Use of synthetic genetics to replicate an infectious disease agent is a scientific accomplishment that many microbiologists and clinical laboratory managers expected would happen
Microbiologists and infectious disease doctors are quite familiar with Escherichia coli (E. coli). The bacterium has caused much human sickness and even death around the globe, and its antibiotic resistant strains are becoming increasingly difficult to eradicate.
Now, scientists in England have created a synthetic “recoded” version of E. coli bacteria that is being used in a positive way—to fight disease. Their discovery is being heralded as an important breakthrough in the quest to custom-alter DNA to create synthetic forms of life that one day could be designed to fight specific infections, create new drugs, or produce tools to diagnose or treat disease.
Scientists worldwide working in the field of synthetic genomics are looking for ways to modify genomes in order to produce new weapons against infection and disease. This research could eventually produce methods for doctors—after diagnosing a patient’s specific strain of bacteria—to then use custom-altered DNA as an effective weapon against that patient’s specific bacterial infection.
This latest milestone is the result of a five-year quest by researchers at the Medical Research Council Laboratory of Molecular Biology (MRC-LMB) in Cambridge, England, to create a man-made version of the intestinal bacteria by redesigning its four-million-base-pair genetic code.
The MRC-LMB lab’s success marks the first time a living
organism has been created with a compressed genetic code.
The researchers published their findings in the journal Nature.
“This is a landmark in the emerging field of synthetic
genomics and finally applies the technology to the laboratory’s workhorse
bacterium,” they wrote. “Synthetic genomics offers a new way of life, while at
the same time moving synthetic biology towards a future in which genomes can be
written to design.”
All known forms of life on Earth contain 64 codons—a specific sequence of three consecutive nucleotides that corresponds with a specific amino acid or stop signal during protein synthesis. Jason Chin, PhD, Program Lead at MRC-LMB, said biologists long have questioned why there are 20 amino acids encoded by 64 codons.
“Is there any function to having more than one codon to encode each amino acid?” Chin asked during an interview with the Cambridge Independent. “What would happen if you made an organism that used a reduced set of codons?”
The MRC-LMB research team took an important step toward
answering that question. Their synthetic E. coli strain, dubbed Syn61,
was recoded through “genome-wide substitution of target codons by defined
synonyms.” To do so, researchers mastered a new piece-by-piece technique that
enabled them to recode 18,214 codons to create an organism with a 61-codon
genome that functions without a previously essential transfer RNA.
“Our synthetic genome implements a defined recoding and refactoring scheme–with simple corrections at just seven positions–to replace every known occurrence of two sense codons and a stop codon in the genome,” lead author Julius Fredens, PhD, a post-doctoral research associate at MRC, and colleagues, wrote in their paper.
Science Alert reports that the laboratory-created version of E. coli (above) “isn’t quite a dead ringer for its ancestor. The cells are a touch longer, and they reproduce 1.6 times slower. But the edited E. coli seems healthy and produces the same range and quantity of proteins as the non-edited versions.” (Photo copyright: Jason Chin/STAT.)
Joshua Atkinson, PhD, a postdoctoral research associate at Rice University in Houston, labeled the breakthrough a “tour de force” in the field of synthetic genomics. “This achievement sets a new world record in synthetic genomics by yielding a genome that is four times larger than the pioneering synthesis of the one-million-base-pair Mycoplasma mycoides genome,” he stated in Synthetic Biology.
“Synthetic genomics is enabling the simplification of
recoded organisms; the previous study minimized the total number of genes and
this new study simplified the way those genes are encoded.”
Manmade Bacteria That are Immune to Infections
Researchers from the J.
Craig Venter Institute in Rockville, Maryland, created the first synthetic
genome in 2010. According to an article in Nature,
the Venter Institute successfully synthesized the Mycoplasma mycoides genome
and used it “reboot” a cell from a different species of bacterium.
The MRC-LMB team’s success may prove more significant.
“This new synthetic E. coli should not be able to decode DNA from any other organism and therefore it should not be possible to infect it with a virus,” the MRC-LMB stated in a news release heralding the lab’s breakthrough. “With E. coli already being an important workhorse of biotechnology and biological research, this study is the first time any commonly used model organism has had its genome designed and fully synthesized and this synthetic version could become an important resource for future development of new types of molecules.”
Because the MRC-LMB team was able to remove transfer RNA and
release factors that decode three codons from the E. coli bacteria,
their achievement may be the springboard to designing manmade bacteria that are
immune to infections or could be turned into new drugs.
“This may enable these codons to be cleanly reassigned and
facilitate the incorporation of multiple non-canonical amino acids. This
greatly expands the scope of using non-canonical amino acids as unique tools
for biological research,” the MRC-LMB news release added.
