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  • richardmitnick 11:03 am on August 23, 2016 Permalink | Reply
    Tags: , , , Scripps Institute   

    From Scripps: “A Look Deep Inside the Human Brain Reveals a Surprise” 

    Scripps
    Scripps Research Institute

    8.23.16
    No writer credit

    In the field of neuroscience, researchers often make the assumption that information they obtain from a tiny brain sample is true for the entire brain.

    Now, a team of scientists at The Scripps Research Institute (TSRI), University of California, San Diego (UC San Diego) and Illumina, Inc., has completed the first large-scale assessment of the way thousands of single neuronal nuclei produce proteins from genetic information (“transcription”) – revealing a surprising diversity in the process. The findings could improve both our understanding of the brain’s normal functioning and how it’s damaged by diseases such as Alzheimer’s, Parkinson’s, ALS and depression.

    [The study is published in Science.]

    The researchers accomplished this feat by isolating and analyzing 3,200 single human neurons, more than 10-fold greater than prior publications, from six Brodmann Areas (larger regions having functional roles) of the human brain.

    “Through a wonderful scientific collaboration, we found an enormous amount of transcriptomic diversity from cell to cell that will be relevant to understanding the normal brain and its diseases such as Alzheimer’s, Parkinson’s, ALS and depression,” said TSRI Professor and neuroscientist Jerold Chun, who co-led the study with bioengineers Kun Zhang and Wei Wang of UC San Diego and Jian-Bing Fan of Illumina.

    While parts of the cerebral cortex look different under a microscope – with different cell shapes and densities that form cortical layers and larger regions having functional roles called “Brodmann Areas” – most researchers treat neurons as a fairly uniform group in their studies. “From a tiny brain sample, researchers often make assumptions that obtained information is true for the entire brain,” said Dr. Chun.

    But the brain isn’t like other organs, Dr. Chun explained. There’s a growing understanding that individual brain cells are unique, and a possibility has been that the microscopic differences among cerebral cortical areas may also reflect unique transcriptomic differences – i.e., differences in the expressed genes, or messenger RNAs (mRNAs), which carry copies of the DNA code outside the nucleus and determine which proteins the cell makes.

    With the help of newly developed tools to isolate and sequence individual cell nuclei (where genetic material is housed in a cell), the researchers deciphered the minute quantities of mRNA within each nucleus, revealing that various combinations of the 16 subtypes tended to cluster in cortical layers and Brodmann Areas, helping explain why these regions look and function differently.

    Neurons exhibited anticipated similarities, yet also many differences in their transcriptomic profiles, revealing single neurons with shared, as well as unique, characteristics that likely lead to differences in cellular function.

    “Now we can actually point to an enormous amount of molecular heterogeneity in single neurons of the brain,” said Gwendolyn E. Kaeser, a UC San Diego Biomedical Sciences Graduate Program student studying in Dr. Chun’s lab at TSRI and co-first author of the study.

    Interestingly, some of these differences in gene expression have roots in very early brain development taking place before birth. The researchers found markers on some neurons showing that they originated from a specific region of fetal brain called the ganglionic eminence, which generates inhibitory neurons destined for the cerebral cortex. These neurons may have particular relevance to developmental brain disorders.

    In future studies, the researchers hope to investigate how single-neuron DNA and mRNA differ in single neurons, groups and between human brains – and how these may be influenced by factors such as stress, medications or disease.

    See the full article here .

    Please help promote STEM in your local schools.

    STEM Icon

    Stem Education Coalition

    The Scripps Research Institute (TSRI), one of the world’s largest, private, non-profit research organizations, stands at the forefront of basic biomedical science, a vital segment of medical research that seeks to comprehend the most fundamental processes of life. Over the last decades, the institute has established a lengthy track record of major contributions to the betterment of health and the human condition.

    The institute — which is located on campuses in La Jolla, California, and Jupiter, Florida — has become internationally recognized for its research into immunology, molecular and cellular biology, chemistry, neurosciences, autoimmune diseases, cardiovascular diseases, virology, and synthetic vaccine development. Particularly significant is the institute’s study of the basic structure and design of biological molecules; in this arena TSRI is among a handful of the world’s leading centers.

    The institute’s educational programs are also first rate. TSRI’s Graduate Program is consistently ranked among the best in the nation in its fields of biology and chemistry.

     
  • richardmitnick 12:21 pm on August 18, 2016 Permalink | Reply
    Tags: , , Scripps Institute, TSRI Scientists Find Potential Treatment for 'Painful Blindness' Form of Dry Eye   

    From Scripps: “TSRI Scientists Find Potential Treatment for ‘Painful Blindness’ Form of Dry Eye” 

    Scripps
    Scripps Research Institute

    August 18, 2016
    No writer credit

    1
    The Scripps Research Institute team found “progenitor” cells isolated from healthy lacrimal glands can improve the appearance and function of diseased tissue. (Image courtesy of TSRI’s Makarenkova lab.)

    The eye’s lacrimal gland is small but mighty. This gland produces moisture needed to heal eye injuries and clear out harmful dust, bacteria and other invaders.

    If the lacrimal gland is injured or damaged by aging, pollution or even certain pharmaceutical drugs, a person can experience a debilitating condition called aqueous deficiency dry eye (ADDE)—sometimes called “painful blindness.”

    Now a new study in animal models, led by scientists at The Scripps Research Institute (TSRI), suggests that lacrimal glands can be repaired by injecting a kind of regenerative “progenitor” cell.

    “This is the first step in developing future therapies for the lacrimal gland,” said TSRI biologist Helen Makarenkova, who led the study.

    The findings were published this week in the online Early Edition of the journal Stem Cells Translational Medicine.

    Up for the Challenge

    If injured, a healthy lacrimal gland naturally regenerates itself in about seven days. When diseased and chronically inflamed, however, regeneration stops—and scientists are not sure why.

    In the new study, Makarenkova and her colleagues looked at whether they could kick start regeneration by injecting progenitor cells into the lobes that make up the lacrimal gland. Progenitor cells are similar to stem cells in their ability to differentiate into different kinds of tissue. In this study, the researchers used progenitor cells that were poised to become epithelial tissue, a key component of the lacrimal gland.

    The researchers knew they faced a major challenge: sorting and separating “sticky” epithelial cell progenitors without destroying them.

    “We had to figure out how to dissociate the tissue into single cells without completely obliterating everything,” said Anastasia Gromova, the study’s first author, now a graduate student at the University of California, San Diego, who spearheaded the project while interning at TSRI during her undergraduate years.

    The researchers solved this problem by developing markers to label the cells of interest and then testing different enzymes and other reagents to draw them out of tissues.

    Restoring Eye Health

    With these cells in hand, the researchers injected them into the lacrimal glands of mouse models of Sjogren’s syndrome, an autoimmune disease that results in ADDE, dry mouth and other symptoms. The team used only older, female mice because ADDE most commonly strikes that demographic in humans.

