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PATH TRANS 1.5 07/09/24 GENETIC DISORDERS ALBERT JOSEPH LUPISAN, MD ○ Deletions and insertions...

PATH TRANS 1.5 07/09/24 GENETIC DISORDERS ALBERT JOSEPH LUPISAN, MD ○ Deletions and insertions OUTLINE ○ Translocations* I. Introduction to Genetic Disorders ○ Copy number changes* a. Mutations ○ Trinucleotide repeats II. Mendelian Disorders * These aren’t mutations but the coding genes undergo structural a. AD Diseases variations b. AR Diseases c. Codominance d. X-linked Disorders 🩺 There are changes in protein-coding genes other than changes in the DNA sequences, which are represented by e. Examples of Mendelian Disorders III. IV. Complex Multigenic Disorders Chromosomal Disorders 🩺 copy-number changes and translocation DNA alterations usually result in either the non-expression of V. Single-Gene Disorders with Non-Classic Inheritance a. Disorders Caused by Trinucleotide-Repeat Mutations 🩺 proteins or he expression of defective or harmful ones One of the products is there is impaired regulation of gene expression because of the expression of RNAs b. Disorders Caused by Mutations in Mitochondrial Genes c. Disorders Associated with Genomic Imprinting d. Disorders Associated with Gonadal Mosaicism POINT MUTATIONS VI. References Missense mutations: single base is substituted with a different base; therefore, alters the code/different codon resulting into LEGEND different amino acid 1 ○ Conservative1 ⭐ ❓ 🩺 📖 🩺 Must Know Good to Know Lecturer Book Silent/ No disease → new amino acid is biochemically similar Causes little change in the protein function/ no pathologic effect I. INTRODUCTION TO GENETIC DISORDERS 🩺 ○ Nonconservative1 New amino acid is biochemically different🩺 Sickle Cell disease: Glutamate → valine Results in a less stable hemoglobin molecule that 🩺 makes the RBCs sickle shape under stressful conditions Nonsense mutations ○ Change of an amino acid codon to a chain terminator or stop codon is produced1 Translation → abruptly stops, so the protein product is 🩺 prematurely shorter than normal, rendering it functionally useless Figure 1. Terminology 2 🩺 Similar to a deletion of a DNA sequence and is seen in Abnormalities arises from the genome many genetic disorders ○ Usual characteristics associated are hereditary ○ Deletion of protein segments Hereditary/ Familial: Derived from one’s parents, transmitted in Some Beta Thalassemias the germline Congenital: Present at birth DELETIONS & INSERTIONS All hereditary/ familial disorders are genetic, while not all congenital diseases are genetic Subtraction or addition of base pair in the DNA respective Not all genetic diseases are hereditary/ familial Base pairs involved are a multiple of 3 ○ Genetic abnormality can arise during gametogenesis or early ○ During translation, there will be additional or less amino fetal development acids in the translated protein but the rest of the protein is 🩺 Not all genetic diseases are congenital translated correctly → it may or may not have a significant ○ Some of them present later in life (adulthood) effect on the protein’s function Genetics disorders are attributable to mutations ○ Without frameshift → reading frame is intact Base pairs involved are not a multiple of 3 🩺 ○ There is a shift in the way the sequence is translated → A. MUTATIONS significantly altered protein compared to the intended one Permanent changes in the DNA ○ With frameshift (more severe) → altered reading frame Germ cell mutations → offsprings → Inherited diseases Somatic cells mutations does not cause hereditary diseases1 Can affect all levels of gene expression Categories ○ Point mutations within exons ○ Mutations within introns [GROUP 12] Arcenal, Bersabe, Macalintal, Tang, Velasco 1 of 12  II. MENDELIAN DISORDERS A. AUTOSOMAL DOMINANT (AD) DISEASES Virtually all are caused by single-gene mutations with large effects One copy of the mutated allele is enough to produce a pathology 🩺 Pleiotropism and the other normal allele cannot compensate for that loss of ○ One mutant gene, multiple end effects function Mutations in only one gene accounts for all the Loss of one copy of the gene cannot be compensated by the 🩺 associated phenotypic changes and clinical other normal copy manifestations More commonly loss-of-function, but some are gain-of-function Genetic heterogeneity (e.g. Huntington disease) 🩺 ○ Different mutant genes, same end effect ○ Profound childhood deafness Table 2. Autosomal Dominant Disorders 1 System Disorder Nervous Huntington disease Neurofibromatosis Myotonic dystrophy Tuberous sclerosis Urinary Polycystic kidney disease Gastrointestinal Familial polyposis coli Hematopoietic Hereditary spherocytosis Von Willebrand disease Skeletal Marfan syndrome Ehlers-Danlos syndrome (some variants) Osteogenesis imperfecta Achondroplasia Metabolic Familial hypercholesterolemia Acute intermittent porphyria Figure 2. Mendelian Patterns of Inheritance 2 Mutations involving single genes typically follow one of three B. AUTOSOMAL RECESSIVE (AR) DISEASES 🩺 patterns1 Require homozygous inheritance of both mutant genes in order to ○ Autosomal dominant produce disease ○ Autosomal Recessive “Margin of safety” → requirement for homozygosity to produce ○ X-linked disease 🩺 ○ A single functioning allele is enough to compensate for the loss of function in the other affected allele Most familiar AR diseases affect genes for enzymes but some 🩺 affect genes for structural genes as in the case of globin gene mutations like in thalassemias Some code for structural proteins (e.g., sickle cell anemia and thalassemias) Table 3. Autosomal Recessive Disorders2 System Disorder Metabolic Cystic fibrosis Phenylketonuria Galactosemia Figure 3. Autosomal Dominant vs Autosomal Recessive 2 Homocystinuria 🩺 Left punnett squares: Autosomal dominant pattern of inheritance Lysosomal storage diseases α1-Antitrypsin deficiency ○ Affected Parent + Unaffected Parent = a roughly equal Wilson disease proportion of affected and unaffected offsprings Hemochromatosis Glycogen storage diseases 🩺 Right punnett squares: Autosomal recessive pattern of inheritance Hematopoietic Sickle cell anemia ○ 