Genomic Imprinting and Uniparental Disomy in Medicine

Genomic Imprinting and Uniparental Disomy in Medicine: Clinical and Molecular Aspects

Eric Engel, Stylianos E. Antonarkis

Copyright # 2002 Wiley-Liss, Inc. ISBNs: 0-471-35126-1 (Hardback); 0-471-22193-7 (Electronic)

Chapter 11

Epilogue of an

Unfinished Story

The important thing is not to stop questioning.

Albert Einstein (1879–1955)

The discovery of the fascinating phenomena of uniparental disomy (UPD) and genomic imprinting generated a plethora of important biological questions that need to be addressed in the next few years. The answers to these questions will enhance our understanding of the importance of parental-specific gene expression, its contribution to normal development, and association with disease phenotypes.

Clearly, the UPD and genomic imprinting is an unfolding and thus unfinished story and much more fun in understanding both lies ahead in the years to come. The list of yet unanswered questions is long and some of these questions are presented below. This list is by no means exhaustive and only represents the biased views of the authors.

UPD and Human Disorders

How many genes (and which ones) are imprinted from the maternal and the paternal genome?

How many additional disorders are due to UPD or imprinted gene dysfunction?

What is the role of segmental UPD in somatic cells? What is the spectrum of human disorders due to segmental UPD?

What is the involvement of UPD in embryonic lethality?

What is the involvement of UPD in male or female sterility (subfertility)?

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272 EPILOGUE OF AN UNFINISHED STORY

The Genetic Control of UPD and Imprinting

How exactly is parental-specific gene expression generated in the germ cells and maintained in the somatic cells?

Are there cis-genomic sequences that distinguish=mark an imprinted gene or an imprinted genomic region?

What is the biochemical basis of gene silencing in the imprinted chromosomal regions?

How is the imprinting mechanism regulated? What are the different levels of control?

Which are the proteins involved in the recognition of imprinted genes and regulate their expression?

Treatment of UPD=Imprinting-Related Phenotypes

Can we treat abnormalities of imprinting? Could we imagine to exogenously regulate the paternal or maternal expression of a given gene?

Evolutionary Significance

What is the evolutionary significance of parental imprinting?

The completion of the initial phase of the sequence of the entire human genome (International Human Genome Sequencing Consortium, 2001; Venter and et al., 2001) and the identification of all genes will greatly enhance the knowledge on UPD and imprinting. It is anticipated that we will soon identify not only the complete set of genes with parental-specific gene expression, but also the sequences necessary for the regulation of imprinting. The discovery of large numbers of DNA polymorphisms of the human genome, both SNPs (single nucleotide polymorphisms) (The International SNP Map Working Group, 2001; Mullikin et al., 2000; Deutsch et al., 2001) and SSRs (short-sequence repeats) (NIH=CEPH Collaborative Mapping Group, 1992), that could distinguish chromosomal or protein alleles will enhance our chances to identify additional disorders with full or segmental UPD. Furthermore, the sequence of the mouse chromosomes and the identification of murine homologues of the human imprinted genes [see, e.g., (Onyango et al., 2000)] will provide more experimental opportunities for in vivo testing of hypotheses in embryos that could not be done in humans. The advances in methods of comparison of global gene expression (Brown and Botstein, 1999; Velculescu et al., 1995) will also facilitate the study of imprinted genes in cells, tissues, and organs at different developmental stages in health and disease. Finally, the methods for global analysis of proteins (Pandey and Mann, 2000) would assist in the characterization of gene products of imprinted genes.

SEGMENTAL UPDS ARE PERHAPS COMMON AND PATHOGENETICALLY IMPORTANT

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The mouse model will continue to be an excellent experimental organism to study UPD and imprinting (see Chapter 10) and many more transgenic and knock-out mice will be developed in the years to come that would undoubtedly elucidate many processes and answer many questions. But, what are the differences (in terms of imprinting) between us and the mouse? Could we study all the human pathologies using the mouse model or do we need to invest in human embryo research to understand aspects of human disorders that we cannot study in the mouse?

The sequence of the genomes of other laboratory model organisms, such as the fruitfly Drosophila (Adams et al., 2000) and the C. Elegans worm (The C. Elegans Sequencing Consortium, 1998), also provides an opportunity to study the function of the human homologues of the genes with parental-specific expression. An obvious question is that of the significance of imprinting in these organisms. If such phenomenon exists in these model organisms, then the laboratory investigation of many imprinting-related questions may be done in these species.

Below we enumerate some future topics of research of clinical significance.

ARE THERE LETHAL UPDs?

It is likely that some of the UPDs so far undetected are embryonic lethal and therefore selected against. Thirteen years after the description of the first clinical case of UPD, none has been found for human chromosomes 12, 18, and 19 (see Chapter 4). In other instances, only one of the two parental types has been observed (i.e., only the maternal or paternal UPD for a given chromosome); this also raises the issue of viability as a function of the parental source of UPD. To mention but one example, the somatic segmental UPD11p15.5 was only observed for the paternally derived chromosome 11; the maternal segmental UPD11p15.5 should have been theoretically equally observed. The fact that this is not the case argues for either the lethality of the phenotype, or selective disadvantage of the somatic cells or no phenotype at all.

