There are numerous diseases which arise from expansions in (CAG)_n repeats, which encode glutamine. In a coding region, a (CAG)_n repeat expansion can either inactivate a protein or exhibit a dominant phenotype due to poly-glutamine’s toxic effects; examples include Huntington Disease and Spinocerebellar Ataxia (SCA) type I. In a non-coding region, a (CAG)_n repeat expansion can interfere with chromatin structure and disrupt transcriptional regulation, and/or exhibit a dominant phenotype by distracting splicing factors with the triplet repeat; examples include Myotonic Dystrophy, Fragile X Syndrome and other SCA forms.

Patients with Chronic Myelogenous Leukemia have undergone a translocation between chromosomes 9 and 22 to form a Philadelphia chromosome (so named due to where it was discovered) containing the tip of chromosome 9 and a portion of chromosome 22, and with an activated oncogene.

Thalassemias are a heterogeneous group of hemoglobinopathies whereby a reduction in synthesis/stability of α or β globin chain causes α- or β-thalassemia, respectively. The clinical problem is excess β peptides (in α-thalassemia) or excess α peptides (in β-thalassemia); this imbalanced α:β ratio leads to early cell destruction and iron overload. The chain produced at a normal rate becomes relatively overabundant, eventually precipitating in the cell, damaging the membrane and causing premature hemolysis.

The heterozygote advantage is that thalassemias weaken red blood cells and confer some resistance to malaria. Upon infection, the cell just dies and prevents spread. Individuals that are α^-α^-/α^-α^- die in utero, although this does not include heterozygous mutations in different globin genes. Expression of the globin gene locus is managed by a locus control region (LCR).

β-thalassemia

β-globin deficiency. Mostly due to single base-pair substitutions in the β-globin genes. Much more heterogenous than α thalassemias, even in high frequency populations. Complex β thalassemias involve β globin plus one or more of the genes from the β globin cluster LCR. β globin cluster is totally dependent on its LCR for expression.

α thalassemia

Due to α-globin deficiency. Excess γ-globin chain form g4 tetramer (Hb Bart’s). Excess β-globin chains form b4 tetramer ( Hb H). These are ineffective oxygen carriers.

Nearly all disease genes have mutant alleles which affect splicing of the mRNA, rather than protein coding. Exon skipping can arise via mutations in the 5′ splice site, the 3′ splice site, and/or exonic or intronic splicing enhancers. Activation of cryptic splice sites (thus shortening the exon) can arise via mutated exonic splicing enhancers. Examples of diseases due to mRNA splicing errors include Familial Isolated Growth Hormone Deficiency (mutations in the GH-1 gene), Cystic Fibrosis (mutations in the CFTR gene), Spinal Muscular Atrophy and some thalassemias (mutations in the β-globin gene that activate a cryptic 3′ splice site).

Spinal Muscular Atrophy is the most common genetic cause of infant death, occurring in 1 in 6,000-10,000 births. This is an autosomal recessive disorder caused by mutations in the SMN1 gene, encoding a protein involved in snRNP maturation. Humans have undergone an SMN gene duplication generating the SMN2 gene. Even though it encodes an identical protein, the presence of SMN2 cannot compensate for the loss of SMN1 in spinal muscular atrophy, because its splicing is abnormal and it does not produce functional protein.

Splicing targeted therapies are being tested for Spinal Muscular Atrophy. A single C to T mutation in an exonic splicing enhancer of SMN2 exon 7 causes exon skipping and production of a truncated protein from 80% of the SMN2 mRNA. If drugs or other therapies could be found that increase exon 7 splicing of SMN2, one could potentially treat the disease even without correcting the SMN1 defect.

A hemoglobinopathy is any disorder of hemoglobin, the red blood cell protein which binds oxygen. Oxyhemoglobin has a reduced orion (does not carry oxygen); methemoglobin has an oxidized iron (carries oxygen). Methemoglobin reductase reverses the oxidation, thus unload the oxygen. Some mutant hemoglobin is resistant to methemoglobin reductase, and the heme iron thus remains permanently oxidized. Heterozygotes accumulate methemoglobin, leading to asymptomatic cyanosis (blue skin). Homozygotes are completely unable to unload oxygen and have thus not been found. Separate from reductase-resistant methemoglobin are diseases where hemoglobin has altered oxygen affinity. For example, Hb Kempsey binds oxygen very strongly and cannot unload oxygen to tissues. Encoded by an autosomal dominant, Hb Kempsey heterozygotes over-proliferate RBCs in an attempt to resolve low oxygen levels in tissues; HB Kempsey is lethal for homozygotes.

