Genetics

What is an autosomal recessive inherited disease?

Children inherit one chromosome of a pair from each parent. The chromosome inherited from the father is a mix of his pair of chromosomes, and the one from the mother is a mix of her pair of chromosomes. We have 23 pairs of chromosomes in total, the structures which contain the large macromolecule DNA. DNA is a genetic code, or blueprint, for cells. It is arranged in sections, called genes, most of which contain the code for making proteins. There are therefore two copies of most genes. To cause NCL both copies of a gene must be faulty. This is why the NCLs are called autosomal recessive genetic diseases. Parents of children with NCL each have one faulty copy. To some of their children the healthy copy is passed on and to others the faulty copy is passed on. This is a completely random process. Children may therefore have two healthy copies, one healthy and one faulty copy, or two faulty copies. Only a child who inherits two faulty copies will develop NCL. For this type of inheritance there is a 1 in 4 chance that a child will be affected. Some families will have no affected children (and therefore will not know that they are carrying a faulty gene), but some families have one, two or even more affected children.

How many genes cause Batten disease?

In the early 1990s it was thought that there were four main types of NCL that began in infancy (between 6-18 months), late infancy (2-4 years), at a juvenile age (6-10 years) or in adulthood. Since it was clear from the inheritance pattern that the NCLs were genetic diseases caused by the presence of two faulty copies of a gene, it was thought that there were therefore four genes that could cause NCL. These were called CLN1 (causing infantile NCL), CLN2 (causing late infantile NCL), CLN3 (causing juvenile NCL) and CLN4 (causing adult NCL,). By comparing the DNA from families with the same type of NCL, it is possible to pinpoint the position on the chromosome of the faulty gene. This is a process called genetic mapping. From this it is then possible to identify the gene. In 1995 the first genes that cause NCL were identified. Since then using this and other scientific methods, more NCL genes have been identified. During this work it became clear that more than four genes cause NCL. By 2008 at least eight genes that cause NCL in children had been identified. These are the CLN10/CTSD, CLN1, CLN2, CLN3, CLN5, CLN6, CLN7, CLN8 genes and possibly also the CLCN6 gene. It is known what protein is encoded by each gene and for some it is known what function the protein is involved in, but for others this is not yet clear. The CLN10/CTSD gene causes the earliest onset NCL, which affects babies at birth or even before they are born as well as milder cases that start in late infancy or even in the teenage years. The CLN1 gene causes infantile NCL, and also milder cases with start in late infancy, at a juvenile age and even in adulthood. CLN2, CLN5, CLN6, CLN7 and CLN8 all cause NCL that almost always start in late infancy. CLN2 is referred to as the classic late infantile gene and CLN5, CLN6, CLN7 and CLN8 are referred to as variant late infantile genes because the disease course is slightly different to that caused by CLN2. These four types of variant LINCL are virtually indistinguishable clinically so are sometimes called Finnish, Czech or Turkish variant LINCL respectively because they were first described in families from these countries. CLN3 causes NCL that begins at a juvenile age. Recently two patients with late onset (teenage and adulthood) were described with single mutations in CLCN6.

Are there more NCL genes?

There are families with NCL where the gene that causes the disease does not appear to be one of the known genes so it is almost certain that there are more genes to be identified. These include genes causing NCL that starts in late infancy, and the gene or genes that cause most of the adult cases (CLN4). There are also some pateints whose disease started in the juvenile age range that are thought to have mutations in an unknown CLN9 gene. Animals also get Batten disease. Some of these have been bred to genetically map the genes responsible. There are animals where the gene has been identified and is the same as a known human gene. Other animals have NCL in mutations not known to cause NCL in humans. These animals will be useful to study what happens in the brain during the disease and to try out new treatments or therapies. It is also possible to introduce a fault in a gene to mimic what happens in the disease. This has been done for the known NCL genes in mice and also for other genes that cause NCL-like disease.

What happens when a gene is faulty?

Genes are made up of a repeated sequence of chemical structures commonly referred to as 'bases'. They contain the instructions to make proteins, the building block of the structures and molecules that cause and control all the chemical reactions that occur in cells. The sequence of bases are arranged as a triplet code. Proteins are made up of small molecules called amino acids that are joined together to make the protein. There are approximately 20 different amino acids, each of which is coded for by one or more of the triplet codes. There are also three triplet codes that tell the cell to stop adding any more amino acids because the protein is complete. A gene is faulty when something interrupts the code so that as the cell cannot make a protein with the correct sequence of amino acids. These faults, or mutations, range from the large changes where the whole or a large portion of the gene has been lost to just one single base being lost or changed or a new one added. Changing one base changes the code so that the wrong amino acid is added (a 'missense' mutation), or may change to code to a 'stop' so that the cell finishes the protein too early (a 'nonsense' mutation). If an extra base is added or lost then the frame of the code changes so that the cell reads the code 'out of frame' and completely the wrong sequence of amino acids are added from that point until a 'stop' signal is reached. Sometimes bases are changed outside the part of the gene that encodes the amino acid sequence but which affect the process of copying the gene into an intermediate molecule called mRNA that is the actual template that the cell reads the code from. These mutations may be 'splicing' mutations (the gene is arranged along the chromosome in small sections that need to be copied and joined together to make the mRNA molecule) or changes in regions of the chromosome that tell the cell where a gene is and when to use it (regulatory or promoter mutations).