    The treated mice showed a significant increase in tear production, indicating—for the first time—that epithelial cell progenitors could repair the lacrimal gland. Further tests suggested that epithelial cell progenitors helped by restoring the connection between cells called myoepithelial contractile cells and the lacrimal gland’s secretory cells, which produce tears.

    The next step in this research will be to study how long the improvement in the lacrimal gland lasts after progenitor cell injections. Makarenkova said the eventual goal is to develop therapies to boost a patient’s own regenerative abilities.

    In addition to Makarenkova and Gromova, authors of the study, “Lacrimal Gland Repair Using Progenitor Cells,” were Dmitry A. Voronov of TSRI, the Russian Academy of Sciences and the A.N. Belozersky Institute of Physico-Chemical Biology of the Lomonosov Moscow State University; Miya Yoshida and Suharika Thotakura of TSRI; Robyn Meech of Flinders University; and Darlene A. Dartt of the Schepens Eye Research Institute/Massachusetts Eye and Ear, Harvard Medical School.

    The research was supported by the National Institutes of Health’s National Eye Institute (grant EY021292), the Russian Foundation for Basic Research (grant 12-04-01621-a) and an Australian Research Council (ARC) Future Fellowship.

    See the full article here .

    Please help promote STEM in your local schools.

    STEM Icon

    Stem Education Coalition

    The Scripps Research Institute (TSRI), one of the world’s largest, private, non-profit research organizations, stands at the forefront of basic biomedical science, a vital segment of medical research that seeks to comprehend the most fundamental processes of life. Over the last decades, the institute has established a lengthy track record of major contributions to the betterment of health and the human condition.

    The institute — which is located on campuses in La Jolla, California, and Jupiter, Florida — has become internationally recognized for its research into immunology, molecular and cellular biology, chemistry, neurosciences, autoimmune diseases, cardiovascular diseases, virology, and synthetic vaccine development. Particularly significant is the institute’s study of the basic structure and design of biological molecules; in this arena TSRI is among a handful of the world’s leading centers.

    The institute’s educational programs are also first rate. TSRI’s Graduate Program is consistently ranked among the best in the nation in its fields of biology and chemistry.

     
  • richardmitnick 1:27 pm on August 16, 2016 Permalink | Reply
    Tags: , Primordial ‘RNA World’, Scripps Institute   

    From Scripps: “TSRI Scientists Take Big Step Toward Recreating Primordial ‘RNA World’ of Four Billion Years Ago” 

    Scripps
    Scripps Research Institute

    August 15, 2016

    Scientists at The Scripps Research Institute (TSRI) have taken a big step toward the laboratory re-creation of the “RNA world,” which is generally believed to have preceded modern life forms based on DNA and proteins.

    “This is probably the first time some of these complex RNA molecules have been synthesized with a ribozyme [a special RNA enzyme] since the end of the RNA world four billion years ago,” said TSRI Professor Gerald F. Joyce, the senior author of the study.

    The results from the study, reported this week in the online Early Edition of the Proceedings of the National Academy of Sciences, show the scientists have succeeded in creating a ribozyme that can basically serve both to amplify genetic information and to generate functional molecules.

    The new ribozyme can replicate short lengths of RNA efficiently and perform transcription on even longer RNAs to make functional RNA molecules with complex structures—coming close to what scientists imagine in terms of an RNA replicator that could have supported life before modern biology, where protein enzymes now handle gene replication and transcription.

    Taking Up a Decades-Old Challenge

    In the new study, Joyce and TSRI Research Associate David P. Horning set out to use test-tube evolution techniques to tackle the decades-old challenge of creating an enzyme that could both replicate and transcribe RNA and thus support an RNA world.

    The team started with an enzyme that had been developed and improved upon by other researchers since the early 1990s. The class I RNA polymerase ribozyme, as it has come to be known, can perform the basic task of RNA synthesis—required for transcribing an RNA template into a functional RNA molecule—by binding to a strand of RNA and using it as a template to stitch together a complementary RNA strand.

    But prior forms of the ribozyme had been very limited in the RNA sequences they could handle, and couldn’t transcribe RNAs that have even moderately complex structures. Because of those limitations, they also could not perform full replication of RNA, which requires the transcription of a complementary strand back into a copy of the original.

    Horning and Joyce drew upon several improvements described in previous research and then added random mutations to create a population of roughly 100 trillion distinct variants of the molecule. Mimicking the evolutionary process of natural selection, they set up a system to isolate only the variant ribozymes that could synthesize—from the respective RNA templates—two different and challenging RNA molecules, which have mixed sequences and complex structures, and have functions in the sense that they bind tightly to specific target molecules.

    “The selection was based on the ability of these newly synthesized RNAs to actually function by binding to their targets,” said Horning. “To be able to make these functional RNAs, the ribozyme effectively had to evolve to become versatile in terms of the sequence and the structure of the RNA it could handle.”

    Best Performer

    The best performer after two dozen rounds of selection, polymerase ribozyme 24-3, proved capable of synthesizing not only the two target-binding RNAs but also several other structurally complex RNA molecules that exist in nature—as functional remnants of the ancient RNA world—including a yeast version of a “transfer RNA” molecule that has an essential protein-making role in all cells.

    “We found that the new ribozyme can handle most sequences and all but the most difficult structures, so we can use it to make a variety of functional RNA molecules,” Joyce said.

    Even when synthesizing the limited RNA sequences that the original class I RNA polymerase ribozyme could handle, ribozyme 24-3 proved capable of stitching them together about 100 times faster than its ancestor could.

    Turning to the much harder task of replication, the TSRI researchers found that ribozyme 24-3 could copy RNAs of up to two dozen nucleotides, achieving what biologists call “exponential replication” and creating as many as 40,000 copies of a target RNA within 24 hours.

    The 24-3 ribozyme is thus the first ever to combine the two basic capabilities—RNA synthesis and RNA replication—necessary for a pre-protein, pre-DNA world of RNA life.

    To generate and sustain a true “RNA world,” the new ribozyme will have to be improved further to enable the replication of longer, more complex RNA molecules—crucially including the polymerase ribozyme itself. The Joyce laboratory is now driving its ribozyme toward that goal with further test-tube evolution experiments.

    “A polymerase ribozyme that achieves exponential amplification of itself will meet the criteria for being alive,” Joyce said. “That’s a summit that’s now within sight.”

    Funding for the study, “Amplification of RNA by an RNA polymerase ribozyme,” was provided by the National Aeronautics and Space Administration (NNX14AK15G) and the Simons Foundation (287624).

    See the full article here .

    Please help promote STEM in your local schools.

    STEM Icon

    Stem Education Coalition

    The Scripps Research Institute (TSRI), one of the world’s largest, private, non-profit research organizations, stands at the forefront of basic biomedical science, a vital segment of medical research that seeks to comprehend the most fundamental processes of life. Over the last decades, the institute has established a lengthy track record of major contributions to the betterment of health and the human condition.

