Update on chromosome 15 duplications: idic(15) and interstitial duplications: The duplication 15q syndrome

N. Carolyn Schanen, M.D., Ph.D.

This paper was presented by Dr. Schanen at the 2005 IDEAS Conference. Dr. Schanen is the Head of Human Genetics Research for Nemours Biomedical Research. She sits on the professional advisory board for IDEAS.

How common are duplications of chromosome 15?
Several types of studies have been done to address this question. First, population studies have been done to examine the frequency of extra chromosomes, often called marker chromosomes, in newborns. Based on those studies, 1 in 8000 people carry an extra chromosome that came from chromosome 15. The most common type of marker chromosome 15 is tiny and contains few active genes, thus they do not usually cause any problems and are only identified incidentally when chromosome testing is done for other reasons¹. In rare cases, the presence of this extra chromosome can cause errors in sorting of the chromosomes into the egg or sperm cells, and thus leading to either Prader Willi or Angelman syndromes.

Studies have also been done to specifically examine the role of chromosome 15q duplications in several neurologic and developmental disorders. Moeschler and colleagues (2002) looked for duplications in 400 children with developmental delay and found evidence for duplications in two children (a third child may also have had a duplication but they did not further analyze the chromosomes so it is not clear whether it is really a duplication)². In contrast, no duplications were found in a study of 285 patients with moderate to severe mental retardation (although they found other abnormalities of chromosome 15)³. A large study of 3392 patients referred for developmental delay or autism of whom only 540 underwent DNA testing as well as chromosome testing found that ~1/600 cases had an interstitial duplications although they did not mention whether patients with idic(15) chromosomes were also found⁴. Two studies that included a total of 226 patients with autism found duplications in ~3% of the patients^{5, 6} while only one patient with a duplication was found in a group of 118 patients with epilepsy⁷.

What causes them? Why do they occur? When did that happen?
We are learning a lot about the structural features of the long arm of chromosome 15 that predisposes it to rearrange and make duplication chromosomes (these same features cause it to delete the same segments of DNA). Chromosomes normally line up during the formation of an egg or sperm and exchange segments of DNA. This alignment occurs early in the formation of the egg and sperm, but because of differences in how these cells develop that is different for an egg or a sperm. In an egg, this alignment while the mother is a fetus in her mother’s uterus. In sperm this occurs continuously from puberty through adult life.

The alignments have to be done precisely or there will be DNA that is lost or gained during the exchange. To line up correctly, the chromosomes line up based on the sequences of their DNA. On chromosome 15, there are repeated regions that share nearly identical DNA sequence. These sequence repeats lead to duplications and copying errors by predisposing to misalignment of the paired chromosomes.
Since errors in lining up contribute to the generation of the duplication chromosome, and this step occurs in the early stages of development of the germ cells (eggs and sperm), it is likely that duplications that arise on the maternal chromosome 15 origninated while the mother was in her mother’s uterus.

There are five main positions that are involved in the generation of duplication chromosomes because of clusters of repetitive DNA sequences along the arm of the chromosome. Importantly, these repeated regions contain active genes, so understanding the positions that are involved in making the duplication chromosomes may help us understand the variability in the symptoms of people who carry duplications- the symptoms may depend on the regions that are duplicated, which repeat was involved and possibly the specific position of the exchange within the repeat.

We know that the part of chromosome 15 is involved in two other disorders, Prader Willi syndrome and Angelman syndrome, how does research on those disorders help us understand duplications of chromosome 15?
Prader Willi and Angelman syndromes are most often caused by deletions of chromosome 15q11-q13. The differences in the symptoms that occur in these disorders are based upon the parental origin of the chromosome that is deleted. Studies in these disorders have focused on determination of which genes in the region are used differently on maternally-derived versus paternally derived chromosomes. This process is called imprinting and is very likely to be important in idic(15) and int dup(15). There are several genes that are active only from the paternal chromosome and two genes that are known to only be active on the maternal chromosome 15. The control region that regulates parent-of-origin specific expression is included in the region that commonly is duplicated in idic(15) and int dup(15). One gene in the region is involved in pigmentation (P gene) and several recent papers have noted unusual skin pigmentation in patients with duplications. In patients with Prader Willi and Angelman syndrome, decreased pigmentation has been noted frequently⁸. The extra copies of the P gene in dup(15) syndromes, may lead to increased pigmentation in some children⁹.