SEGMENTAL UPDs ARE PERHAPS COMMON AND

PATHOGENETICALLY IMPORTANT

The UPD for a segment of a chromosome is likely to occur as a result of the rare mitotic reciprocal somatic crossing-over. Except from the segmental clonal UPD11p mentioned above, such UPDs have been reported for chromosome 14 (Martin et al., 1999) and for either 6p (Lopez-Gutierrez et al., 1998) or part of 6q (Das et al., 2000). The identification of additional examples is not trivial, considering the limited size of the chromosome segments involved. Although the molecular structure may predispose some chromosomal areas to rearrangements (Ji et al., 2000), one would predict that segmental UPD resulting from homologous chromatid pairing and exchanges could be more frequent than currently appreciated.

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The role of such somatic segmental UPDs may also become important as one step in the sequential events of genetic changes involved in cancer as already noted in some cases (White et al., 1996; Rousseau-Merck et al., 1999). Loss of heterozygosity is usually the hallmark of such cases.

FREQUENCY OF UPD

The frequency of UPD is currently unknown and may remain unknown for some time. Biases toward the assessment of this frequency include (at opposite ends of the spectrum) nonviability for some UPDs and lack of phenotypic expression for others. One of the authors (Engel, 1998) estimated a frequency of about 1=33,000 births for the cases of meiotic origin UPD (of chromosomes 15 and 6) and of somatic origin (UPD11p, in WBS). This estimated frequency only includes 4 of the 33 types of UPD currently identified, so that one would guess a UPD of some type may occur in the range of 1 in 3000–5000 viable births. More studies including large series of newborn babies, spontaneously aborted fetuses, pregnancies of mothers of advanced age (Ginsburg et al., 2000), and targeted phenotypic groups (i.e., people with handicaps, cognitive impairment, cancers) may provide a more accurate estimate of UPD frequency in health and disease.

ELUCIDATION OF MECHANISMS INVOLVED IN UPD AND ITS ‘‘CORRECTION’’

It seems reasonable to infer that most cases of UPD for entire chromosomes result from two unrelated coincidental errors in meiosis or mitosis. It would be of interest to study potential predispositions for such events due to the nature of chromosomal centromeres, location and frequency of recombination events, or the proteins involved in chromosomal segregation and recombination. In addition, the mechanism of the events for correction of chromosome aneuploidies may reveal fundamental phenomena of gene copy counting and gene product imbalance.

ADDITIONAL DIAGNOSTIC TESTS

The elucidation of the molecular bases of UPDs is likely to provide more diagnostic tests in patients with unrecognized syndromes. For example, the discovery of the imprinted genes on chromosomes 6q, 7, or 14 associated with emerging phenotypes will provide more diagnostic options and tools. The abundance of DNA polymorphisms and the automation of their detection are likely to enhance our ability to recognize segmental and full UPD for any chromosomal region.

THE EVOLUTIONARY ROLE OF IMPRINTING

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NEW UPD SYNDROMES

In recent years, some new syndromes emerged as a result of the detection of UPD (see Chapter 5). Other conditions (such as paternal or maternal UPD14, maternal UPD2 and maternal UPD16) are in the process of being better characterized. Undoubtedly, many surprises and exciting molecular etiologies lie ahead in the elucidation of causes of hereditary or congenital conditions.

IMPLICATION OF UPD IN RECESSIVE DISORDERS

The isodisomy UPD uncovers mutant alleles for recessive disorders (see Table 1, Chapter 4 for a list). In the few instances where recessive disorders have been screened serially to document the parental source of the mutation, a frequency of single mutant allele duplications by UPD (so-called reduction to homozygosity) has been obtained in around one case out of 50 [1=55 in cystic fibrosis (Voss et al., 1989); 2=54 in cartilage hair hypoplasia (Sulisalo et al., 1997); and 1=61 for junctional epidermolysis bullosa (Pulkkinen et al., 1997)]. The genetic counseling of these cases is certainly different from that of the usual recessive inheritance. We anticipate that the chromosomal regions of isodisomy UPD would be extensively studied for homozygosity of polymorphic alleles of all the genes of the region for associations of these alleles with normal or abnormal phenotypic characteristics.

THE EVOLUTIONARY ROLE OF IMPRINTING

Various theories have been proposed for the evolutionary significance of genomic imprinting. A discussion of the evolutionary aspects of imprinting is beyond the scope of this book. The reader is referred to the original literature for a more thorough discussion. Briefly, the following hypotheses have been proposed:

A parental competition between paternal and maternal genes to balance the developing potential of an offspring (Moore and Haig, 1991)

A host-defense mechanism akin to methylation of ‘‘foreign’’ DNA methylation (Barlow, 1993)

A suppressive regulation of chromosomal aneuploidy to control malignant clonal developments in gonadal and somatic tissues (Varmuza and Mann, 1994; Thomas, 1995)

A preferential gene expression pattern for the conservation of some traits inherited from one parent only (Engel, 1997)

It is apparent that all of the above are only theories and hypotheses. Clearer understanding will require more detailed knowledge of the molecular events of imprinting and its regulation in different species.

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We hope that some of the readers of this book will become so fascinated with the parental-specific contribution to gene expression that they, in turn, devote part of their professional life to contributions to this field and advance our knowledge and understanding of this phenomenon. To these people, and those who care for patients with the UPD-imprinting-related disorders, we dedicate this book.

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