2 unaffected parents = offspring affected with a disease, Thalassemias although most of the other children are unaffected Endocrine Congenital adrenal hyperplasia Skeletal Ehlers-danlos syndrome (some variants) Alkaptonuria Table 1. Autosomal Dominant vs. Autosomal Recessive 2 Nervous Neurogenic muscular atrophies Autosomal Dominant (AD) Autosomal Recessive (AR) Friedreich ataxia At least one parent is affected Both parents are usually Spinal muscular atrophy unaffected Variable penetrance Commonly with complete C. CODOMINANCE penetrance Refers to co-expression of both phenotypes from both alleles Variable expressivity Mostly uniform expression Neither AD or AR Many have delayed or adult onset Onset is frequently early in life/congenital Refers to a pattern of inheritance in both alleles express their 🩺 Many involve genes coding for Many involve genes coding for phenotypes equally and thus neither the traits are dominant or 🩺 structural proteins or regulatory enzymes (e.g., inborn errors of recessive proteins affecting metabolic metabolism) A well known example is the human ABO blood type system pathways [GROUP 12] Arcenal, Bersabe, Macalintal, Tang, Velasco 2 of 12  See APPENDIX A for Table of Biochemical & Molecular Basis of Some Mendelian Disorders E. EXAMPLES OF MENDELIAN DISORDERS MARFAN SYNDROME 🩺 Lead to altered structural proteins 🩺 70-85% familial → autosomal dominant ○ The rest are sporadic due to newly arising mutations Mutations in FBN1 gene → decreased amount of fibrillin-1 Figure 4. Codominance 2 Basis for clinical manifestations: ○ Decreased fibrillin-1 (esp. Aorta, ligaments, lens) → D. X-LINKED DISORDERS weakened elastic fibers/connective tissue Diseases that result from mutations in genes located in the X ○ Increased TGF-beta bioavailability → increased inflammation and metalloproteinase activity 🩺 chromosome and thus have an inherent dependence on the sex of the offspring on whether or not they will be expressed In general X-linked diseases are more common in sons because 🩺 of the requirement of homozygosity for daughters to express the disease Males with a mutant X chromosome gene are said to be 🩺 hemizygous while females that are heterozygous for the mutant gene are called carriers If a mother is affected all of her sons are automatically affected meanwhile the frequency of the disease becomes more or less 🩺 equal for both sexes in the X-linked DOMINANT pattern of inheritance In fact sometimes the frequency of the disease is increaed more 🩺 in daughters than sons, this occurs when an affected but heterozygous mother and unaffected father produce offspring Figure 6. Marfan Syndrome 2 Clinical manifestations ○ Skeletal abnormalities (e.g., tall stature, dolichocephaly, spinal deformities (kyphosis or scoliosis), pectus excavatum/carinum, etc.) ○ Skin changes (more stretchable) ○ Ocular changes (e.g., ectopic lentils) 🩺 Finding particularly helpful in establishing the Figure 5. Types of X-linked disorders2 diagnosis ○ Cardiovascular lesions (e.g. mitral valve prolapse, aortic dilation) → most life-threatening X-LINKED RECESSIVE More commonly death in marfan syndrome patients More frequent/common than X-Linked dominant disorders occur due to aortic dissection which is a result of 🩺 Examples of X-linked dominant disorders are vitamin D 🩺 progressive aortic dilatation stemming from the dependent rickets and alport syndrome 🩺 weakened vessel walls Heterozygous females (carriers) may exhibit some degree of Marfan syndrome exhibits variable expressivity phenotypic changes due to random X chromosome inactivation (Lyon hypothesis) ○ Ex: G6PD deficiency One peculiar phenomenon in x-linked diseases is that carriers can potentially manifest disease characteristics as if they are homozygous for the disease trait, this is due to the random 🩺 inactivation of x chromosomes in the cells of the female individual as explained by the Leon hypothesis Table 4. X-Linked Recessive Disorders2 System Disorder Musculoskeletal Duchenne muscular dystrophy Blood Hemophilia A and B Chronic granulomatous disease Glucose-6-phosphate dehydrogenase deficiency Immune Agammaglobulinemia Wiskott-Aldrich syndrome Metabolic Diabetes insipidus Lesch-Nyhan syndrome Nervous Fragile X syndrome [GROUP 12] Arcenal, Bersabe, Macalintal, Tang, Velasco 3 of 12  Figure 8. Familial Hypercholesterolemia 2 Figure 7. Marfan Syndrome 2 FAMILIAL HYPERCHOLESTEROLEMIA (FH) 🩺 Autosomal dominant ○ Characterized by defective receptors or transportins Most common mutation: LDLR gene ○ Decreased LDL receptors Other mutations: 🩺 ○ Genes for ApoB - decreased ApoB ApoB – ligands of LDL that binds to LDL receptor Decreased LDL receptor and ApoB → Decreased receptor binding of LDL to the hepatocytes and ultimately the none transfer of LDL Figure 9. The low-density lipoprotein (LDL) receptor pathway and LDL cholesterol stays in the plasma in the regulation of cholesterol metabolism 2 ApoB-100, Apolipoprotein B-100 (ApoB); HMG CoA, 3-hydroxy-3-methylglutaryl bloodstream coenzyme A 🩺 ○ PCSK9 gene - increased enzyme activity PCSK9 – similarly decreases the number LDLR but instead upregulating the activity of PCSK9 which is 🩺 Most important in these cells are the hepatocytes ○ Responsible mostly in LDL clearance responsible for recycling LDLR LDLR gene mutations also lead to increased LDL synthesis Main effect: Hypercholesterolemia in the blood → Various FH mutations are classified into types according to atherosclerosis and cardiovascular disorders (e.g. Myocardial resulting abnormal function 🩺 Infarction) Diversion of LDL into mononuclear phagocyte system and vessel ○ All in all the mutations effect is the accumulation of 🩺 walls → xanthomas and atherosclerosis cholesterol in the blood because LDL can’t be transfer in ○ Besides the impaired clearance of LDL from the blood, the hepatocytes or other target cells. LDL synthesis is also stimulated by this mutations because of precursor of LDL which are IDL (Intermediate Density Lipoproteins) is also using the same LDLR. Instead of being taken up by hepatocytes and other cells with these receptors, IDL are then shunted to form LDL. Excess LDL are then shunted toward the scavenger receptor mediated pathway that mainly involves macrophages and vessel walls. 