Diseases such as cancer and other chronic ailments are the result of copy-number changes in our genome, that is, when certain genes are accidentally duplicated to create extra copies or when genes are deleted so that they exist in fewer copies than normal.
In addition to potential hazards to our health, changes in gene copy-number are also important for the evolution of our genomes. Unnecessary or harmful genetic material can be discarded, and the extra gene copies can undergo further changes as they are passed on through generations. These changes can result in the emergence of new genes that code for novel traits.
In their foundational project “Mutational and transcriptional landscape of spontaneous gene duplications and deletions in Caenorhabditis elegans,” published in the July 10 issue of theProceedings of the National Academy of Sciences USA, a team led by Texas A&M College of Veterinary Medicine & Biomedical Sciences (CVM) researchers have used a species of nematode (C. elegans), a self-fertilizing non-parasitic roundworm, to take a closer look at the rate of genetic evolution.
Understanding the functional consequences of these changes could ultimately impact human disease by further extending the possibility for personalized medicine in the future.
For their project, the team—including associate professors Vaishali Katju and Ulfar Bergthorsson and their postdoctoral student Anke Konrad, all in the CVM’s Department of Veterinary Integrative Biosciences —established experimental populations of C. elegans populations, all descended from a single ancestral roundworm.
In order to facilitate natural selection, which is driven by competition among individuals with genetic differences, experimental lines were maintained with three different population sizes.
By sequencing the genomes of these experimental lines after a four-and-a-half-year period of evolution in the laboratory, the researchers were able to identify copy-number variants that arose and characterize how they changed the expression of duplicated genes. The team found that the rate of copy-number changes in C. elegans was “extraordinarily high.”
“Mutations fuel evolution. For evolution to occur, genetic variation is needed for selection, to pick one genotype over another. Mutation creates this genetic variation,” Katju said. “The problem is that, initially, when mutations arise, they tend to have deleterious, or detrimental, effects on the organism’s fitness. So, the very process that you want to study—and one that impinges on all aspects of biology—which is the mutations and the genetic variation they create, are largely weeded out in natural populations before you even get to see them.”
The team worked around this complication by minimizing the opportunity for natural selection in lines maintained at the smallest population size—one individual at each new generation.
Finding a lot of variation, the researchers worked to get a baseline rate of mutation and found that copy-number duplications occurred at a rate of greater than 1 in 100,000 per gene per generation.
“If we imagine a population of million individuals, then in every generation, more than 10 individuals would acquire an extra copy of one of their genes that might either have harmful consequences or perhaps, be the progenitor of a new gene with a different function,” Katju said. “This is why we are all different with respect to the number of genes that we carry. Some of us are missing genes that others carry and many of us carry extra genes that most of us do not have. Which genes are present in fewer or more copies than normal is one of the reasons we are all unique.
“For more than a century, evolutionary biologists have studied genetic variations and found there to be many classes of mutations, but the main contributor to genetic variation has been thought to be point mutations or base substitutions—where one nucleotide base of DNA gets substituted for another. For example, an A changes to a T, or a T gets substituted by a G,” Katju said.
Population genomic studies looking at various human populations, or different populations of other species, show that the entire genome is littered with copy-number changes; this abundant form of genetic variation is owed to the high rates of origin of gene duplications and deletions.
“Point mutations happen at every nucleotide with a probability of one in a billion, but any gene can be duplicated with a probability of greater than one in a million. This is a great difference in the rates of origin of these two classes of mutation,” Bergthorsson said. “Basically, this high rate of duplications and deletions arising spontaneously in each generation is what creates this massive amount of differences between individuals, possibly more than the genetic contribution of base substitutions.”
Because it would take 8,000 years for humans to create the number of generations that the team was able to produce from roundworms in just over four years, model organisms like C. elegans, with short generation times, provide significant advantages in the study of genetics. However, by examining the results of the both DNA and RNA sequencing conducted by the team, implications can be derived that could have massive effects on human medicine.
Understanding the reason for some of the more unique phenomena they observed—such as a modest-to-complete recovery in the sickest of their generational lines after maintaining large population sizes, or a chromothripsis, the shattering of an entire chromosome that is often seen in cancer progression, that spontaneously occurred and caused a generational line to go extinct—are among the functional aspects that need to be further studied.
“Our future research program is now taking individual mutations and trying to use CRISPR/Cas9 genome editing technology to actually create the mutation in a wild-type, or an ancestral background,” Katju said. “We know exactly what kind of duplications occur. To engineer this duplication in a wild-type background and be able to look at its functional effects will help determine the consequences of having one or several extra copies of a gene for the organism… That’s the new frontier, in a way.”
“I think this is going to be the future in medicine—a personalized medicine approach, where people take the knowledge of somebody’s genome and use that to determine the best course of action,” Bergthorsson said. “If you only look at things we normally understand as mutations, changes in the sequences of the DNA, then we will miss out on a very important aspect of genetic variation, which is not just change in sequence but changes in dosage, changes in how much you have of something.
“In many instances, more is actually different. It’s not just more of the same sequence; it actually results in something new, often with the deleterious consequences, but sometimes with beneficial consequences,” he continued. “So, I think, for future development of personalized medicine, keeping an emphasis on understanding the consequences of this gene-level variation in populations is very important.”