Neurometabolic Hereditary Diseases of Adults

This practical book describes only neurometabolic hereditary diseases which have a specific treatment and encourages the general neurologist to think of the most common neurometabolic hereditary diseases, which he might have seen and never considered in the differential diagnosis. Information regarding how to deal with diseases with special therapy is provided (i.e. enzymatic replacement therapy in Fabry disease and Pompe disease), as is information on diseases which are not easily recognized (i.e. Niemann-Pick disease type C), and diseases with clinical features mimicking other common neurodegenrative diseases (i.e. Wilson's disease). Neurometabolic Hereditary Diseases is written with a clinical focus for adult neurologists working in general hospitals.

• Language: English
• Publisher: Springer
• Release date: Jun 4, 2018
• ISBN: 9783319761480

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© Springer International Publishing AG, part of Springer Nature 2018

Alessandro P. Burlina (ed.)Neurometabolic Hereditary Diseases of Adultshttps://doi.org/10.1007/978-3-319-76148-0_1

1. Principles of Human Genetics and Mendelian Inheritance

Dominique P. Germain¹   and Iulia E. Jurca-Simina¹, ²

(1)

Division of Medical Genetics, University of Versailles, Montigny, France

(2)

Center of Genomic Medicine, Victor Babes University of Medicine and Pharmacy, Timisoara, Romania

Dominique P. Germain

Email: [e-mail]

Email: [e-mail]

Basic Concepts of Human Genetics

Every species has a particular series of inherited characteristics (traits) , which determines a developmental plan and distinguishes one species from another. Differences between individuals of the same species ( variations ) are the result of genetic, epigenetic, and/or environmental factors. As the molecular support of heredity of any living organism, genes are transmitted from parents to offspring during the process of reproduction . A gene is the basic physical and functional unit of heredity. The concept of gene was recently redefined as a locatable region of genomic sequence, corresponding to a unit of inheritance, associated with regulatory regions, transcribed regions, and/or other functional sequence regions [1].

In 1869, Friedrich Miescher identified the desoxyribonucleic acid (DNA) as the chemical basis of genes. The genetic information is encoded in DNA, found in each nucleated cell of the organism and mitochondria. In 1953, James Watson and Francis Crick proposed the three-dimensional double-helix structure of DNA, made of two long chains of nucleotide subunits twisted around each other. Each nucleotide contains any of the four bases: adenine (A), thymine (T), guanine (G), or cytosine (C). The bases are complementary (2-paired) on the two DNA strands: A matches with T, and G matches with C [2]. Any change in the genetic material, whatever a base or a sequence of bases, is named a variant or a mutation , and is considered to be the ultimate source of diversity among organisms.

Most visible phenotypic traits result from the interaction of genes together and with environmental factors. This relationship is complex, the proportion and manner in which they affect each other remains largely unknown, but obeys to the following principles:

1.

Every gene can affect more than one trait (pleiotropy),

2.

Every trait can be influenced by the interaction of two or more different genes (epistasis), and

3.

Many traits are significantly affected by environmental factors as well as by genes: for example, the capabilities of children with phenylketonuria can be brought to normal by dietary treatment.

The development of genomics allowed the complete set of genetic information ( genome ) in humans to be deciphered through the human genome project finalized in 2003, further expanding our ability to understand genes involved in physiological functions and diseases [3]. The genetic information is encoded in DNA sequences associated to histone proteins as chromatin in cell nuclei and, for a small part, within circular DNA molecules located in mitochondria. During cellular division (mitosis) , DNA compresses and organizes itself into structures called chromosomes , each of them having a central constriction ( centromere ), a short (p) and a long arm (q). Human organisms are diploid , having two sets of 23 chromosomes that contain one copy of each gene ( allele ), at the same position (locus) on each chromosome (Table 1.1). The human genome contains both coding (genes) and noncoding DNA , the importance of the latter was recently emphasized [4]. Haploid human genomes found in egg and sperm cells consist of three billions of base pairs of DNA, while diploid genomes in somatic cells have twice that DNA content. There are an estimated 17,300–20,000 human protein-coding genes [5] (Table 1.1). Although the sequence of the human genome has now been almost completely determined, many gene functions are not yet fully understood. Our understanding of how genomes direct development, normal physiology, and disease in higher organisms has been hindered by a lack of suitable tools for precise and efficient gene engineering. The simple two-component CRISPR-Cas9 system , using Watson-Crick base pairing by a guide RNA to identify target DNA sequences, is a novel innovative technology. By introducing site-specific modifications in the genomes of cells and organisms, CRISPR-Cas9 has triggered a revolution in which laboratories around the world are using the technology for innovative applications in biology [6].

