Chemistry of Life Processes Institute

Sheridan, IL, United States

Chemistry of Life Processes Institute

Sheridan, IL, United States
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News Article | December 12, 2016
Site: phys.org

"Right now, one of the most promising frontiers in cancer treatment is immunotherapy—harnessing the immune system to combat a wide range of cancers," said Joshua N. Leonard, the senior author of the study. "The simple cell rewiring we've done ultimately could help overcome immunosuppression at the tumor site, one of the most intransigent barriers to making progress in this field." When cancer is present, molecules secreted at tumor sites render many immune cells inactive. The Northwestern researchers genetically engineered human immune cells to sense the tumor-derived molecules in the immediate environment and to respond by becoming more active, not less. This customized function, which is not observed in nature, is clinically attractive and relevant to cancer immunotherapy. The general approach for rewiring cellular input and output functions should be useful in fighting other diseases, not just cancer. "This work is motivated by clinical observations, in which we may know why something goes wrong in the body, and how this may be corrected, but we lack the tools to translate those insights into a therapy," Leonard said. "With the technology we have developed, we can first imagine a cell function we wish existed, and then our approach enables us to build—by design—a cell that carries out that function." Currently, scientists and engineers lack the ability to program cells to exhibit all the functions that, from a clinical standpoint, physicians might wish them to exhibit, such as becoming active only when next to a tumor. This study addresses that gap, Leonard said. Leonard, who focuses on integrating synthetic biology into medicine, is an associate professor of chemical and biological engineering at the McCormick School of Engineering. He is a member of the Robert H. Lurie Comprehensive Cancer Center of Northwestern University. The research comes out of a rich collaboration that Leonard's team has with clinical oncologists, immunologists and basic cancer researchers at Northwestern University Feinberg School of Medicine as well as other synthetic biologists. The study, to be published Dec. 12 by the journal Nature Chemical Biology, provides details of the first synthetic biology technology enabling researchers to rewire how mammalian cells sense and respond to a broad class of physiologically relevant cues. Kelly A. Schwarz, a graduate student in Leonard's research group, is the study's first author. "This work is exciting because it addresses a key technical gap in the field," Schwarz said. "There is great promise for using engineered cells as programmable therapies, and it is going to take technologies such as this to truly realize that goal." Starting with human T cells in culture, the research team genetically engineered changes in the cells' input and output, including adding a sensing mode, and built a cell that is relevant to cancer immunotherapy. Specifically, the engineered cells sense vascular endothelial growth factor (VEGF), a protein found in tumors that directly manipulates and in some ways suppresses the immune response. When the rewired cells sense VEGF in their environment, these cells, instead of being suppressed, respond by secreting interleukin 2 (IL-2), a protein that stimulates nearby immune cells to become activated specifically at that site. Normal unmodified T cells do not produce IL-2 when exposed to VEGF, so the engineered behavior is both useful and novel. This work was carried out in cells in culture, and the technology next will be tested in animal studies. While Leonard's team has initially focused on the application of this cell programming technology to enabling cancer immunotherapy, it can be readily extended to distinct cellular engineering goals and therapeutic applications. Leonard's "parts" are also intentionally modular, such that they can be combined with other synthetic biology innovations to write more sophisticated cellular programs. "To truly accelerate the rate at which we can translate scientific insights into treatments, we need technologies that let us rapidly try out new ideas, in this case by building living cells that manifest a desired biological function," said Leonard, who also is a founding member of the Center for Synthetic Biology and a member of the Chemistry of Life Processes Institute. "Our technology also provides a powerful new tool for fundamental research, enabling biologists to test otherwise untestable theories about how cells coordinate their functions in complex, multicellular organisms," he said. Related to this research, Leonard was an invited conferee at a special meeting held in October, "Systems and Synthetic Biology for Designing Rational Cancer Immunotherapies," as part of President Obama and Vice President Biden's Cancer Moonshot Initiative.