Though synthetic genomics impact on clinical laboratory diagnostics is yet to be known, medical laboratory leaders should be mindful of the potential for rapid innovation in this field as proof-of-concept laboratory innovations are translated into real-world applications.
Technology allows retrievable information to be recorded directly into the genomes of living bacteria, but will this technology have value in clinical laboratory testing?
Researchers at Harvard Medical School have successfully used CRISPR technology to encode an image and a short film into the Deoxyribonucleic acid (DNA) of bacteria. Their goal is to develop a way to record and store retrievable information in the genomes of living bacteria. A story in the Harvard Gazette described the new technology as a sort of “biological hard drive.”
It remains to be seen how this technology might impact medical laboratories and pathology groups. Nevertheless, their accomplishment is another example of how CRISPR technology is leading to new insights and capabilities that will advance genetic medicine and genetic testing.
Recording Complex Biological Events in the Genomes of Bacteria
Clustered Regularly Interspaced Short Palindromic Repeats (CRISPR) are DNA sequences containing short, repetitive base sequences found in the genomes of bacteria and other micro-organisms that can facilitate the modification of genes within organisms. The term CRISPR also can refer to the whole CRISPR-Cas9 system, which can be programmed to pinpoint certain areas of genetic code and to modify DNA at exact locations.
Led by George Church, PhD, faculty member and Professor of Genetics at Harvard Medical School, the team of researchers at the Wyss Institute for Biologically Inspired Engineering at Harvard University in Cambridge, Mass., constructed a molecular recorder based on CRISPR that enables cells to obtain DNA information and produce a memory in the genome of bacteria. With it, they inserted a GIF image and a five-frame movie into the bacteria’s DNA.
“As promising as this was, we did not know what would happen when we tried to track about 100 sequences at once, or if it would work at all,” noted Seth Shipman, PhD, Postdoctoral Fellow, and one of the authors of the study in the Harvard Gazette story. “This was critical since we are aiming to use this system to record complex biological events as our ultimate goal.”
Translating Digital Information into DNA Code
The team transferred an image of a human hand and five frames of a movie of a running horse onto nucleotides to imbed data into the genomes of bacteria. This produced a code relating to the pixels of each image. CRISPR was then used to insert genetic code into the DNA of Escherichia coli (E-coli) bacteria. The researchers discovered that CRISPR did have the ability to encode complex information into living cells.
“The information is not contained in a single cell, so each individual cell may only see certain bits or pieces of the movie. So, what we had to do was reconstruct the whole movie from the different pieces,” stated Shipman in a BBC News article. “Maybe a single cell saw a few pixels from frame one and a few pixels from frame four … so we had to look at the relation of all those pieces of information in the genomes of these living cells and say, ‘Can we reconstruct the entire movie over time?’”
The team used an image of a digitized human hand because it embodies the type of intricate data they wish to use in future experiments. A movie also was used because it has a timing component, which could prove to be beneficial in understanding how a cell and its environment may change over time. The researchers chose one of the first motion pictures ever recorded—moving images of a galloping horse by Eadweard Muybridge, a British photographer and inventor from the late 19th century.
“We designed strategies that essentially translate the digital information contained in each pixel of an image or frame, as well as the frame number, into a DNA code that, with additional sequences, is incorporated into spacers. Each frame thus becomes a collection of spacers,” Shipman explained in the Harvard Gazette story. “We then provided spacer collections for consecutive frames chronologically to a population of bacteria which, using Cas1/Cas2 activity, added them to the CRISPR arrays in their genomes. And after retrieving all arrays again from the bacterial population by DNA sequencing, we finally were able to reconstruct all frames of the galloping horse movie and the order they appeared in.”
In the video above, Wyss Institute and Harvard Medical School researchers George Church, PhD, and Seth Shipman, PhD, explain how they engineered a new CRISPR system-based technology that enables the chronological recording of digital information, like that representing still and moving images, in living bacteria. Click on the image above to view the video. It is still too early to determine how this technology may be useful to pathologists and clinical laboratory scientists. (Caption and video copyright: Wyss Institute at Harvard University.)
“In this study, we show that two proteins of the CRISPR system, Cas1 and Cas2, that we have engineered into a molecular recording tool, together with new understanding of the sequence requirements for optimal spacers, enables a significantly scaled-up potential for acquiring memories and depositing them in the genome as information that can be provided by researchers from the outside, or that, in the future, could be formed from the cells natural experiences,” stated Church in the Harvard Gazette story. “Harnessed further, this approach could present a way to cue different types of living cells in their natural tissue environments into recording the formative changes they are undergoing into a synthetically created memory hotspot in their genomes.”