How many mutations are there?

All the mutations known that cause NCL are listed in the NCL Mutation Database within this web site. More than 150 mutations are known. Some of these occur in just one family. Others in a few or even many families. For each mutation it is important to know how may families carry that mutation and where these families come from. This has shown that for some genes almost all the families in the world have the same mutation in at least one of the copies of the faulty gene (eg the '1 kb deletion' in the CLN3 gene). For other mutations families with the same type of NCL originating from the same country have the same mutation (eg mutation T75P in CLN1 in families with juvenile onset NCL).

What about diagnostics?

It is important to know which type of NCL an affected child has. This can be done at the DNA level by identifying the NCL gene and even the exact mutations in each copy of the faulty gene. It is easier to do this for some of the NCL genes than others. It is easiest to implement a simple DNA-based test for common mutations, so most DNA-based tests that are used or likely to be used routinely will detect the presence of the most common mutation(s) in the NCL gene. The test used in each country may vary according to the mutations found in that country. It is more tricky and time-consuming to look through the whole of a gene for a rare mutation. For three of the genes it is possible to test directly for the presence of functional protein. The CLN1/PPT1, CLN2/TPPI and CLN10/CTSD genes encode enzymes which are proteins that catalyse specific chemical reactions. Using blood or even saliva or urine it is possible detect the activity of these enzymes. An affected child will have no activity, an unaffected person normal activity, and a carrier a level of activity approximately half-way in between.

Why is it important to know which gene is faulty?

If the gene and the underlying mutations that cause NCL in a patient are known then it will be possible to predict the general disease course. This will be particularly useful for families where an affected child has a 'mild' mutation. It will enable planning for future disease-related needs as well as the normal planning for family life, education, career choice etc. As an example a particular mutation in CLN3 (E295K) causes onset of visual failure in the juvenile age range, but there may be no other problems for several decades, in contrast with other mutations in CLN3 where a child may have trouble walking in their teens. In addition knowing the exact mutations may influence the choice of treatment and in the future the most appropriate therapy. For the rest of the family knowing the mutations enables carrier testing and prenatal testing. Some families find that the ability to plan for a child unaffected with Batten disease allows them to contemplate more children which in turn enhances the quality of family life both with an affected child and also gives them hope and brightens their outlook for the future.

Do the genes have something in common?

It is only recently that a biological theme is emerging for the NCLs. The storage material accumulates in cellular structures called lysosomes which is where unwanted material is broken down so that where possible the basic building blocks can be re-used. The CLN1/PPT1, CLN2/TTPI and CLN10/CTSD enzymes are located here and are involved in this degradation process. The CLN3, CLN5 and CLN7 proteins are also in the lysosome, so in some, as yet unknown, way they must contribute to this process. The CLN6 and CLN8 proteins are located elsewhere in the cell, in the endoplasmic reticulum (ER) for CLN6 and the ER and ER Golgi intermediate compartment (ERGIC) for CLN8. The ER is where the actual synthesis of proteins destined for the lysosome (and other places in the cell) occurs. Proteins pass through the ERGIC enroute for the lysosome. So CLN6 and CLN8 may be helping some components along their journey to the lysosome. The cells most affected in Batten disease are the brain neurones. It is not known why this is but there is some evidence that at least some of the NCL proteins may be present in structures in addition to the lysosomes in brain cells. Perhaps it is their special role in brain cells that is being affected most in Batten disease, causing these cells to die.

What research is being done to identify new genes?

For this, samples from families that are not a known type of NCL are being collected so that enough of the same type can be grouped together to make a genetic linkage approach possible. DNA is extracted from blood or cell lines for genetic linkage studies. Initially each family is tested for linkage to known NCL genes. Then, if this is negative, genetic markers across the whole genome are used to pinpoint which chromosome region the new gene or gene(s) is located. The best kind of families for this research approach are those that are consanguineous or inbred as it makes it easier to detect the region that contains the gene. Families that have more than one affected child or lots of unaffected children are also most useful.