Clinically significant structural variants of normal hemoglobin are synthesized in the proper amount, but have structural defects which can cause or interfere any of the mechanisms described below. Structural variants are typically caused by point mutations, and are responsible for Sickle Cell Disease. Recall that Amino1#Amino2 means ‘Amino1′ replaced ‘Amino2′ at position ‘#’ on the polypeptide.

A hydatid cyst (also known as a mole) is a mass of placenta-derived cells resembling a grape cluster. Complete hydatidiform moles contain only paternal chromosomes but have a 46,XX karyotype. Complete hydatidiform moles (or complete moles, for short) develop into a hydatid cyst. Complete moles contain no normal placenta and no fetus. Ovarian tetranomas are cases with only maternal chromosomes which exist only as benign tumors.

Partial hydatidiform moles (or partial moles, for short) are triploids containing either an extra maternal chromosome set or an extra paternal chromosome set. Cases with an extra set of maternal chromosomes are severely retarded with small, fribrotic placentas. Cases with an extra set of paternal chromosomes have abundant trophoblast (“pre-placental”) growth and poor embryonic development.

X-Linked Severe Combined Immunodeficiency (SCID) stems from a mutation in either common γ chain gene or IL-7 receptor-α gene. A mutation in the common γ chain gene leads to an inability to bind (and hence respond) to cytokines IL-2,4,7,9,15,21. Without activity of those cytokines, the individual cannot produce T cells, B cells nor NK cells; the patient has bubble boy disease and almost no ability to fend off infection. A mutation in the IL-7 receptor-α gene leads to a lack of T cells but present B cells and NK cells. Based on this — and the paragraph above — it is clear that IL-7 is critical for T cell formation, but not B cell nor NK cell formation.

It is worth noting that mice require IL-7 for both T cell and B cell formation. SCID mice are extremely useful research tools. Lacking B and T cells, they are unable to mount an adaptive immune response. Thus, they do not reject transplanted tissues and are also useful for studying how to restore hematopoiesis. Also, SCID has been successfully treated via gene therapy techniques to introduce a functioning common γ chain gene into hematopoietic stem cells.

Down Syndrome (aka trisomy 21) is one of only three thoroughly-studied viable non-mosaic autosomal disorders (the others being trisomies 13 and 18), all of which result in stunted growth, mental retardation and multiple congenital deformities. The phenotype of Down Syndrome involves: hypotonia (low muscle tone) at birth; dysmorphic facial features; folded, low-set ears; flat nasal bridge; mental retardation, with an average adult IQ or 30-60; and, in about a third of all cases, congenital heart disease.

Down Syndrome is the most frequent and studied chromosomal disorder, and can arise in several different ways. All of these avenues somehow involve trisomy of Chromosome 21, and are detailed below.

Trisomy 18 is one of only three thoroughly-studied viable non-mosaic autosomal disorders (the others being trisomies 18 and 21), all of which result in stunted growth, mental retardation and multiple congenital deformities. Trisomy 18 frequently arises via translocation of all or most of Chromosome 18. Trisomy 18′s phenotype is mental retardation in all cases, with most cases also involving: severe heart malformation; a receded jaw (overbite); low-set malformed ears; rocker-like feet; and hypertonia, usually leading to unique clenched fists characteristic of trisomy 18.

Trisomy 13 — occurring in 1 in ∼20,000 births — is one of only three thoroughly-studied viable non-mosaic autosomal disorders (the others being trisomies 18 and 21), all of which result in stunted growth, mental retardation and multiple congenital deformities. Trisomy 13 (aka Patau Syndrome) leads to severe growth and mental retardation, usually accompanied by: a sloped forehead; malformed ears; clenched fists and rocker-bottom feet (as in trisomy 18); congenital heart defects; urogenital defects; and polycystic kidneys. Most trisomy 13 individuals gain their extra chromosome via maternal nondisjunction in meiosis I.

Many thanks to ThereseAnn, the commenter who provided incredible links to learn more about trisomy 13. I urge StudentReader.com visitors to peruse LivingWithTrisomy13.org, a site about fellow human beings living with Trisomy 13.