News Article | December 12, 2016
Site: www.eurekalert.org

A major challenge in truly targeted cancer therapy is cancer's suppression of the immune system. Northwestern University synthetic biologists now have developed a general method for "rewiring" immune cells to flip this action around. "Right now, one of the most promising frontiers in cancer treatment is immunotherapy -- harnessing the immune system to combat a wide range of cancers," said Joshua N. Leonard, the senior author of the study. "The simple cell rewiring we've done ultimately could help overcome immunosuppression at the tumor site, one of the most intransigent barriers to making progress in this field." When cancer is present, molecules secreted at tumor sites render many immune cells inactive. The Northwestern researchers genetically engineered human immune cells to sense the tumor-derived molecules in the immediate environment and to respond by becoming more active, not less. This customized function, which is not observed in nature, is clinically attractive and relevant to cancer immunotherapy. The general approach for rewiring cellular input and output functions should be useful in fighting other diseases, not just cancer. "This work is motivated by clinical observations, in which we may know why something goes wrong in the body, and how this may be corrected, but we lack the tools to translate those insights into a therapy," Leonard said. "With the technology we have developed, we can first imagine a cell function we wish existed, and then our approach enables us to build -- by design -- a cell that carries out that function." Currently, scientists and engineers lack the ability to program cells to exhibit all the functions that, from a clinical standpoint, physicians might wish them to exhibit, such as becoming active only when next to a tumor. This study addresses that gap, Leonard said. Leonard, who focuses on integrating synthetic biology into medicine, is an associate professor of chemical and biological engineering at the McCormick School of Engineering. He is a member of the Robert H. Lurie Comprehensive Cancer Center of Northwestern University. The research comes out of a rich collaboration that Leonard's team has with clinical oncologists, immunologists and basic cancer researchers at Northwestern University Feinberg School of Medicine as well as other synthetic biologists. The study, to be published Dec. 12 by the journal Nature Chemical Biology, provides details of the first synthetic biology technology enabling researchers to rewire how mammalian cells sense and respond to a broad class of physiologically relevant cues. Kelly A. Schwarz, a graduate student in Leonard's research group, is the study's first author. "This work is exciting because it addresses a key technical gap in the field," Schwarz said. "There is great promise for using engineered cells as programmable therapies, and it is going to take technologies such as this to truly realize that goal." Starting with human T cells in culture, the research team genetically engineered changes in the cells' input and output, including adding a sensing mode, and built a cell that is relevant to cancer immunotherapy. Specifically, the engineered cells sense vascular endothelial growth factor (VEGF), a protein found in tumors that directly manipulates and in some ways suppresses the immune response. When the rewired cells sense VEGF in their environment, these cells, instead of being suppressed, respond by secreting interleukin 2 (IL-2), a protein that stimulates nearby immune cells to become activated specifically at that site. Normal unmodified T cells do not produce IL-2 when exposed to VEGF, so the engineered behavior is both useful and novel. This work was carried out in cells in culture, and the technology next will be tested in animal studies. While Leonard's team has initially focused on the application of this cell programming technology to enabling cancer immunotherapy, it can be readily extended to distinct cellular engineering goals and therapeutic applications. Leonard's "parts" are also intentionally modular, such that they can be combined with other synthetic biology innovations to write more sophisticated cellular programs. "To truly accelerate the rate at which we can translate scientific insights into treatments, we need technologies that let us rapidly try out new ideas, in this case by building living cells that manifest a desired biological function," said Leonard, who also is a founding member of the Center for Synthetic Biology and a member of the Chemistry of Life Processes Institute. "Our technology also provides a powerful new tool for fundamental research, enabling biologists to test otherwise untestable theories about how cells coordinate their functions in complex, multicellular organisms," he said. Related to this research, Leonard was an invited conferee at a special meeting held in October, "Systems and Synthetic Biology for Designing Rational Cancer Immunotherapies," as part of President Obama and Vice President Biden's Cancer Moonshot Initiative. The paper is titled "Rewiring Human Cellular Input-Output Using Modular Extracellular Sensors." In addition to Leonard and Schwarz, other authors are Nichole M. Daringer and Taylor B. Dolberg, both of Northwestern.


Marvin R.G.,Chemistry of Life Processes Institute | Wolford J.L.,Northwestern University | Kidd M.J.,University of Michigan | Murphy S.,University of Washington | And 7 more authors.
Chemistry and Biology | Year: 2012

Dynamic fluxes in the concentration of ions and small molecules are fundamental features of cell signaling, differentiation, and development. Similar roles for fluxes in transition metal concentrations are less well established. Here, we show that massive zinc fluxes are essential in the infection cycle of an intracellular eukaryotic parasite. Using single-cell quantitative imaging, we show that growth of the blood-stage Plasmodium falciparum parasite requires acquisition of 30 million zinc atoms per erythrocyte before host cell rupture, corresponding to a 400% increase in total zinc concentration. Zinc accumulates in a freely available form in parasitophorous compartments outside the food vacuole, including mitochondria. Restriction of zinc availability via small molecule treatment causes a drop in mitochondrial membrane potential and severely inhibits parasite growth. Thus, extraordinary zinc acquisition and trafficking are essential for parasite development. © 2012 Elsevier Ltd All rights reserved.


