Overcoming the challenges of cancer drug resistance through bacterial-mediated therapy.

Despite tremendous efforts to fight cancer, it remains a major public health problem and a leading cause of death worldwide. With increased knowledge of cancer pathways and improved technological platforms, precision therapeutics that specifically target aberrant cancer pathways have improved patient outcomes. Nevertheless, a primary cause of unsuccessful cancer therapy remains cancer drug resistance. In this review, we summarize the broad classes of resistance to cancer therapy, particularly pharmacokinetics, the tumor microenvironment, and drug resistance mechanisms. Furthermore, we describe how bacterial-mediated cancer therapy, a bygone mode of treatment, has been revitalized by synthetic biology and is uniquely suited to address the primary resistance mechanisms that confound traditional therapies. Through genetic engineering, we discuss how bacteria can be potent anticancer agents given their tumor targeting potential, anti-tumor activity, safety, and coordinated delivery of anti-cancer drugs

Genetically programmable pathogen sense and destroy/

Thesis (Ph. D.)--Massachusetts Institute of Technology, Dept. of Biological Engineering, 2012.This electronic version was submitted by the student author. The certified thesis is available in the Institute Archives and Special Collections.Cataloged from student submitted PDF version of thesis.Includes bibliographical references (p. 123-134).Twenty five percent of all the deaths worldwide are caused by infectious diseases. They are also the biggest cause of mortality among children under five years of age. Among them diarrheal diseases alone cause as many deaths as AIDS or TB and malaria combined. Also up to 80% of traveler's diarrhea is bacterial in nature. Vibrio cholerae (cholera), Salmonella spp (typhoid fever), Shigella spp (shigellosis) and a variety of enteropathogenic Escherichia coli strains are among the principle bacterial agents that cause this type of diarrhea. Improvements in hygiene and access to adequate nutrition are good strategies but immunization against specific diseases still offers the best solution to fight these infections. Unfortunately the wide diversity of bacterial and viral agents that cause diarrhea complicates accurate diagnosis and makes the development of vaccines difficult. Antibiotics used in timely manner and in appropriate doses can be effective but the diagnosis is usually made too late for the therapy to be effective. Moreover frequent use of over-the-counter drugs without any medical supervision has led to multidrug resistance in most of the bacterial strains. To counter this problem I demonstrate a proof of principle of a novel cell therapy against Pseudomonas Aeruginosa (major cause of urinary tract disease and hospital infections). Using principles of Synthetic Biology I genetically modified a probiotic strain of E. coli to specifically detect PAO₁ and respond by secreting a novel, pathogen-specific engineered toxin. Additionally, I translated the bacterial system into mammalian cells and established a foundation for an adaptive system where the sentinel cells secrete an alternate toxin if the pathogen becomes resistant to the first one. Finally, based on this system I proposed designs against highly pathogenic strains of Shigella, Salmonella and Vibrio cholerae. This cell therapy remains inert until a threat is detected, and then serves as an early detection and rapid response agent. Furthermore this platform can be tuned to release minimum but sufficient amounts of very narrow spectrum antimicrobial proteins to control the early stages of infection before the disease becomes systemic. Therefore this system's rapid, automated and highly specific response can be helpful in reducing the occurrence of dose dependent resistance. This approach offers a single integrated solution to eradicating multiple threats with a strategy that is a rapid, selective, and highly sensitive.by Saurabh Gupta.Ph.D

Engineered bacteria as therapeutic agents

Although bacteria are generally regarded as the causative agents of infectious diseases, most bacteria inhabiting the human body are non-pathogenic and some of them can be turned, after proper engineering, into ‘smart’ living therapeutics of defined properties for the treatment of different illnesses. This review focuses on recent developments to engineer bacteria for the treatment of diverse human pathologies, including inflammatory bowel diseases, autoimmune disorders, cancer, metabolic diseases and obesity, as well as to combat bacterial and viral infections. We discuss significant advances provided by synthetic biology to fully reprogram bacteria as human therapeutics, including novel measures for strict biocontainment.Ministerio de Economía y Competitividad (MINECO) (BIO2014- 60305R and BIO2011-26689), BACFITERed (SAF2014-56716-REDT)Comunidad Autónoma de Madrid (S2010-BMD-2312)La Caixa FoundationMINECO (BES-2009-02405)Peer reviewe

Programmable molecular scissors: Applications of a new tool for genome editing in biotech.

