Sunday, February 21, 2016

Monogenic Rare Diseases are Surprisingly Complex

"How is it that you keep mutating and can still be the same virus?" - Chuck Palahniuk, in his novel, Invisible Monsters

Monogenic diseases, caused by an aberration in a single gene, account for the majority of rare diseases. Monogenic diseases are the simplest diseases occurring in any organism, and one would think that once we identify the protein coded by the mutant gene, we would fully understand the disease. Nothing could be further from the truth. Knowing the gene, and its protein, may bring us to the root of the disease, but it does not explain how the disease develops; it does not explain the pathogenesis of the disease.

In point of fact, we know very little about the pathogenesis of most of the rare, monogenic diseases. When we try to study the pathogenesis of rare diseases, we quickly learn that they are much more complex than we had imagined. The complexity derives from the general biological properties of genes and of the cellular processes that influence the expression of genes. Let us examine a partial list of factors that add to the complexity of monogenic diseases.

1. A single gene may produce a protein product whose function varies depending on the specific site and type of mutation in the gene. Hence, variations in a gene can produce different diseases.

For example, different mutations of the same gene, desmoplakin, cause the following diseases:
- Arrhythmogenic right ventricular dysplasia 8
- Dilated cardiomyopathy with woolly hair and keratoderma
- Lethal acantholytic epidermolysis bullosa
- Keratosis palmoplantaris striata II
- Skin fragility-woolly hair syndrome

There are hundreds of examples of single genes that can produce more than one disease. Appendix I from my book, Rare Diseases and Orphan Drugs, contains a list of approximately 170 genes, with each gene known to be the underlying cause of more than one listed genetic diseases.

The disease caused by a gene may change depending on whether the gene is expressed as a germline mutation or a somatic mutation. In the case of the MYCN gene, a germline mutation resulting in MYCN gene haploinsufficiency (i.e., for which one gene is non-functional while the gene on its matching chromosome expresses a normal gene product) may produce Feingold syndrome, a developmental disorder characterized by microcephaly, limb malformations, esophageal and duodenal atresias, and other developmental alterations. The same gene, occurring in somatic cells (i.e., as new mutations in tissue cells of adult organisms), as an amplified gene, is associated with neuroblastoma formation.

In some cases, the diseases produced by a specific genetic mutation will change depending on the mutation's parental lineage. Prader-Willi syndrome is a genetic disease characterized by growth disorders (e.g., low muscle tone, short stature, extreme obesity, and cognitive disabilities). Angelman syndrome is a genetic disease characterized by neurologic disturbances (e.g., seizures, sleep disturbances, hand-flapping), and a typifying happy demeanor. Both diseases can occur in either gender and both diseases are caused by the same microdeletion at 15q11-13. When the microdeletion occurs on the paternally-derived chromosome, the disease that results is Prader-Willi syndrome. When the microdeletion occurs on the maternally-derived chromosome, the disease that results is Angelman syndrome.

In some cases, variation in the sites of mutations in a gene do not produce different diseases, but may account for one disease with different levels of severity. For example, in the case of Wiskott-Aldrich syndrome, mutations that truncate the protein product of the WAS gene will produce severe disease, while mutations that produce changes in single amino acids, without changing the length of the protein, will tend to produce mild disease (1).

In some cases, the gain or loss of methylation at a gene site may produce disorders of nearly opposite clinical features. For example, H19 differentially methylated region is a site on chromosome 11p15.5 in which microdeletions occur in some cases of Beckwith-Wiedemann syndrome and Russell-Silver syndrome. Opposite methylation patterns in the H19 differentially methylated region will cause Beckwith-Wiedemann syndrome when there is gain-of-methylation and Russell-Silver syndrome when there is loss-of-methylation (2). Beckwith-Wiedemann syndrome is characterized by tissue overgrowth and tumor formation (3). Russell-Silver syndrome is characterized by dwarfism.

2. A single gene may encode a regulatory protein that effects many other proteins, to produce a disease that affects many different tissues, through unrelated mechanisms. It may be difficult or impossible to determine all the different proteins and pathways that are altered by a defective regulatory gene.

In general, diseases due to genes encoding transcription factors are characterized by multiple anomalies of development and growth. Transcription factors are proteins that bind to specific DNA sequences to control the transcription of DNA to RNA. A mutation in a single transcription factor can produce a phenotypically complex syndrome. For example a mutation in the gene encoding transcription factor TBX5 causes Holt-Oram syndrome, consisting of hand malformations, heart defects and other malformations.

3. A protein with a single function may exert a pleiotypic response in different types of cells and tissues, causing may different phenotypic changes in tissues, to produce a seemingly complex disease phenotype.