Are most duplications are inherited from the mother?
For idic(15) and int dup(15), the symptoms are more obvious if the chromosome came from the mother, because they include the learning disabilities, autistic features, muscle tone changed, and minor facial features. Thus, there is some degree of bias for identifying patients with the maternally derived duplications- they are a lot easier to recognize and more likely to get chromosome testing done. One study in 2004 identified a case of a paternal duplication associated with autism as well¹⁰. Nonetheless, it seems likely that duplications occur more frequently on the maternal chromosome although we are likely to be missing many patients with paternally derived duplication chromosomes. This would be in keeping with what has been reported for the deletions in Prader Willi and Angelman syndromes where the deletions are more common on maternal chromosome and thus lead to Angelman syndrome (estimated at ~1/15,000) and paternal deletions that lead to Prader Willi syndrome are estimated at ~1/30,000.

What do we know about the region that gets duplicated?
The most commonly duplicated region contains at least 20 genes. Of these, two genes are known to be expressed from the maternal copy of chromosome 15 and at least 5 are known to be expressed from the paternal copy of the chromosome. Because maternally derived duplications tend to cause more significant developmental problems, these genes are likely to be important in duplications of chromosome 15. The two genes known (so far) are UBE3A and ATP10A (aka ATP10C). Importantly, the imprinting process that regulates activity of these genes from the specific chromosomes is most apparent in brain, while in other tissues in the body both maternal and paternal genes are active. Note: One of the world’s experts on UBE3A is Dr. Art Beaudet from Baylor College of Medicine, who will be attending the meeting.

The UBE3A gene encodes a protein that is involved in degradation of other proteins in the cell. Loss of protein product arising from errors in the gene or deletion of the gene causes Angelman syndrome. It is expressed by many cells in the body (which actually express both copies of the gene) and nerve cells in the brain, which only use the maternal copy. This gene is present in 4 copies in most children with idic(15) and 3 copies in most patients with interstitial duplications. Studies done by Laura Herzing’s lab have shown that the extra copies of the gene are active in patients with idic(15) chromosomes¹¹.

The ATP10A gene makes a protein that is thought to be involved in moving calcium in and out of cells. It is expressed by the brain and most people with idic(15) chromosomes carry two additional copies of the gene while most children with interstitial duplications have one extra copies.

There are also 3 GABA receptor genes in the region that is commonly duplicated. GABA receptors are neurotransmitter receptors that are inhibitory in function and play important roles in virtually brain functions. A functional GABA receptor is composed of several parts, and it is believed that expressing extra copies of some components will lead to fewer functional receptors although this needs to be tested. In mice, abnormal over- or underexpression of individual parts of GABA receptors often leads to seizures, thus it is likely that the increased numbers of receptors are part of what predisposes kids with duplications of 15q11-q13 to seizures. Many seizure medications target the GABAergc system to try to inhibit seizure activity.

Have there been any studies on treatments for children with chromosome 15 duplications?
A group at the University of California, Davis, reported three families, which included five people with interstitial duplications of chromosome 15. The children had ADHD, PDD or Autism¹². 3/5 were treated with methylphenidate (Ritalin) for their ADHD symptoms and responded well. One of these children had also been given a trial of adderall but did not respond as well so was placed back on methylphenidate. Respiridone had mixed effects- for one child it was beneficial and one responded poorly (no details given). Fluoxetine was not beneficial for and of the 3 children treated with it- two had aggressive behaviors and one was reported as not responding. Since the last meeting in 2003, no larger studies have been done to see which medications work best for the behavioral parts of the dup(15) symptoms. Based on the discussions on your list serve and the clinical data that we accumulated as part of our study, we suspect that patients with chromosome 15 duplications may tolerate medications differently and may be more sensitive to side effects for some classes of medications, such at the serotonin reuptake inhibitor type medications (SSRI). Thus, these should be used with caution and any new medication should be instituted in a controlled setting, with slow titration of levels and with a clear endpoint as to what the expected outcome for treatment is. This includes supplements.

