Rare inherited coagulation and fibrinolytic defects that challenge diagnostic laboratories

Model Explains Disorders Caused By Improper Transmission Of Chromosomes

Parents of healthy newborns often remark on the miracle of life. The joining of egg and sperm to create such delightful creatures can seem dazzlingly beautiful if the chromosome information from each parent has been translated properly into the embryo and newborn.

The darker side is that when extra copies of chromosomes or fewer than the normal 46 (23 from each parent) are present, tragic birth defects can occur. Now, scientists at the University of Georgia have developed a model system for plants and animals that shows the loss of a key structural protein can lead to the premature separation of one DNA copy called a chromatid.

The new model shows for the first time that the loss of this protein can lead to aneuploidy—the name given to birth disorders caused by extra or too few chromosomes. Disorders caused by errors in the proper transmission of chromosomes from each parent are uncommon but tragic nonetheless. Best known may be Down Syndrome, which is caused by an extra copy of chromosome 21. Many errors in chromosome transmission are so severe that miscarriages usually occur.

"As we know, human females have all the eggs they will ever have from the time of birth, and so as they age, the protein structures on chromosomes also age," said Kelly Dawe, a geneticist and plant biologist at UGA. "If an egg is fertilized late in life, the final stages of chromosome separation may not occur properly. The goal of the work, which was done in maize, is to find out which parts of the chromosomes are most sensitive to failure. We now believe that proteins in a structure called the kinetochore are among the most sensitive to degradation or mutation. That may be a clue as to why older women have more problems with these kinds of chromosomal disorders when giving birth than younger women."

The research was published today in the journal Nature Cell Biology. Co-author on the paper is former University of Georgia graduate student Xuexian Li.

Irregularities in chromosome number are usually caused during a biological event called meiosis, in which the number of chromosomes per cell is halved and, in animals, results in the formation of gametes or sex cells. While the biology of meiosis has been known for more than a century, major questions remain about how all the constituent cell parts must coordinate to make the process successful.

During the two stages of meiosis, chromosomes are first separated by type, ensuring that only one of each gene is represented and then separated in half again in preparation for fertilization. The authors showed that the first stage is orchestrated in part by the kinetochore that attaches chromosomes to the rest of the cell. When they suppressed a kinetochore protein called MIS12, the chromosomes no longer separated by type and jumped to the second stage before completing the first. These failures closely mimic those seen in eggs from older women.

The cell division processes that Dawe and Li studied have implications for other diseases—such as cancer—as well. And yet a genuine payoff may come in the form of genetically improved lines of corn.

Dawe's work opens the possibility of a more positive outcome: the ability to engineer so-called "artificial chromosomes" with useful genes into corn varieties. Though that may be years off, it could offer a way to create lines that could resist drought, disease and insect pests without harming the environment.

Researchers are racing to design artificial chromosomes that behave like natural ones. With such an engineered chromosome, the positives traits researchers could give to corn plants would be almost limitless.

"You could really put genes in there at will, stacking traits that would make the plants able to withstand problems that now limit production greatly all over the world," said Dawe. "But to get from theory to practice, we will need a much clearer understanding of meiosis."

Unfortunately, most early generation artificial chromosomes have failed at meiosis in a nearly identical manner as plants with reduced MIS12. By manipulating MIS12 or other similar proteins, Dawe hopes to correct these defects.

Some Genetic Disorders May Be Caused By Defects We Couldn't Detect

You have two copies of each chromosome, one from your mom and one from your dad. And your parents' two copies get scrambled together before they get passed on to you, so the copy of chromosome 1 you got from your mom is a unique composite of the two copies she got from her two parents. Same with the copy of chromosome 1 you got from your dad.

This process is called recombination, and the mixing of genes it allows is one of the primary benefits of sexual reproduction. According to geneticists, anyway. But now it seems that recombination is responsible for more genetic issues than we had previously surmised.

Like elections and everything else in this world, recombination doesn't always go smoothly, and different types of errors can happen. Genetic sequences can get inverted or duplicated when they are moved from one chromosome to another; or they can get spliced into the wrong place, disrupting a gene. These errors have clinical ramifications, often resulting in neurodevelopmental disorders, especially autism spectrum disorders and intellectual disability.

Chromosomal abnormalities are often still diagnosed by looking through a microscope at the actual chromosome (a process called karyotyping), despite the advent of sophisticated DNA tests. It is a powerful technique, but it is limited to changes that are big enough to disrupt the structure of a chromosome. If the cytogenic abnormality is small and balanced—if it occurs without any gross gain or loss of genetic material to the chromosome—it won't be seen.

An international consortium of researchers mapped the sites of chromosomal abnormalities in 248 people with various congenital abnormalities, and their sequencing analysis revised the breakpoint identified by karyotyping in ninety-three percent of cases. This doesn't mean that karyotyping is wrong, just that it's very inexact compared to checking out the actual DNA.

Hunt For Chromosomal Errors Which Cause Genetic Diseases

Commercially available gene chips have been used by a pediatric research team to scrutinize all of a patient's chromosomes in order to identify small defects that lead to genetic diseases .

Because currently used genetic tests usually cannot detect these abnormalities, the new research may lead to more accurate diagnosis of congenital diseases, including puzzling disorders that lead to mental retardation.

"For years, many children who have multiple congenital problems, such as developmental delays, heart defects and facial abnormalities, have gone undiagnosed because they may not have an easily recognizable syndrome," said study leader Tamin H. Shaikh, Ph.D., a molecular geneticist at The Children's Hospital of Philadelphia.

