The 80 scientists and engineers that comprise the consortium believe synthetic biology can address key challenges in health and medicine, but technical hurdles remain
Synthetic biology now has a 20-year development roadmap. Many predict this fast-moving field of science will deliver valuable products that can be used in diagnostics—including clinical laboratory tests, therapeutics, and other healthcare products.
Eighty scientists from universities and companies around the world that comprise the Engineering Biology Research Consortium (EBRC) recently published the 20-year roadmap. They designed it to “provide researchers and other stakeholders (including government funders)” with what they hope will be “a go-to resource for engineering/synthetic biology research and related endeavors,” states the EBRC Roadmap website.
Medical laboratories and clinical pathologists may soon have new tools and therapies for targeting specific diseases. The EBRC defines synthetic biology as “the design and construction of new biological entities such as enzymes, genetic circuits, and cells or the redesign of existing biological systems. Synthetic biology builds on the advances in molecular, cell, and systems biology and seeks to transform biology in the same way that synthesis transformed chemistry and integrated circuit design transformed computing.”
Synthetic biology is an expanding field and there are predictions that it may produce research findings that can be adapted for use in clinical pathology diagnostics and treatment for chronic diseases, such as cancer.
Another goal of the roadmap is to encourage federal
government funding for synthetic biology.
“The question for government is: If all of these avenues are now open for biotechnology development, how does the US stay ahead in those developments as a country?” said Douglas Friedman, EBRC’s Executive Director, in a news release. “This field has the ability to be truly impactful for society and we need to identify engineering biology as a national priority, organize around that national priority, and take action based on it.”
Designing or Redesigning Life Forms for Specific
Applications
Synthetic biology is an interdisciplinary field that combines
elements of engineering, biology, chemistry, and computer science. It enables
the design and construction of new life forms—or redesign of existing ones—for
a multitude of applications in medicine and other fields.
Another recent example comes from the Wyss Institute at Harvard. Scientist there developed a direct-to-consumer molecular diagnostics platform called INSPECTR that, they say, uses programmable synthetic biosensors to detect infectious pathogens or host cells.
The Wyss Institute says on its website that the platform can
be packaged as a low-cost, direct-to-consumer test similar to a home pregnancy
test. “This novel approach combines the specificity, rapid development, and
broad applicability of a molecular diagnostic with the low-cost, stability, and
direct-to-consumer applicability of lateral flow immunoassays.”
In March, Harvard announced that it had licensed the technology to Sherlock Biosciences.
Howard Salis, PhD (above), Associate Professor of biological engineering and chemical engineering at Pennsylvania State University (Penn State), co-chaired the EBRC Roadmapping Working Group that produced the roadmap. In a Penn State news story, Salis explained synthetic biology’s potential. “There are both traditional and startup companies leveraging synthetic biology technologies to develop novel biotech products,” he said. “Organisms that produce biorenewable materials; diagnostics to detect the Zika virus, Ebola and tuberculosis; and soil bacteria that fix nitrogen into ammonia for improved plant growth.” (Photo copyright: Twitter.)
Fundamental Challenges with Synthetic Biology
The proponents of synthetic biology hope to make it easier
to design and build these systems, in much the same way computer engineers
design integrated circuits and processors. The EBRC Roadmap may help scientist
worldwide achieve this goal.
However, in “What is Synthetic/Engineering Biology?” the EBRC also identifies the fundamental challenges facing the field. Namely, the complexity and unpredictability inherent in biology, and a limited understanding of how biological components interact.
The EBRC roadmap report, “Engineering Biology: A Research
Roadmap for the Next-Generation Bioeconomy,” covers five categories of applications:
Health and medicine are of primary interest to pathologists.
Synthetic Biology in Health and Medicine
The Health and Medicine section of the report identifies
four broad societal challenges that the EBRC believes can be addressed by
synthetic biology. For each, the report specifies engineering biology
objectives, including efforts to develop new diagnostic technologies. They
include:
Existing and emerging infectious diseases: Objectives include development of tools for treating infections, improving immunity, reducing dependence on antibiotics, and diagnosing antimicrobial-resistant infections. The authors also foresee tools for rapid characterization and response to “known and unknown pathogens in real time at population scales.”
Non-communicable diseases and disorders, including cancer, heart disease, and diabetes: Objectives include development of biosensors that will measure metabolites and other biomolecules in vivo. Also: tools for identifying patient-specific drugs; tools for delivering gene therapies; and genetic circuits that will foster tissue formation and repair.
