Understanding why some mutations impair normal bodily functions and contribute to cancer may lead to new clinical laboratory diagnostics
New insight into the human genome may help explain the ageing process and provide clues to improving human longevity that can be useful to clinical laboratories and researchers developing cancer diagnostics. A recent study conducted at the Wellcome Sanger Institute in Cambridge, United Kingdom, suggests that the speed of DNA errors in genetic mutations may play a critical role in the lifespan and survival of a species.
To perform their research, the scientists analyzed genomes from the intestines of 16 mammalian species looking for genetic changes. Known as somatic mutations, these mutations are a natural process that occur in all cells during the life of an organism and are typically harmless. However, some somatic mutations can impair the normal function of a cell and even play a role in causing cancer.
“Aging is a complex process, the result of multiple forms of molecular damage in our cells and tissues. Somatic mutations have been speculated to contribute to ageing since the 1950s, but studying them had remained difficult,” said Inigo Martincorena, PhD (above), Group Leader, Sanger Institute and one of the authors of the study. Greater understanding of the role DNA mutations play in cancer could lead to new clinical laboratory tools and diagnostics. (Photo copyright: Wellcome Sanger Institute.)
Lifespans versus Body Mass
The mammalian subjects examined in the study incorporated a wide range of lifespans and body masses and included humans, giraffes, tigers, mice, and the highly cancer-resistant naked mole-rat. The average number of somatic mutations at the end of a lifespan was around 3,200 for all the species studied, despite vast differences in age and body mass. It appears that species with longer lifespans can slow down their rate of genetic mutations.
The average lifespan of the humans used for the study was 83.6 years and they had a somatic mutation rate of 47 per year. Mice examined for the research endured 796 of the mutations annually and only lived for 3.7 years.
Species with similar amounts of the mutations had comparable lifespans. For example, the small, naked mole-rats analyzed experienced 93 mutations per year and lived to be 25 years of age. On the other hand, much larger giraffes encountered 99 mutations each year and had a lifespan of 24 years.
“With the recent advances in DNA sequencing technologies, we can finally investigate the roles that somatic mutations play in ageing and in multiple diseases,” said Inigo Martincorena, PhD, Group Leader, Sanger Institute, one of the authors of the study in a press release. He added, “That this diverse range of mammals end their lives with a similar number of mutations in their cells is an exciting and intriguing discovery.”
The scientists analyzed the patterns of the mutations and found that the somatic mutations accumulated linearly over time. They also discovered that the mutations were caused by similar mechanisms and the number acquired were relatively similar across all the species, despite a difference in diet and life histories. For example, a giraffe is typically 40,000 times larger than a mouse, but both species accumulate a similar number of somatic mutations during their lifetimes.
“The fact that differences in somatic mutation rate seem to be explained by differences in lifespan, rather than body size, suggests that although adjusting the mutation rate sounds like an elegant way of controlling the incidence of cancer across species, evolution has not actually chosen this path,” said Adrian Baez-Ortega, PhD, postdoctoral researcher at the Sanger Institute and one of the paper’s authors, in the press release.
“It is quite possible that every time a species evolves a larger size than its ancestors—as in giraffes, elephants, and whales—evolution might come up with a different solution to this problem. We will need to study these species in greater detail to find out,” he speculated.
Why Some Species Live Longer than Others
The researchers also found that the rate of somatic mutations decreased as the lifespan of each species increased which suggests the mutations have a likely role in ageing. It appears that humans and animals perish after accumulating a similar number of these genetic mutations which implies that the speed of the mutations is vital in ascertaining lifespan and could explain why some species live substantially longer than others.
“To find a similar pattern of genetic changes in animals as different from one another as a mouse and a tiger was surprising. But the most exciting aspect of the study has to be finding that lifespan is inversely proportional to the somatic mutation rate,” said Alex Cagan, PhD, Postdoctoral Fellow at the Sanger Institute and one of the authors of the study in the press release.