Sickle cell hemoglobin (HbS) results from a single nucleotide substitution which changes the codon of the sixth β-globin amino acid from glutamic acid to valine (GAG→GTG: Glu6Val) and is the causative agent of sickle cell disease when homozygous. Homozygotes have α₂^Aβ₂^S hemoglobin. Heterozygotes (said to have sickle cell trait) have α₂^Aβ₂^S (HbS), α₂^Aβ₂^A (HbA) and α₂^Aβ₂^Sβ₂^A (HbS/HbA hybrid) hemoglobin, and are clinically normal despite mild symptoms under low oxygen pressure. In Sickle Cell Disease, the HbS β chains form chains, aggregating into long fibers which deform the cell, impair its function and result in hemolysis for homozygotes.

Hyperphenylalaninemias are enzymopathies (enzyme inactivity) and aminoacidopathies (inappropriate amino acid processing) that lead to an increase in phenylalanine blood levels due to improper pheylalanine catabolism. They are all autosomal recessive and exemplified by phenylketonuria and phenylalanine hydroxylase deficiency. All hyperphenylalaninemias stem from loss of function in phenylalanine hydroxylase (PAH or PheH, a liver enzyme which catabolizes phenylalanine to tryosine) and/or genes required to synthesize its cofactor, tetrahydrobiopterin (BH₄).

Classic phenylketonuria (PKU) stems from an autosomal recessive PAH mutation that renders it inactive. Unable to degrade phenylalanine, PKU patients accumulate phenylalanine in their body fluids and the ensuing hyperphenylalaninemia damages the developing nervous system and mature brain. It is treated by complete diet restriction of phenylalanine; if no phenylalanine is ingested, then it cannot accumulate in the body. Phenylalanine hydroxylase variants are frequently benign, with many people being heterozygous at the gene encoding PAH. The few clinically significant PAH alleles can lead to near-complete PAH activity (classic PKU) or variant PKU (aka non-PKU hyperphenylalaninemia). Variant PKU occurs when PAH carries enough residual activity to lessen the disease phenotype, or prevent the disease despite elevated phenylalanine blood levels.

Rarely, a patient with hyperphenylalaninemia will have normal PAH but be unable to properly synthesize or recycle its cofactor, tetrahydrobiopterin (BH₄). Since BH₄ is necessary for the activity of other enzymes, phenylalanine restriction alone will not fully treat the patient. Fortunately, normal BH₄ can be administered in large oral doses that allow normal development and even unrestricted consumption of phenylalanine. In addition, BH₄ administration can help lower phenylalanine blood levels in patients whose PAH has a weak BH₄ affinity.

Hyperphenylalaninemias lead to mental retardation due to an imbalance of amino acids crossing the blood brain barrier. With too much phenylalanine in the bloodstream, other amino acids are outcompeted and their levels in the brain significantly decrease. This decrease in brain levels of other amino acids leads to disruption of brain development and, to a lesser extent, mature brain function. Patients with PKU are allowed slight flexibility in their diet during adulthood, as elevated phenylalanine blood levels will not have as detrimental an effect after development. However, elevated phenylalanine levels are detrimental for fetal life. Thus, females with hyperphenylalaninemia expecting to conceive must vigorously restrict their phenylalanine consumption to avoid severe developmental retardation in their offspring.

Lysosomes are membrane-bound organelles which contain hydrolases that degrade unneeded proteins and infectious bacteria. When these substrates accumulate without degradation inside the lysosome, the cells die lysosomal storage diseases (a subset of enzymopathies ensue. Affected tissues grow noticeably large, and mental dysfunction occurs in diseased brains. Tay-Sachs disease is a group of disorders where hexosaminidase A (hexA) cannot degrade the sphingolipid GM₂ ganglioside. Since GM₂ ganglioside synthesis is most prevalent in the brain, it is most severely affected by Tay-Sachs.

hexA

Normal hexA consists of α and β subunits (encoded by HEXA and HEXB) that associates with an activator protein to cleave GM₂ ganglioside. Disruption of the α subunit leads to Tay-Sachs disease; disruption of the β subunit o the activator protein leads to, respectively, Sandhoff disease and activator protein deficiency. Tay-Sachs homozygotes are clinically normal at first, but mentally deteriorate by 3-6 months of age and die by 2-4 years. HEXA alleles with some residual activity can lead to late onset, motor dysfunction, psychosis or sometimes no disease at all.