🩺 Treated with anti lipid drugs (e.g., statins) ○ Which act on various steps of cholesterol metabolism to decrease these amount. [GROUP 12] Arcenal, Bersabe, Macalintal, Tang, Velasco 4 of 12  Main pathologic effects: ○ Accumulation of insoluble metabolites (primary 🩺 accumulation/storage) Where enzyme deficiency there, is incomplete metabolism of substance → accumulates in lysosomes enlarging and affecting other cellular functions because they start to crowd out other organelles. ○ Impaired autophagy and mitochondrial and lysosomal 🩺 functions (secondary storage) Accumulation of toxic metabolites in generation of free radicals → cell death Pathologic effects depend on: ○ Which tissue where most of the substance is found 🩺 ○ Where degradation of the substance normally occurs Examples: Tay-Sachs disease ○ The enzyme defect results in accumulation of gangliosides which is found in neurons and retina ○ Primarily involved neuronal signs and Figure 10. Classification of Low-Density Lipoprotein (Ldl) Receptor symptoms Mutations Based on Abnormal Function of the Mutant Protein 1 These mutations disrupt the receptor’s synthesis in the endoplasmic reticulum, Niemann-pick disease type A and gaucher disease transport to the Golgi complex, binding of apoprotein ligands, clustering in coated type 1 pits, and recycling in endosomes. Not shown is class VI mutation, in which initial ○ Mainly found in tissues rich in targeting of the receptor to the basolateral membrane fails to occur. Each class is macrophages such as spleen, liver and heterogeneous at the DNA level. lymph nodes. ○ In these cases, organomegaly is a LYSOSOMAL STORAGE DISEASES typical presentation not neuropathies Large, heterogenous group of genetic disorders with lysosomal enzyme deficiencies Lysosomal enzymes: ○ Acid hydrolases produced in Golgi complex that worked best in the acidic milieu of lysosomes ○ Designed to function for intracellular organelles not 🩺 extracellularly They normally function for digestion of phagocytosed particles and important process of autophagy. Figure 11. Pathogenesis of Lysosomal Storage Diseases 1 In the example shown, a complex substrate is normally degraded by a series of lysosomal enzymes (A, B, and C) into soluble end products. If there is a deficiency or malfunction of one of the enzymes (e.g., B), catabolism is incomplete, and insoluble intermediates accumulate in the lysosomes. In addition to this primary storage, secondary storage and toxic effects result from defective autophagy See APPENDIX B for Table of Lysosomal Storage Diseases Figure 11. Synthesis & Intracellular Transport of Lysosomal Enzymes 1 [GROUP 12] Arcenal, Bersabe, Macalintal, Tang, Velasco 5 of 12  Some notable features of lysosomal storage disorders: III. COMPLEX MULTIGENIC DISORDERS ○ Generally autosomal recessive Risk for disease is affected by multiple genes and environmental ○ Some are more common in specific populations like factors Ashkenazi Jews (e.g., Tay Sachs disease, Niemann-Pick ○ Diseases that are largely affected by the interactions of disease types A and B) multiple gene effects and environmental factors ○ Gaucher disease – most common disorder ○ Example: diabetes, autoimmune diseases ○ Associations with other diseases: ○ Risk of occurrence depends on the alleles expressed by the Gaucher disease – Parkinson disease genes Niemann-Pick type C disease – Alzheimer disease Polymorphisms 🩺 ○ Prognosis: from curable and manageable to early death ○ Each polymorphism has a contribution to the disease Current treatment options: ○ A shift towards the end of the bell curve would increase the Enzyme mutase therapy probability of the disease Substrate reduction therapy ○ Not specific to one disorder, and are often associated with Gene therapy other diseases Stem cell transplants ○ Alleles occurring in low frequencies in the population Some have disproportionate effects on disease risk GLYCOGEN STORAGE DISEASES Some are associated with multiple diseases (GLYCOGENOSES) Sometimes difficult to establish External factors play a significant/ major role in this type of Mostly autosomal recessive with some X-linked disorders 🩺 Main effect: impaired synthesis or degradation of glycogen In order for the diseases to be considered complex and ○ Poor mobilization of glucose and consequently there is multigenic, other modes of inheritance should be definitely 🩺 hypoglycemia excluded ○ Glycogen accumulation in cells → organomegaly Subgroups: ○ Hepatic forms (e.g., von Gierke disease or type I) ○ Myopathic forms (e.g., McArdle disease or type V) 🩺 ○ Miscellaneous (e.g., Pompe disease or type II) Most common are hepatic and myopathic – since liver and skeletal muscles are main sites of glycogen metabolism Figure 15. Complex Multigenic Disorders 2 IV. CHROMOSOMAL DISORDERS Figure 16. G-banded karyotype from a normal male (46,XY). Also shown is the banding pattern of the X chromosome with nomenclature of arms, regions, bands, and sub-bands 2 Figure 13. (A) Normal glycogen metabolism in the liver and skeletal muscles. (B) Effects of an inherited deficiency of hepatic enzymes involved Normal karyotype in glycogen metabolism. (C) Consequences of a genetic deficiency in the enzymes that metabolize glycogen in skeletal muscles 1 ○ Human somatic cells contain 46 chromosomes 22 homologous pairs of autosomes See APPENDIX C. for Table of Principal Subgroups of 2 sex chromosomes Glycogenoses XX: female XY: male [GROUP 12] Arcenal, Bersabe, Macalintal, Tang, Velasco 6 of 12  G-banding Chromosome 22q11.2 deletion syndrome ○ Uses the Giemsa stain ○ CATCH-22 syndrome (see red initials in the table) ○ Aids in subdividing chromosome arms into regions, bands, ○ Represents two recognized syndromes that were previously and sub-bands thought to be unrelated Abnormal number/ structure of chromosomes: DiGeorge Syndrome ○ Aneuploidy Velocardiofacial Syndrome Chromosome number that is not a multiple of 23 ○ Variable presentation Caused by unequal distribution of chromosomes during ○ Common to both is the high risk for psychotic disorders such cell