“This suggests that somatic mutations may play a role in ageing, although alternative explanations may be possible. Over the next few years, it will be fascinating to extend these studies into even more diverse species, such as insects or plants,” he noted.
Benefit of Understanding Ageing and Death
The scientists believe this study may provide insight to understanding the ageing process and the inevitability and timing of death. They surmise that ageing is likely to be caused by the aggregation of multiple types of damage to the cells and tissues suffered throughout a lifetime, including somatic mutations.
Some companies that offer genetic tests claim their products can predict longevity, despite the lack of widely accepted evidence that such tests are accurate within an acceptable range. Further research is needed to confirm that the findings of the Wellcome Sanger Institute study are relevant to understand the ageing process.
If the results are validated, though, it is probable that new direct-to-consumer (DTC) genetic tests will be developed, which could be a new revenue source for clinical laboratories.
In fact, the UB study suggests traditional anatomical methods for determining the evolutionary relationships between species may not be as accurate as once thought, an article in SciTechDaily reported.
Nevertheless, the UB’s research into convergent evolution is unlocking new insights into how genes evolve over time and this new knowledge may help researchers develop genetic tests that more accurately identify different diseases and health conditions.
Additionally, studies that bring a better understanding of how beneficial genetic mutations work their way into a species’ genome might also aid researchers in developing personalized clinical laboratory testing and therapies based on manipulating a patient’s genetic sequences in ways that would be beneficial.
Gene Sequencing More Accurate at Determining Evolutionary Relationships
The UB study suggests that existing evolutionary (phylogenetic) trees may need to be reconsidered. To put a finer point on the findings, a UB news release on the study states, “determining evolutionary trees of organisms by comparing anatomy rather than gene sequences is misleading.”
The UB scientists used genetic sequencing to quickly—and more cost effectively—determine evolutionary relationships as compared to traditional morphology (anatomy and structure), according to the news release.
They found genetic data that revealed surprising relationships about where the sequenced species originated, and which differed with prior conclusions that were drawn based on the species’ appearance. The findings suggest there may be need to “overturn centuries of scientific work in classifying relation of species by physical traits,” the UB scientists said.
“For over a hundred years, we’ve been classifying organisms according to how they look and are put together anatomically, but molecular data often tells us a rather different story,” said Matthew Wills, PhD (above), Professor of Evolutionary Paleobiology, Milner Center for Education at the University of Bath, in the news release. “Our study proves statistically that if you build an evolutionary tree of animals based on their molecular data, it often fits much better with their geographical distribution.” This new use of genetic sequencing could lead to improved precision medicine treatments and clinical laboratory testing. (Photo copyright: University of Bath.)
Molecular Data Leads to New Insights into Convergent Evolution
The UB study’s use of genetic sequencing led the researchers to a greater understanding of convergent evolution, defined by “a characteristic evolving separately in two genetically unrelated groups of organisms,” according to UB.
For example, wings are a widely developed characteristic. But they are not necessarily a sign of relatedness when it comes to birds, bats, and insects.
“Now with molecular data, we can see that convergent evolution happens all the time—things we thought were closely related often turn out to be far apart on the tree of life,” Wills said, adding, “Individuals within a family don’t always look similar; it’s the same with evolutionary trees, too.”
Family Trees: Morphology Versus Molecular
In their paper, the UB researchers acknowledged the importance of phylogenies (evolutionary history of species) in areas of biology, including medicine. They aimed to study a better way to produce accurate phylogenetic trees.
“Phylogenetic relationships are inferred principally from two classes of data: morphological and molecular,” they wrote, adding, “The superiority of molecular trees has rarely been assessed empirically.”
So, they set out to compare the two approaches to building evolutionary trees:
Traditional morphology analysis, and
Phylogenetic trees developed using molecular data.
Using 48 pairs of morphological and molecular trees, they mapped data geographically.
“We show that, on average, molecular trees provide a better fit to biogeographic data than their morphological counterparts, and that biogeographic congruence increases over research time,” the researchers wrote.