Environmental health threats, such as toxins, pollution, and injury: Objectives include systems that will integrate wearable tech with living cells, improve interaction with prosthetics, prevent rejection of transplanted organs, and detect and repair of biochemical damage.
Healthcare access and personalized medicine: The authors believe that synthetic biology can enable personalized treatments and make new therapies more affordable.
Technical Themes
In addition to these applications, the report identifies
four “technical themes,” broad categories of technology that will spur the
advancement of synthetic biology:
Gene editing, synthesis, and assembly: This refers to tools for producing chromosomal DNA and engineering whole genomes.
Biomolecule, pathway, and circuit engineering: This “focuses on the importance, challenges, and goals of engineering individual biomolecules themselves to have expanded or new functions,” the roadmap states. This theme also covers efforts to combine biological components, both natural and non-natural, into larger, more-complex systems.
Host and consortia engineering: This “spans the development of cell-free systems, synthetic cells, single-cell organisms, multicellular tissues and whole organisms, and microbial consortia and biomes,” the roadmap states.
Data Integration, modeling, and automation: This refers to the ability to apply engineering principles of Design, Build, Test and Learn to synthetic biology.
The roadmap also describes the current state of each
technology and projects likely milestones at two, five, 10, and 20 years into
the future. The 2- and 5-year milestones are based on “current or recently
implemented funding programs, as well as existing infrastructure and facilities
resources,” the report says.
The longer-term milestones are more ambitious and may
require “significant technical advancements and/or increased funding and
resources and new and improved infrastructure.”
Synthetic biology is a significant technology that could
bring about major changes in clinical pathology diagnostics and treatments.
It’s well worth watching.
Scientists with Francis Crick Institute and Ragon Institute have successfully created human antibodies in vitro that can be made to recognize specific antigens in the human body; Could lead to new treatments for cancer and other infectious diseases
It’s been long-recognized that the ability to design human antibodies customized to recognize specific antigens could be a game-changer in the diagnosis and treatment of many diseases. It would enable the creation of useful new clinical laboratory tests, vaccines, and similar therapeutic modalities.
Now an international research team has published the findings of its novel technique that was developed to generate human antibodies in vitro. The research was conducted at the Ragon Institute of Massachusetts General Hospital (MGH), Massachusetts Institute of Technology (MIT), Harvard, and the Francis Crick Institute in London.
Antibodies and antigens are used in a large number of clinical laboratory and anatomic pathology tests and assays. In many cases, animal antibodies/antigens are used in test kits because they attract and bind to specific human antibodies/antigens that are biomarkers for diagnoses. Thus, as this technology is validated and further developed, it could be the source of useful biomarkers for lab tests as well as for vaccines.
Antibodies—also referred to as immunoglobulins—are made by the body’s B-lymphocytes (B cells) in response to antigens, such as bacteria, viruses, or other harmful substances. Each antibody has a special bearing on a particular antigen. For example, the human immunodeficiency virus (HIV) antibody and HIV antigen (p24) test screens and diagnoses people for HIV infection, explained LabTestsOnline.
Many medical laboratory tests use animal antibodies and antigens. But what if human antibodies could be generated and stimulated to recognize specific human antigens? That’s what the researchers believe they have done, according to a press release.
The Ragon Institute at MGH, MIT, and Harvard (above) was established in 2009 to find an HIV vaccine and to be a worldwide leader in the study of immunology. The Francis Crick Institute, formed in 2015, is a biomedical research institute using biology to understand health and disease. (Photo copyright: The Ragon Institute.)
The researchers know the novel technique they developed for generating human antibodies in vitro needs further development and validation. If this happens, the technique could one day be the source of useful biomarkers for medical lab tests, and may be a way to prevent infectious diseases.
“Specifically, it should allow the production of these antibodies within a shorter time frame in vitro and without the need for vaccination or blood/serum donation from recently infected or vaccinated individuals,” said Facundo D. Batista, PhD, in the press release. Batista is Principle Investigator with the Ragon Institute and led the research teams. “In addition, our method offers the potential to accelerate the development of new vaccines by allowing the efficient evaluation of candidate target antigens.”
Researchers Aim to Make Human Antibodies in Medical Laboratory
This international team of researchers sought to replicate in the lab—using patient blood samples—a natural human process for creation of antibodies from B cells. This is the process they wished to replicate:
· Antibodies are made by the body’s B cells;
· An antigen molecule is recognized by a B cell;
· Plasma cells (able to secrete antibodies) develop;
· An antibody binds to a particular antigen to fight an infection.
