Mapping the Human Genome, Groundwork for a New Era of Medicine

Interview with Dr. Jamie Cuticchia, Founder of the Ontario-Based Centre for Bioinformatics Supercomputing

Dr. Jamie Cuticchia is the Head of the Bioinformatics program at the Hospital for Sick Children in Toronto. Since 1997, Dr. Cuticchia has actively and successfully developed this program, which is designed to turn trillions of pieces of biological information into usable knowledge. Dr. Cuticchia kindly agreed to share his thoughts on the future of medicine, bioinformatics, and Canada's role in the overall genome project.

Q: Dr. Cuticchia, we have just seen two rival groups announce that they won the race to sequence the Human Genome. How can they have "won the race", if the complete sequence will not be available until 2003? Who are these two groups? Has the race been "won" and who won it?

A: The "race", which has been heralded by the press for the past year or so, has been between the private effort by Celera Genomics and the public sequencing effort lead by Francis Collins at NIH but including researchers in Europe as well. Celera claims to have the genome sequenced and now is in effect assembling the pieces. This is like saying that they have located all the pieces, but the puzzle still isn't complete. The public effort has gone a more methodical way by sequencing on a clone-by-clone basis, which in effect combines sequencing and assembly.

Genethics: The Ethical and Legal Side of Referral for Genetic Testing and Counselling

David Kaplan, MSc(HA)
Joint Centre for Bioethics
Faculty of Medicine, University of Toronto

As the international quest to map and sequence the entire human genome continues, myriad medi-cal conditions of a genetic origin will be recognized, and tests to identify individuals at risk for these conditions will become available. An enormous amount of medical information can be gleaned from testing a person's genetic material. Health care providers could use this information to predict, and possibly prevent, future disability and disease. For over a decade, physicians have referred patients for genetic testing. In the early part of the last decade, this testing was often done without proper counselling. Numerous questions should be considered before referring an individual for genetic counselling and testing. Which patients should be sent for genetic testing and for which diseases should testing be available? Do traditional ethical and legal concepts of patient confidentiality, consent and disclosure apply to genetic information in the same manner as they apply to a patient's medical history? Are physicians liable for negligent counselling on the part of a non-physician genetic counsellor? This paper will highlight the ethical issues and legal implications of referring adult patients for genetic testing and counselling.

Aging: The Dance of a Few Genes

Anna Liachenko, BSc, MSc
Managing Editor,
Geriatrics & Aging

A number of groundbreaking studies seem to suggest that only a few genes are responsible for the multiple changes in our bodies, which lead to the gradual physiological decline, we call aging. The small number of genes involved in aging supports a thesis that was first proposed by Dr. George Martin of the University of Washington.

Using a new technology called oligonucleotide microarrays (or gene chips), to detect the rates of gene transcription, Dr. Richard A. Lerner together with Dr. Peter G. Schultz and other colleagues, recently examined 6000 genes expressed in human fibroblasts from both young and aging humans. They found that only 61 genes consistently showed changes in levels of expression with aging. More than half of these genes were involved in either cell cycle progression or remodeling of extracellular matrix. These cellular markers of aging may be fibro-blast-specific or at least mitotically-active-tissue specific as they are different from those found in post-mitotic tissues. Indeed, Dr. Tomas A. Prolla, who examined transcription rates in post-mitotic mouse gastrocnemius muscle, found a different (but, interestingly, just as narrow) subset of genes, for which the transcription rates were significantly altered with age.

In light of the small number of genes that presumably are able to cause the decline of multiple physiological systems, it is interesting to look at a group of genetic disorders called progerias. Progeria means early aging, in Greek.

Reversal of Fortune: The Fate of Huntington’s Disease

Kimby N. Barton, MSc
Assistant Editor,
Geriatrics & Aging

Dramatic results presented in Cell have demonstrated that turning off the expression of a mutated protein in mice with Huntington's disease, results in either a cessation or a reversion of the symptoms associated with the disease.

Huntington's disease (HD) is an autosomal dominant inherited disorder characterized by motor disturbances such as chorea and dystonia, personality changes, and cognitive decline. These symptoms seem to result from neural degeneration, which occurs primarily in the striatum and cortex of the brain. HD typically manifests in mid-life and death follows 10 to 20 years after disease onset. Currently, no specific cure or treatment is available.

HD is caused by an expansion of glutamine (CAG) repeats near the 5' end of the gene that codes for a protein called huntingtin. The translated protein then contains an expanded glutamine (polyQ) sequence in the N-terminal portion. Normal individuals possess a polyQ length of approximately 6 to 34 repeats whereas individuals with more than 40 repeats develop HD. The longer the polyQ expansion, the earlier the onset of symptoms.