"Until recently, our laboratory technology was not sufficiently refined to detect many of these small rearrangements in chromosomes," added Dr. Shaikh. "Now we have a better tool for finding the abnormal gene or genes that give rise to a disorder." The research is published in the May 2006 issue of Human Mutation.

For many of these rare disorders caused by small errors in chromosomes, improved diagnosis does not mean that physicians can provide more effective treatments, at least not immediately. In the long run, adds Dr. Shaikh, better knowledge of the underlying genetic cause of a disease may provide targets for designing future therapies.

Conventional genetic tests have limited resolving power in detecting many chromosomal arrangements. In karyotyping, chromosomes are stained and examined under microscopes, but only larger rearrangements are visible, such as extensive deletions, or the presence of an extra chromosome, as occurs in Down syndrome. Another technique, subtelomere analysis, finds smaller, submicroscopic abnormalities, but only in the regions directly below the telomeres, at the end of each chromosome.

Recent advances in diagnostic gene chips, used by Dr. Shaikh's team, allow more precise analysis of very small DNA alterations throughout all of a patient's chromosomes.

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-- Gene Chips Detect Tiny Structural Defects in Genomic Diseases --

Conditions that originate in alterations of chromosome architecture have been called "genomic diseases." The smallest of these structural defects are microdeletions, a loss of a small amount of genetic material, or microduplications, an excess of genetic material.

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Individually, many genomic diseases are rare, but collectively, they may occur in one in 1,000 live births. Frequently the gene aberrations harm multiple organ systems. For example, patients with chromosome 22q11.2 deletion syndrome may have heart defects, impaired immunity and developmental delay. Deletions of several genes in Prader-Willi syndrome may cause obesity and mental retardation.

To seek out miniscule rearrangements in chromosomes, the Children's Hospital team employed the types of gene chips, or microarrays, originally designed to identify genes involved in common, complex diseases like diabetes and hypertension. Microarrays contain short fragments of DNA, called oligonucleotides, that bind to complementary stretches of DNA within a sample being tested. These microarrays hold more than 100,000 DNA oligonucleotides, which allow researchers to rapidly analyze a person's whole genome — the entire complement of DNA in a cell nucleus.

"These microarrays provide more rapid and precise results than karyotyping, and offer as much as 50 times higher resolution than other, more commonly used microarrays, such as bacterial artificial chromosome arrays," said Dr. Shaikh. "Our study is one of the first to report using these microarrays in a clinical setting to detect constitutional rearrangements which lead to severe birth defects." Constitutional rearrangements occur in all of a person's cells.

-- As Technology Improves, Smaller Defects Should Be Detectable --

In the current paper, the research team first validated the microarray by using it to test samples from two patients with known chromosomal rearrangements and well-characterized genetic diseases. In a blinded analysis, the experiment found the correct location of the abnormal regions.

In the second part of the study, the researchers studied samples from 10 patients with multiple congenital anomalies, all of whom had previously normal results from karyotype and subtelomeric testing. The team identified novel submicroscopic deletions in two patients. These deletions, one on chromosome 1 and the other on chromosome 3, were not detected in the patients' parents, providing strong evidence that the deletions were the underlying cause of the multiple defects seen in the children.

Dr. Shaikh's laboratory has subsequently used the microarray to analyze DNA samples from more than 60 patients, and have detected novel microdeletions and microduplications in 25 percent of the cases. He also has received a grant to investigate chromosomal rearrangements in bipolar disease, a complex disorder thought to involve interactions among multiple genes.

Dr. Shaikh is currently collaborating with other researchers at Children's Hospital to evaluate other, higher-density gene chips (holding more than 500,000 oligonucleotides), which provide greater resolution. His team is also developing better computational tools to evaluate data from these chips. "Our ability to detect even smaller rearrangements will only get better as there are improvements in the resolution of the microarrays and the computational tools required to analyze and mine the data generated," said Dr. Shaikh.

As he pursues ongoing studies to enroll and study more patients with congenital defects, Dr. Shaikh collaborates with Elaine H. Zackai, M.D., director of Clinical Genetics at Children's Hospital. "It is extremely rewarding to finally have tools to identify heretofore undetectable, cryptic rearrangements and to be able to provide a diagnosis for the patients and their families," said Dr. Zackai.

The National Institutes of Health supported this research, as did the Ethel Brown Foerderer Fund at Children's Hospital. Dr. Shaikh's co-authors, all from The Children's Hospital of Philadelphia, are Jeffrey E. Ming, M.D., Elizabeth Geiger, Alison C. James, Karen L. Ciprero, Manjunath Nimmakayalu, Ph.D., Yi Zhang, Andrew Huang, Madhavi Vaddi, Eric Rappaport, Ph.D., and Elaine H. Zackai, M.D. Drs. Shaikh, Ming and Zackai also are faculty members of the University of Pennsylvania School of Medicine.

About The Children's Hospital of Philadelphia: The Children's Hospital of Philadelphia was founded in 1855 as the nation's first pediatric hospital. Through its long-standing commitment to providing exceptional patient care, training new generations of pediatric healthcare professionals and pioneering major research initiatives, Children's Hospital has fostered many discoveries that have benefited children worldwide. Its pediatric research program is among the largest in the country, ranking second in National Institutes of Health funding. In addition, its unique family-centered care and public service programs have brought the 430-bed hospital recognition as a leading advocate for children and adolescents. For more information, visit http://www.Chop.Edu.

Source: Newswise

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