“B lymphocytes (B cells) play a critical role in adaptive immunity, providing protection from pathogens through the production of specific antibodies. B cells recognize and respond to pathogen-derived antigens through surface B cell receptors,” the researchers wrote in The Journal of Experimental Medicine (JEM).
Nanoparticles Key to the Approach
But finding an exact antigen is only one part of the B cell’s job. In the lab, B cells also need a trigger that enables them to grow and develop into plasma cells, which are key to fighting disease, the researchers noted.
“The in vitro activation of B cells in an antigen-dependent manner is difficult to achieve,” the authors stated in the JEM. “To overcome limitations, we developed a novel in vitro strategy to stimulate human B cells with streptavidin nanoparticles conjugated to both CpG and antigen. B cells producing antigen-specific antibodies were identified, quantified, and characterized to determine the antibody repertoire.”
According to the press release, “CpG oligonucleotides internalize into B cells that recognize the specific antigen.”
The statement, which garnered worldwide attention, noted the following steps taken by the researchers:
· B cells from patient blood samples were isolated;
· Then, they were treated with tiny nanoparticles coated with both CpG oligonucleotides and the right antigen;
· These DNA molecules are unique, because they can activate toll-like receptor 9 (TLR9);
· TLR9 develops into antibody-secreting plasma cells.
Results: Antibodies for Tetanus, Influenza, HIV
This method, according to the scientists, could be used in further research to develop antibodies to treat infectious diseases and cancer.
· “The team successfully demonstrated their approach using various bacterial and viral antigens, including the tetanus toxoid and proteins from several strains of influenza A;
· “In each case, the researchers were able to produce specific, high-affinity antibodies in just a few days. Some of the anti-influenza antibodies generated by the technique recognized multiple strains of the virus and were able to neutralize its ability to infect cells;
· “The procedure does not depend on the donors having been previously exposed to any of these antigens through vaccination or infection; and,
· “Researchers were able to generate anti-HIV antibodies from B cells isolated from HIV-free patients.”
Research Suggests More Possibilities
While this highly scientific study may not be on the radar of most anatomic pathologists and medical laboratory leaders at the moment, it holds enormous promise to produce cures for infectious disease and more effective cancer treatments. This research project also demonstrates how new techniques using antibodies have the potential to create an entirely new generation of clinical laboratory assays that improve diagnostic accuracy and better inform physicians when they consider the most appropriate therapies for their patients.
As science learns more about the human genome, new companies are being formed to offer consumers at-home microbiology test kits, a development many microbiologists consider worrisome
Can consumers rely on the accuracy of at-home microbiology tests that promise to give them useful information about their microbiome? That’s just one question being asked by clinical laboratory scientists and microbiologists in response to the proliferation of companies offering such tests.
Advances in gene sequencing technology, new insights into the human microbiome, and more sophisticated software to analyze test data are fueling the growth of companies that want to offer consumers at-home microbiology test kits. And no less an authority than the American Academy of Microbiology (ASM) states in a 2017 report, that knowledge of the microbiome can revolutionize healthcare as “insights acquired from NGS [next-generation sequencing] methods can be exploited to improve our health as individuals and the greater public health.”
The move towards more “precision medicine” in terms of diagnostics and treatments, according to the ASM, is based in part on microbial genomic testing, which when combined with a patient’s medical history, clinical signs, symptoms, and human genomic information, can help “create treatment pathways that are individualized and tailored for each patient.”
However, critics worry about overreach given current limitations in the analysis and diagnosis of microbiome data produced by testing, particularly in connection to the rising number of consumer self-testing services aimed at the general public.
No Science to Back Up Claims of Accuracy for At-Home Microbiology Tests
A recent article from the MIT Technology Review, notes that these at-home microbiology testing services, while exciting, can only offer limited information—despite claims. Companies such as Thryve, for example, offer visitors to their website a $99 gut health kit, which they recommend using four times per year. The goal is to use the data to target regimens of supplements and “correct” problems the testing identifies.
Another company, uBiome, offers physician-ordered and customer-requested test kits that the company suggests can determine risk factors for disease. However, critics suggest science cannot currently back up those claims. Concerns about the value of such consumer self-testing, the legitimacy of recommendations based on “diagnoses,” and basic health privacy are leading to serious concerns within the scientific community.