    The institute — which is located on campuses in La Jolla, California, and Jupiter, Florida — has become internationally recognized for its research into immunology, molecular and cellular biology, chemistry, neurosciences, autoimmune diseases, cardiovascular diseases, virology, and synthetic vaccine development. Particularly significant is the institute’s study of the basic structure and design of biological molecules; in this arena TSRI is among a handful of the world’s leading centers.

    The institute’s educational programs are also first rate. TSRI’s Graduate Program is consistently ranked among the best in the nation in its fields of biology and chemistry.

     
  • richardmitnick 3:25 pm on August 12, 2016 Permalink | Reply
    Tags: , , , , Scripps Institute   

    From Scripps: “Team Pinpoints Ebola’s Weak Spots” 

    Scripps
    Scripps Research Institute

    8.12.16
    Madeline McCurry-Schmidt

    Scientists at The Scripps Research Institute (TSRI) now have a high-resolution view of exactly how the experimental therapy ZMapp™ targets Ebola virus.

    The new study is also the first to show how an antibody in the ZMapp™ “drug cocktail” targets a second Ebola virus protein, called sGP, whose vulnerable spots had previously been unknown.

    “This sGP protein is tremendously important,” said TSRI Professor Erica Ollmann Saphire, who co-led the study with TSRI Associate Professor Andrew Ward. “This is the roadmap we need to target the right molecules in infection.”

    “Determining the proper balance in targeting these two Ebola proteins will be key to building improved therapeutics,” added Ward.

    The study was published August 8, 2016 in the journal Nature Microbiology.

    1
    The team succeeded in showing how experimental therapy ZMapp™ targets the Ebola virus, here pictured targeting the virus’s GP protein. (Image courtesy of Andrew Ward and Jesper Pallesen.)

    Zooming in on ZMapp™

    Scientists need detailed images of Ebola virus’s molecular structure. Like enemy reconnaissance, structures can show where Ebola is vulnerable and how medical treatments can neutralize it.

    TSRI scientists are harnessing an imaging technique called cryo-electron microscopy (in which a sample is pelted with electrons) to create high-resolution, 3-D images of Ebola virus and the antibodies that fight it.

    “We’re at the cutting edge of our ability to resolve high-resolution protein complexes,” said TSRI Research Associate C. Daniel Murin, co-first author of the new study with TSRI Research Associate Jesper Pallesen.

    In the new study, the researchers used cryo-electron microscopy to see exactly how Ebola virus interacts with the three antibodies in the ZMapp™ experimental therapy produced by Mapp Biopharmaceutical, also a study collaborator.

    The researchers had imaged these interactions at a low resolution in a 2014 study, but the new study revealed substantially more details, including the exact angles the antibodies use to approach the molecule on the surface of the virus, termed its surface glycoprotein (GP), and the individual amino acid contact points at which the antibodies bind GP. This information provides new clues to researchers trying to make the antibodies even more effective.

    “The three components of ZMapp™, now resolved at high-resolution, can be further engineered in a structure-based manner for improved potency,” said Ward.

    Solving an Elusive Structure

    Next, the researchers took a closer look at one of the three antibodies that make up ZMapp™, called 13C6. This antibody is unique because it can also target the soluble Ebola protein sGP.

    sGP’s role in infection is a mystery. Ebola virus makes the protein profusely, indicating that it is important, but then sGP appears just to float in a person’s blood serum. One theory is that sGP may be essential in the natural host “reservoir.”

    “Eighty to ninety percent of what Ebola virus makes in infection is this shed molecule,” said Saphire. “It’s like a smoke screen, and we need to know where it is similar to our target GP and where it is different.”

    To add to the mystery, Ebola makes GP and sGP using the same gene. A small difference in the way the gene is read changes how the molecules are shaped and changes their roles.

    One obstacle to understanding sGP is that it is too small to be seen with cryo-electron microscopes. To solve this problem, the researchers added “bulk” by pairing sGP with antibodies, including 13C6. This allowed them to kill two birds with one stone—they could see sGP’s structure while also studying how antibodies interact with it.

    The new image shows the binding sites, or “epitopes,” the antibody targets. “We can see hot spots on this virus that we can hit,” said Pallesen.

    This study is the latest research from the Viral Hemorrhagic Fever Consortium, an international partnership of research institutes led by Saphire. The researchers said collaboration with the consortium was key to this study, allowing scientists to share samples and data, including viral genetic sequences isolated from patients in the most recent Ebola outbreak.

    In addition to Saphire, Ward, Murin and Pallesen, authors of the study, Structures of Ebola virus GP and sGP in complex with therapeutic antibodies, were Natalia de Val, Christopher A. Cottrell, Kathryn M. Hastie, Hannah Turner and Marnie Fusco of TSRI; Kristian G. Andersen of TSRI and the Scripps Translational Science Institute; Andrew I. Flyak and James E. Crowe of Vanderbilt University and Larry Zeitlin of Mapp Biopharmaceutical.

    This study was supported by the National Institutes of Health (NIH, grant R01 AI067927), the NIH’s National Institute of Allergy and Infectious Diseases (grants U19AI109762 and U19AI109711) and the National Science Foundation.

    See the full article here .

    You can Help Stamp Out EBOLA.

    This WCG project rubs at Scripps Institute

    Outsmart Ebola Together

    You can help researchers at The Scripps Research Institute find a cure for Ebola by donating your computing power to this project and encouraging others to join.

    Visit World Community Grid (WCG). Download and install the BOINC software on which it runs. Attach to the Outsmart Ebola Together project. This will allow WCG to use your computer’s free CPU cycles to process computational data for the project.

    WCGLarge
    WCG Logo New

    BOINCLarge
    BOINC WallPaper

    While you are at WCG and BOINC, check out the other very worthwhile projects running on this software. All project results are “open source”, free for the use of scientists world while to advance health and other issues of mankind.

    Please help promote STEM in your local schools.

    STEM Icon

    Stem Education Coalition

    The Scripps Research Institute (TSRI), one of the world’s largest, private, non-profit research organizations, stands at the forefront of basic biomedical science, a vital segment of medical research that seeks to comprehend the most fundamental processes of life. Over the last decades, the institute has established a lengthy track record of major contributions to the betterment of health and the human condition.

    The institute — which is located on campuses in La Jolla, California, and Jupiter, Florida — has become internationally recognized for its research into immunology, molecular and cellular biology, chemistry, neurosciences, autoimmune diseases, cardiovascular diseases, virology, and synthetic vaccine development. Particularly significant is the institute’s study of the basic structure and design of biological molecules; in this arena TSRI is among a handful of the world’s leading centers.

    The institute’s educational programs are also first rate. TSRI’s Graduate Program is consistently ranked among the best in the nation in its fields of biology and chemistry.