Table 1.1

Estimated number of genes and base pairs on each human chromosome

Gene Expression

The transformation process from DNA information to protein synthesis is called gene expression and requires the presence of RNA. This complex process includes the transcription of DNA into pre-messenger ribonucleic acid (pre-mRNA), pre-mRNA splicing into mRNA, translation of mRNA into proteins, and post-translational modifications of proteins. Structurally, RNA is assembled as one chain of nucleotides, mostly found in nature folded as a single-strand. RNA contains a different ose than DNA (ribose instead of deoxyribose) and the base uracil (U) instead of thymine (T).

The process in which DNA codes for mRNA and mRNA codes for proteins is seen as the central dogma of molecular genetics.

During translation , a segment of three adjoining bases (codon) of RNA is translated into one amino acid or a stop codon, as determined by the genetic code (Table 1.2).

Table 1.2

The genetic code for nuclear DNA

Each codon codes for an amino acid. Abbreviations for the 20 standard amino acids: Phe (F) Phenylalanine, Leu (L) Leucine, Ile (I) Isoleucine, Met (M) Methionine, Val (V) Valine, Ser (S) Serine, Pro (P) Proline, Thr (T) Threonine, Ala (A) Alanine, Tyr (Y) Tyrosine, His (H) Histidine, Gln (Q) Glutamine, Asn (N) Asparagine, Lys (K) Lysine, Asp (D) Aspartic acid, Glu (E) Glutamic acid, Cys (C) Cysteine, Trp (W) Tryptophan, Arg (R) Arginine, Ser (S) Serine, Gly (G) Glycine. In ribonucleic acids (RNA), thymine (T) is replaced by uracil (U)

The ribosome is the cellular subunit, which hosts the translation process. The messenger RNA (mRNA) is used as a template for protein synthesis. The physical link between the nucleotide sequence of nucleic acids (mRNA) and the amino acid sequence of proteins is made by the transfer RNA (tRNAs) molecules. When a specific codon in the mRNA is recognized, a particular amino acid subunit is incorporated into the nascent polypeptide. The polypeptide synthesis is modulated by specific codons: a start codon (AUG or initiator codon) which codes for methionine and three stop codons (UAA, UGA, or UAG) which result in the termination of the protein synthesis. Nascent proteins commonly require physiological chaperone proteins to reach their mature final form, as the information contained by mRNA is incomplete.

Mutations/Variants

Any cellular process that makes use of a DNA sequence can be affected by a mutation. Changes of one or more codons in coding portions of DNA may alter the amino acid sequence of the synthesized protein. Even a variant in noncoding regions of DNA also has the potential to alter the expression of genes, for example by altering the strength of promoter [7]. This can result in a protein that is partially or totally functionally defective, or in the complete absence of the protein. In contrast, some mutations have no effect or produce new versions of proteins that may result in a survival advantage to the organisms (gain of function) [8].

The term wild type refers to the typical form of a species as it is naturally found. It can mean an organism, or a nucleotide sequence, a set of genes, a gene, a gene product (protein). Originally, the wild type gene was conceptualized as the standard normal allele at a locus, in contrast to any non-standard, mutant allele.

