The Mysterious World of the Human Genome
Page 12
By the late 1980s, geneticists working with the fruit fly discovered a battery of genes that determined the identity of the different segments of the insect body in strict order from the head to the “tail” end during the embryological formation of the insect body within the egg. They called these “homeobox” or “Hox” genes (the name of a gene is conventionally italicized whereas the name of its transcribed protein is written in ordinary script). Subsequent research would discover that these same Hox genes in similar order along a specific chromosome were critically important to the development of the animal body plan during embryological development. We humans, like all vertebrate animals, follow a Hox-determined developmental plan that creates a right and a left side. This gives us our “bilateral” symmetry. We might compare this, for example, to the exotically beautiful sea creatures, called echinoderms, such as starfish and sea urchins, which have a radial pattern of symmetry similar to the segments of an orange or the flower head of a daisy.
As the human embryo grows from the initial ball of cells, our Hox genes will determine at which point to place the head, and within the head the eyes, the nose, the jaws; and then, vertebra by vertebra, the seven bones that constitute the neck. Then, vertebra by vertebra again, the twelve bones that designate the thorax, with the offshoots of upper limbs and ribs; in similar fashion, the five lumbar vertebrae that will support the abdomen; and finally the fused vertebrae of sacrum, which supports the pelvis and lower limbs—all in appropriate position along the central axis of our bilateral body plan. The evolution of Hox genes was clearly a vital evolutionary step in the evolution of the animal kingdom. So vital is their function that they have been steadfastly conserved by natural selection over vast time periods of evolution. For example, even though the common ancestor of humans and insects inhabited the oceans roughly 600 million years ago, if we were to replace the Hox gene for the specification of the insect eye with its human equivalent in the insect zygote, the human gene would still locate the development of the insect eye.
Hox genes code for proteins, but Hox proteins are not enzymes, nor do they function in a structural capacity—such as making up skin or the structures of kidneys, heart, or bone. Instead, they regulate the expression, or “transcription,” of other genes. Hence they are dubbed “transcription factors.” The Hox-coded proteins bind themselves to key nucleotide sequences within the chromosomes, known as “enhancers,” where they act by switching the target genes off or on. In time, scientists came to discover many such “regulatory genes” that play important roles during embryological development, as well as in normal human physiology throughout life. Key genes, such as the Hox cluster, initiate a process that leads to a series of developmental steps involving signaling hormones and transcription factors. Key to understanding such systems is the fact that one key gene may activate many secondary genes, each further activating multiple more, so that it ends up with a cascade of hundreds of genes that constitute what is called a “developmental pathway.” This ensures that a region in the embryo becomes the brain or a limb, a kidney or a toenail. In fact, if we consider the construction of a complex tissue, such as a kidney or a limb, it is evident that this will contain many different kinds of cells and tissues. For example, a developing leg will include the construction of skin, muscle, bone, nerves, and blood vessels—so its embryological development must involve the coordination of many different regulatory pathways, perhaps with local signaling between tissues. A failure of any individual component is likely to lead to catastrophe. Thalidomide was a popular over-the-counter drug used to treat nausea in pregnancy in the 1950s and early 1960s. Within a few years of widespread use, approximately 10,000 children were born with severely malformed limbs—so-called “phocomelia.” The failure of the normal blood vessel development within the developing limb buds was the root cause of the thalidomide tragedy.
At the time of publication of Brenner's paper, in the early 1970s, we understood little of this genetic regulation of human development. We knew, of course, that the human brain was still relatively undeveloped at birth, continuing to grow and develop for perhaps two or three years into infant life. And while we were aware of the glandular changes that brought about and resulted from puberty, we had little or no understanding of its genetic regulation. Today we know that puberty involves very profound changes, both at the genetic and epigenetic level—in effect, we return to the controlled turmoil of embryogenesis, in what geneticists now recognize to be a major and dramatic phase of “postembryonic development.” There are so many similarities in the genetic regulation and the profound bodily changes between human puberty and the astonishing metamorphoses we see in the lives of moths and butterflies, some scientists regard puberty as a variety of metamorphosis.
Prepubertal boys and girls have much the same proportion of muscle mass, skeletal mass, and body fat. But now, with the reawakening of the same powerful developmental epigenetic and genetic pathways that controlled embryological development, the bodies of boys and girls undergo dramatic physical change, including rapid growth and major changes in muscle and fat distribution that differ between the sexes. By the end of puberty, men have 1.5 times the skeletal and muscle mass of women, whereas women now possess twice as much body fat as men. These obvious physical changes are accompanied by cellular and tissue changes involving sexual organs and related organs, such as the breasts in women and the prostate glands in men. Puberty is brought about by signaling pulses of gonadotrophin-releasing hormone (GnRH), which is released by the hypothalamic portion of the brain. This stimulates the master gland, the pituitary, to increase the secretion and release of the sex gland stimulating hormones, or gonadotrophins, which travel through the blood stream to the ovaries and testes, where they provoke increasing blood levels of estrogens and androgens. If sometimes the pubertal adolescent appears moody and confused, it is hardly surprising given the massive physical and hormonal changes that are coming about. Only recently have we recognized that puberty is also associated with hormone-driven major rewiring of the neural circuits of the adolescent brain, triggering changes toward adult behavior.