Lysosomes are membrane-bound organelles which contain hydrolases that degrade unneeded proteins and infectious bacteria. When these substrates accumulate without degradation inside the lysosome, the cells die lysosomal storage diseases (a subset of enzymopathies ensue. Hurler Syndrome is a mucopolysaccharidose, a kind of disease involving accumulation of mucopolysaccharides (or glcyosaminoglycans) within lysosomes due to deficiencies in degradative enzymes. An autosomal recessive disease, Hurler Syndrome is caused by extreme impairment of the enzyme α-L-iduronidase, leading to facial dysmorphia, developmental retardation and death by ∼10 years. In Scheie Syndrome, also autosomal recessive, α-L-iduronidase has residual activity and patients sometimes have normal life spans and normal intelligence (despite facial dysmorphia).

Hunter Syndrome is a phenotypically similar mycopolysaccharidose, but is X-linked recessive and impairs iduronate sulfatase (not α-L-iduronidase). Hurler Syndrome fibroblasts synthesize normal iduronate sulfatase, and Hunter Sydrome fibroblasts synthesize normal α-L-iduronidase. When grown together in culture, they uptake secreted proteins and thereby complement each other to produce non-diseased cells. Complementation analysis is the study of genetic complementation, where mutant gene products can complement each other to neutralize disease.

Duchenne Muscular Dystrophy (DMD) is untreatable, severe, deteriorative and relatively common X-linked recessive disorder caused by a mutation of the structural protein dystrophin. DMD causes worsening muscle weakness, with wheelchair confinement by ∼12 years and death by ∼20 years. Females very rarely have DMD, since it is lethal in males and thus cannot be passed on to XX progeny; however, females with Turner Syndrome or X chromosome translocations have been known to have DMD. About 1/3 of DMD patients have new mutations, while 2/3 have maternal inheritance of the DMD allele.

At ∼2,300 kilobases (1.5% of the X chromosome), the gene encoding dystrophin is among the largest in the animal kingdom. It contains 79 exons, and its 7 tissue-specific promoters allow differential splicing into tissue-specific and developmentally regulated isoforms. Dystrophin is a massive complex with a myriad of functions that maintain muscle integrity. Most DMD patients have deletions in either the 5′ or central regions, while most other patients have randomly distributed point mutations. Due to its sheer size, the gene for dystrophin has one of the highest frequencies of mutation.

PCR analysis of carriers and fetuses can identify deletions in dystrophin, and molecular sequencing can identify point mutations. Also, linked markers are useful for prenatal diagnosis when direct analysis does not detect a mutation. If a DMD patient is the first affected family member and a mutant dystrophin allele is not found in his mother, then most of the time it is due to a new mutation. However, ∼10% of such cases are in fact due to maternal germline mosaicism, meaning only some of her cells carry the mutant allele; this is significant due to an increased risk of recurrence.

Cystic Fibrosis (CF) is caused by an autosomal recessive mutation of the cystic fibrosis transmembrane regulator gene (CFTR), which was identified via positional cloning. Cystic fibrosis is due to abnormal fluid and electrolyte transport across epithelial apical (pointed) membranes. This leads to disease of the lung, pancrea, intestine, hepatobiliary tree and male genital tract. Noticeable when kissing a baby with cystic fibrosis, loss of CFTR activity leads to chloride and sodium build-up in sweat glands. Also, the mucous layer of the lung becomes ‘sticky’ and traps pathogens, leading to chronic pulmonary infections..

The first sign of cystic fibrosis is usually high concentration of sodium and chloride in sweat. The average patient survives to ∼33 years, eventually succumbing to chronic lung and heart infections, and maldigestion due to a deficiency of pancreatic enzymes. Many males are infertile due to absence of a vas deferens; most females have near-normal fertility. Postnatal lower intestinal tract obstruction also may occur, treatable by surgery. Some individuals with mutations in the CFTR may have just one or all of these phenotypes.

CFTR

Present on Chromosome 7 (7q31, to be precise), the CFTR gene is ∼190kB and encodes the large 170kD cystic fibrosis transmembrane conductance regulator (CFTR) protein. Likely an ABC transporter, it contains a chloride channel with five domains: two membrane-spanning domains, each of which contain six transmembrane sequences; two nucleotide-binding domains which bind and hydrolyze ATP to power opening and closing the channel; and a regulatory domain, mediated via phosphorylation.