     
  • richardmitnick 11:39 am on August 12, 2016 Permalink | Reply
    Tags: , , New Study Shines Light on Mutations Responsible for Debilitating Heart Conditions, Scripps Institute   

    From Scripps: “New Study Shines Light on Mutations Responsible for Debilitating Heart Conditions” 

    Scripps
    Scripps Research Institute

    August 11, 2016

    1
    Binding to the plasma membrane induces metavinculin dimerization which stabilizes cardiac adhesion sites. The metavinculin mutation causing the most severe cardiomyopathy prevents metavinculin dimerization. The lipids are shown as spheres and the metavinculin tail domain as a cartoon with the 5 alpha-helices (H1-H5) of the 5-helix bundle colored spectrally (H1, red; H2, orange; H3, yellow; H4, green; H5, blue). (Image courtesy of the Izard lab.)

    The leading cause of death in the world remains cardiovascular diseases, which are responsible for more than one third of overall mortality, according to the World Health Organization. Obesity and diet are obvious culprits behind heart disease but, over the past decade, research has also pointed to genetic factors, specifically mutations in cell adhesion components—the forces that bind cells together.

    In a new study, scientists from the Florida campus of The Scripps Research Institute offer new molecular insights into how the interaction between specific genetic mutations and a cytoskeletal protein critical for the proper development and maintenance of heart tissue can lead to conditions such as dilated cardiomyopathy (DCM) and hypertrophic cardiomyopathy (HCM)—and ultimately heart failure.

    The new study, which was led by Associate Professor T. Izard of the Florida campus of TSRI, is published this week in an early online edition of the journal Proceedings of the National Academy of Sciences. The new insights could aid in the development of drug therapies to strengthen the hearts of patients suffering from age-related heart failure.

    The study focuses on the protein vinculin and a variant form known as metavinculin, which is found only in muscle tissue. Vinculin has been shown to reinforce the myocardial cell cytoskeleton, improving heart muscle contractility and prolonging life, while metavinculin plays an essential role in the development and function of the heart.

    Both vinculin and metavinculin regulate cell adhesion and migration by linking the cell’s cytoskeleton to adhesion receptor complexes via a process known as dimerization—the joining of two similar subunits. Control of the dimerization process is crucial for normal protein function in cell adhesion sites.

    But mutations in the variant metavinculin, either inherited or spontaneous, corrupt this process, altering dimerization and, the study suggests, producing a decreased ability to stabilize critical cell adhesions, weakening the heart muscle over time.

    The first author of the study, Differential Lipid Binding of Vinculin Isoforms Promotes Quasiequivalent Dimerization, is Krishna Chinthalapudi of TSRI. Other authors include Erumbi S. Rangarajan of TSRI and David T. Brown of the University of Mississippi Medical Center.

    The laboratory is supported by the National Institutes of Health, the Department of Defense, the American Heart Association and the State of Florida.

    See the full article here .

    Please help promote STEM in your local schools.

    STEM Icon

    Stem Education Coalition

    The Scripps Research Institute (TSRI), one of the world’s largest, private, non-profit research organizations, stands at the forefront of basic biomedical science, a vital segment of medical research that seeks to comprehend the most fundamental processes of life. Over the last decades, the institute has established a lengthy track record of major contributions to the betterment of health and the human condition.

    The institute — which is located on campuses in La Jolla, California, and Jupiter, Florida — has become internationally recognized for its research into immunology, molecular and cellular biology, chemistry, neurosciences, autoimmune diseases, cardiovascular diseases, virology, and synthetic vaccine development. Particularly significant is the institute’s study of the basic structure and design of biological molecules; in this arena TSRI is among a handful of the world’s leading centers.

    The institute’s educational programs are also first rate. TSRI’s Graduate Program is consistently ranked among the best in the nation in its fields of biology and chemistry.

     
  • richardmitnick 5:15 pm on August 1, 2016 Permalink | Reply
    Tags: , , Scripps Institute, TSRI Study Points Way to Better Vaccines and New Autoimmune Therapies   

    From Scripps: “Found: A Potential New Way to Sway the Immune System” 

    Scripps
    Scripps Research Institute

    August 1, 2016
    No writer credit found

    TSRI Study Points Way to Better Vaccines and New Autoimmune Therapies

    A new international collaboration involving scientists at The Scripps Research Institute (TSRI) opens a door to influencing the immune system, which would be useful to boost the effectiveness of vaccines or to counter autoimmune diseases such as lupus and rheumatoid arthritis.

    The research, published August 1, 2016, in The Journal of Experimental Medicine, focused on a molecule called microRNA-155 (miR-155), a key player in the immune system’s production of disease-fighting antibodies.

    “It’s very exciting to see exactly how this molecule works in the body,” said TSRI Associate Professor Changchun Xiao, who co-led the study with Professor Wen-Hsien Liu of Xiamen University in Fuijan province, China.

    An Immune System Tango

    Our cells rely on molecules called microRNAs (miRNAs) as a sort of “dimmer switches” to carefully regulate protein levels and combat disease.

    “People know miRNAs are involved in immune response, but they don’t know which miRNAs and how exactly,” explained TSRI Research Associate Zhe Huang, study co-first author with Liu and Seung Goo Kang of TSRI and Kangwon National University.

    In the new study, the researchers focused on the roles of miRNAs during the critical period when the immune system first detects “invaders” such as viruses or bacteria. At this time, cells called T follicular helpers proliferate and migrate to a different area of the lymph organs to interact with B cells.

    “They do a sort of tango,” said Xiao.

    This interaction prompts B cells to mature and produce effective antibodies, eventually offering long-term protection against infection.

    “The next time you encounter that virus, for example, the body can respond quickly,” said Xiao.

    Identifying a Dancer

    Using a technique called deep sequencing, the team identified miR-155 as a potential part of this process. Studies in mouse models suggested that miR-155 works by repressing a protein called Peli1. This leaves a molecule called c-Rel free to jump in and promote normal T cell proliferation.

    This finding could help scientists improve current vaccines. While vaccines are life-saving, some vaccines wear off after a decade or only cover around 80 percent of those vaccinated.

    “If you could increase T cell proliferation using a molecule that mimics miR-155, maybe you could boost that to 90 to 95 percent,” said Xiao. He also sees potential for using miR-155 to help in creating longer-lasting vaccines.

    The research may also apply to treating autoimmune diseases, which occur when antibodies mistakenly attack the body’s own tissues. Xiao and his colleagues think an mRNA inhibitor could dial back miR-155’s response when T cell proliferation and antibody production is in overdrive.

    For the next stage of this research, Xiao plans to collaborate with scientists on the Florida campus of TSRI to test possible miRNA inhibitors against autoimmune disease.

    In addition to Xiao, Huang, Liu and Kang, authors of the study, “A miR-155-Peli1-c-Rel pathway controls the generation and function of T follicular helper cells,” were Cheng-Jang Wu and Li-Fan Lu of the University of California, San Diego; Yi Liu and Alexander Hoffmann of the University of California, Los Angeles; Shunbin Xu of Wayne State University; Guo Fu and Nengming Xiao of Xiamen University; Ye Zheng of The Salk Institute for Biological Studies; and Hyun Yong Jin, Christian J. Maine, Jovan Shepherd, Mohsen Sabouri-Ghomi and Alicia Gonzalez-Martin of TSRI.