Biogeography a Better Gauge of Relatedness than Anatomy
The study also found animals on molecular trees lived geographically closer as compared to groups on morphological trees.
For example, molecular studies put aardvarks, elephants, golden moles, swimming manatees, and elephant shews in an Afrotheria group, named for Africa, which is where they came from. Therefore, the biogeography matches, however the appearances of these mammals clearly do not, the UB scientists point out.
“What’s most exciting is that we find strong statistical proof of molecular trees fitting better not just in groups like Afrotheria, but across the tree of life in birds, reptiles, insects, and plants,” said Jack Oyston PhD, UB Department of Biology and Biochemistry Research Associate and first author of the study, in the news release.
The researchers believe their findings support the accuracy of genetic-themed trees.
“It being such a widespread pattern makes it much more potentially useful as a general test of different evolutionary trees. But it also shows just how pervasive convergent evolution has been when it comes to misleading us,” Oyston added.
Advantages of Molecular Data
In their Nature Communications Biology paper, the UB scientists wrote that molecular data offer up these advantages over morphology:
Widely available in vast quantity.
Opportunity exists to “search, repurpose, and reanalyze sequenced data alongside novel sequences.”
Less subjectivity in researchers’ analysis.
Well-developed data at the ready and “still in their infancy.”
The University of Bath’s study of convergent evolution, phylogenetic trees, and comparison of molecular data versus morphology, has implications for medical laboratories. Should their research lead to new insights into how genes evolve over time, diagnostics professionals may have new information to identity diseases and work with others to precisely treat patients.
Nanorate sequencing allows researchers to identify changes to individual genetic sequencing letters among millions of DNA letters contained in a single cell
Detecting genetic mutations in cells requires genomic sequencing that, until now, has not been accurate enough to spot minute changes in DNA sequences. Many clinical laboratory scientists know this restricted the ability of genetic scientists to identify cancerous mutations early in individual cells.
Now, researchers at the Wellcome Sanger Institute in the United Kingdom have developed a new method of genetic sequencing that “makes it possible to more accurately investigate how genetic changes occur in human tissues,” according to Genetic Engineering and Biotechnology News (GEN).
This development suggests a new, more sensitive tool may soon be available for anatomic pathologists to speed evaluation of pre-cancerous and cancerous tissues, thereby achieving earlier detection of disease and clinical intervention.
Called Nanorate Sequencing (NanoSeq for short), the new technology enables researchers to detect genetic changes in any human tissues “with unprecedented accuracy,” according to a news release.
How Somatic Mutations Drive Cancer, Aging, and Other Diseases
NanoSeq enables the detection of new mutations in most human cells—the non-dividing cells—GEN explained, calling Wellcome Sangar Institute’s new technology a “breakthrough” in the use of duplex sequencing.
Until now, genomic sequencing has not been “accurate enough” for this level of detection, Sanger stated in the news release. Thus, there was little opportunity to enhance exploration of new mutations in the majority of human cells.
Further, the findings of the Sanger study suggest that cell division may not be the primary cause of somatic mutations (changes in the DNA sequence of a biological cell).
In their paper, the researchers discussed the importance of somatic mutations. “Somatic mutations drive the development of cancer and may contribute to aging and other diseases. Despite their importance, the difficulty of detecting mutations that are only present in single cells or small clones has limited our knowledge of somatic mutagenesis to a minority of tissues.
“Here, to overcome these limitations, we developed Nanorate Sequencing (NanoSeq), a duplex sequencing protocol with error rates of less than five errors per billion base pairs in single DNA molecules from cell populations. This rate is two orders of magnitude lower than typical somatic mutation loads, enabling the study of somatic mutations in any tissue independently of clonality,” the researchers wrote in Nature.
Refining Duplex Sequencing and Improving PCR Testing
In their study, Sanger researchers assessed duplex sequencing and found errors concentrated at DNA fragment ends. To them, this suggested “flaws” in preparation for DNA sequencing.
