Thân gửi các Bạn trong Diễn Ðàn Dược Khoa.

A- MỤC ÐÍCH NGHIÊN CỨU BỘ GENE :

B- KẾT QUẢ VỀ BỘ GENE CỦA NHÂN LOẠI :

C- NHỮNG ỨNG DỤNG:

1- Bản đồ gene vŕ việc chẩn đoán bệnh lý:

2- Tìm các gene liên hệ đến bệnh lý:

2- Tìm các gene và dược phâm có tính chất trị liệu:

3- Ðiện toán sinh-học (bio-informatics):

A- VÀI CẢM NGHĨ :

Thân chào,

Nguyễn Ðức Thái

June 30, 2000

Thai D. Nguyen, PhD

Glaucoma Research

Dept. of Ophthalmology/UCSF

On the occasion of the announcement of the near completion of The Human Genome Project by Celera Genomics and The National Institute of Health's Human Genome Program on June 26, 2000 in Washington DC.

An unprecedented landmark in the history of biological research as well as of mankind has been recently been achieved. It relates to the announcement of the near completion of The Human Genome Project by Celera Genomics and of the National Human Genome Research Institute of the National Institute of Health (NIH). Here, we review this special event and share some thoughts with the Pharmacy Forum on the Human Genome Project and the influences that it could have on the future of medical practice as well as pharmaceutical research.

Gene is the basic element of biology, accordingly research of the human genome is fundamental importance by nature. Genes reside within the cell's nucleus made up of DNA consisted of four basic chemicals A (adenine), C (cytosine), G (guanine) and T (thymine). The cell is regarded as a computer in which genes are located at its nuclei and continuously sending out signals that determine the cell structure as well as control its complex functions. In brief, there are enormous numbers of genes and each responsible for a cell function. Historically, the quest for knowledge of genes within the human genome has evolved via different stages. In the beginning, applications of cloning methodology, genes have been identified one by one from disease research and from research topics varied from laboratory to laboratory. Cancer genes were found by researchers working on oncology; similarly genes relating to high blood pressure, diabetic, development, aging etc. were obtained by experts in each of these areas. Since the development of recombinant DNA technology in the beginning of 1980s, a numerous genes have been discovered. From these, a wealth of knowledge on the mechanism of disease processes, have been established together with their effectiveness in treatments. The fast growing of biotechnology companies with time is a way of ascertaining the importance of genes and our society. Nevertheless, the numbers of gene discovered represent only a minor portion of the numbers of genes potentially found within our cells. Few thousands gene have been reported as compared to possibly nearly 100,000 genes estimated in the cell. In reality, the test to achieve the number of genes and their locations are enormous since genes occupy a very minor portion of the total cellular DNA. Searching for the total genes by classical cloning approach would require numerous centuries and associated with huge expenses. In response to the need of advancing the science with a fast pace, The Human Genome Project has been conceived in the mid-1980s and operated in October 1990 leading by Dr. James Watson, who is also one of the two who made the DNA discovery. The Human Genome Project aimed to gain a better knowledge of the human genetic makeup with focus on determining the exact order of the 3 billion base pairs of the human DNA at a cost estimated to be 3 billion dollars. The Human Genome Project has been a global research effort for nearly 15 years combining various human genome centers of industrialized nations including America, Japan, England, Germany, French, China and other countries. In addition to The Human Genome Project, a new type of biotechnology companies has emerged known as genomic companies due to the economical importance of the human genome. Their engagements have changed the landscape of the genome project and created a phenomenon competition environment in the race to uncover the secret code of man.

On Monday June 26, 2000 two genome research scientists both from America, Drs. Craig Venture, J. and Francis Collins have made announcements on the completion of their work for the Human Genome Project. The announcement was made at the White House in the presence of President Bill Clinton. Dr. Venter represented Celera Genomics, a newly formed company, and Dr. Collins represented the National Human Genome Research Institute of the NIH. The work of Dr. Collins' group represented the original efforts of the human genome research, which has an international status, however, its results are not as completed as those of Dr. Venter. Dr. Venture's participation in the human genome project has changed the structure of the already highly competitive of the project. Dr. Venter has worked on genomic studies at the NIH and at The Human Genome Sciences, Inc. prior to establishing Celera Genomics only recently in 1997. Although coming late into the game, Dr. Venter has made the accomplishment within a phenomenon record of 3 years (1 year earlier than his plan) to become the first to make the announcement for the completion of the human genome research. His secrecy for this once-and-for-all victory in the international race for mankind: determination, enthusiasm and visionary. Of particularly interest to us, is the fact that Dr. Venter has experienced the Vietnam War during the Tet offense in 1968. The Vietnam experience has made him a steel man at work and a whole hearted man in life. He mentioned that Vietnam has made him to appreciate every moment of life. His slogan: " Make every minute of your day and everyday of your life count". On his success, Dr. Venter undertook the shotgun DNA sequencing approach which involved breaking down the genome in random DNA fragments, sequence the fragments and resembling them by aligning overlapping pieces. In principle, this appears as a simple and direct approach, but in practice, it is a huge task for the size of over 3 billion base pairs of the human genome. To facilitate the task, Dr. Venter associated with PE Biosystems to have access to their super-computer system. Other human genome centers employed various methods, which required multiple stages. Some have laboriously cloned the genome DNA into large fragments (using BAC, or YAC, yeast artificial clone) to begin with, or established the physical map of the genome, mapping with the STS (satellite sequence tag) prior the sequencing work.