division as schizophrenia and bipolar disorders Due to nondisjunction or anaphase lag Although there is proper disjunction in the Table 5. Chromosome 22q11.2 Deletion Syndrome 2 beginning of the anaphase. There is one part of DiGeorge Syndrome Velocardiofacial Syndrome the chromosome pair that may lag during the Thymic hypoplasia → T-cell Facial dysmorphism separation and becomes excluded, leading the immunodeficiency Cleft palate same effect as nondisjunction Parathyroid hypoplasia → Cardiovascular anomalies ○ Monosomies, trisomies, etc. Hypocalcemia Learning disabilities Monosomy Cardiac malformations Immunodeficiency (seen in Involves an autosome which generally causes loss Facial Abnormalities some cases only) of too much genetic information to permit live birth Atopy and autoimmunity or even embryogenesis Extra/ lack of chromosomes V. SINGLE-GENE DISORDERS WITH Autosomal monosomies are generally not compatible NON-CLASSIC INHERITANCE with life Autosomal trisomies lead to early death A. DISORDERS CAUSED BY Sex chromosomal aneuploidies are generally TRINUCLEOTIDE-REPEAT MUTATIONS compatible with life Trinucleotide-Repeat Mutations ○ If occurring post-zygotically → mosaicism ○ Unstable DNA sequences composed of repetitions of three Early in fetal development base paisr that usually include G and/or C base pairs Involves some cells with normal and abnormal ○ Found in coding and noncoding regions of the DNA karyotypes due to a cytogenetic disorder ○ As they are transmitted in each generation, they expand in numbers ○ Expansions are usually affected by sex depending on the sex since this occurs either during oogenesis or spermatogenesis Excessive trinucleotide repeats in exons or introns → clinical disease Generally cause neurodegenerative and neuromuscular disorders Figure 17. Chromosomal abnormalities 2 Various structural changes in chromosomes: ○ Cell death Due to loss of significant amounts of DNA ○ Inherited conditions and syndromes ○ Neoplasms Most frequently associated with cytogenetic abnormalities Figure 19. Disorders Caused by Trinucleotide-repeat Mutations 2 See APPENDIX D for Table of Examples Trinucleotide-Repeat Disorders Figure 18. Types of Chromosomal Rearrangements1 [GROUP 12] Arcenal, Bersabe, Macalintal, Tang, Velasco 7 of 12 FRAGILE X SYNDROME progressive amplification of the repeats will become full mutations and finally cross the threshold needed for disease. Most common genetic cause of intellectual disability in males; 2nd Male are more commonly affected most common overall behind Down Syndrome ○ X linked diseases > Senior Males CGG repeat mutation in FMRI gene, located in X chromosome ○ Only about half of females are affected by full mutations, and ○ Two related disorders; Fragile X Tremor Ataxia and Fragile X even then the presentation is usually milder. associated with primary ovarian insufficiency, have similar Transmission and Amplification of CGG repeats through mutations, but different pathophysiology and clinical generations shows why the risk of disease is much higher in sons features. and grandsons compared to that in siblings, male siblings, or Clinical Features: brothers. ○ Marked intellectual disability ○ This Accounts for the phenomenon called Anticipation, Most Common and Prominent Clinical Feature Which is the finding that the clinical presentation of the ○ Macro-orchidism disease becomes more severe as it is further and further Large Testicles passed down the generations. ○ Long face with large mandible and large, everted ears ○ Hyperextensible joints, high-arched palate, mitral valve prolapse, etc. HOW DOES THE CGG MUTATION CAUSE DISEASE FMR Protein or FMRP, is a product of the FMR1 gene. FMR1 gene codes for FMRP ○ Most abundant in the brain and testes FMRP facilitates the transport of mRNA’s from the nucleus to axons and dendrites Full CGG mutations affecting the untranslated region of the FMR1 gene lead to methylation and therefore silencing of the gene. Full mutations → FMR1 methylation Decreased FMRP Decreased mRNA transport to dendrites and axons Unregulated protein synthesis in synapses → loss of synaptic plasticity → impaired learning and memory Figure 21. Fragile X Syndrome 2 Figure 23. FMRP Model 2 B. DISORDERS CAUSED BY MUTATIONS IN MITOCHONDRIAL GENES Figure 22. Fragile X Pedigree 2 Mitochondrial genes are maternally inherited This Pedigree explains the genetics of Fragile X and ○ Many code for enzymes related to oxidative phosphorylation Trinucleotide-Repeat Disorders. Though the majority code for translation RNA or tRNA, many mitochondrial genes code for enzymes that are In the Normal population, CGG repeats are few. Some individuals, related to oxidative phosphorylation. these are higher in number, but they are not yet enough to cause Mitochondrial DNA is inherited by the zygote from the disease. old, and so it is said to be maternally inherited. Because PREMUTATION of this, mitochondrial mutations are passed by affected ○ Inherited by females, the number of repeats can be mothers to all her offspring. potentially amplified during oogenesis. While affected fathers cannot pass them to offspring at ○ These repeats are unstable DNA sequences, that's why they all. Unless of course the mother is affected. However, can be potentially amplified during division. mitochondrial gene inheritance has some unique Fragile X Syndrome, This does not occur in spermatogenesis, So features. So each mitochondrion has thousands of male carriers do not amplify the permutations. copies of mitochondrial DNA, and not all of these ○ The permutations are transmitted by carrier females in copies have had the same amounts of wild time and subsequent generations, there is a high probability that the mutated. [GROUP 12] Arcenal, Bersabe, Macalintal, Tang, Velasco 8 of 12  ○ Heteroplasmy and “threshold effect” This is important because in order for a cell to exhibit pathology from abnormal oxidative function, it must have some amount of mutant DNA enough to cause the dysfunction. So this is called the threshold effect. So this is similar to the concept that we saw earlier, in the clavicle of the type C repeated disorders wherein you need to