Duplex sequencing is an established technique “which sequences both strands of a DNA molecule to remove sequencing and polymerase chain reaction (PCR) errors,” explained a Science Advisory Board article.
“Detecting somatic mutations that are only present in one or a few cells is incredibly technically challenging. You have to find a single letter change among tens of millions of DNA letters and previous sequencing methods were simply not accurate enough,” said Robert Osborne, PhD (above), former Principal Staff Scientist at Sanger who led development of NanoSeq, in the news release. Osborne is now COO of Biofidelity, a cancer diagnostics developer in Cambridge, United Kingdom. This research may eventually give clinical laboratories and surgical pathologists useful new tools that enable earlier, more accurate diagnosis of cancer. (Photo copyright: Cambridge Independent.)
Re-evaluating Mutagenesis and Cell Division with NanoSeq
It took the Sanger researchers four years to create NanoSeq. They “carefully refined” duplex sequencing methods using more specific enzymes to aid DNA cutting and bioinformatics analysis, Clinical OMICS noted.
Then, they put NanoSeq’s sensitivity to the test. They wanted to know if its low error rate meant that NanoSeq could enable study of somatic mutations in any tissue. This would be important, they noted, because genetic mutations naturally occur in cells in a range of 15 to 40 mutations per year with some changes leading to cancer.
The scientists compared the rate and pattern of mutation in both stem cells (renewing cells supplying non-dividing cells) and non-dividing cells (the majority of cells) in blood, colon, brain, and muscle tissues.
The Sanger study found:
Mutations in slowly dividing stem cells are on track with progenitor cells, which are more rapidly dividing cells.
Cell division may not be the “dominant process causing mutations in blood cells.”
Analysis of non-dividing neurons and rarely-dividing muscle cells found “mutations accumulate throughout life in cells without cell division and at a similar pace” to blood cells.
“It is often assumed that cell division is the main factor in the occurrence of somatic mutations, with a greater number of divisions creating a greater number of mutations. But our analysis found that blood cells that had divided many times more than others featured the same rates and patterns of mutation. This changes how we think about mutagenesis and suggests that other biological mechanisms besides cell divisions are key,” said Federico Abascal, PhD, First Author and Sanger Postdoctoral Fellow, in the news release.
Using NanoSeq to Scale Up Somatic Mutation Analyses
“NanoSeq will also make it easier, cheaper, and less invasive to study somatic mutation on a much larger scale. Rather than analyzing biopsies from small numbers of patients and only being able to look at stem cells or tumor tissue, now we can study samples from hundreds of patients and observe somatic mutations in any tissue,” said Inigo Martincorena, PhD, Senior Author and Sanger Group Leader, in the news release.
More research is needed before NanoSeq finds its way to diagnosing cancer by anatomic pathology groups. Still, for diagnostics professionals and clinical laboratory leaders, NanoSeq is an interesting development. It appears to be a way for scientists to see genetic changes in single cells and mutations in a handful of cells that evolve into cancerous tumors, as compared to those that do not.
The Sanger scientists plan to pursue larger follow-up NanoSeq studies.
Unlike most other CRISPR/Cas-9 therapies that are ex vivo treatments in which cells are modified outside the body, this study was successful with an in vivo treatment
Use of CRISPR-Cas9 gene editing technology for therapeutic purposes can be a boon for clinical laboratories. Not only is this application a step forward in the march toward precision medicine, but it can give clinical labs the essential role of sequencing a patient’s DNA to help the referring physician identify how CRISPR-Cas9 can be used to edit the patient’s DNA to treat specific health conditions.
Most pathologists and medical lab managers know that CRISPR-Cas9 gene editing technology has been touted as one of the most significant advances in the development of therapies for inherited genetic diseases and other conditions. Now, a pair of biotech companies have announced a milestone for CRISPR-Cas9 with early clinical data involving a treatment delivered intravenously (in vivo).