Targeted genome editing is an advanced technique that enables precise modification of the nucleic acid sequences in a genome. Genome editing is typically performed using tools, such as molecular scissors, to cut a defined location in a specific gene. Genome editing has impacted various fields of biotechnology, such as agriculture; biopharmaceutical production; studies on the structure, regulation, and function of the genome; and the creation of transgenic organisms and cell lines. Although genome editing is used frequently, it has several limitations. Here, we provide an overview of well-studied genome-editing nucleases, including single-stranded oligodeoxynucleotides (ssODNs), transcription activator-like effector nucleases (TALENs), zinc-finger nucleases (ZFNs), and CRISPR-Cas9 RNA-guided nucleases (CRISPR-Cas9). To this end, we describe the progress toward editable nuclease-based therapies and discuss the minimization of off-target mutagenesis. Future prospects of this challenging scientific field are also discussed.This work was supported by the KU-Research Professor Program of Konkuk University. This study was partially supported by a grant from the National Research Foundation of Korea (NRF) funded by the Ministry of Science, ICT & Future Planning, South Korea (grant 2016R1E1A1A01940995)

Synthetic biology devices for in vitro and in vivo diagnostics

There is a growing need to enhance our capabilities in medical and environmental diagnostics. Synthetic biologists have begun to focus their biomolecular engineering approaches toward this goal, offering promising results that could lead to the development of new classes of inexpensive, rapidly deployable diagnostics. Many conventional diagnostics rely on antibody-based platforms that, although exquisitely sensitive, are slow and costly to generate and cannot readily confront rapidly emerging pathogens or be applied to orphan diseases. Synthetic biology, with its rational and short design-to-production cycles, has the potential to overcome many of these limitations. Synthetic biology devices, such as engineered gene circuits, bring new capabilities to molecular diagnostics, expanding the molecular detection palette, creating dynamic sensors, and untethering reactions from laboratory equipment. The field is also beginning to move toward in vivo diagnostics, which could provide near real-time surveillance of multiple pathological conditions. Here, we describe current efforts in synthetic biology, focusing on the translation of promising technologies into pragmatic diagnostic tools and platforms.United States. Defense Threat Reduction Agency (Grant HDTRA1-14-1- 0006)United States. Office of Naval Research. Multidisciplinary University Research InitiativeUnited States. Air Force Office of Scientific Research (Grant FA9550-14-1-0060)Wyss Institute for Biologically Inspired EngineeringHoward Hughes Medical Institut

The Failure of Federal Biotechnology Regulation

The recent court case and state ballot measures regarding mandatory labels for Genetically Modified Organisms (“GMOs”) suggest the need for a deeper conversation about the federal framework for regulating biotechnology. What is it about GMOs that consumers feel they have the “right to know?” Why has a generation of federal biotechnology regulation failed to satisfy consumer concerns? Are those concerns irrational, or is the regulatory structure inadequate? This Article argues that many consumer concerns underlying the labeling movement raise important scientific and extra- scientific questions that have been apparent since the advent of the technology in the 1980s. Moreover, these concerns persist because the Coordinated Framework for Regulation of Biotechnology has failed to respond to them effectively. The Coordinated Framework was based on statutes that pre-existed the technology and thus poorly fit the unique risks of genetic engineering. Today, genetic engineering is on the verge of a radical shift in technology, a shift that has already begun to burst the seams of those old statutes, leaving agencies with no regulatory authority at all over new products. This Article reviews the evidence behind persistent concerns about GMOs, considers the failures of the Coordinated Framework to address the most valid of those concerns, and canvasses policy questions that Congress must consider to more effectively tailor agency authority to address the risks and to enhance the potential of this rapidly-changing field of technology

Principles of genetic circuit design

Cells navigate environments, communicate and build complex patterns by initiating gene expression in response to specific signals. Engineers seek to harness this capability to program cells to perform tasks or create chemicals and materials that match the complexity seen in nature. This Review describes new tools that aid the construction of genetic circuits. Circuit dynamics can be influenced by the choice of regulators and changed with expression 'tuning knobs'. We collate the failure modes encountered when assembling circuits, quantify their impact on performance and review mitigation efforts. Finally, we discuss the constraints that arise from circuits having to operate within a living cell. Collectively, better tools, well-characterized parts and a comprehensive understanding of how to compose circuits are leading to a breakthrough in the ability to program living cells for advanced applications, from living therapeutics to the atomic manufacturing of functional materials.National Institute of General Medical Sciences (U.S.) (Grant P50 GM098792)National Institute of General Medical Sciences (U.S.) (Grant R01 GM095765)National Science Foundation (U.S.). Synthetic Biology Engineering Research Center (EEC0540879)Life Technologies, Inc. (A114510)National Science Foundation (U.S.). Graduate Research FellowshipUnited States. Office of Naval Research. Multidisciplinary University Research Initiative (Grant 4500000552