accumulate enough mutations in order to produce the disease. ○ Variable expression due to random distribution in daughter cells So in a patient, not all daughter cells inherit the same proportion of wild type and mutant DNA that the parent cell had.This is because during cell division, the copies of mitochondrial DNA are randomly distributed between the daughter cells. And therefore, the phenotypic expression of mitochondrial gene mutations is variable. It's not one is to one inheritance. Figure 24. Pedigree of Leber 1 LEBER HEREDITARY OPTIC NEUROPATHY Mitochondrial gene disorders mainly affect tissues of the CNS, Skeletal and Cardiac Muscles, Liver and Kidneys because there are the cell types that are highly dependent on oxidative phosphorylation, Neurodegenerative Disease → bilateral loss of central vision/blindness Visual impairment begins in early adulthood (onsent) Figure 25. Diagrammatic Representation of Prader-Willi & Angelman Syndromes2 ○ Eventually progress to bilateral blindness. This diagram shows the effect of Imprinting disorder associated with genomic Some have cardiac conduction defects and minor neurologic imprinting exemplified by the genetic disorders Angelman syndrome and manifestations. Prader-Willi Syndrome. Both are located at Chromosome 15. C. DISORDERS ASSOCIATED WITH GENOMIC The UBE3A gene or CUBE3A gene is maternally imprinted. The IMPRINTING copy of the UBE3A gene is inactivated by default. And so the Genomic Imprinting maternal UBE3A gene is the only one functioning. ○ A relatively recent concept discovered due to studies of In contrast, the so-called Prader-Willi genes are maternally some unusually related genetic disorders. imprinted, only the paternal copies are functional. ○ Process of inactivating certain genes during gametogenesis When the deletions in the Maternal chromosome 15 region → “imprinted” allele involve the gene where UBE3A is located, then there is no The imprinted allele is kept inactivated from the time it remaining functional copy of UBE3A because the paternal copy is first occurred in a sperm or ovum up to zygote imprinted by default. This results in Angelman Syndrome. formation, up to its propagation to all the somatic cells When deletions in the paternal chromosome 15 involve the making up the individual or the offspring. location where Prader-Willi genes are, then the resulting disease ○ Depends on which parent the allele came from is Prader-Willi Syndrome. e.g., if the imprinted allele came from the mother, then it ○ In this case, the remaining maternal copies of Prader-Willi is “maternally imprinted” genes are imprinted and are thus nonfunctional by default. ○ Implicated in genetic and neoplastic disorders ○ Deletions are not the only way by which these disorders can occur. ○ Another way is called uniparental disomy wherein there is the inheritance of both alleles from only one parent and there is none from the other parent. For example both copies of chromosome 15 were inherited from the father, then both copies of the UBE3A are imprinted and nonfunctional. ○ Similarly, this will also result in Angelman Syndrome. [GROUP 12] Arcenal, Bersabe, Macalintal, Tang, Velasco 9 of 12  Another method by which these kinds of disorders appear is VI. REFERENCES defective imprinting. Wherein a gene is imprinted as if it came 1. Robbins and Cotran Pathologic Basis of Disease 10th Edition from the other parent. 2. Lupisan, A. J. L., (2024). Genetic Disorders [Lecture PPT] ○ So when a maternal chromosome, with a mistaken paternal imprint is combined with a paternal chromosome with a correct paternal imprint, the result is that all UBE3A genes are imprinted by default. All leads similarly to Angelman SYndrome. Table 6. Angelman Syndrome vs Prader-Willi Syndrome Angelman Syndrome Prader-Willi Syndrome Intellectual disability Intellectual Disability Microcephaly Short Stature Ataxic Gait Hypotonia Seizures Hyperphagia and obesity Inappropriate laughter (“Happy Small hands and Feet Puppets”) Hypogonadism UBE3A gene → Ubiquitin ligase SNORP family of genes → small nuclear RNAs AngelMAn Syndrome PRAder- Willi Syndrome MAternal allele is DELETED, PAternal allele is DELETED, Paternal allele is impaired Maternal allele is imprinted The genes involved in Angelman Syndrome produces a ubiquitin ligase, the absence of which affects synaptic function and synaptic plasticity that accounts for much of the neurologic manifestations. In contrast, sets of genes are implicated in Prader-Willi, the SNORP family of genes which encode for small nucleolar RNAs that function in post-translational modification of RNAs. D. DISORDERS CAUSED BY GONADAL MOSAICISM The Exception that occurs in autosomal dominant cases is when even though both parents are unaffected, one or more offspring have the disease and may be passed further in subsequent generations in non-autosomal dominant matter. GENETIC MOSAIC ○ In this case, When a mutation occurs after the formation of the Zygote, the cells of the individual will have different genotypes. Postzygotic mutations can result in different cell types having different genotypes within an individual, aka genetic mosaicism ○ Gonadal stem cells may be specifically affected -> affected offspring despite unaffected parent Gonadal cells will inherit the mutation, but the rest of the individual’s somatic cells are unaffected. Ex: Osteogenesis Imperfecta Figure 26. Gonadal Mosaicism 2 [GROUP 12] Arcenal, Bersabe, Macalintal, Tang, Velasco 10 of 12  APPENDIX APPENDIX A. Biochemical & Molecular Basis of Some Mendelian Disorders Table 7. Biochemical & Molecular Basis of Some Mendelian Disorders 1 Protein Type/Function Example Molecular Lesion Disease Enzyme Phenylalanine hydroxylase Splice-site mutation: reduced amount Phenylketonuria Hexosaminidase A Splice-site mutation or frameshift Tay-Sachs disease mutation with stop codon: reduced amount Adenosine deaminase Point mutations: abnormal protein with Severe combined immunodeficiency reduced activity Enzyme inhibitor α1-Antitrypsin Missense mutations: impaired secretion Emphysema and liver disease from liver to serum Receptor Low-density lipoprotein receptor Deletions, point