The pathogenesis of HD is poorly understood. It is believed that somehow the expansion of the polyQ sequence in the N-terminal portion of the protein results in a deleterious gain of function mechanism. Neuronal nuclear aggregates are found in the brains of patients with the disease as well as in transgenic animal models studied to date. These aggregates contain the mutant huntingtin protein and are also often found to be ubiquitinated suggesting that they have been targeted for proteasomal degradation. However, it remains to be determined whether these nuclear aggregates are themselves responsible for the neural degeneration or whether they are merely a byproduct of some other toxic response.

The most interesting part of the study, was when the researchers were able to turn the mutant protein 'off'. Adding an antibiotic to water consumed by the mice, turned off gene expression of the mutated protein. Amazingly, suppression of the mutant protein in mice between the ages of 18 and 34 weeks either halted or reversed the different aspects of the HD-like phenotype. Specifically, the neuronal and nuclear aggregates in the brain disappeared, the number of reactive astrocytes decreased, and the progressive striatal atrophy along with the decrease in D1 receptor levels was halted. In addition, stopping the expression of the HD gene prevented the further exacerbation of the HD behavioural characteristics and ameliorated their condition to a degree approaching those in control mice.

This is the first study that has ever demonstrated that the symptoms and characteristics of HD are reversible, implying that irreversible changes which commit the cell to neuronal dysfunction or death have not necessarily taken place. The findings also suggest that therapeutic approaches to target and specifically destroy the mutant huntingtin protein may be effective in returning patients with HD to a normal phenotype. Understanding the mechanisms responsible for this disease may provide new targets for therapeutic interventions in patients suffering from HD and other progressive neurodegenerative disorders.

Source

1. Yamamoto A., Lucas JJ. and Hen R. 2000. Cell. 101:57-66.

Not Much on Chromosome 21

Last month, a multinational consortium reported the completion of the sequencing of chromosome 21, the smallest human chromosome. A description of the sequence soon followed. Chromosome 21 represents approximately 1 to 1.5% of the total human genome. It was expected to be relatively gene-poor based on the fact that trisomy 21 is one of the only viable human trisomies. Surprisingly, researchers found that it contained even fewer genes than they had expected; only 225 genes were identified, compared with the 545 found on chromosome 22. The total length of the sequence is 33.8 million base pairs (or megabases, Mb).

Chromosome 21 has been of particular interest since it was discovered in 1959 that Down's syndrome occurs when there are three copies of the chromosome. The complete sequence analysis is expected to have profound implications for research in this area in terms of bringing about both improved understanding of the pathogenesis of diseases and speeding up the development of new therapeutic approaches. Individuals with Down's syndrome exhibit several phenotypes other than mental retardation, including congenital heart disease and early-onset Alzheimer's disease, all of which are, ultimately, the product of the three copies of genes on chromosome 21 instead of two. It is believed that only a subset of genes on chromosome 21 may be involved in the Down's syndrome phenotype and that these gene products may be more sensitive than others to gene dosage imbalance. The gene catalogue now allows the hypothesis-driven selection of different sets of candidates, which can then be used to study the molecular pathophysiology of the gene dosage effects.

Mutations in 14 known genes on chromosome 21 have been identified as the causes of several monogenetic disorders, although the loci for several other monogenetic disorders have not yet been cloned. The gene catalogue and mapping coordinates will help in the identification of these loci, and the mutation analysis of candidate genes in patients will lead to the cloning of the responsible genes. The challenge now is to unravel the function of all the genes on chromosome 21.

Source

1. Hatori et al. Nature 2000. 405:311-319.

Of Mice and Men

Celera Corporation announced in early June that they had sequenced over 1 billion base pairs of the mouse genome. The mouse genome is similar in size to the human genome, approximately 3 billion base pairs, and decoding it will be vital to interpreting many aspects of the human genome. Mice and humans share most of the same genes and it will be possible to make comparisons between the two genomes as well as to perform extensive knock-out studies on mice, both of which will provide an exceptional vehicle for genetic analysis.

Genomics Initiative Moves Geriatric Medicine to Centre Stage

The final human genome sequence is a watershed event in human and medical history. The next pivotal event will be to correlate this information to specific diseases. Perhaps the most significant revelation that has so far emerged from modern genomic studies is that we are all descendants of a remarkably small family group that emerged perhaps less than 100,000 years ago. Although we are closely related, sharing 99.9% of mankind's genetic make-up, the remaining 0.1% of genetic variation accounts for many of the diseases which afflict man, and for the different ways humans respond to medications. Individualized medicine will revolve around the newly-achieved understanding of the clinical implications stemming from this 0.1% of variation. These variations are called single nucleotide polymorphisms SNPs (pronounced SNIPs). These SNPs occur in one out of every thousand base pairs that make up the three to four billion units of the human genome. The challenge of future genomics will be to correlate these tiny variations with disease.