Some psychologists have proposed that individual differences in adult behavior and the risk of sex-related psychopathies may derive from variations in timing and in the interactions between the hormones of puberty and the brain rewiring at this critical period of adolescence.
By the early 1990s, biologists had a basic understanding of how genes worked. They knew that genes coded for several different types of protein. Some played key roles in our internal chemistry, as enzymes, while others were structural components in cell membranes, the tissues of skin, eyes, hair, and nails. Geneticists had plotted where hundreds of genes were to be found on the 46 human chromosomes. They were accumulating substantial knowledge about genetic regulation. They were also beginning to realize that there were additional systems of regulation that were not DNA-determined. There was growing evidence of non-DNA-based systems that could influence the expression of DNA from outside the genome—systems that might be capable of changing during the life and experience of the individual. These would in time come to be understood as part of the epigenetic regulatory system, which will be described in a later chapter.
The revolution that had begun in 1953 with the discovery of the structure of DNA had given rise to the novel discipline of molecular biology, with its manifold extrapolations to medicine and biology. We had discovered more of the labyrinthine inner workings of human heredity, embryological development, and the workings of cells, tissues, and organs at the biochemical level in just a few decades, than we had in all of previous history. There was also growing evidence that viruses had invaded our human genome, from the presence of viral genetic sequences and even whole viral genomes. While some geneticists regarded these as junk, the fossils of infection from long ago, others believed they might be contributing in some functional ways.
Thousands of genes had been discovered using the laborious techniques of mutation in experimental anima
l models. But, given that the human body incorporated an estimated 80,000 to 120,000 proteins, on the basis of one-gene-one-protein, there should be as many genes encoding all those proteins. This suggested that there must be vast numbers of unknown genes yet to be discovered. What geneticists now needed to know extended beyond the sequencing of individual genes. The next logical step must be the exploration of the structure of every chromosome, and beyond that, the exploration of the entire nuclear genome. Without such exploration, we could not determine how the system worked as a whole. Only with the sequencing of the entire human genome would we understand what lay at the core of our being—to paraphrase Bronowski, what genetic gifts made us so unique among the animals. All that we needed to take this final almighty step was the political will to fund the exercise, together with more efficient techniques of reading DNA sequences.
Back in the mid-1970s, a Cambridge-based British biochemist, Fred Sanger, already a Nobel Laureate in Chemistry for work on the structure of proteins, had pioneered novel techniques of automated DNA sequencing that were subsequently named after him: “Sanger sequencing.” Sanger used these techniques to determine the first complete genome of an organism—the same organism I studied as a student and doctor: the bacteriophage virus known as ΦX174. This won him a second Nobel Prize in Chemistry, the only Nobel Laureate ever to win two prizes in chemistry. While Sanger's methodology became the standard technique for DNA sequencing in laboratories throughout the world, discovering the structure of tens of thousands of genes, it was, in Sanger's own admission, slow and laborious to conduct, requiring the scientists to read off the results on printouts and demanding wasteful quantities of radioactive phosphorus, which was used to label the nucleotides. In the mid-1980s, Leroy Hood and colleagues at Caltech in America introduced a faster and easier methodology that labeled the nucleotides with four different-colored fluorescent dyes that could be read by a laser within a machine. Others developed techniques of replicating genetic sequences using cultures of E. coli bacteria so that small amounts of DNA could be amplified to make sequencing easier. The genome could now be broken down into smaller sequences that could be amplified to many copies in bacteria and then sequenced in automated machines.
In 1984, the political component achieved critical mass when the United States Department of Energy proposed that they would fund the sequencing of the entire human genome, with its 6.6 billion nucleotide sequences. The name of the project was decided by a committee: it would be “The Human Genome Project.”
The scope of the project was daunting, but it was also fantastically ambitious, inspiring, and exciting. By 1987, the proposal had been debated and clarified, with a crystal clear statement of purpose: “The ultimate goal of this initiative is to understand the human genome, knowledge of which is as necessary to the continuing progress of medicine and other health sciences as knowledge of human anatomy has been for the present state of medicine.”
Exclusively American to start with, the project later expanded to include many other countries, ultimately growing into the largest collaborative biological project in scientific history. With so many different scientists and scientific groups involved, it was inevitable that there would be conflicting opinions on how to go about it. Some thought we should undertake a chromosome at a time, but this would stretch to maybe ten or even fifteen years to complete. Some politicians failed to grasp the importance of the project and bridled at the likely financial cost, which would rise to billions of dollars. Some people may have been somewhat daunted by the prospect of such a monumental step into the unknown.