Ethics and Realistic Expectations
One additional criticism of consumer self-testing of microbiomes involves privacy. An NPR article on the American Gut Project (AGP), which Dark Daily reported on in previous e-briefings, notes that those tested may be disclosing quite a bit of information about themselves. The article’s author points out basic privacy and value concerns about the AGP. American Gut Project is a crowd-funded “citizen science project,” and part of the larger global Earth Microbiome Project, described as a “massively collaborative effort to characterize microbial life on this planet.” (See Dark Daily, “Get the Poop on Organisms Living in Your Gut with a New Consumer Laboratory Test Offered by American Gut and uBiome,” September 9, 2015.)
One example of an at-home microbiology test marketed to consumers is the SmartGut by uBiome (above). It is “a microbiome screening test that uses precision sequencing technology to identify key microorganisms in your gut, both pathogenic and commensal.” (Photo copyright: uBiome.)
In her blog post on the Center for Microbiome Informatics and Therapeutics’ website, Tami Lieberman, PhD, claims that “microbiome profiling is messy (and I’m not just talking about the sample collection).” Lieberman submitted samples to American Gut and uBiome for her article. Lieberman’s skepticism of the services is based on two things:
1. There is no “gold standard” for microbiome DNA profiling technology or analysis methods at this time; and,
2. Human microbiomes are in her words, “a moving target, changing with age and diet.”
Thus, the best these services can provide, Lieberman argues, is a snapshot of gut microbes at one period of time. Additionally, she claims there is a danger in trying to interpret personal microbiome data. And, Lieberman is not alone in her criticism.
Science Must Be ‘On Guard’ Against Hype about the Usefulness of Microbiome Tests
Martin Blaser, MD, PhD, Director of the Human Microbiome Project at New York University, also criticizes at-home self-tests of microbiomes. In a New York Times article, Blaser points out that the enormous amount of data generated by microbiome testing is “basically uninterpretable” at this time. According to Blaser, scientists can chart the presence, absence, and levels of specific microbiomes and note correlations, but there is no way to know if changes to microbiomes in a particular patient signal disease risk, progression, or development.
The study of microbiomes is still in its nascent stages, so despite there being significant information correlating the presence or absence of specific microbes to diseases, Blaser states that scientists are currently unsure of what that correlation implies. They simply know the correlations exist.
The “gold rush” of companies offering consumers an at-home microbiology test requires skepticism, notes Hanage. He further urges researchers, press officers, and journalists to remain objective. Hanage writes, “Press officers must stop exaggerating results, and journalists must stop swallowing them whole.” Hanage warns that scientists should be on guard against the “buzz around the field” distorting scientific priorities and misleading the public at large. So, while studies of the human microbiome do carry vast potential for medical laboratories and pathologists to change healthcare and healthcare diagnostics, a healthy dose of skepticism is still the best medicine.
U.S. Patent and Trademark Office will hold hearings to determine whether University of California Berkeley, or Broad Institute of Harvard and MIT, should receive patents for new genomic engineering technique
In the race to master gene-editing in ways that will advance genetic medicine and patient care, one of the hottest technologies is CRISPR, which stands for Clustered Regularly Interspaced Short Palindromic Repeats. But now a patent fight has the potential to complicate how pathologists and other scientists use this exciting technology.
This dispute over the CRISPR patent—a tool that has been hailed as one of the biggest biotech breakthroughs of the decade—will likely be settled in the coming months by the United States Patent and Trademark Office (USPTO).
The USPTO will be reviewing key patents awarded for what is called CRISPR/Cas9. The technology is already generating novel therapies for diseases, which should create new opportunities for pathologists and medical laboratories. (more…)
Lab-on-a-chip technology could reduce the time needed to identify infection-causing bacteria and for physicians to prescribe correct antibiotics
Pathology groups and medical laboratories may see their role in the patient-care process grow if researchers succeed in developing culture-independent diagnostic tools that quickly identify bacterial infections as well as pinpoint the antibiotics needed to treat them.
In the battle against antibiotic-resistant infections (AKA “super bugs”) the National Institutes of Health (NIH) is funding nine research projects aimed at thwarting the growing problem of life-threatening infections that no longer are controlled or killed by today’s arsenal of drugs.
Common Practices in Hospitals Leading to Super Bugs
Currently, when infections are suspected in hospitals or other settings where illness can quickly spread, samples are sent to a central medical laboratory where it may take up to three days to determine what germ is causing the infection. Because of that delay, physicians often prescribe broad-spectrum antibiotics based on a patient’s symptoms rather than lab test results, a practice that can lead to the growth of antibiotic-resistant microbes. (more…)