DNA structure can have three basic types of mutations: substitutions , deletions , and insertions (among which duplications ) which appear isolated or in combination. Each of these structural changes can apply for only one or a few nucleotides, entire genes, or chromosomal segments with multiple genes.

Mutations can also be alternatively classified according to their size and impact on the protein structure between two major type of genetic disorders: genomic disorders and monogenic diseases.

Genetic Disorders

A genetic disorder is any disease caused by an abnormality in an individual’s genome, from large-scale chromosomal changes to point mutations including:

genomic disorders resulting from copy number losses (or microdeletions) and copy number gains (or microduplication syndromes), or uniparental disomies (UPD),

monogenic disorders (Mendelian inherited disorders, triplet repeat expansion and mitochondrial disorders),

Approximately 7000 monogenic diseases are known, most of them following Mendelian inheritance.

Genomic disorders are large scale rearrangements in the structure of a chromosome which include:

Copy number variants (CNV) which are duplications or deletions of large regions of genetic material. Microduplications increase the number of copies of a chromosomal segment, augmenting the dosage of the genes located in those regions. Microdeletions of chromosomes result in the loss of the genes located in those regions, leading to a partial loss of function of the protein products when the organisms cannot assure enough normal gene product (haploinsufficiency) or to a complete loss of function in cases of a deletion occurring in association with an amorphic mutation on the other allele, and can be observed in certain type of cancers: e.g. inherited germinal mutation in RB1 on one allele in association to an acquired somatic microdeletion of chromosome 13 in the tumoral cells of the retina (loss of heterozygosity or Knudson theory).

Reciprocal translocations are structural changes consisting of exchange of genetic regions between two non-homologous chromosomes, which do not necessarily cause pathology if there is neither gain nor loss of genetic material (balanced translocations). However, when balanced reciprocal translocation bring together previously separate regions, this may result in expression of fusion genes with oncogenic properties such as the BCR-ABL fusion gene due to t(9, 22)(q34;q11) in chronic myeloid leukemia. When the breakpoint occurs inside a gene, reciprocal translocations can also be responsible for a monogenic disease.

Robertsonian translocations are fusions of two acrocentric (chromosomes 13, 14, 15, 21, 22, and Y) chromosomes centromers with subsequent loss of their short arms (p).

Interstitial deletions are genomic diseases consisting in segmental chromosomal losses which do not involve the telomeres. They can be responsible for contiguous gene syndromes (e.g., 22q11, 22q13, Smith-Magenis syndrome, Williams syndrome).

Chromosomal inversionscan be paracentric or pericentric and can be disease causing (e.g., hemophilia B, Hunter syndrome) or benign (chromosome 9: inv(9)(p13q13)).

Uniparental disomies (UPD).

Monogenic Genetic Diseases

They are due to mutation(s) in a single gene that can be responsible for a gain or a loss of function and include:

Substitutions

(a)

Missense mutations are point mutations consisting in the substitution (not always disease-causing) of an amino acid by a different one (e.g., the homozygous p.Glu6Val missense mutation in the beta globin gene, HBB, is responsible for sickle cell anemia)

The most frequent mutation responsible for Gaucher disease in the Ashkenazi Jewish population is an A-to-G transition at nucleotide c.1226 of the complementary DNA (cDNA) of the acid beta glucosidase gene (GBA) resulting in the change of asparagine by serine at codon 370 (p.Asn370Ser). This mutation is associated only with type 1 Gaucher disease since residual β-glucosidase activity associated with this mutation protects from cerebral involvement. Another T-to-C transition at nucleotide c.1448 replaces leucine by proline at codon 444 (p.Leu444Pro). This mutation is panethnic and often, but not always, found in association with the neuronopathic forms of Gaucher disease when present in the homozygous state [9].

The most frequent mutation responsible for the non-classic phenotype of Fabry disease in Western countries is a G-to-A transition at nucleotide c.644 of the cDNA of the α-galactosidase gene (GLA) resulting in the change of asparagine by serine at codon 215 (p.Asn215Ser). This mutation is associated with a late-onset form of Fabry disease and is amenable to chaperon therapy [10].