mutations: reduction of Familial hypercholesterolemia synthesis, transport to cell surface, or binding to low-density lipoprotein Vitamin D receptor Point mutations: failure of normal Vitamin D–resistant rickets signaling Transport Oxygen Hemoglobin Deletions: reduced amount α-Thalassemia Defective mRNA processing: reduced β-Thalassemia amount Point mutations: abnormal structure Sickle cell anemia Ion channels Cystic fibrosis transmembrane Deletions and other mutations: Cystic fibrosis conductance regulator nonfunctional or misfolded proteins Structural Extracellular Collagen Deletions or point mutations cause Osteogenesis imperfecta reduced amount of normal collagen or normal amounts of defective collagen Ehlers-Danlos syndromes Fibrillin Missense mutations Marfan syndrome Cell membrane Dystrophin Deletion with reduced synthesis Duchenne/Becker muscular dystrophy Spectrin, ankyrin, or protein 4.1 Heterogeneous Hereditary spherocytosis Hemostasis Factor VIII Deletions, insertions, nonsense Hemophilia A mutations, and others: reduced synthesis or abnormal factor VIII Growth regulation Rb protein Deletions Hereditary retinoblastoma Neurofibromin Heterogeneous Neurofibromatosis type 1 APPENDIX B. Lysosomal Storage Diseases Table 8. Lysosomal Storage Diseases 1 Disease Enzyme Deficiency Major Accumulating Metabolites Glycogenosis Type 2—Pompe disease Glycogen α-1,4-Glucosidase (lysosomal glucosidase) Sphingolipidoses GM1 gangliosidosis GM1 ganglioside β-galactosidase GM1 ganglioside, galactose-containing Type 1—infantile, generalized oligosaccharides Type 2—juvenile GM2 gangliosidosis Tay-Sachs disease Hexosaminidase A GM2 ganglioside Sandhoff disease Hexosaminidase A and B GM2 ganglioside, globoside GM2 gangliosidosis variant AB Ganglioside activator protein GM2 ganglioside Sulfatidoses Metachromatic leukodystrophy Arylsulfatase A Sulfatide Multiple sulfatase deficiency Arylsulfatase A, B, C; steroid sulfatase; iduronate Sulfatide, steroid sulfate, heparan sulfate, sulfatase; heparan N-sulfatase dermatan sulfate Krabbe disease Galactosylceramidase Galactocerebroside Fabry disease α-Galactosidase A Ceramide trihexoside Gaucher disease Glucocerebrosidase Glucocerebroside Niemann-Pick disease: types A and B Sphingomyelinase Sphingomyelin Mucopolysaccharidoses (MPSs) MPS I-H (Hurler) α-L-Iduronidase Dermatan sulfate, heparan sulfate MPS II (Hunter) Iduronate 2-sulphatase Mucolipidoses (MLs) I-cell disease (ML II) and pseudo-Hurler Deficiency of phosphorylating enzymes essential Mucopolysaccharide, glycolipid polydystrophy for the formation of mannose-6-phosphate recognition marker; acid hydrolases lacking the recognition marker cannot be targeted to the lysosomes, but are secreted extracellularly Other diseases of complex carbohydrates Fucosidosis α-Fucosidase Fucose-containing sphingolipids and glycoprotein [GROUP 12] Arcenal, Bersabe, Macalintal, Tang, Velasco 11 of 12  fragments Mannosidosis α-Mannosidase Mannose-containing oligosaccharides Aspartylglycosaminuria Aspartylglycosamine amide hydrolase Aspartyl-2-deoxy-2-acetamido-glycosylamine Other lysosomal storage diseases Wolman disease Acid lipase Cholesterol esters, triglycerides APPENDIX C. Principal Subgroups of Glycogenoses Table 9. Principal Subgroups of Glycogenoses 1 Clinicopathologic Specific Type Enzyme Deficiency Morphologic Changes Clinical Features Category Hepatic type Hepatorenal—von Gierke Glucose-6-phosphata Hepatomegaly—intracytoplasmic In untreated patients: failure to disease (type I) se accumulations of glycogen and thrive, stunted growth, small amounts of lipid; intranuclear hepatomegaly, and renomegaly glycogen Hypoglycemia due to failure of Renomegaly—intracytoplasmic glucose mobilization, often accumulations of glycogen in cortical leading to convulsions tubular epithelial cells Hyperlipidemia and hyperuricemia resulting from deranged glucose metabolism; many patients develop gout and skin xanthomas Bleeding tendency due to platelet dysfunction With treatment: most survive and develop late complications (e.g., hepatic adenomas) Myopathic type McArdle disease (type V) Muscle Skeletal muscle Painful cramps associated with phosphorylase only—accumulations of glycogen strenuous exercise; myoglobinuria predominant in subsarcolemmal occurs in 50% of cases; onset in location adulthood (>20 years); muscular exercise fails to raise lactate level in venous blood; serum creatine kinase always elevated; compatible with normal longevity Miscellaneous types Generalized Lysosomal acid Mild hepatomegaly — ballooning of Massive cardiomegaly, muscle glycogenosis— Pompe alpha-glucosidase lysosomes with glycogen, creating hypotonia, and cardiorespiratory disease (type II) lacy cytoplasmic pattern failure within 2 years; a milder adult Cardiomegaly—glycogen within form with only skeletal muscle sarcoplasm as well as involvement, presenting with membrane-bound chronic myopathy; enzyme Skeletal muscle—similar to changes replacement therapy available in heart APPENDIX D. Examples of Trinucleotide-Repeat Disorders Table 10. Examples of Trinucleotide-Repeat Disorders 1 No. Repeats Gene Locus Protein Repeat Disease Normal Disease Expansions Affecting Noncoding Regions Fragile X syndrome FMRI (FRAXA) Xq27.3 FMR-1 protein (FMRP CGG 6–55 55–200 (pre); >230 (full) Friedreich ataxia FXN 9q21.1 Frataxin GAA 7–34 34–80 (pre); >100 (full) Myotonic dystrophy DMPK 19q13.3 Myotonic dystrophy protein kinase CTG 5–37 34–80 (pre); >100 (full) (DMPK) Expansions Affecting Coding Regions Spinobulbar muscular atrophy AR Xq12 Androgen receptor (AR) CAG 5–34 37–70 (Kennedy disease) Huntington disease HTT 4p16.3 Huntingtin CAG 6–35 39–250 Dentatorubral-pallidoluysian atrophy ATNL 12p13.31 Atrophin-1 CAG 7–35 49–88 (Haw River syndrome) Spinocerebellar ataxia type 1 ATXN1 6p23 Ataxin-1 CAG 6–44 >39 Spinocerebellar ataxia type 2 ATXN2 12q24.1 Ataxin-2 CAG 13–33 >31 Spinocerebellar ataxia type 3 ATXN3 14q21 Ataxin-3 CAG 12–40 55–84 (Machado-Joseph disease) Spinocerebellar ataxia type 6 Ataxin-6 19p13.3 α1A-Voltage-dependent calcium CAG 4–18 21–33 channel subunit Spinocerebellar ataxia type 7 Ataxin-7 3p14.1 Ataxin-7 CAG 4–35 21–33 [GROUP 