Xue F.,Chemistry of Life Processes Institute | Fang J.,Chemistry of Life Processes Institute | Lewis W.W.,Chemistry of Life Processes Institute | Martasek P.,University of Texas Health Science Center at San Antonio | And 3 more authors.
Bioorganic and Medicinal Chemistry Letters | Year: 2010

Recently, a series of potent and selective neuronal nitric oxide synthase inhibitors containing two basic nitrogen atoms was reported (Ji, H.; Stanton, B. Z.; Igarashi, J.; Li, H.; Martásek, P.; Roman, L. J.; Poulos, T. L.; Silverman, R. B. J. Am. Chem. Soc. 2008, 130, 3900-3914). In an effort to improve their bioavailability, three compounds (2a-c) were designed with electron-withdrawing groups near one of the basic nitrogen atoms to lower its pKa. Inhibition studies with these compounds showed that two of them not only retained most of the potency and selectivity of the best analogue of the earlier series, but also showed improved membrane permeability based on data from a cell-based assay. © 2009 Elsevier Ltd. All rights reserved.


Trippier P.C.,Northwestern University | Trippier P.C.,Texas Tech University | Zhao K.T.,Northwestern University | Fox S.G.,Chemistry of Life Processes Institute | And 7 more authors.
ACS Chemical Neuroscience | Year: 2014

(Chemical Equation Presented) Amyotrophic lateral sclerosis (ALS) is a progressive and ultimately fatal neurodegenerative disease. Pyrazolone containing small molecules have shown significant disease attenuating efficacy in cellular and murine models of ALS. Pyrazolone based affinity probes were synthesized to identify high affi nity binding partners and ascertain a potential biological mode of action. Probes were confirmed to be neuroprotective in PC12-SOD1G93A cells. PC12-SOD1G93A cell lysates were used for protein pull-down, affinity purification, and subsequent proteomic analysis using LC-MS/MS. Proteomics identified the 26S proteasome regulatory subunit 4 (PSMC1), 26S proteasome regulatory subunit 6B (PSMC4), and T-complex protein 1 (TCP-1) as putative protein targets. Coincubation with appropriate competitors confirmed the authenticity of the proteomics results. Activation of the proteasome by pyrazolones was demonstrated in the absence of exogenous proteasome inhibitor and by restoration of cellular protein degradation of a fluorogenic proteasome substrate in PC12-SOD1G93A cells. Importantly, supplementary studies indicated that these molecules do not induce a heat shock response. We propose that pyrazolones represent a rare class of molecules that enhance proteasomal activation in the absence of a heat shock response and may have therapeutic potential in ALS. © 2014 American Chemical Society.


Catherman A.D.,Chemistry of Life Processes Institute | Durbin K.R.,Chemistry of Life Processes Institute | Ahl D.R.,Chemistry of Life Processes Institute | Early B.P.,Chemistry of Life Processes Institute | And 4 more authors.
Molecular and Cellular Proteomics | Year: 2013

Top-down proteomics is emerging as a viable method for the routine identification of hundreds to thousands of proteins. In this work we report the largest top-down study to date, with the identification of 1,220 proteins from the transformed human cell line H1299 at a false discovery rate of 1%. Multiple separation strategies were utilized, including the focused isolation of mitochondria, resulting in significantly improved proteome coverage relative to previous work. In all, 347 mitochondrial proteins were identified, including ~50% of the mitochondrial proteome below 30 kDa and over 75% of the subunits constituting the large complexes of oxidative phosphorylation. Three hundred of the identified proteins were found to be integral membrane proteins containing between 1 and 12 transmembrane helices, requiring no specific enrichment or modified LC-MS parameters. Over 5,000 proteoforms were observed, many harboring post-translational modifications, including over a dozen proteins containing lipid anchors (some previously unknown) and many others with phosphorylation and methylation modifications. Comparison between untreated and senescent H1299 cells revealed several changes to the proteome, including the hyperphosphorylation of HMGA2. This work illustrates the burgeoning ability of top-down proteomics to characterize large numbers of intact proteoforms in a highthroughput fashion. © 2013 by The American Society for Biochemistry and Molecular Biology, Inc.


Savaryn J.P.,Chemistry of Life Processes Institute | Catherman A.D.,Chemistry of Life Processes Institute | Thomas P.M.,Chemistry of Life Processes Institute | Abecassis M.M.,Comprehensive Transplant Center | And 2 more authors.
Genome Medicine | Year: 2013

Proteomic technology has advanced steadily since the development of 'soft-ionization' techniques for mass-spectrometry-based molecular identification more than two decades ago. Now, the large-scale analysis of proteins (proteomics) is a mainstay of biological research and clinical translation, with researchers seeking molecular diagnostics, as well as protein-based markers for personalized medicine. Proteomic strategies using the protease trypsin (known as bottom-up proteomics) were the first to be developed and optimized and form the dominant approach at present. However, researchers are now beginning to understand the limitations of bottom-up techniques, namely the inability to characterize and quantify intact protein molecules from a complex mixture of digested peptides. To overcome these limitations, several laboratories are taking a whole-protein-based approach, in which intact protein molecules are the analytical targets for characterization and quantification. We discuss these top-down techniques and how they have been applied to clinical research and are likely to be applied in the near future. Given the recent improvements in mass-spectrometry-based proteomics and stronger cooperation between researchers, clinicians and statisticians, both peptide-based (bottom-up) strategies and whole-protein-based (top-down) strategies are set to complement each other and help researchers and clinicians better understand and detect complex disease phenotypes. © 2013 BioMed Central Ltd.