Consider the example of the rare disease, ligneous conjunctivitis. Ligneous conjunctivitis is caused by a deficiency of a single protein, plasminogen. Plasmin, the activated form of plasminogen, breaks down fibrin, a protein produced during coagulation and clot formation. In the absence of plasminogen, fibrin accumulates in various sites, and the accumulating fibrin dries out as a hard material. On the surface of the eyes, dried fibrin elicits inflammation, leading to a thick, hardened focus of conjunctivitis (i.e., ligneous conjunctivitis). Accumulating fibrin in the middle ear and the tracheo-bronchial mucosa (of the lungs), leads to inflammation at these sites. In the brain, an occlusive hydrocephalus may occur, due to fibrin deposits blocking the normal flow and clearance of cerebrospinal fluid in the brain ventricles. In retrospect, the pathogenesis of ligneous conjunctivitis is simple to understand. All of the pleiotrophic effects are the result of a deficiency of a single protein, with a single function, that happens to be expressed in several different organs to produce a variety of clinical conditions that are closely related to one another; but not obviously so. Ligneous conjunctivitis is an example of the simplest form of pleiotropism, wherein seemingly unrelated phenotypes result from an alteration in a single expressed protein, and a single functional pathway.

Another example of pleiotypia resulting from a gene with a single function is found in the WHIM syndrome. WHIM is an acronym for Warts, Hypogammaglobulinemia, Infections and Myelokathexis (congenital leukopenia and neutropenia). We now know that WHIM is a combined immunodeficiency disease caused by an alteration in the chemokine receptor gene CXCR4 (4). Warts result from a lowered immune repression of papillomaviruses. Likewise, the other phenotypic components of the disease arise from the aberrant chemokine. Though the altered CXCR4 gene produces a syndrome with a complex phenotype, it does so through the action of one protein with one function.

4. A protein with a single function may exert a single type of response, but that response may depend on the genetic and epigenetic conditions under which the protein is expressed. Hence, different individuals, each with their own unique genome and epigenome, will respond differently to the same genetic aberration.

If a disease were truly caused by an aberration of a single gene, then all of the consequences of the genetic aberration would be identical, in every person with the gene. In fact, some monogenic diseases have remarkably uniform clinical phenotypes in affected populations (e.g., sickle cell disease). What would happen if the same genetic aberration were recapitulated in a mouse. If the mouse homolog served the same purpose as the human gene, and if the gene were the sole cause of the disease, then you might expect the disease to be the same, in man and mouse.

Lesch-Nyhan disease is a rare syndrome caused by a deficiency of HGPRT (hypoxanthine-guanine phosphporibosyl transferase), an enzyme involved in purine metabolism. In humans, HGPRT deficiency results in high levels of uric acid, with resultant renal disease and gout. A vast array of neurologic and psychologic signs accompany the syndrome, including self-mutilation. Neurologic features tend to increase as the affected child ages. The same HGPRT deficiency of humans can be produced in mice. Mice with HGPRT deficiency do not have disease. As far as anyone can tell, mice with HGPRT deficiency are totally normal (5). How can this be? A single gene cannot cause a disease, all by itself. Every monogenic disease is expressed in a complex system wherein the defective gene is a participant in various pathways that eventually lead to a disease. The mouse, evidently, has a set of pathways that compensates for the deficiency in HGPRT.

Diabetes is usually a common polygenic disease. There are rare subtypes of type 2 diabetes that have a monogenic origin. As you would expect, these rare subtypes arise in children, and have a Mendelian pattern of inheritance. One such monogenic form of diabetes is MODY-8 (maturity-onset diabetes of the young), caused by a mutation in the carboxyl-ester lipase gene. This same mutation was delivered to a transgenic mouse, intended as an animal model for MODY. Mice carrying the same altered gene as the human failed to develop any signs of diabetes, or pancreatic damage, or any dysfunction caused by the mutated gene (6).

Though there is often striking phenotypic homogeneity among humans with the same genetic defect, there are many exceptions. Modifier genes can influence the time of onset of disease, the severity of disease, and the clinical phenotype of genetic diseases (7).

5. A single protein encoded by a single gene may have many different biological effects and functions, and these functions may differ based on the cell type in which the protein is expressed, the stage of development in which the protein is expressed, and the cellular milieu (e.g., concentrations of substrate or protein inhibitors) for a given cell type, at a particular moment in time. Hence, a specific aberration in a single gene may produce different diseases, depending on factors that are difficult to anticipate or analyze.

Sometimes, one gene may code for a protein that has multiple different roles, thus producing diseases of widely disparate clinical phenotypes. For example, nuclear lamina (lamin a/c) has several biological roles: controlling nuclear shape; influencing transcription; and organizing heterochromatin. Mutations in the LMNA gene cause more than 10 different clinical syndromes, including neuromuscular and cardiac disorders, premature aging disorders, and lipodystrophy. Likewise, the polyfunctional TP53 gene has been linked to 11 clinically distinguishable cancer related disorders (8).