    The study was supported by the PEW Charitable Trusts; Cancer Research Institute; Lupus Research Institute; National Institutes of Health (grants R01AI087634, R01AI089854, R56AI110403, R56AI121155, R01AI103646 and R01AI108651); National Natural Science Foundation of China (grants 31570882, 31570883 and 31570911); 1000 Young Talents Program of China (grant K08008); the Fundamental Research Funds for the Central Universities of the People’s Republic of China (grant 20720150065); Basic Science Research Program through the National Research Foundation of Korea (NRF) funded by the Ministry of Science, ICT & Future Planning (grant NRF-2015R1C1A1A01052387, S.G.K.) and a 2016 Research Grant from Kangwon National University.

    See the full article here .

    Please help promote STEM in your local schools.

    STEM Icon

    Stem Education Coalition

    The Scripps Research Institute (TSRI), one of the world’s largest, private, non-profit research organizations, stands at the forefront of basic biomedical science, a vital segment of medical research that seeks to comprehend the most fundamental processes of life. Over the last decades, the institute has established a lengthy track record of major contributions to the betterment of health and the human condition.

    The institute — which is located on campuses in La Jolla, California, and Jupiter, Florida — has become internationally recognized for its research into immunology, molecular and cellular biology, chemistry, neurosciences, autoimmune diseases, cardiovascular diseases, virology, and synthetic vaccine development. Particularly significant is the institute’s study of the basic structure and design of biological molecules; in this arena TSRI is among a handful of the world’s leading centers.

    The institute’s educational programs are also first rate. TSRI’s Graduate Program is consistently ranked among the best in the nation in its fields of biology and chemistry.

     
  • richardmitnick 9:05 am on July 28, 2016 Permalink | Reply
    Tags: , Scripps Institute, SR10171, Type 2 diabetes   

    From Scripps: “Study Suggests New Drug Candidate Could Treat Both Type 2 Diabetes and Bone Loss” 

    Scripps
    Scripps Research Institute

    July 27, 2016

    In addition to its more obvious ills, type 2 diabetes is a condition closely associated with bone fractures, increasing the risk of fractures twofold. To make matters worse, certain anti-diabetic drugs further increase this risk, particularly in postmenopausal women, severely limiting their treatment options.

    A new study, co-led by Patrick R. Griffin, a professor on the Florida campus of The Scripps Research Institute (TSRI), and B. Lecka-Czernik, a professor at the University of Toledo, has shown that a new class of drug candidates developed at TSRI increases bone mass by expanding bone formation (deposition of new bone) and bone turnover (a normal process of replacement of old bone). A proper balance of these two processes is critical to healthy bone maintanence, and this balance is frequently negatively affected in diabetic patients.

    The result is a new dual-targeting drug candidate—or, as Griffin describes, “one drug addressing multiple therapeutic indications”—that could treat both diabetes and bone disease. The compound has been referenced as “SR10171.”

    The study was published recently online ahead of print by the journal EBioMedicine.

    Diabetes affects more than 29 million people in the United States, according to a 2012 report from the American Diabetes Association. Between 2010 and 2012, the incidence rate was about 1.7 to 1.9 million per year, and in 2013, estimated direct medical costs of the disease were $176 billion.

    Over the past decade, Griffin and his colleague, TSRI Associate Professor Theodore Kamenecka, have focused on the details of molecules that increase sensitivity to insulin (a hormone that regulates blood sugar). Using newly discovered information, the researchers made significant advances in developing a family of drug candidates that target a receptor known as peroxisome proliferator-activated receptors gamma (PPARγ), a key regulator of stem cells controlling bone formation and bone resorption and a master regulator of fat.

    Anti-diabetic drugs known as glitazones (TZDs) target the PPARγ protein, but that interaction leads to severe bone loss and increased fractures. Stem cells in the bone marrow can differentiate either into bone cells or fat cells, and the glitazones drive them to fat at the expense of bone.

    But SR10171 is designed to avoid this troubling outcome. In animal models treated with the compound, fat formation in the bone marrow was successfully blocked independent of their metabolic state (healthy or diabetic).

    “Using structural biology technigues and rational design synthetic chemistry, SR10171 was constructed to engage the PPARγ protein in a unique way possessing an optimal balance with the receptor’s other family member, PPARa, to treat diabetes and, at the same time, improve bone health,” Griffin said. “This targeted polypharmacological approach demonstrates that the target isn’t the problem if you target it correctly.”

    The compound increases bone mass by protecting and increasing the activity of bone cells in various stages of normal bone mantanence, utilizing mechanisms that overlap those that regulate whole-body energy metabolism.

    “SR10171 improves bone mass regardless of body mass index, normal to obese,” Griffin added. “So you could use such a drug to treat osteoporosis whether patients are diabetic or not.”

    The first author of the study, PPARG Post-Translational Modifications Regulate Bone Formation and Bone Resorption, is L.A. Stechschulte of the University of Toledo, Ohio. Other authors include P.J. Czernik, Z.C. Rotter and F.N. Tausif of the University of Toledo; C.A. Corzo, D.P. Marciano, A. Asteian, J. Zheng and T.M. Kamenecka of TSRI; J. B. Bruning of The University of Adelaide, Australia; and C.J. Rosen of the Maine Medical Center Research Institute.

    The study was supported by the National Institutes of Health (grant numbers DK080261 and DK105825); the American Diabetes Association (award 7-13-BS-089), the Abrams Charitable Trust and the Klorfine Family Fellowship.

    See the full article here .

    Please help promote STEM in your local schools.

    STEM Icon

    Stem Education Coalition

    The Scripps Research Institute (TSRI), one of the world’s largest, private, non-profit research organizations, stands at the forefront of basic biomedical science, a vital segment of medical research that seeks to comprehend the most fundamental processes of life. Over the last decades, the institute has established a lengthy track record of major contributions to the betterment of health and the human condition.

    The institute — which is located on campuses in La Jolla, California, and Jupiter, Florida — has become internationally recognized for its research into immunology, molecular and cellular biology, chemistry, neurosciences, autoimmune diseases, cardiovascular diseases, virology, and synthetic vaccine development. Particularly significant is the institute’s study of the basic structure and design of biological molecules; in this arena TSRI is among a handful of the world’s leading centers.

    The institute’s educational programs are also first rate. TSRI’s Graduate Program is consistently ranked among the best in the nation in its fields of biology and chemistry.