But by the early 1990s, the die was cast. In 1990, two major funding agencies, the DOE and the National Institutes of Health (or NIH), coordinated their plans. That same year, James Dewey Watson, joint discoverer of the structure of DNA, was appointed head of the NIH program. Watson's prestige, the backing of the US National Academy of Sciences, the support of many academically influential molecular biologists, and the governmental and other official sponsorship of something like $2.6 billion, now underpinned the project. Watson immediately encouraged the internationalization of their plans, enlisting the help of the UK, Germany, and France, with contributions from many other European centers, as well as Japan, China, and Australia. In the UK, the Wellcome Trust became a major charity partner with the US public bodies.
With the major opus now organized, coordinated, funded, and ready to roll, the banks of computers and the automated sequencing machines kicked into action. It was still the general assumption that the project would take fifteen years to complete, but that would change with the intervention of an unexpected rival from the business sector—an American, commercially sponsored organization named “Celera Genomics.” The competition from a rival, privately sponsored organization would throw an unwelcome wrench into some of the most conservatively organized plans.
I feel this is an historic moment. This is the most important scientific effort that humankind has ever mounted…It will change biology for all time.
FRANCIS COLLINS
On Sunday, February 12, 2001, the two rival organizations, Celera Genomics and the publicly funded Human Genome Project—embodying many different governmental and major charitable bodies in the US, UK, Germany, Japan, and France—announced simultaneously that they had completed the first comprehensive analysis of the human genome. It created a wave of excitement throughout the world's media. In the United States, President Clinton led the chorus that would be joined by Prime Minister Tony Blair in the UK, and by similar national leaders and leading scientific figures in every country, proclaiming that a new epoch of knowledge and scientific exploration had arrived. In the UK, Roger Highfield, science editor of the Daily Telegraph, put it bluntly: “Science Rivals Open the Book of Life.” In the words of Andy Coghlan and Michael Le Page, writing for New Scientist, the genome would soon be as familiar to schoolchildren as the periodic table of the elements. There could be no doubting that it signaled a new milestone in genetic science, the most powerful and logical development to follow the breakthroughs on DNA. And like the DNA story, there were new issues of rivalry and conflict between the discovering groups.
As director of the Human Genome Project, Watson had internationalized the scope of the undertaking, meanwhile engendering the gratitude and dedicated support of academic scientists throughout the world. He had also devoted a small but significant allocation of funds to include sociological, religious, and ethical concerns in the minds of lay intellectuals and politicians. Celera Genomics was seen by some within scientific academia as a brash interloper, led by an entrepreneurial scientist, J. Craig Venter—but to his credit Venter had, through insight and sheer force of personality, already succeeded in a litany of impressive breakthroughs involving new fields of genetic discovery. Like Watson, Crick, and Wilkins, Venter would also admit that he had been inspired by Schrödinger's book.
Growing up as part of academia, Venter had worked for the US National Institutes of Health in a lab immediately below that of Marshall Nirenberg, who had contributed to the discovery of the histone code. In 1992, impatient with the slow progress of academia, Venter set up his own commercial laboratory, the Institute for Genomic Research, or TIGR. He was now free to combine automated sequencing with his group's newly invented “shotgun” approach, in which incredibly lengthy genetic sequences found in living genomes could be broken down into smaller fragments. By breaking down the same genome again and again, and breaking the sequences in different regions, his team could use the inevitable overlapping sections to piece together the fragments so that the entire sequence of, say, a microbe, or a human chromosome and so on, to the entire genome, could eventually be stitched together.
This “shotgun sequencing” technique had the potential to speed things up, but it was derided as potentially inaccurate by Venter's academic rivals. Nevertheless, by 1995, Venter was ready to publish his first success—the first ever completely sequenced genome of a bacterium, Haemophilus influenzae, which causes respiratory a
nd other infections. This was followed by the genome of the ulcer-causing bug, Helicobacter pylori, and, in March 2000, the first insect genomic sequence—that of Thomas Hunt Morgan's famous experimental subject, the fruit fly. The skeptical world of academia was rocked back onto its metaphorical heels.
In May 1998, Venter had teamed up with Perkin Elmer to amalgamate his Institute for Genomic Research with Elmer's PE Corporation and formed a new company, Celera Genomics. Celera, as its Latin derivative implies, conveyed the objective of “speed.” Its remit, as Venter made clear, was not biotechnology per se but the provision of information. In the words of James Shreeve, who wrote the history of this extraordinary period, Celera's market product would be a massive database of DNA, with the human genome sequence as its heart. Thus Venter, and the new company, had as their very raison d’être a vested interest in rivaling the publicly sponsored Human Genome Project.
In 1992, James Watson had a major disagreement with Bernadine Healy, then director of the National Institutes of Health, who had been put in charge of the Human Genome Project. Healy supported the dictates of Congress that NIH discoveries should, where possible, be supported by patents. Watson heatedly disagreed. Watson derided Healy until, “tired of his insulting remarks,” she fired him. That same year, Watson was replaced as director of the Human Genome Project by the more diplomatically savvy Francis Collins. In the UK, the Wellcome Trust had set the ball rolling by funding a major sequencing laboratory near Cambridge, the Sanger Centre, which would work in a coordinated synchronicity with NIH on the Human Genome Project.