Approximately 2% of white (European) populations carry a cystic fibrosis disease allele, although carriers are almost nonexistent in other populations. The most frequent CFTR defect is δF508, a missense mutation that reduces ATP binding and accounts for 70% of all CF alleles in white populations. Patients homozygous for δF508, or with premature stop codons in CFTR all have insufficient pancreatic activity, but differing pulmonary (lung) disease. Two alleles of a modifier gene encoding transforming growth factor β1 (TGFβ1) are frequent in cystic fibrosis patients with severe pulmonary disease. Also, a cystic fibrosis genocopy (aka phenocopy — an identical phenotype for different genetic reasons) is a mutation in SCNN1, which encodes an epithelial sodium channel. With ∼85% of CFTR disease alleles identified, DNA diagnosis is useful prenatally and to identify carriers amongst relatives of a patient with no familial history of cystic fibrosis. However, the only current treatments for cystic fibrosis are antibiotics, exercise and a nutritious diet.

Fragile X Syndrome is an X-linked mutation in FMR1, which encodes an abundant neuron protein named FMRP. Almost every FMR1 mutation is an expansion of the CGG-repeat sequence in the 5′ untranslated region of the gene. Normal individuals between 6 and 50 CGG repeats, while diseased patients have over 200 repeats. So many repeats does not happen within one generation; it takes several expansions (premutations) over several generations to acquire hundreds of CGG repeats (full mutation). Having over 200 CGG repeats leads to hypermethylation of the repeat region and the adjacent FMR1 promoter, leading to obliteration of FMRP expression. Mental retardation ensues, with a more severe phenotype in males than females. AGG triplets nestled between CGG repeats inhibit AGG expansion; thus, individuals with reduced AGG triplets are predisposed to become carriers of a diseased FMR1 allele.

Almost all males and ∼50% of females with a disease allele will have the Fragile X phenotype. Some patients have a mixture of premutant and full mutant cells (repeat length mosaicism) due to a worsening genotype with every round of mitosis. Patients with over 200 CGG repeats but lacking methylation in some of their cells (repeat methylation mosaicism) or none of their cells range from normal to fully affected. When analyzing a pedigree, increasing prevalence of the disease in successive generations and inheritance from unaffected mothers are both signs of fragile X syndrome.

Huntington Disease (HD) is an autosomal dominant, late-onset, progressively neurodegenerative disorder caused by mutation of the ubiquitously expressed HD gene. Normal HD alleles have 10 to 26 CAG repeats, while disease HD alleles typically contain more than 36 CAG repeats; 97% of disease alleles are inherited, while 3% of disease alleles are new mutations arising from inherited premutations of 20 to 35 repeats. The function of huntingtin — the gene product of HD — is unclear, and it is also unknown how huntingtin encoded by a disease allele leads to the Huntington Disease phenotype.

Age of onset is inversely proportional to the number of CAG repeats in the HD allele. Juvenile onset ensues from over 60 CAG repeats, adult onset ensues from 40-55 CAG repeats and reduced penetrance (possibly no disease phenotype) ensues from 36-41 CAG repeats. Alleles with more than 36 repeats expand during paternal transmission, with somewhat less expansion during maternal transmission. The phenotype includes cognitive loss, behavioral instability and even schizophrenia. As death approaches, motor skills fail such that incontinence and mutism develops; however, behavioral disturbances lessen. The only current treatment for Huntington Disease is pharmacologic treatment of behavioral instability, and lots of support.

Patients with two defective retinoblastoma (Rb) alleles invariably develop retinoblatomas, leading to its discovery as a tumor suppressor. E2F is a key host cell transcription factor in activating cellular genes required for synthesis of dNTPs, DNA polymerases, and other proteins required for cells to begin S-phase. Also, E2F binds and activates transcription from the adenovirus E2 promoter. The E2 region encodes viral proteins required for adenovirus DNA replication. In uninfected cells, retinoblastoma (aka Rb) is bound to E2F and inactivates it; in infected cells, Rb is not bound to E2F — the adenovirus protein E1A binds to retinoblastoma and removes it from E2F. Since E1A deactivates retinoblastoma by binding it and displacing it from E2F, it accomplishes the equivalent of mutations in both retinoblastoma alleles: there is no functional cellular retinoblastoma. SV40 and polyomavirus Large T-antigen also binds Rb; mutations of SV40 and polyomavirus Large-T that did not bind retinoblastoma did not transform cells. p110 is another tumor suppressor that was found to be absolutely identical to retinoblastoma.