A Pandora’s box
Ten years ago, when the Human Genome Project was completed, scientists thought they had written the book on humankind’s DNA. But they now realize the system is ‘mind-blowing’ in its complexity — and it will be decades before all the chapters are fully und
It was like God’s own jigsaw puzzle.
Built up over evolutionary eons, it featured 46 spiralling, ladder-like structures, some three billion pieces, and it took thousands of scientists working around the globe 13 years to complete.
But that, it turned out, was the easy part. The Human Genome Project — which was presented in its final form 10 years ago this month — provided a map of mankind’s DNA. But it also opened up a Pandora’s box of boggling complexity in the biological sciences and medicine that will take decades more to unravel.
“It’s mind-blowing actually,” says Dr. Jeff Wrana, a top cancer researcher at the University of Toronto.
“It’s one of those things, you know, ‘be careful what you wish for.’ ” What genome cartographers had wished for at the project’s 1990 incep- tion — what the genetic tea leaves had led them to expect — was something far simpler than what they found.
Going into the project, and as it progressed, the same sequencing strategies that were building the map of human DNA were also producing full genomic charts for yeast, fruit flies and a family of tiny worms.
That particular worm, known as C. elegans, is a homely creature, too small to fit on a fishing hook. And its genome — simply the entire nucleic DNA content of any given species — showed it possessed about 19,000 genes.
Genes are the blueprint segments of DNA, which is spread out in humans along 23 pairs of double helix chromosomes located within the nucleus of each of our cells.
The encoding strands of the genetic material, genes are interspaced intermittently along those chromosomes
and direct an organism’s construction, growth, metabolism and even some of its behaviours.
And the obvious fact that humans were so much more complicated in all those areas than worms — with our limbs, our eyes, our giant brains — surely meant that we should possess multiple times more of them than the compost-dwelling crawlers.
Coupled with research that had identified a multitude of genetic building instructions — molecules known as RNAs — scientists figured we might boast 50,000, 70,000, 100,000 genes or more.
And the genome project showed? We were in the worm range — about 20,000 or so.
“That was a surprise, that was a big surprise,” says Howard Lipshitz, the University of Toronto’s head of molecular genetics.
“The estimates up to then were that there were probably going to be at least 10 times as many genes in humans.”
The thinking, going in, was that many of the expected genes would be independent actors. Want a kidney cell? Here’s a gene. Have bladder cancer? Here’s your gene mutation.
What the genome project showed was that the human genes — to achieve our complexity, to produce all those RNA messengers — must be phenomenal multi-taskers.
And the instructions that can make one gene perform up to 1,000 different functions must be profoundly complex and varied.
THE HUMAN GENOME Project, which cost between $1 billion and $3 billion depending on what you include, aimed to create “a book” that was written in the entire, three-billion base-pair lettering of human DNA, says Lipshitz.
“And I think the most succinct outcome was (said) by (genome pioneer) Eric Lander . . . who put it in seven words after (the project) was completed,” says Lipshitz.
“He said ‘genome, bought the book, hard to read.’ And it’s true, now we’ve got the book, now we’ve got the words and the hard part is figuring out the logic and what all the sentences mean.”
While certainly full of surprises and disappointments, what that vastly complicated text made clear was that scientists were now facing nature’s true biological reality, says U of T biochemist Benjamin Blencowe, director of the Donnelly Sequencing Centre at U of T.
“It showed us what the real landscape is,” Blencowe says.
And with a new and alien landscape to inhabit, researchers turned to taming it.
What interrelations between genes were responsible for their multiple actions? What role, if any, did the vast stretches of DNA — once referred to by some scientist as junk — that lay between the genes play in their shifting functions?
Where did the genetic directions come from?
One of these directional sources, it has been shown, was simply the bodily setting that genes find themselves in.
During early embryonic development, for example, physical setting is the main DNA director, telling genes to produce the appropriate organ or tissue in the appropriate body location.
“If we want to make a kidney, we don’t have a whole set of genes that are instructions for making a kidney, we don’t have a different set of genes that are instructions for making a heart,” Wrana says.
“What we have is literally a kind of mechanic’s tool box that we apply in different ways . . . so the same genes that are critical for a kidney are the same genes that are being used to make a heart.”
For Wrana, who works out of the Simon Lunenfeld Research Institute at Mount Sinai Hospital, this situational insight led to a key cancer breakthrough.
In a study released last December, Wrana’s team showed that cancer cells, which carry mutant genes, were coaxed to spread, or metastasize, by the normal, healthy cells that surrounded them.
“Basically the normal cells and the cancer cells are engaged in a dialogue which is controlling (spread),” Wrana said at the time.