12] Arcenal, Bersabe, Macalintal, Tang, Velasco 12 of 12  PATH TRANS 1.4 26/08/24 DISEASES OF THE IMMUNE SYSTEM JON PAOLO TAN, MD, DPSP OUTLINE Major components: ○ Epithelial barriers I. Immunity a. Innate Immunity ○ Skin, gastrointestinal, respiratory tracts b. Adaptive Immunity ○ Phagocytic cells (neutrophils and macrophages), dendritic II. Lymphocytes cells, NK cells a. Lymphocyte Diversity ○ Plasma proteins (complement) III. Tissues of the Immune System a. Generative Lymphoid Organs b. Peripheral Lymphoid Organs PATTERN RECOGNITION RECEPTORS IV. Major Histocompatibility Complex Molecules Pattern Recognition Receptors are receptors that recognize a. Class I MHC Molecules pathogen/ damage associated molecules b. Class II MHC Molecules Pattern-associated molecular receptors recognize: V. Cytokines: Messenger Molecules of the Immune System ○ Pathogen-associated molecular patterns: VI. Adaptive Immunity Microbial components shared among related microbes a. Cell-Mediated Immunity Essential for infectivity b. Humoral Immunity VII. Hypersensitivity ○ Damage-associated molecular patterns: a. Immediate (Type I) Hypersensitivity Molecules released by dead/damaged cells Recognized b. Antibody-Mediated (Type II) Hypersensitivity by cells of innate immunity c. Immune Complex-Mediated (Type III) Hypersensitivity d. T-Cell Mediated (Type IV) Hypersensitivity VIII. Autoimmune Diseases TOLL- LIKE RECEPTORS (TLR) IX. Immunologic Tolerance Extracellular a. Central Tolerance Activate 2 sets of transcription factors: b. Peripheral Tolerance ○ NF-kB → cytokines and adhesion molecules X. Autoimmunity ○ Interferon regulatory factors → antiviral cytokines (type I a. General Features of Autoimmune Diseases interferon) b. Systemic Lupus Erythematosus (Discussed in SGD) c. Sjogren Syndrome d. Systemic Sclerosis (Scleroderma) NOD-LIKE RECEPTORS (NLR) XI. Transplant Pathology Cytosolic a. Mechanism of Recognition & Rejection of Allografts Recognize necrotic cell products, ion disturbances and microbial b. Patterns of Graft Rejection products c. Increasing Graft Survival Signal via cytosolic multiprotein complex (inflammasome) XII. Immunodeficiency Syndromes a. Defects in Innate Immunity b. Defects in Adaptive Immunity C-TYPE LECTIN RECEPTORS (CLR) XIII. Secondary Immunodeficiencies Expressed on plasma membrane of macrophages and dendritic a. HIV/AIDS (Discussed in SGD) cells b. Amyloidosis Elicit inflammatory reactions to fungi XIV. References RIG-LIKE RECEPTORS (RLR) LEGEND Cytosol of most cell types Detect nucleic acid of viruses Must Know Good to Know Lecturer Book G-PROTEIN COUPLED RECEPTORS (GPCR) Found in neutrophils, macrophages and leukocytes I. IMMUNITY Recognize proteins with N-formylmethionyl residues (found in all Immunity is defined as the protection from infectious pathogens bacterial proteins) ○ Innate immunity (natural) ○ Adaptive immunity (acquired) MANNOSE RECEPTORS Recognize microbial sugars A. INNATE IMMUNITY Induce phagocytosis Always present Innate mechanisms poised to react immediately NATURAL KILLER CELLS “THE FIRST LINE OF DEFENSE” Recognize and destroy severely stressed or abnormal cells 3 stages: ○ Virus-infected cells and tumor cells ○ Recognition of microbes and damaged cells Approximately 5% - 10% of peripheral blood lymphocytes ○ Activation of various mechanisms Regulated by signals from activating and inhibitory receptors ○ Elimination of unwanted substances Express CD16 ○ Confers antibody-dependent cellular cytotoxicity (ADCC) [GROUP 4] Berces, Calpo, Co, Esturco, Lopez 1 of 12 REACTIONS OF INNATE IMMUNITY Consists of spatially separated segments Inflammation: During lymphocyte maturation ○ Cytokines and complement activation → Inflammation, ○ Segments recombine randomly → variation in genes → recruitment of leukocytes variations in receptors Antiviral defense: ○ Type 1 interferons → act on infected and uninfected cells → T LYMPHOCYTES activate enzymes → degrade viral nucleic acids → inhibit viral Helper T lymphocytes replication ○ Stimulate B lymphocytes to make antibodies, activate other ○ “Antiviral state” WBCs Provides danger signals that stimulate subsequent more powerful Cytotoxic T lymphocytes – kill infected cells adaptive immune response Regulatory T lymphocytes No memory or fine antigen specificity ○ Limit immune responses and prevent reactions against self- 100 different receptors for 1000 molecular patterns antigens Develop in thymus B. ADAPTIVE IMMUNITY Mature T cells Consists of lymphocytes and their products (including antibodies) ○ 60-70% found in blood, T-cell zones of peripheral lymphoid 2 types of adaptive immunity: organs ○ Humoral immunity protects against extracellular microbes and toxins, B-cell mediated ○ Cell-mediated (cellular) defense against intracellular microbes, T-cell mediated II. LYMPHOCYTES Circulate via the lymphatic and blood circulation Allows them to home in on infections “Naive” lymphocytes ○ Immunologically inexperienced; not yet met their antigen Effector cells ○ Eliminate microbes Memory cells ○ React rapidly and strongly to microbe in case it returns Figure 2. Natural Killer Cells 1 B LYMPHOCYTES Only cells in body capable of producing antibody molecules Develop from precursors in bone marrow Mature B cells constitute around 10-20% Recognize antigen via B-cell antigen receptor complex Activated B-cells → plasma cells Single plasma cell ○ secrete hundreds to thousands of antibody molecules per second DENDRITIC CELLS Antigen presenting cell Most important for initiating T-cell responses against protein antigens Figure 1. Natural Killer Cells 1 Have fine cytoplasmic processes resembling dendrites Found in germinal centers of lymphoid follicles (follicular dendritic A. LYMPHOCYTE DIVERSITY cell) Clonal selection Langerhans cells – immature dendritic cells within epidermis ○ Each lymphocyte expresses receptors for a single antigen These lymphocytes exist even before exposure to antigen MACROPHAGES Can recognize hundreds of millions of antigens Mononuclear phagocyte system Clone Function as antigen presenting cells to T-cells ○ Lymphocytes of the same specificity T cells activate macrophages and enhance their ability