Rule - A single pleiotropic gene is likely to be associated with several phenotypically unrelated diseases.
Brief Rationale - Genes with pleiotropic pathological effects, and genes that alter a pathway that operates in many different types of cells, are likely to play a role in the pathogenesis of more than one disease, simply because they perturb many different cellular processes.

A bull in a china shop will do more damage than a mouse in a china shop. For example, The APOE gene encodes apolipoprotein E, which is involved in the synthesis of lipoproteins. One common allele of the APOE locus, e4, increases the risk of two common diseases with no obvious biological relationship: Alzheimer disease and heart disease (9), (10). A rare locus of APOE is a associated with longevity (11).

6. The pathogenesis of a monogenic disease may be complex, requiring many events to occur in a particular sequence, over a period of time, culminating in a disease phenotype. Deviations from the usual steps in pathogenesis may delay or eliminate the occurrence of disease.

Many of the rare monogenic diseases express a characteristic clinical phenotype at birth (e.g., birth defects), or in early childhood. A minority of rare, monogenic diseases are not expressed until adulthood. What can we infer from this observation?

Rule - Monogenic rare diseases that express in late adolescence, or in adulthood, are likely to require additional events (i.e., somatic genetic mutations, toxic exposures, or the accumulation of molecular species or cellular alterations caused by the original genetic defect) that occur over time.
Brief Rationale - If this were not the case, every inherited genetic defect would be expected to express itself clinically at birth or in early childhood.

The many inherited cancer syndromes produce tumors in a younger age group than the same tumors that occur sporadically. Still, these inherited tumors tend to occur in early or mid-adulthood, not at or near birth. Cancer is a multi-step process. An inherited mutation that accounts for one step in the process may shorten the time for development of the cancer, but it cannot eliminate the remaining steps.

Huntington disease is a rare monogenic inherited disease that usually begins in adults between 35 and 45 years of age. It is caused by a CAG triplet repeat inside the Huntington gene. The mutant gene slowly poisons brain cells, particularly neurons in the caudate nucleus, putamen, and substantia nigra. The toxic effects of the mutant protein are slow to cause injury, hence the late onset of disease.

Cardiofaciocutaneous syndrome is a rare monogenic inherited disorder characterized by a set of distinctive congenital abnormalities involving the face, heart, and other organs. It is caused by mutations in any of several different genes, including BRAF. In a zebrafish model of cardiofaciocutaneous syndrome, fish embryos express the BRAF disease allele. Treatment of the affected embryos with inhibitors of the pathway affected by the BRAF mutation will restore normal development in these fish (12). The inhibitor needed to be administered in a window of time when the BRAF mutation exerted its teratogenic effect. In this case, the pathogenesis of disease could be interrupted by an additional event occurring at a crucial moment of time.

Rare Disease Day is coming up February 29 (a rare day for rare diseases). In honor of the upcoming event, I'll be posting blogs all month, related to the rare diseases and to rare disease funding.

- Jules Berman (copyrighted material)

key words: rare disease, orphan drugs, orphan diseases, zebra diseases, rare disease day, disease complexity, monogenic diseases, complex diseases, common diseases, jules j berman


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[2] Soejima H, Higashimoto K. Epigenetic and genetic alterations of the imprinting disorder Beckwith-Wiedemann syndrome and related disorders. J Hum Genet 58:402-409, 2013.

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[6] Raeder H, Vesterhus M, El Ouaamari A, Paulo JA, McAllister FE, Liew CW, et al. Absence of diabetes and pancreatic exocrine dysfunction in a transgenic model of carboxyl-ester lipase-MODY (maturity-onset diabetes of the young). PLoS One 8:e60229, 2013.

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[10] Corder EH, Saunders AM, Strittmatter WJ, Schmechel DE, Gaskell PC, Small GW, et al. Gene dose of apolipoprotein E type 4 allele and the risk of Alzheimer's disease in late onset families.Science. 261:921-923, 1993.

[11] Beekman M, Blanch H, Perola M, Hervonen A, Bezrukov V, Sikora E, et al. Genome-wide linkage analysis for human longevity: genetics of healthy aging study. Aging Cell 12:184-193, 2013.

[12] Anastasaki C, Estep AL, Marais R, Rauen KA, Patton EE. Kinase-activating and kinase-impaired cardio-facio-cutaneous syndrome alleles have activity during zebrafish development and are sensitive to small molecule inhibitors. Hum Molec Genet 18:2543-2554, 2009.