     
  • richardmitnick 9:39 am on July 14, 2016 Permalink | Reply
    Tags: , , Scripps Institute   

    From Scripps: “Catching Cancer-Causing Mutations in the Act” 

    Scripps
    Scripps Research Institute

    July 2016
    No writer credit found

    Cancer can be caused by mutations in cell DNA, and researchers at The Scripps Research Institute (TSRI) have discovered how one mutation, in a protein known as POT1, causes some of the most aggressive forms of cancer, including leukemia, lymphoma, glioma and melanoma. The research also suggests a possible way to kill these kinds of tumors by targeting an important enzyme.

    1
    Eros Lazzerini Denchi of The Scripps Research Institute co-led the study with Agnel Sfeir of New York University School of Medicine.

    “We’ve found the mechanism through which this mutation leads to a scrambling of the genome,” said TSRI Associate Professor Eros Lazzerini Denchi, who co-led the study with Agnel Sfeir of New York University (NYU) School of Medicine. “That’s when you get really massive tumors.”

    The researchers investigated mutations in a gene that codes for the protein POT1. This protein normally forms a protective cap around the ends of chromosomes (called telomeres), stopping cell machinery from mistakenly damaging the DNA there and causing harmful mutations.

    POT1 is so critical that cells without functional POT1 would rather die than pass on POT1 mutations. Stress in these cells leads to the activation of an enzyme called ATR that triggers programmed cell death.

    Knowing this, scientists in recent years were surprised to find recurrent mutations affecting POT1 in several human cancers, including leukemia and melanoma.

    “Somehow those cells found a way to survive – and thrive,” said Dr. Lazzerini Denchi. “We thought that if we could understand how that happens, maybe we could find a way to kill those cells.”

    Using a mouse model, the researchers found that mutations in POT1 lead to cancer when combined with a mutation in a gene called p53.

    “The cells no longer have the mechanism for dying, and mice develop really aggressive thymic lymphomas,” said Dr. Lazzerini Denchi.

    P53, a well-known tumor suppressor gene, is a cunning accomplice. When mutated, it overrides the protective cell death response initiated by ATR. Then, without POT1 creating a protective cap, the chromosomes are fused together and the DNA is rearranged, driving the accumulation of even more mutations. These mutant cells go on to proliferate and become aggressive tumors. The findings led the team to consider a new strategy for killing these tumors.

    Scientists know that all cells – even cancer cells – will die if they have no ATR. Since tumors with mutant POT1 already have low ATR levels, the researchers think a medicine that knocks out the remaining ATR could kill tumors without affecting healthy cells. “This study shows that by looking at basic biological questions, we can potentially find new ways to treat cancer,” said Dr. Lazzerini Denchi.

    The researchers plan to investigate this new therapeutic approach in future studies.

    See the full article here .

    Please help promote STEM in your local schools.

    STEM Icon

    Stem Education Coalition

    The Scripps Research Institute (TSRI), one of the world’s largest, private, non-profit research organizations, stands at the forefront of basic biomedical science, a vital segment of medical research that seeks to comprehend the most fundamental processes of life. Over the last decades, the institute has established a lengthy track record of major contributions to the betterment of health and the human condition.

    The institute — which is located on campuses in La Jolla, California, and Jupiter, Florida — has become internationally recognized for its research into immunology, molecular and cellular biology, chemistry, neurosciences, autoimmune diseases, cardiovascular diseases, virology, and synthetic vaccine development. Particularly significant is the institute’s study of the basic structure and design of biological molecules; in this arena TSRI is among a handful of the world’s leading centers.

    The institute’s educational programs are also first rate. TSRI’s Graduate Program is consistently ranked among the best in the nation in its fields of biology and chemistry.

     
  • richardmitnick 1:52 pm on July 1, 2016 Permalink | Reply
    Tags: , , Scripps Institute   

    From Scripps: “Researchers Stabilize HIV Structure, Design Potential AIDS Vaccine Candidates” 

    Scripps
    Scripps Research Institute

    July 04, 2016
    Madeline McCurry-Schmidt

    Want to catch a criminal? Show a mugshot on the news.

    Want to stop HIV infections? Get the immune system to recognize and attack the virus’s tell-tale structure.

    1
    “We’ve figured out one of the fundamental reasons why HIV is metastable,” says Assistant Professor Jiang Zhu (left), here with some co-authors of the new studies, Charles Morris (back), Parisa Azadnia (center) and Linling He. (Photo by Cindy Brauer.)

    2
    In a feat of bioengineering, the team designed nanoparticles that could mimic HIV.

    That’s part of the basic approach behind efforts at The Scripps Research Institute (TSRI) to design an AIDS vaccine. This strategy may hinge on finding new ways to stabilize proteins called HIV-1 surface antigens and in designing HIV-like particles to prompt the body to fight the real virus.

    Now two new studies led by TSRI scientists advance these efforts. The first describes a strategy to stabilize an important HIV structure and potentially create HIV lookalikes for large-scale vaccine production. The second study engineers novel nanoparticles as vaccine candidates, using this new knowledge.

    “This is a big accomplishment in terms of engineering and design,” said TSRI biologist Jiang Zhu.

    Zhu co-led the first study with Ian Wilson, Hansen Professor of Structural Biology and chair of the Department of Integrative Structural and Computational Biology at TSRI, and co-led the second with TSRI Associate Professor Andrew Ward.

    The findings were published June 28, 2016 in the journal Nature Communications.

    Stabilizing HIV

    In the first publication, Zhu and researcher Leo Kong (a study first author now at the National Institutes of Health) built on previous structural studies from the Ward and Wilson labs to investigate a trait called “metastability.” Metastability describes the tense state of the HIV Envelope glycoprotein (Env) trimer when it is poised like a loaded spring to undergo the dramatic changes that allow the virus to enter cells.

    Metastability poses a problem for scientists who want to create a precise image of this viral target and see what the human immune system is up against.

    Metastability also stands in the way of naturally occurring immunity and vaccine production. For the adaptive immune system to work in either case, it needs to recognize a functional, stable version of a virus’s proteins—a sort of mugshot—so it can produce antibodies and attack the actual virus upon encountering it.

    Unfortunately, because of the virus’s metastability, or shape-shifting tendency, structures of HIV’s proteins have proven difficult to establish for use in vaccine design. The Ward and Wilson groups at TSRI have previously determined cryo-EM and x-ray structures for other Env constructs; however, current methods to stabilize Env in one strain of HIV won’t necessarily stabilize it in another, making it hard to design an arsenal of Env proteins to help elicit “broadly neutralizing antibodies” that could fight many types of HIV.

    To advance the vaccine effort, TSRI researchers wanted to track down the root cause of metastability, and Jiang and Kong hypothesized that altering a key region of Env would improve its overall properties.

    They hypothesized that a region of the Env called HR1 could be linked to metastability.

    “The HR1 basically resembles a highly bent twig that is ready to spring back straight,” said Kong. “This small bend in the HR1 region is likely ground zero for metastability. In most published Env structures, this region appears disordered when mutated or loosely packed when in its native form. From these observations, it seemed reasonable that rewiring the HR1 bend could greatly stabilize Env.”