to kill Somatic recombination/ rearrangement of genes that encode ingested microbes receptor proteins Participate in effector phase of humoral immunity - phagocytose Receptor genes cells/microbes opsonized by complement or Ig [GROUP 4] Berces, Calpo, Co, Esturco, Lopez 2 of 12 NATURAL KILLER CELLS A. CLASS 1 MHC MOLECULES Destroy irreversible stressed and abnormal cells (virus-infected Expressed on all nucleated cells and platelets and tumor cells) Heterodimers of alpha chain and beta-2 microglobulin CD16 and CD56 identify NK cells Alpha chains encoded by 3 genes: HLA-A, HLA-B,HLA-C CD16-Fc receptor for IgG: ability to lyse IgG coated target cells Present peptides derived from proteins (viral and tumor antigens) (antibody-dependent cell-mediated cytotoxicity) located in the cytoplasm and usually produced in cell Recognized by CD8+ T lymphocytes Eliminate viruses B. CLASS II MHC MOLECULES Encoded in a region HLA-D 3 subregions: HLA-DP, HLA-DQ, HLA-DR Consists of a noncovalently associated alpha and beta chain (both polymorphic) Present only in Antigen Presenting Cells (dendritic cells), macrophages, B-cells Bind to peptides from proteins synthesized outside of cells, ingested into cells Present antigens that are internalized into vesicles Recognized by CD4+ T cells (helper cells) Figure 3. Natural Killer Cells 1 In diagram A, if the inhibitory receptor is engaged and the activating receptor is not engaged, there is NO cell killing. INNATE LYMPHOID CELLS Lymphocytes that lack TCR, but produce T-cell cytokines NK cells are considered the first-defined ILC Early defense against infections Recognition and elimination of stressed cells (stress surveillance) Shaping the later adaptive immune response by providing cytokines Figure 4. MHC Class I and MHC Class II Molecules 1 III. TISSUES OF IMMUNE SYSTEM A. GENERATIVE LYMPHOID ORGANS V. CYTOKINES: MESSENGER MOLECULES OF Where T and B lymphocytes mature and become competent to IMMUNE SYSTEM respond to antigens Mediates cellular interactions and functions of leukocytes Thymus (T cell) and bone marrow (B cell) Autocrine, paracrine or endocrine functions Innate immune responses - TNF, IL-1, IL-12, type I IFNs, IFNy, B. PERIPHERAL LYMPHOID ORGANS some limit and terminate immune responses (TGF-beta and IL-10) When T cell and B cell mature, they go to the peripheral Colony-stimulating factors - stimulate hematopoiesis (GM-CSF lymphoid organs and IL-7) Adaptive immune responses to microbes are initiated Interleukins - molecularly defined cytokines Lymph nodes, spleen, and mucosal and cutaneous lymphoid tissues IV. MAJOR HISTOCOMPATIBILITY COMPLEX (MHC) MOLECULES Display peptide fragments of protein antigens for recognition by antigen-specific T cells In humans, MHC molecules are called human leukocyte antigens (HLA) 2 major classes: Class I MHC and Class II MHC [GROUP 4] Berces, Calpo, Co, Esturco, Lopez 3 of 12  VI. ADAPTIVE IMMUNITY B. HUMORAL IMMUNITY A. CELL-MEDIATED IMMUNITY Activated B-cells → plasma cells (secrete antibodies) T-cell dependent response: ○ B-cells ingest microbes, present antigens bound to MHC class II ○ T-helper binds to antigens, secrete cytokines and CD40L → stimulate B-cells T-cell independent response: ○ antigens that cannot be recognized by T-cells ○ these have multiple identical antigenic determinants that are able to engage B-cell antigen receptors Protein antigens → production of IgA, IgG, IgE Isotype switching - production of functionally different antibodies with the SAME specificity ○ provides plasticity in antibody response Affinity maturation - production of antibodies with higher and higher affinity for the antigen Figure 5. Cell-Mediated Immunity 1 Your dendritic cells capture microbial antigens and transport it into secondary lymphoid organs (E.g. lymph node) Once inside the lymph node, the dendritic cells mature and express high levels of MHC molecules. It then activates your T- cells and differentiate either into an effector or memory T cells Then, they begin to migrate to the site of the infection The effector T cells can either secrete cytokines causing macrophage activation leading to inflammation, or they can become cytotoxic T-lymphocyte and kill infected cells with microbes Figure 7. Combating Infections by Humoral Immunity 1 VII. HYPERSENSITIVITY Injurious immune reactions Hypersensitivity reactions - elicited by exogenous environmental antigens ir endogenous self antigens Results from imbalance between effector mechanisms of immune responses and control mechanisms Associated with inherit energy of particular susceptibility genes Same mechanism of injury with effector mechanisms of defense Figure 6. Cytokines Produced by CD4+ 1 See APPENDIX A. for the Mechanisms of Hypersensitivity Table 1. Cytokines produced by CD4+ Reactions Major Cytokines IFN-γ IL-4, IL-5, IL-17, IL-22 Produced IL-13 A. IMMEDIATE (TYPE 1) HYPERSENSITIVITY Cytokines that induce IFN-γ, IL-12 IL4 TGF-β, IL-6, IL-1, Rapid immunologic reaction (allergy) this subset IL-23 Occurs in a previously sensitized individual Immunological Macrophage Stimulation Recruitment of Triggered by binding of an antigen to IgE antibody on mast cell reactions triggered activation, of IgE neutrophils, surface stimulation of production, monocytes IgG antibody activation 2 phases: production of mast ○ Immediate response (vasodilation, vascular leakage) cells and ○ Late phase reaction (2-24 hours later and may last for several eosinophils days) Host defense against Intracellular Helminthic Extracellular Excessive TH2 responses and stimulated IgE production microbes parasites bacteria, fungi Role in disease Autoimmune Allergies Autoimmune and and other other chronic chronic inflammatory inflammatory diseases (such as diseases (such IBD, psoriasis, MS) as IBD, psoriasis, granulomatous inflammation) [GROUP 4] Berces, Calpo, Co, Esturco, Lopez 4 of 12  Non-atopic allergy-triggered by non-antigenic stimuli (extreme temperature & exercise), 20-30% Table 2. Immediate (Type 1) Hypersensitivity Clinical Syndrome Clinical and Pathological Manifestations Anaphylaxis Fall in blood pressure (shock) caused by vascular dilation; airway obstruction due to