As with other therapies, determining which patients are suitable candidates for specific treatments is key to the therapy’s success. Therefore, clinical laboratories will play a critical role in identifying those patients who would most likely benefit from a CRISPR-delivered therapy.
Such is the goal of precision medicine. As methods are refined that can correct unwelcome genetic mutations in a patient, the need to do genetic testing to identify and diagnose whether a patient has a specific gene mutation associated with a specific disease will increase.
Cleveland Clinic describes ATTR amyloidosis as a “protein misfolding disorder” involving transthyretin (TTR), a protein made in the liver. The disease leads to deposits of the protein in the heart, nerves, or other organs.
According to Intellia and Regeneron, NTLA-2001 is designed to inactivate the gene that produces the protein.
The interim clinical trial data indicated that one 0.3 mg per kilogram dose of the therapy reduced serum TTR by an average of 87% at day 28. A smaller dose of 0.1 mg per kilogram reduced TTR by an average of 52%. The researchers reported “few adverse events” in the six study patients, “and those that did occur were mild in grade.”
Current treatments, the companies stated, must be administered regularly and typically reduce TTR by about 80%.
“These are the first ever clinical data suggesting that we can precisely edit target cells within the body to treat genetic disease with a single intravenous infusion of CRISPR,” said Intellia President and CEO John Leonard, MD, in a press release. “The interim results support our belief that NTLA-2001 has the potential to halt and reverse the devastating complications of ATTR amyloidosis with a single dose.”
He added that “solving the challenge of targeted delivery of CRISPR-Cas9 to the liver, as we have with NTLA-2001, also unlocks the door to treating a wide array of other genetic diseases with our modular platform, and we intend to move quickly to advance and expand our pipeline.”
“It’s an important moment for the field,” MIT biomedical engineer Daniel Anderson, PhD (above), told Nature. Anderson is Professor, Chemical Engineering and Institute for Medical Engineering and Science at the Koch Institute for Integrative Cancer Research at MIT. “It’s a whole new era of medicine,” he added. Advances in the use of CRISPR-Cas9 for therapeutic purposes will create the need for clinical laboratories to sequence patients’ DNA to help physicians determine the best uses for a CRISPR-Cas9 treatment protocol. (Photo copyright: Massachusetts Institute of Technology.)
In Part 2 of the Phase 1 trial, Intellia plans to evaluate the new therapy at higher doses. After the trial is complete, “the company plans to move to pivotal studies for both polyneuropathy and cardiomyopathy manifestations of ATTR amyloidosis,” the press release states.
Previous clinical trials reported results for ex vivo treatments in which cells were removed from the body, modified with CRISPR-Cas9 techniques, and then reinfused. “But to be able to edit genes directly in the body would open the door to treating a wider range of diseases,” Nature reported.
How CRISPR-Cas9 Works
On its website, CRISPR Therapeutics, a company co-founded by Emmanuelle Charpentier, PhD, a director at the Max Planck Institute for Infection Biology in Berlin, and inventor of CRISPR-Cas9 gene editing, explained that the technology “edits genes by precisely cutting DNA and then letting natural DNA repair processes take over.” It can remove fragments of DNA responsible for causing diseases, as well as repairing damaged genes or inserting new ones.
The therapies have two components: Cas9, an enzyme that cuts the DNA, and Guide RNA (gRNA), which specifies where the DNA should be cut.
Charpentier and biochemist Jennifer Doudna, PhD, Nobel Laureate, Professor of Chemistry, Professor of Biochemistry and Molecular Biology, and Li Ka Shing Chancellor’s Professor in Biomedical and Health at the University of California Berkeley, received the 2020 Nobel Prize in Chemistry for their work on CRISPR-Cas9, STAT reported.
It is important to pathologists and medical laboratory managers to understand that multiple technologies are being advanced and improved at a remarkable pace. That includes the technologies of next-generation sequencing, use of gene-editing tools like CRISPR-Cas9, and advances in artificial intelligence, machine learning, and neural networks.