Encoding Information into Cells for Clinical Laboratory Testing and Therapy
The team plans to focus on creating molecular recording devices for other cell types and on enhancing their current CRISPR recorder to memorize biological information.
“One day, we may be able to follow all the developmental decisions that a differentiating neuron is taking from an early stem cell to a highly-specialized type of cell in the brain, leading to a better understanding of how basic biological and developmental processes are choreographed,” stated Shipman in the Harvard Gazette story. Ultimately, the approach could lead to better methods for generating cells for regenerative therapy, disease modeling, drug testing, and clinical laboratory testing.
According to Shipman in the BBC News article, these cells could “encode information about what’s going on in the cell and what’s going on in the cell environment by writing that information into their own genome.”
This field of research is still new and its full potential is not yet understood. However, if this capability can be developed, there could be opportunities for pathologists and molecular chemists to develop methods for in vivo monitoring of a patient’s cell function. These methods could prove to be an unexpected new way for clinical laboratories to add value and become more engaged with the clinical care team.
Use of these new technologies creates opportunities for clinical laboratories and pathologists to add more value when collaborating with physicians to advance patient care
Ongoing improvements in point-of-care testing are encouraging one major academic medical center to apply this mode of testing to the diagnosis of hospital-acquired infections (HAIs). This development should be of interest to clinical laboratory professionals and pathologists, since it has the potential to create a different way to identify patients with HAIs than medical lab tests done in the central laboratory.
Massachusetts General Hospital (MGH), Harvard Medical School’s (HMS’) largest teaching hospital, has developed a prototype diagnostic system that works with doctors’ smartphones or mobile computers. The hand-held system can identify pathogens responsible for specific healthcare-acquired infections (HAIs) at the point of care within two hours, according to an MGH statement.
The researchers noted that 600,000 patients develop HAIs each year, 10% of which die, and that costs related to HAIs can reach $100 to $150 billion per year. However, as Dark Daily reported, the Centers for Medicare and Medicaid Services (CMS) does not reimburse hospitals for certain HAIs. (See Dark Daily, “Consumer Reports Ranks Smaller and Non-Teaching Hospitals Highest in Infection Prevention,” October, 30, 2015.) Thus, the critical need to identify from where the infection originated, which generates a significant proportion of samples tested at the clinical laboratories of the nation’s hospitals and health systems.
Therefore, pathologists and medical laboratory scientists will understand that shifting some of that specimen volume to point-of-care testing will change the overall economics of hospital laboratories.
Optical test cubes are placed on an electronic base station that transmits data to a smartphone or computer, where results are displayed. “In a pilot clinical test, PAD accuracy was comparable to that of bacterial culture. In contrast to the culture, the PAD assay was fast (under two hours), multiplexed, and cost effective (under $2 per assay), wrote the MGH researchers in the journal Science Advances. (more…)
New vaccine has potential to reduce volume of clinical laboratory testing for bacterial and viral infections
By now, nearly all pathologists and clinical laboratory scientists acknowledge that advances in molecular diagnostics and genetic testing are contributing to significant improvements in patient care. Now comes news of a comparable breakthrough in another field of medicine with the potential to protect many individuals from pneumonia and similar infectious diseases.
A new way to develop vaccines made the news recently. Researchers at the University of Buffalo (UB) in New York have found a new way to reduce infections of specific and widespread Streptococcus pneumoniae (pneumococcus) diseases.
This cutting-edge pneumococcal vaccine allows Streptococcus pneumoniae to colonize and live inside the body as long as there is no risk to the host. When a threat is detected, the vaccine establishes an immune system response to annihilate the disease-causing bacteria. (more…)
Researchers at Florida Atlantic University believe this technology could also be used to detect bacteria in food and water and to follow patients’ progress after leaving acute or outpatient care
New technology could shift the paradigm in infectious disease testing by clinical laboratories, while also giving hospitals a faster way to identify hospital-acquired infections (HAIs) and monitor patients for infections post-discharge. The diagnostic technology is built into a special “biosensing film” made of cellulose paper and a flexible polymer.
Researchers at Florida Atlantic University (FAU) developed the biosensing film. They say it can detect and discern HIV, Staphylococcus aureus, E-coli and other bacteria in blood, plasma, and saliva. The test is inexpensive, disposable, and portable. Best of all (at least for developing countries, remote locations, and places that have few resources), it requires no expensive infrastructure or a clinical laboratory.
And yes, the biosensing film is designed to work in tandem with a smartphone app. But in this case, the mobile app is only part of the story. The real genius is the piece of lightweight, flexible, “electronic paper” or “biosensing film” used with the app. The film acts as a platform that detects infections, both viral and bacterial.