“The tumour cells are tweaking the normal cells, causing them . . . to misbehave a little bit and causing those normal cells to produce signals, words if you will, that flow back to the tumour cells and promote the tumour cells’ growth.”
This type of interplay between cancers and their surroundings, between cancer genes and the rest of the genome, between any number of factors, makes the disease far more complicated than previously believed.
“Now we have to think about cancer not as one disease, but as many, many diseases,” Wrana says.
He also says cancers must now be viewed as shifting systems that have multiple genetic and environmental strategies and can deflect most magicbullet treatments.
Another source of gene direction, Lipshitz says, has proven to be the vast DNA segments that sit between them — the 98 per cent of the human genome that was once thought largely a vestigial, evolutionary artifact. “And it’s that DNA between the (genes) which determines . . . where and when the genes will be turned on and off. But we’re still trying to figure all that out,” he says.
Parts of this erstwhile junk, it has been shown, are not inert, but actually encode their own RNAs. While the RNA produced by genes can go out and create the proteins that make up tissues or enzymes, however, its junk-made counterparts can trigger that genetic activity.
IF THE GENOME PROJECT has injected daunting complexity into biology, however, it’s also proven an immensely useful research tool, many scientists say.
“Every single day, every scientist who does any biology uses that data,” says Stephen Scherer, director of the Centre for Applied Genomics at The Hospital for Sick Children. “It’s had a huge impact.” The main benefits coming out of the project were twofold, says Scherer, also director of the U of T’s McLaughlin Centre for Molecular Medicine.
“One was the concept that the scientific community could come together in biology and generate this incredible resource that now everyone uses,” says Scherer, who helped map chromosome seven during the project.
Second, he says, the original project prompted the creation of more muscular DNA sequencers that can now rapidly and cheaply generate personal genomes.
“There are certainly tens of thousands of human genomes that have now been sequenced in one way or another,” he says.
And for all of these, scientists have the original project map to compare and contrast them to in searching for genetic diseases or other traits.
Scherer’s own, post-project work has used these sequencers to show that humans actually possess a varied number of copies — Copy Number Variables or CNVs — of many of their genes. With the Human Genome Project, scientists built a better understanding of mankind’s DNA.
“Every single day, every scientist who does any biology uses that data. It’s had a huge impact.” STEPHEN SCHERER DIRECTOR OF THE CENTRE FOR APPLIED GENOMICS AT THE HOSPITAL FOR SICK CHILDREN
These CNVs describe any genetic anomaly that shifts the number of copies of a gene a person has above or below the typical two they inherit — one from their mother, one from their father.
“If it is copy number variable, you vary away from the typical two copies,” Scherer explains.
“So, you either have one copy or, in some cases, zero copies, and in other cases three or four. And CNVs could help doctors to personalize the dose of a particular drug.” CNVs can have a huge impact on how an individual might handle cancer chemotherapies, for example, and will be a critical diagnostic factor in the emerging field of personalized medicine.
Blencowe has used the genome map extensively for research into one of the main methods genes use to multi-task, referred to as alternative splicing.
This method involves genes cutting and splicing the RNA messengers they create into diverse new configurations, that in turn specify proteins tailored for specified functions, says Blencowe.
Genes within a cell’s nucleus work by acting as a template, throwing open their DNA sequences as an assembly point for strands of messenger RNA.
These messenger strands then go out into a cell and create a protein, plucking out the correct, amino acid ingredients and stitching them together according to their genetically encoded instructions.
The resulting protein will then help to build an organ or direct a bodily function.
In his groundbreaking research, Blencowe used the genome project’s DNA sequence data as a reference to help show that more than 95 per cent of human genes utilized the alternative splicing strategy.
This work helped Blencowe’s team decipher a genetic code that controls the splicing process and to discover critical splicing switches that control cell fate and embryonic development.
“It was transformative,” Lipshitz says of the genome project.
“When I started my lab more than 25 years ago, to clone and study and sequence a single gene from the fruit fly took months to years. Now we just log on to the (project) database and it’s there.”
WRANA DOES NOT DESPAIR that the profound complexity revealed by the genome project may be too great to overcome — in cancer or in broader biology.
But he admits that it’s going to be a long and laborious slog.
“I think we’re just starting to begin to comprehend just how complicated this system is,” he says.
“And so that’s really requiring us to start developing new ways of analyzing and thinking about the system.”
In the end, Wrana says, the project has changed biology forever.
“Sequencing the genome is driving a paradigm shift, really in the way ‘paradigm shift’ is meant to be used,” he says.