What has our study of chromosome 15 duplications found?
We are looking at various components of the structure of the duplicated chromosomes as well as the symptoms manifest by the child. So far we have gotten samples from 82 people with duplications of chromosome 15 and have done clinical assessments on 60 people. We have also assessed 12 cases that we do not have DNA samples to study.

Nicholas Wang, (now PhD, 2004) performed his doctoral work designing a tool to rapidly assess the size of the duplications and number of copies of the regions that are present. This tool is called array comparative genomic hybridization (array CGH) and involves taking specific pieces of DNA from chromosome 15 and sticking them to a glass slide. The DNA from the person with the duplication is then tagged with a fluorescent green dye and DNA from the parent is then tagged with a fluorescent red dye. The DNAs are then mixed together in equal amounts and allowed to stick to the DNA on the glass slide. They should stick specifically to the ones that they match by sequence. If the number of copies of a specific sequence are the same between the parent and the child, the fluorescence signal from the slide emits yellow light- indicating that both stuck to the slide in about the same amount. If there is a region that is present in higher copy because of the duplication, the green DNA from the patient will be more likely to stick- so there is a bias is the signal toward green.

Using a laser to capture the amount of green to red signal for each of the spots of DNA on the glass slide and quantitiating the relative signal difference, Nick was able to distinguish whether there were 1, 2, 3, or 4 extra copies of the duplication regions. His work allowed us to sort out the differences in the BP4:BP5 versus BP3:BP3 duplications¹³. (He is now at the Lawrence Berkeley lab in Berkeley California.)

Chromosome findings:
Although most reports describe idic(15) chromosomes as mirror images, which would mean that they carry two additional copies of the DNA in the region, we see that most of them are asymmetric and lead to one extra copy of part of the region and two extra copies of other parts of the region. The most common form occurs between an exchange between BP5 and BP4.
Most common form (BP4-BP5)

Second most common form (BP3:BP3)

Of our samples, most are idic(15) but we have several familial cases of int dup(15).

We have not formally analyzed the clinical data but the simple overview of clinical data does not show an obvious correlation of the size of the duplication region with the severity of the symptoms. Detailed analyses are planned when we complete the clinical testing.

Clinical findings:
As noted in the previous meeting, we have been working with the research group at Duke to examine the symptoms of kids with duplications of chromosome 15 compared with typically developing kids and kids that have autism but no chromosome abnormality. Looking at the first 41 kids, we find a remarkable variability in how the kids are doing when we sort them by age. In general, kids with typical interstitial duplications have milder cognitive symptoms and fewer seizures. Children with idic(15) chromosomes tend to sit and walk later than both typically developing and other autistic kids, 95% were walking by age 5 years and the onset of language peaks around age 4-5 years. 14/41 children had their first word by age 5 years, 2 began using words between 5-10 years and one acquired his/her first word after age 10 y. Phrase speech was present in 12/41 children. The average age at first word is 28 months and first phrase 45 months. The children who had better “joint attention” skills (the ability to direct someone else’s attention to something that you are interested in) had better language scores. We also looked at some adaptive skills and 9/41 achieved bladder control by age 78 months (6.5 y, range 30-78m) and 8/41 were toilet trained for bowel and bladder functions by 84 months (7 y, range 30-84 m). We plan to extend these analyses on the larger group when we have completed the clinical assessment.

Supplemental figure to show model of how idic(15) chromosomes form

References

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