Uzarski J.S.,Northwestern University | Xia Y.,Salk Institute for Biological Studies | Belmonte J.C.I.,Salk Institute for Biological Studies | Wertheim J.A.,Northwestern University | Wertheim J.A.,Chemistry of Life Processes Institute
Current Opinion in Nephrology and Hypertension | Year: 2014

The severe shortage of suitable donor kidneys limits organ transplantation to a small fraction of patients suffering from end-stage renal failure. Engineering autologous kidney grafts on-demand would potentially alleviate this shortage, thereby reducing healthcare costs, improving quality of life, and increasing longevity for patients suffering from renal failure. RECENT FINDINGS: Over the past 2 years, several studies have demonstrated that structurally intact extracellular matrix (ECM) scaffolds can be derived from human or animal kidneys through decellularization, a process in which detergent or enzyme solutions are perfused through the renal vasculature to remove the native cells. The future clinical paradigm would be to repopulate these decellularized kidney matrices with patient-derived renal stem cells to regenerate a functional kidney graft. Recent research aiming toward this goal has focused on the optimization of decellularization protocols, design of bioreactor systems to seed cells into appropriate compartments of the renal ECM to nurture their growth to restore kidney function, and differentiation of pluripotent stem cells (PSCs) into renal progenitor lineages. SUMMARY: New research efforts utilizing bio-mimetic perfusion bioreactor systems to repopulate decellularized kidney scaffolds, coupled with the differentiation of PSCs into renal progenitor cell populations, indicate substantial progress toward the ultimate goal of building a functional kidney graft on-demand. © 2014 Wolters Kluwer Health | Lippincott Williams & Wilkins.


Serrano M.C.,Chemistry of Life Processes Institute | Ameer G.A.,CSIC - Institute of Materials Science | Ameer G.A.,Northwestern University
Macromolecular Bioscience | Year: 2012

Shape-memory polymers (SMP) are versatile stimuli-responsive materials that can switch, upon stimulation, from a temporary to a permanent shape. This advanced functionality makes SMP suitable and promising materials for diverse technological applications, including the fabrication of smart biomedical devices. In this paper, advances in the design of SMP are discussed, with emphasis on materials investigated for medical applications. Future directions necessary to bring SMP closer to their clinical application are also highlighted. © 2012 WILEY-VCH Verlag GmbH & Co. KGaA, Weinheim.


Zhang Y.,University of Chicago | Kenny H.A.,University of Chicago | Swindell E.P.,Chemistry of Life Processes Institute | Mitra A.K.,University of Chicago | And 8 more authors.
Molecular Cancer Therapeutics | Year: 2013

The urokinase system is overexpressed in epithelial ovarian cancer cells and is expressed at low levels in normal cells. To develop a platform for intracellular and targeted delivery of therapeutics in ovarian cancer, we conjugated urokinase plasminogen activator (uPA) antibodies to liposomal nanobins. The arsenic trioxide- loaded nanobins had favorable physicochemical properties and the ability to bind specifically to uPA. Confocal microscopy showed that the uPA-targeted nanobins were internalized by ovarian cancer cells, whereas both inductively coupled plasma optical mass spectrometry (ICP-MS) and fluorescence-activated cell sorting (FACS) analyses confirmed more than four-fold higher uptake of targeted nanobins when compared with untargeted nanobins. In a coculture assay, the targeted nanobins showed efficient uptake in ovarian cancer cells but not in the normal primary omental mesothelial cells. Moreover, this uptake could be blocked by either downregulating uPA receptor expression in the ovarian cancer cells using short-hairpin RNA (shRNA) or by competition with free uPA or uPA antibody. In proof-of-concept experiments, mice bearing orthotopic ovarian tumors showed a greater reduction in tumor burdenwhentreated with targeted nanobins than with untargeted nanobins (47% vs. 27%; P < 0.001). The targeted nanobins more effectively inhibited tumor cell growth both in vitro and in vivo compared with untargeted nanobins, inducing caspase-mediated apoptosis and impairing stem cell marker, aldehyde dehydrogenase-1A1 (ALDH1A1), expression. Ex vivo fluorescence imaging of tumors and organs corroborated these results, showing preferential localization of the targeted nanobins to the tumor. These findings suggest that uPA-targeted nanobins capable of specifically and efficiently delivering payloads to cancer cells could serve as the foundation for a new targeted cancer therapy using protease receptors. © 2013 AACR.

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