The announcement revealed that our genome has 3.12 billion base pair and 97% of these were sequenced, among these 85 % of the sequences were mapped by the orders that they are constructed in the cell. About 3% of our total DNA have genes, the remained 97% does not, thus termed "non-functional DNA". The 3% of DNA have between 60,000 to 100,000 genes. Other findings from The Human Genome Sciences, Inc. estimated the gene number could be over 120,000. Interestingly, our genomes are 99.9% identical among different ethnic. It is expected that the remained sequences and mapping would be achieved within the next two years. Although this is a small sequence, they happen to be in regions of the genome which is not readily for sequencing. The characterizations of genes based on the established sequences remain to be a long-term efforts for biological research since the genes are proven by its expression and functions, not by sequencing alone.

To get an idea about the complexity of the genome, one could imagine that it would need 200 books of 500 pages each to record all of the human genome sequences, among these, only 3 thousand pages has genes which scattered among the 200 books. Our genes are closely related to other animal kingdoms in numbers as well as in structures. The closest DNA to human is that of chimpanzees with 99% homology. The numbers of genes reduce in simpler forms of life among these worm has 20,000 genes, yeast has 6,000 and tuberculosis has 4,000 genes. In a recent report, a new gene was found within the "non-functional DNA region". This unexpected discovery could be quite interesting as it signified that more secrecy to be revealed and their nature could turn out to be novel and importance. The information obtained from these reports is quite close to estimations made in the past. The estimations, however, were neither verified nor documented as a data base for applications.

The Human Genome Project has accomplished its mission by providing a systematic establishment for the DNA database of the genome sequences. Simply speaking, the genome project has provided gene researchers with a map of the human genome that allows them to move from one part of the genome to the other parts without being lost. Besides, genes cluster together like the human society with varieties of sizes, shapes, culture and functions; in this regard, the genome map will provide sources of information for researchers to understand the characteristics of each gene group and how they are related. The genome map is thus an important and necessary direction for researchers to navigate their search, which is expected to be highly rewarded with novel discoveries and applications for mankind.

Applications from the human genome map is as many as one could imagine for. It is anticipated that various disciplines in biological sciences would benefit largely from the leads established from the human genomic map. The applications of the gene map for cell biology would help to advance our knowledge in the cell functions; for pathophysiology, genetics would advance our knowledge on disease genes. In therapeutic research, it is expected that the genome map would facilitate our research for therapeutic genes or methods of treatments to be more rapidly and effective. Ecology studies will also benefit from the gene map as we learn about which genes are response to the environment factors. Other applications relate to cultural values of our society such as genetic selection to create one type of species (eugenics) or human cloning already raised public attention. In this report, we would like to summarize the applications from the human genome project that involve current medical research and believed to have major impacts on the future of medicine.

1- Genome Map and Disease Diagnosis: Gene is the basis of the cell, and cell is a living unit of our body, therefore knowledge of the human gene map could provide significant information about our physiology. Importantly, there are changes on the genome map associated with disease processes that is regarded as signatures predicting the pathophysiology background of an individual. Within nearly two decades, genetics research has been the rosetta stone of disease related genes that have become valuable markers of the gene map due to the mutations that they imprinted. The genetic markers encompass large disease entities from cancer, cardiovascular, ophthalmic diseases, and diabetics to psychiatric disorders.

Another type of markers involving single chemistry changes in the genome, known as SNPs (pronounced snips) or single nucleotide polymorphism. Interestingly, SNPs could be critical markers of the gene map due to their possible associations with disease genes. A major challenge to the medical practice has been the variations in the outcome of drug response in individuals, for some, the medicine brings a cure, for others not or evens side effects. SNPs have been regarded as a major genetic factor responsible for the variations. In fact, this concept has been known in the oriental medicine by which each of us has distinct genetic entity; accordingly, various combination of herbs are prescribed individually. SNPs are being investigated in a large scale to establish information needed for effective therapeutics for individuals of different genetic background, besides researching for novel genes relating to disorders.

In the future medical practice, a genotype map would be common for each of us in which disease-related makers are established, the map would be a routine and key documentation in the clinical files of hospitals and medical offices. Doctors, dentists, pharmacists and other health practitioners will base their judgments on our gene map to make appropriate decisions for the treatments, together with other conventional tests.

2- Research for disease related genes: There are enormous numbers of disorders whose causes remained largely unknown, which in molecular term, the genes have not been found for the disorders. It is expected that this will be changed with a rapid pace, at least for diseases of genetics basis. There have been several gene loci established for genetic disease. It is expected that many of the genes within the loci could be revealed from established sequences of the genome map. They are candidate genes for mutation screenings to identify their possible associations with the disease.

On a larger scale, DeCODE, a genomic company, has been working on identifying genes for disorders of critical illness via deciphering markers of the genomic map using the national clinical database of the Icelander population.