(b)

Nonsense mutations are point mutations that result in a stop codon (UGA, UAG, or UAA) with subsequent nonsense mediated mRNA decay (NMD) or premature end of the protein synthesis.

e.g., In transition c.208C>T in the IDUA gene on chromosome 4, the cytosine (pyrimidine) located at position 208 is substituted by a thymine (pyrimidine) introducing a stop codon at position 70 (p.Gln70* or p.Q70X) and subsequent nonsense-mediated mRNA decay (NMD). Nonsense mediated mRNA decay reduces errors in gene expression by removing mRNA transcripts containing premature stop codons [11]. This is a form of RNA surveillance that is believed to have evolved to protect the body from the possible consequences of truncated proteins interfering with normal function [12]. Nonsense mutation p.Gln70* was found to account for 15% of all mucopolysaccharidosis (MPS) type I alleles; this mutation is associated with the severe clinical phenotype of MPS I (Hurler disease ) when present in the homozygous state.

e.g., A C-to-T transition (c.679C>T) at one of the CpG dinucleotides of the GLA gene, which are known mutational hot spots, leads to the recurrent p.Arg227* nonsense mutation responsible for the classic form of Fabry disease [13].

(c)

Frameshift mutations are deletions or insertions of a number of nucleotides that is not a multiple of 3 from/in a DNA sequence, leading to an alteration in the reading frame of the gene (frameshift) and frequently resulting in a premature stop codon with nonsense mediated mRNA decay or protein truncation (e.g., the duplication of the guanine located at position c.84 of the complementary DNA (c.84insG) of the GBA gene at locus 1q21 leads to a frameshift in the reading frame leading to Gaucher disease when found in a homozygote (type 2 Gaucher disease) or a compound heterozygote for a different GBA mutant allele.

(d)

Splice mutations are mutations that substitute nucleotides in specific sites involved in the splicing of introns from precursor messenger RNA into a mature mRNA. Mutations in the canonicalconsensus splice sites located at the exon–intron boundaries (GT at the donor site and AG at the acceptor site) may lead to retention of segments of intronic DNA in the mRNA or to entire exons being spliced out of the mRNA (exon skipping). Eukaryotic genomes naturally contain a number of splice sites, known as cryptic splice sites which are generally dormant or used only at low levels unless activated by mutation in nearby authentic (or advantageous) splice sites. If activated, cryptic splice sites may be used, resulting in genetic diseases [14]. In addition, base substitutions resulting in apparently silent missense mutations can cause aberrant splicing through mutation of exon splicing enhancer sequences.

Triplet-repeat expansions (repetitions of a DNA segment consisting of three nucleotides) are a distinct category also known as dynamic mutations (the number of repeats may increase from one generation to another). For example, Huntington disease exhibits an autosomal dominant pattern of inheritance and is associated with increased CAG repeats in the HD gene located on human chromosome 4. Individuals with more than 36 CAG repeats express a progressive motor, cognitive and psychiatric dysfunction. Myotonic dystrophy due to an expanded CTG triplet at the 3′ of the DMPK gene is also an autosomal dominant neurological disease which exhibits a reduced age of onset and increased severity of the disease over generations in families (anticipation). This is due to the fact that the length of the CTG repeats increases with each successive generation especially when the mutation is passed on to an offspring through the maternal lineage, possibly culminating in congenital Steinert disease in the latter.

Variants of unknown significance (VUS) represent ambiguous or uncertain mutations for which pathogenicity has neither been demonstrated nor excluded in published literature, mutation databases, or in the clinic. Next generation sequencing (NGS) , often identifies such allelic variants in the 20,000–22,000 known genes: e.g., p.(Leu3Pro), p.(Arg118Cys), p.(Ser126Gly), p.(Arg143Thr) are variants of unknown significance of the GLA gene, which are likely benign, in contrast to pathogenic, disease-causing, variants of GLA that are responsible for Fabry disease. Such variants of unknown significance present a clinical interpretation challenge raising genetic counseling dilemmas [13].