To this end, in April of 1999, the SNP consortium was formed by a group of pharmaceutical firms, research institutes, and the Wellcome trust. The SNP consortium is founded upon a database of information garnered from the genetic screening of 300,000 individuals. SNP maps would allow for genetic clustering studies to be quickly performed which could then be compared against individual genetic profiles, using inexpensive means such as gene chips.

A recently announced new consortium in the UK backed by the Medical Research Council (MRC) and Wellcome Trust will greatly outstrip the SNP consortium in terms of its mandate. Drawing on the organized resources of the centralized British healthcare system, the UK plans to enlist 500,000 physician-recommended individuals in order to form a national database. The British medical system has health records on the enlisted patients and their families extending back more than fifty years. Combining the health records with the SNP information will allow vast amounts of information to be harnessed and correlated with individuals who bear similar genetic markers. The database is going to be directed at individuals aged 40-70 years, and will concentrate on "late-onset diseases, developing and targeting new treatments and assessing an individual's risk so that preventive measures can be taken."

Source

1. Scientific American. June 2000.

Uncovering the Genetic Basis of Osteoporosis

Philip Dopp, BSc

The disturbing statistics with regard to the prevalence of osteoporosis among older women are well known. By 65 years of age, one in four women have experienced an osteoporotic fracture, and the rate of incidence rises to one in two by the age of 75. The incidence of hip fractures among women in the United States is 2 per 1000 patient years by the age of 65 and 30 per 1000 patient years by the age of 85.1 More importantly, hip fractures in the elderly are associated with a high mortality rate. Both men and women are between two and five times more likely to die during the first 12 months following a hip fracture when compared to age and sex matched controls without hip fractures. Given this and other serious consequences, there is much interest in discovering factors that can prevent or slow the rate of development of this disease.¹

Pathophysiology of Osteoporosis
Osteoporosis is the generalized, progressive diminution in bone tissue mass per unit volume which causes skeletal weakness, even though the remaining bone is normal morphologically. It is well known that factors that decrease bone mineral density (BMD) and increase the risk of osteoporotic fractures include family history, white race, female gender, estrogen deficiency, low dietary levels of calcium and vitamin D, limited physical activity or immobility and medications such as corticosteroids.^1,2 Currently, there has been an increased interest in determining the role that genetic factors play in the pathogenesis of osteoporosis.

Late-onset Variant of Familial Hypertrophic Cardiomyopathy Identified

Internet Databases Offer Easy Access to Relevant Genetic Information

Kathleen Jaques Bennett, BSc, BSc, MSc

Familial hypertrophic cardiomyopathy (FHCM) is an inherited disorder that results in the thickening and stiffening of the myocardium, primarily in the left ventricle.¹ This disorder runs in families and may appear late in life. FHCM is produced by mutations in at least eight autosomal genes that are responsible for the synthesis of the sarcomeric filament proteins. These genes vary in terms of where the mutations are located.² FHCM is present in less than 0.5% of the population and has been associated with sudden death.³ The disorder varies both in its severity and in its clinical features, with more variants still being identified. There is some phenotypic heterogeneity with FHCM but the disorder is highly correlated in its physical expression to the mutation and its location, especially within families. Internet-based databases now exist to describe the characteristics of FHCM, specific mutations and loci, the epidemiology and the type of hypertrophy and the prognosis.⁴ FHCM has been a disorder associated with young people but was recently identified as having a late-onset variant that develops after age 50. This late-onset FHCM results from mutations in the gene for cardiac myosin-binding protein C (MBP-C) and cardiac troponin T (TNN-T).

A Milestone in Human History

Human Genome Project Nears Completion--Vast Implications for Medical and Biological Sciences

J. Sedmihradsky BSc, MA

Genetic technology has been in the news regularly in recent years, thanks to the enormous advances that have been made in the technological world. The genes linked to diseases such as Alzheimer's disease, Parkinson's disease, asthma and various cancers have been identified and in some cases, patented. By identifying the genes associated with different diseases, researchers may be able to learn more about disease mechanisms and discover new therapies or possible cures.

The Human Genome Project
The Human Genome Project (HGP) is an international research project aimed at establishing an accurate map of all the genes in human DNA. Anticipated outcomes of the project include better understanding, treatment, cure and possible prevention of over four thousand genetic diseases. Advances in forestry, biotechnology and agriculture are also expected,¹ as researchers have studied the genetic makeup of several non-human organisms for purposes of furthering the mapping of human DNA. Project planning began in the mid-1980s but most of the research has taken place since the implementation of the HGP in 1990. The project was initially estimated to span a period of 15 years, from 1990 to 2005,² but the expected completion date was recently moved forward to 2003.