Other methods of identifying disease genes involves screening expression of genes in disease state versus the control (healthy condition). Microarray, DNA/protein chips allow researchers to make distinction on genes relating to these conditions.

3-Research for genes and pharmacological compounds of therapeutic values: While a number of genes cause disease, many of them deliver medical benefits including prevention and treatments. Some of these genes provide benefits via pharmacological compounds, they are called target genes. Up to date, there are about 500 target genes being discovered ranging from G-proteins, metabolic enzymes to ion channels. It is estimated that a much larger numbers from 3,000-10,000 target genes in the human genome and these targets, once discovered, would lead to many new therapeutic applications. The gene map will play a major role in our efforts to identify these genes for medical uses. Researchers nowadays have tools to express a large numbers of proteins simultaneously from the genome, making pharmacological research a new era. The advancement aims to identify molecules of selective activities and also would help to reduce the time and cost (which used to run from 10-20 years with hundred of millions of dollars).

Based on the principle of drug and protein interactions are required for pharmacological effects, a number of projects have made achievements via the applications of protein chips for drug screenings. The chip technology allows depositions of several ten thousands of proteins on a chip and chemicals could be mixed together, a computer system is then employed to scan for possible interactions. SNPs technology is expected to be an important part among the applications of the gene map for pharmacological research. Pharmacogenomics has evolved from the genomics sciences to advance the research for safer and more effective pharmaceutical products.

In addition, genes of therapeutic values could also be found via selection criteria. For examples genes code for secretory proteins or proteins interacting with other proteins are of potentials. Other methods including assaying for gene functions known as functional geneomics or investigating the molecular shapes of the proteins known as proteonomics which identify functional motifs of the proteins.

4-Bio-informatics: A recent field of biological sciences, and is also the most promising for biomedical research. Bio-informatics combines biology and computer assisted approach, thus also known as computational biology. Cell is a network of biological dynamics and complexity. The biological network composed of genes and pathways that they interact to produce biological outcomes. Bio-informatics establishes the gene structures, functions and their interactions via computation of a large number of data. The genome map together with other technologies including the gene chips, differential display, SAGE (serial analysis of gene expression) are expected to be major tools for bio-informatic research to understand disease processes in the complex picture. A single gene does not, by itself, cause a cellular phenotypic change that resulting in disease, but rather a set of genes are involved. For therapeutic purposes, bio-informatics targets multiple genes and aims to reset the biological network to its healthy state. Bio-informatics also aims to characterize genetic variations of individuals and their differential gene expression profile to set stage for individualized therapies.

In summary, the human genome map will have pivotal impacts on biomedical research as well as its applications in medical practice. The use of mutation and SNP map would lead to prediction and effective diagnosis for various diseases; the identifications of disease genes or therapeutic genes would provide specific molecular targets for treatments. Bio-informatics will reveal the genes in their complex functions within the cell net work that will lead to a new paradigm in medical research.

1. A Reflection:

The outcomes from the human genome research concluded a major achievement by Celera Genomics and The Human Genome Project of the NIH. On a broader view, this is also the achievement made from contributions of many research centers in various parts of the world, many of these occurred within the last two decades of the 20-century. Besides its colossal dimension, the human genome project has been an important symbolism of collaborative efforts for over a decade among many countries in serving science and mankind.

The human gene map reveals to us that from the beginning, there was a harmony and close connection among peoples on the planet earth, indicating from the 99.9% DNA homology among us. Looking toward the future, we all hope that besides its immense impacts on the future of sciences, the human genome research will continue to enlighten us with new knowledge about our origin, and form the foundation for continuing collaborative efforts among countries to build the world with peace, prosperity in the new millennium.

For Vietnam, we are particularly encouraged by the milestone set by the Human Genome Project for the potential opportunities and applications that it would offer to our future research. Among these, information on the genetic diversities of the genome map are of special importance to understand our origin at the genetic level; SNP technology would be of major interest to help study medical, pharmacological variations relating to our race; the technology could also be useful to investigate biological resources in Vietnam that are believed to be highly diversified and regional. From our research, we hope to offer the scientific communities knowledge on the genetic nature of the Vietnamese, which is a part of the variations that make our world a kaleidoscope wonder.

Thai D. Nguyen, PhD

- For references to the genomic research, please refer to information available in various genomic centers including Genome Database (GDB) (for genetic database); European Molecular Biology Laboratory Nucleotide Sequence (EMBL), DNA Database of Japan (DDBJ) (for gene structure data base); GeneMark, Genscan (for new gene discoveries); Merk Gene Index (for human gene expression); The Millenium Pharmaceuticals, Human Genome Sciences (for gene microarray and therapies); Orchid Biosciences, Variagenics (for SNPs); Lexicon Genetics, Exelixis (for functional genomics); Genomic Solution (for proteonomics); Caliper Technologies, Aclara (for protein/DNA chips); Incyte Pharmaceuticals, Inc., InforMax, Inc., Pangea System Inc. (for bio-informatics) and others. Many other functions related to genomic research are also expected to be found from these research centers.

- The underlines are terms relating to genome research.