At some future point, it can be expected that these technologies will be combined and integrated in a way that allows clinical laboratories to make very early and accurate diagnoses of many health conditions.
Using precision genomics, Mayo researchers hope to develop improved medical laboratory tools for screening, diagnosing, and treating patients with inherited genetic disorders such as accelerated aging
Telomeres increasingly are on the radars of physicians and healthcare consumers alike, as researchers gain more knowledge about these critical nucleotides, and doctors continue to indicate their belief that telomeres could make useful diagnostic tools. If so, that would open up a new channel of precision medicine testing for clinical laboratories and anatomic pathology groups.
Telomeres are DNA strands that protect chromosome end points from degrading as people age. Their job is similar to the way plastic tips keep shoelaces from fraying, researchers at the Mayo Clinic explained in a news release. They have been using precision genomics in their assessment of 17 patients with short telomere syndrome (STS) to uncover the genetic causes of the condition.
Using Genetic Sequencing to Find Causes of Short Telomeres
People with STS could develop conditions including bone marrow failure, liver disease, and lung disease earlier in life than others, the news release pointed out.
However, according to the researchers’ paper, “Management of STSs is fraught with significant challenges such as delayed diagnoses, lack of routinely available diagnostics modalities, and standardized treatment guidelines.”
Nevertheless, some physicians are already leveraging information about telomeres in patient treatment. And many consumers have been turning to telomere diagnostic testing companies to learn the lengths of their own telomeres. They’ve learned that the longer the telomeres the better, as shorter telomeres are associated with accelerated aging.
“The length of certain telomeres gives a history of all the assaults a person has been subject to over the course of her lifetime,” a Wired article noted, quoting Joseph Raffaele, MD, co-founder of PhysioAge Medical Group, a clinical practice in New York City that specializes in “proactive” medicines. He goes on to call telomeres “the new cholesterol.” (Photo copyright: drraffaele.com.)
More Study into STS is Needed
GenomeWeb summarized the Mayo study’s methodology as follows:
“An analysis of data from 17 patients with STS confirmed by flow-FISH (fluorescence in situ hybridization) occurred;
Two were of unknown significance in TERT and RTEL1
Study authors concluded that while some genetic mutations are common to short telomeres, they were found in only about 40% of the people in their study. So, more research is needed to discover other causes of short telomeres.
The study found that when compared to people with normal blood telomeres, people with shorter telomere lengths and more rapidly aging blood cells:
Were 50% more likely to develop new or increasing respiratory symptoms;
Were nine times more likely to die; and,
Had worse health status and quality of life.
“It is known that short telomeres are associated with common morbidities of COPD, but it was not known if there is a relationship between blood telomeres and patient-related outcomes in COPD,” Don Sin, MD, a chest physician who led the research at the Centre for Heart Lung Innovation at St. Paul’s Hospital, stated in a news release.
Other Takes on Telomeres
A Harvard Medical blog noted, however, that short telomeres do not necessarily mean disease is imminent, nor that long ones guarantee optimal health.
“There is mounting evidence that a healthy lifestyle buffers your telomeres,” stated Immaculata De Vivo, PhD, a Harvard Medical School Professor and Genetics Researcher at the Dana-Farber/Harvard Cancer Center, in the blog post.
However, another expert questions the value of measuring telomeres for disease risk.
“In short, telomere lengths are too variable within a population, too variable within an individual, and too sensitive to environmental factors to offer any reliable information for common disease risk,” wrote Ricki Lewis, PhD, in PLOS.
Although there are many pitfalls to overcome, some doctors are pushing to use telomere information in patient treatment, and these studies from the Mayo Clinic and other researchers have contributed important data for diagnostic test developers.
In the end, vast and varied content about telomeres exists and clinical laboratory professionals may be called on to help clarify and assess the information. And that’s the long and the short of it.
