounds, Null or dominant Unknown, but likely to one dominant negative 7-16 mg/dL negative alleles greatly reduce risk heterozygote Tyr142Stop or African American Mean: 28% 90% reduction Public Health Relevance Mean: 15% Cys679Stop heterozygotes: 2.6% (38 mg/dL) Arg46Leu White heterozygotes: 3.2% 50% reduction Modest but lifelong reductions (20 mg/dL) in plasma LDL cholesterol levels of 20 to 40 mg/dL would significantly decrease the incidence of coronary heart disease in the population Investigation of rare genetic disorders can lead to important new knowledge about the genetic contribution to common genetically complex diseases  25 Disease Due to Mutations in Different Classes of Proteins Diseases Involving Enzymes Defects in Receptor Proteins Transport Defects Cystic Fibrosis Disorders of Structural Proteins  26 Transport Defects Cystic Fibrosis Autosomal recessive Presentation: principal effects in lungs and exocrine pancreas and increase sweat sodium and chloride concentration Incidence: 1 per 2,500 white births 1 per 15,000 African American births 1 per 31,000 Asian Americans births  27 Transport Defects Cystic Fibrosis: Molecular Defects chr 7 27 membrane spanning domain stability/activation Null Alleles Folding; can not exit ER  28 Transport Defects Cystic Fibrosis Genocopy Genocopy – Similar phenotypes show varying genotypes on different loci CFTR is the only gene associated with classic CF Mutations in the epithelial sodium channel gene (SCNN1) CF-like pulmonary infections, less severe intestinal disease, elevated sweat chloride levels  29 Disease Due to Mutations in Different Classes of Proteins Diseases Involving Enzymes Defects in Receptor Proteins Transport Defects Disorders of Structural Proteins DMD  30 Disorders of Structural Proteins The Dystrophin Glycoprotein Complex Duchenne Muscular Dystrophy (DMD) Presentation: Muscle weakness at 3-5 years of age, heart and respiratory muscles also are affected as early teens, elevated creatine kinase, moderate decreased in IQ Incidence: 1 in 3300 live male births Inheritance Pattern: X-linked Rec Mutation Rate: 10-4  31 Disorders of Structural Proteins The Dystrophin Glycoprotein Complex: Duchenne Muscular Dystrophy Dystrophin Gene (DMD) is the largest known human gene 2300kb or 1.5% of the X chromosome 79 exons (14kb transcript) and 7 tissue-specific promoters Highest levels of protein in skeletal and cardiac muscle spacer linkage to the protein-protein actin cytoskeleton interactions  32 Phenotypic Heterogeneity DMD and BMD J Med Genet. 2016 Mar;53(3):145-51.  33 DMD – more severe, frameshift variant/premature stop BMD – less severe, in-frame variant https://www.ncbi.nlm.nih.gov/pmc/articles/PMC5006996/ 34 35 36  37 Learning Objectives Examine the molecular and biochemical basis of genetic disease beyond hemoglobinopathies. Reviewing mutations by protein class provided an introduction to multiple disease states, e.g. familial hypercholesterolemia, cystic fibrosis, etc. Explore mutations among classes of proteins. Multiple classes of proteins, e.g. enzymes, receptors, transporters were discussed with examples. Illustrate disease mechanisms with well-known disorders. Examples included familial hypercholesterolemia, cystic fibrosis, and Alzheimer’s Disease which are common in the population.  38 Questions 1. Consider variants discussed in the last lecture. 2. Phenocopy vs genocopy? 3. Speculation 4. Ignore B. 5. Speculation 6. What causes DMD? 7. Concepts from Dr. Howard’s lecture. 8. ND 9. Current and previous lecture(s) concepts. 10. ND 11. ND 12. Examples 13. ND 14. Consider variants discussed in the last lecture.