A variant or mutation is defined as any change in a DNA sequence, while a polymorphism is a non-pathogenic DNA sequence variant that is common in the population. In this case, no single allele is regarded as the standard sequence. Instead there are two or more equally acceptable alternatives. The arbitrary limit between a polymorphism and a variant is a minimal allele frequency (MAF) of 1% (by definition a polymorphism has a MAF > 1% in the population). If the frequency is lower than 1%, the allele is categorized as a variant : e.g., the allele frequency in the normal population of p.Asp313Tyr or p.D313Y is approximated 0.5%. Individuals with this benign variant do not present clinical manifestations of Fabry disease, but can occasionally have reduced plasma α-galactosidase activity (pseudo deficiency of the α-galactosidase, not clinically associated with Fabry disease). Similarly, the p.Glu66Gln (p.E66Q) benign variant of GLA has a minimal allele frequency of 0.5% in Asian populations. Both are non-disease causing GLA variants that should not be treated neither with enzyme replacement therapy nor with chaperon therapy.

Introduction to Mendelian Inheritance

The principles attesting how genes passed from one generation to the next were first described by Gregor Mendel in 1865 in Brno, Czech Republic [15]. Mendel analyzed the pattern of transmission of single traits in generations by crossing different varieties of pea plants (Pisum sativum). Mendel’s laws were rediscovered more than 30 years later when three botanists, de Vries, von Tschermak and Correns, carried out similar experiments with plants and arrived at conclusions similar to those of Mendel. Coming across Mendel’s paper, they interpreted their results in terms of Mendel’s principles who is therefore considered as the founder of genetics through his discovery of the principles of inheritance. Mendel conducted breeding experiments from 1856 to 1863. He observed that when crossing strains bred for opposite traits such as tallness and shortness, all of the offspring in the first generation (F1) were tall. Interbreeding plants in F1 generation led to both tall and short plants in a ratio of 3:1 in F2 (Fig. 1.1). Traits that were expressed in the F1 hybrids were called dominant, only one allele of a pair being required to manifest a phenotype; traits that needed both identical alleles to reappear in the F2 generation were referred to be recessive. This can be described by the notation TT, Tt, and tt, where T is dominant and t is recessive. Plants with the two identical genes used in the initial cross (TT, tt) were described as homozygotes (pure-bred plants), whereas the hybrid F1 plants with one gene for tallness and one for shortness were called heterozygotes. Hence, TT is homozygous dominant, Tt heterozygous, and tt homozygous recessive. Mendel’s conclusion was that every studied trait in offspring was dictated by a pair of factors, each being inherited from one parent [15].

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Fig. 1.1

An illustration of one of Mendel’s breeding experiments . All the offspring in the F1 generation have the Tt genotype and a tall phenotype. In the F2 generation, ratios are 25%, 50% and 25% for TT, Tt and tt genotypes, respectively, with the tall phenotype accounting for ¾ cases

Based on Mendel’s research, three main principles were established, known as Mendel’s laws of uniformity , gametes segregation, and independent assortment [15]. Mendel’s laws are applicable for all autosomes.

The law of uniformity states that crossing two homozygotes for different alleles, each offspring in the F1 generation is identical and heterozygous. The traits do not blend and can reappear later in generations.

The law of gametes segregation refers to the fact that each individual possesses two alleles for a particular trait, and only one of these can be transmitted to one offspring. There are rare exceptions to this rule when the two alleles do not separate through chromosome non-disjunction at the first meiotic division.

The law of independent assortment states that allele pairs are separating independently during the meiosis, leading to a random recombination of the haploid parental genetic material. There are exceptions for genes that are located close together on the same chromosome which tend to be inherited together, because of genetic linkage.

Drawing a Pedigree

In humans it is impossible to control mating; consequently, genetic analysis is achieved through the