    Indeed, when the scientists tweaked HIV’s genetic sequence, they were able to shorten the HR1 region, preventing its transformation and keeping the rest of the structure stable.

    “We’ve figured out one of the fundamental reasons why HIV is metastable,” said Zhu.

    The researchers then demonstrated that their stabilized Env trimers also almost perfectly mimicked the structure of the real HIV trimer, suggesting they could be useful in vaccines. Since rewiring the HR1 should prevent Env undergoing its necessary shape-shifting changes to infect cells, the stabilization strategy also could lead to protein or DNA-based vaccines. Furthermore, the modified trimer also has the potential to be produced in reasonably large quantities and at high purity—important considerations in industrial-scale vaccine production.

    Finally, since many viruses contain metastable Env proteins with HR1-like regions, this TSRI-developed engineering approach may be applicable in the design of vaccines against other viral pathogens such as influenza and Ebola virus.

    New Vaccine Candidates

    In the second paper, the researchers looked into designing nanoparticles that could mimic HIV.

    Particles aren’t new in vaccine design. They provide the backbone of successful vaccines against human papillomavirus (HPV), hepatitis B and hepatitis E—“the most efficacious human vaccines ever made,” according to Zhu.

    These nanoparticles are called virus-like particles (VLPs) and are hollow shells of other proteins found in nature. Scientists have found that they can add viral proteins to the outside of a shell, creating a phony virus. The imposter then prompts the body to produce antibodies for long-term protection against the real virus.

    But as Zhu and his colleagues focused on creating HIV-like VLPs, the Env trimer, once again, presented a challenge.

    The trimer is made of three subunits that come together to form a base with a crown shape on top. The top of the crown is where the tips of the three subunits meet.

    Scientists have found that the immune system cannot produce broadly neutralizing antibodies when a vaccine contains only one part of the trimer. The immune system needs to see intact HIV proteins—also called antigens when they stimulate the immune system to create antibodies—in their native trimeric context.

    To construct an artificial virus, in the new study the researchers added HIV trimers to nanoparticles that naturally lock their own subunits together in clusters of three. As the three subunits come together, the researchers hypothesized, they could bring the HIV antigens together to form a trimer.

    “Our idea was to ‘fuse’ a trimeric HIV-1 antigen to a nanoparticle subunit, so when the subunits ‘self-assemble’ they bring three attached HIV-1 antigens together,” said TSRI Staff Scientist Linling He, who served as co-first author of the study with Natalia de Val, a researcher at TSRI at the time of the study.

    It was a feat of geometry and engineering—and it worked. “It has been really challenging to properly present HIV Env on nanoparticles while keeping its natural trimeric form—but we did it,” said Zhu, “Multiple copies of Env are now displayed on the nanoparticle surface, just like what a real virus would do.”

    The team then tested different nanoparticles and versions of the trimer, including one based on the stabilized Env in the first study, to find the best combinations. Six designs worked well in laboratory tests and now await trials in animal models.

    “We are still pushing hard to find new vaccine candidates to elicit a protective response in humans,” said Wilson. “The challenges going forward are to understand how to use these new vaccine candidates to induce a protective broadly neutralizing antibody response and to develop the appropriate regimens to initiative this response.”

    In addition to Zhu, Wilson, Ward, Kong, He and de Val, authors of the first study, “Uncleaved prefusion-optimized gp140 trimers derived from analysis of HIV-1 envelope metastability,” were Nemil Vora, Charles D. Morris, Parisa Azadnia and Bin Zhou of TSRI; Devin Sok of TSRI, the International AIDS Vaccine Initiative (IAVI) Neutralizing Antibody Center and Collaboration for AIDS Vaccine Discovery (CAVD), and TSRI Center for HIV/AIDS Vaccine Immunology & Immunogen Discovery (CHAVI-ID); and Dennis R. Burton of TSRI, IAVI, CHAVI-ID and the Ragon Institute.

    This study was supported by the NIH National Institute of General Medical Sciences (NIGMS) (grants P41GM103393, U54 GM094586 and AI084817), the NIH National Center for Research Resources (grant P41RR001209), the IAVI Neutralizing Antibody Center and CAVD (grants OPP1084519 and OPP1115782), CHAVI-ID (grant CHAVI-ID UM1 AI100663), the HIV Vaccine Research and Design (HIVRAD) program (grant P01 AI110657), and American Foundation for AIDS Research Mathilde Krim Fellowship in Basic Biomedical Research. Use of the Advanced Photon Source (APS) beamline 23ID-B and Stanford Synchrotron Radiation Lightsource (SSRL) BL12-2 for this study was supported by the U.S. Department of Energy (DOE), Basic Energy Sciences, Office of Science, under contract no. DE-AC02-06CH11357 and the DOE Office of Biological and Environmental Research.

    In addition to the authors listed above, authors of the second study, “Presenting native-like trimeric HIV-1 antigens with self-assembling nanoparticles,” were Therese C. Thinnes and David Nemazee of TSRI.

    This study was supported by the IAVI Neutralizing Antibody Center and CAVD, CHAVI-ID (grant UM1 AI00663), the HIV Vaccine Research and Design (HIVRAD) program (grant P01 AI110657) and the Joint Center of Structural Genomics, funded by the NIGMS Protein Structure Initiative (grants U54 GM094586, AI073148 and AI084817).

    See the full article here .

    YOU CAN HELP IN THE FIGHT AGAINST HIV/AIDS FROM THE COMFORT OF YOUR EASY CHAIR.

    The Fight AIDS at home (FAAH@home) Phase II project is now running at World Community Grid (WCG)

    FAAH Phase II

    WCG runs on your home computer or tablet on software from Berkeley Open Infrastructure for Network Computing [BOINC]. Many other scientific projects run on BOINC software.Visit WCG or BOINC, download and install the software, then at WCG attach to the FAAH@home Phase II project. You will be joining tens of thousands of other “crunchers” processing computational data and saving the scientists literally thousands of hours of work at no real cost to you.

    WCGLarge
    WCG Logo New

    BOINCLarge
    BOINC WallPaper

    Please help promote STEM in your local schools.

    STEM Icon

    Stem Education Coalition

    The Scripps Research Institute (TSRI), one of the world’s largest, private, non-profit research organizations, stands at the forefront of basic biomedical science, a vital segment of medical research that seeks to comprehend the most fundamental processes of life. Over the last decades, the institute has established a lengthy track record of major contributions to the betterment of health and the human condition.

    The institute — which is located on campuses in La Jolla, California, and Jupiter, Florida — has become internationally recognized for its research into immunology, molecular and cellular biology, chemistry, neurosciences, autoimmune diseases, cardiovascular diseases, virology, and synthetic vaccine development. Particularly significant is the institute’s study of the basic structure and design of biological molecules; in this arena TSRI is among a handful of the world’s leading centers.

    The institute’s educational programs are also first rate. TSRI’s Graduate Program is consistently ranked among the best in the nation in its fields of biology and chemistry.

     
  • richardmitnick 2:36 pm on June 17, 2016 Permalink | Reply
    Tags: , New TSRI Method Opens Door to Development of Many New Medicines, Scripps Institute   

    From Scripps: “New TSRI Method Opens Door to Development of Many New Medicines” 

    Scripps
    Scripps Research Institute

    June 20, 2016

    Scientists at The Scripps Research Institute (TSRI) have developed a powerful new method for finding drug candidates that bind to specific proteins.

    The new method, reported recently in Nature, is a significant advance because it can be applied to a large set of proteins at once, even to the thousands of distinct proteins directly in their native cellular environment. The TSRI researchers demonstrated the technique to find “ligands” (binding partners) for many proteins previously thought to bind poorly to small molecules that can be used to determine the functions of their protein targets and can serve as starting compounds for the development of drugs.

    Among the newly discovered ligands are selective inhibitors of two caspase enzymes, which have key roles in multiple diseases but have largely eluded efforts to target them with drugs.

    “Our data suggest that the human proteome is much more broadly targetable with small molecules than has been previously appreciated,” said principal investigator Benjamin F. Cravatt, chair of the Department of Chemical Physiology and member of the Dorris Neuroscience Center and Skaggs Institute for Chemical Biology at TSRI. “That opens up new possibilities for developing scientific probes and ultimately drugs.”

    Putting Fragments to Use

    Researchers have long sought better ways to identify small-molecule ligands for human proteins and to determine which proteins in our cells are inherently “ligandable.” Biologists typically have used complex computer algorithms to predict whether a given class of proteins can bind adequately to small molecules. Pharmaceutical researchers often won’t even try to develop drugs to target proteins that are thought unligandable. Several large protein classes are believed to be in this category, and so far only about 600 of the roughly 20,000 human proteins have been targeted successfully with FDA-approved drugs.

    “There really hasn’t been a way to determine empirically, rather than theoretically, what fraction of the human proteome can be targeted by small molecules,” Cravatt said.

    The new method is partly based on an approach known as fragment-based ligand discovery, which uses candidate ligand molecules about half the size of the small molecules in pill-based drugs. For initial screens to find potential ligands, such “fragment” molecules are much more efficient than drug-sized molecules, requiring much smaller libraries of compounds for a thorough search.

    Cravatt’s team attached candidate fragment molecules to a class of other molecules that, when they can get close enough, react strongly with cysteine amino-acids on proteins, locking the ligands to the proteins with strong “covalent” bonds.

    “You still need an affinity-based interaction, but the covalent bonding event provides a significant boost in potency,” said Keriann M. Backus, a research associate in the Cravatt laboratory who is first author of the study with TSRI Professional Scientific Collaborator Bruno Correia.

    The scientists devised a screening system in which they can apply these covalent-bonding fragment molecules one by one to entire collections of proteins expressed in human cells. The method can even be used with intact, living cells in a culture dish. The system allows researchers to detect and identify which small-molecule fragments have bound covalently to which proteins in the samples and which specific sites on the proteins are responsible for binding.

    Applying a small library of cysteine-reactive fragments to the proteins found in two types of human cancer cells, the scientists found that the fragments successfully “liganded” more than 750 different cysteines found on more than 600 distinct proteins—which equated to more than 20 percent of all the proteins assayed in the samples.

    Many of these proteins belonged to protein classes, such as transcription factors, that have been considered virtually unligandable, and therefore “undruggable.” In fact, about 85 percent of the newly liganded proteins are not listed in a standard database of proteins with known small-molecule ligands.

    “This experiment has effectively expanded what we think of as the ligandable proteome,” said Backus.

    Potential to Develop Probes and Drugs

    The researchers were able to confirm the accuracy of the system, for example, by showing that it can identify the known protein targets of a covalent-binding anti-cancer drug, ibrutinib.

    The team also demonstrated that some of the protein-binding ligand molecules identified with the system have strong biological activity—and thus have the potential to be developed into scientific probes or drugs. Newly discovered ligands for the enzymes IDH1 and IDH2, for example, turned out to block the activity of the normal versions of the enzymes as well as the mutant versions implicated in many cancers.

    In a final set of experiments, the team showed that one of its identified ligands inhibits the activities of caspase-8 and caspase-10, two enzymes that help switch on the cellular self-destruct process known as apoptosis. An excess of apoptosis is thought to contribute to neurodegenerative conditions such as Alzheimer’s and Huntington’s disease, as well as the brain damage occurring in the aftermath of strokes and other brain injuries. By contrast, a lack of apoptosis in certain cells is believed to contribute to cancers and autoimmune diseases. However, scientists don’t understand enough about the roles of these enzymes, since they have been largely unable to find small molecules that selectively inhibit specific caspases.

    In this case, Cravatt’s team found that their initially identified anti-caspase ligand works by binding the precursor forms of caspase-8 and -10. They chemically modified the ligand into one that selectively binds just the precursor of caspase-8, and, using their two ligands as probes, were able to discover new details of how caspase-8 and -10 promote apoptosis in human T-cells.

    “In essence, we demonstrated that our new platform works and that we can use the ligands it identifies to do useful biology,” said Backus.

    Backus and other members of the Cravatt laboratory are now doing several further studies: optimizing many of the newly identified ligands into probes for exploring protein functions; making a more comprehensive catalogue of cysteine-containing proteins that are ligandable; and expanding the method to target other amino-acids besides cysteine.

    “We will be occupied for some time following up on this development,” said Cravatt.

    Other co-authors of the paper, Proteome-wide covalent ligand discovery in native biological systems, were Kenneth M. Lum, Stefano Forli, Benjamin D. Horning, Gonzalo E. González-Páez, Sandip Chatterjee, Bryan R. Lanning, John R. Teijaro, Arthur J. Olson, and Dennis W. Wolan, all of TSRI.

    Funding was provided by the National Institutes of Health (CA087660, GM090294, GM108208, GM069832).

    See the full article here .

    Please help promote STEM in your local schools.

    STEM Icon

    Stem Education Coalition

    The Scripps Research Institute (TSRI), one of the world’s largest, private, non-profit research organizations, stands at the forefront of basic biomedical science, a vital segment of medical research that seeks to comprehend the most fundamental processes of life. Over the last decades, the institute has established a lengthy track record of major contributions to the betterment of health and the human condition.

    The institute — which is located on campuses in La Jolla, California, and Jupiter, Florida — has become internationally recognized for its research into immunology, molecular and cellular biology, chemistry, neurosciences, autoimmune diseases, cardiovascular diseases, virology, and synthetic vaccine development. Particularly significant is the institute’s study of the basic structure and design of biological molecules; in this arena TSRI is among a handful of the world’s leading centers.

    The institute’s educational programs are also first rate. TSRI’s Graduate Program is consistently ranked among the best in the nation in its fields of biology and chemistry.

     
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