Dallas, TX, United States
Dallas, TX, United States

Time filter

Source Type

Zhong R.,Quantitative Biomedical Research Center | Kim H.S.,Yonsei University | Kim M.,Quantitative Biomedical Research Center | Kim M.,Simmons Comprehensive Cancer Center | And 4 more authors.
Nucleic Acids Research | Year: 2014

A challenge for large-scale siRNA loss-of-function studies is the biological pleiotropy resulting from multiple modes of action of siRNA reagents. A major confounding feature of these reagents is the microRNA-like translational quelling resulting from short regions of oligonucleotide complementarity to many different messenger RNAs. We developed a computational approach, deconvolution analysis of RNAi screening data, for automated quantitation of off-target effects in RNAi screening data sets. Substantial reduction of off-target rates was experimentally validated in five distinct biological screens across different genome-wide siRNA libraries. A public-access graphical-user-interface has been constructed to facilitate application of this algorithm. © 2014 The Author(s) 2014. Published by Oxford University Press on behalf of Nucleic Acids Research.


News Article | December 22, 2016
Site: www.eurekalert.org

DALLAS - Dec. 22, 2016 - Researchers at UT Southwestern Medical Center have uncovered the mechanism that cells use to find and destroy an organelle called mitochondria that, when damaged, may lead to genetic problems, cancer, neurodegenerative diseases, inflammatory disease, and aging. Understanding how this process works could potentially lead to new treatments to prevent certain illnesses and even some aspects of aging, said Dr. Beth Levine, Director of the Center for Autophagy Research at UT Southwestern and senior author of the study, published today in Cell. The Center for Autophagy Research -- the only one of its kind in the nation - investigates the process called autophagy in which cells rid themselves of damaged or unnecessary components. Mitochondria are commonly called the "powerhouses of the cell" because these cellular components works like a tiny factory inside cells to convert compounds such as sugars into energy that a cell can use. But mitochondria also have a dark side: Because of their high-energy function, when they are damaged, they release toxic chemicals called reactive oxygen species into the rest of the cell, said Dr. Yongjie Wei, Assistant Professor of Internal Medicine at UT Southwestern and lead co-first author of the study. "The removal of damaged mitochondria by autophagy (a process called mitophagy) is important for cellular health," said Dr. Levine, also Professor of Internal Medicine and Microbiology and a Howard Hughes Medical Institute Investigator. Researchers have to date focused on protein "tags" found on the outer membranes of mitochondria - especially the protein Parkin that attaches these tags -- to explain how the cell's degradative organelles, called autophagosomes, target sick mitochondria, explained Dr. Levine, who holds the Charles Cameron Sprague Distinguished Chair in Biomedical Science. (Autophagosomes are double-membraned vesicles that contain cellular material to be degraded in the process called autophagy.) But UT Southwestern scientists, working with human and mouse cells, discovered that a receptor on an inner mitochondrial membrane actually is more important in guiding these autophagosomes to their prey. In the study, researchers found that a protein called prohibitin 2 (PHB2) resides on the inner membrane of mitochondria, but is exposed when an ailing mitochondrion's outer membrane ruptures. Once the break occurs, the protein LC3, which rides on an autophagosome's exterior like a lookout, is drawn to the PHB2. The LC3 protein then attaches to PHB2, and the autophagosome carries its doomed cargo to a lysosome - yet another organelle found within cells - that acts like a tiny stomach, with enzymes to break down cell waste. The study's finding that PHB2 is crucial in targeting mitochondria for autophagic degradation is new, said Dr. Levine. However, she said, previous research had linked the presence of PHB2 to prevention of cancer, aging effects, neurodegeneration, and inflammation. So, given these beneficial health effects, it makes sense that a key action of PHB2 is to help rid cells of damaging mitochondria that contribute to such disease processes, she said. "By understanding how cells get rid of damaged mitochondria that contribute to cancer, neurodegenerative diseases, and aging, we may be able to develop treatments to prevent those processes," Dr. Levine said. The study also found that PHB2 is necessary for the routine elimination of paternal mitochondrial DNA in developing embryos, leaving only mitochondrial DNA from the mother. This work was done in roundworms, but a recent study performed elsewhere using mouse models demonstrated that mitophagy is also used to remove paternal mitochondria in mammalian embryos, said Dr. Wei-Chung "Daniel" Chiang, a postdoctoral researcher at UT Southwestern and co-first author of the study. Usually, only maternal mitochondrial DNA is passed to offspring, Dr. Levine said. For unknown reasons, the continued presence of paternal mitochondrial DNA signals genetic or health problems in the progeny. In yet another finding, the UTSW research shows that - despite scientists' greater focus on the Parkin protein's role in supporting autophagy -- PHB2 is required for Parkin to work. Other scientists involved in the study were: Dr. Rhea Sumpter, Assistant Professor of Internal Medicine; and Dr. Prashant Mishra, Assistant Professor at the Children's Medical Center Research Institute at UT Southwestern, and the Cecil H. and Ida Green Comprehensive Center for Molecular, Computational, and Systems Biology, and of Pediatrics. The research was supported by grants from the National Institutes of Health, Cancer Prevention and Research Institute of Texas, Leducq Foundation, and a Burroughs Wellcome Career Award for Medical Scientists. UT Southwestern, one of the premier academic medical centers in the nation, integrates pioneering biomedical research with exceptional clinical care and education. The institution's faculty includes many distinguished members, including six who have been awarded Nobel Prizes since 1985. The faculty of almost 2,800 is responsible for groundbreaking medical advances and is committed to translating science-driven research quickly to new clinical treatments. UT Southwestern physicians provide medical care in about 80 specialties to more than 100,000 hospitalized patients and oversee approximately 2.2 million outpatient visits a year.


News Article | December 28, 2016
Site: www.biosciencetechnology.com

Researchers at UT Southwestern Medical Center have uncovered the mechanism that cells use to find and destroy an organelle called mitochondria that, when damaged, may lead to genetic problems, cancer, neurodegenerative diseases, inflammatory disease, and aging. Understanding how this process works could potentially lead to new treatments to prevent certain illnesses and even some aspects of aging, said Dr. Beth Levine, Director of the Center for Autophagy Research at UT Southwestern and senior author of the study, published in Cell. The Center for Autophagy Research -- the only one of its kind in the nation - investigates the process called autophagy in which cells rid themselves of damaged or unnecessary components. Mitochondria are commonly called the "powerhouses of the cell" because these cellular components works like a tiny factory inside cells to convert compounds such as sugars into energy that a cell can use. But mitochondria also have a dark side: Because of their high-energy function, when they are damaged, they release toxic chemicals called reactive oxygen species into the rest of the cell, said Dr. Yongjie Wei, Assistant Professor of Internal Medicine at UT Southwestern and lead co-first author of the study. "The removal of damaged mitochondria by autophagy (a process called mitophagy) is important for cellular health," said Dr. Levine, also Professor of Internal Medicine and Microbiology and a Howard Hughes Medical Institute Investigator. Researchers have to date focused on protein "tags" found on the outer membranes of mitochondria - especially the protein Parkin that attaches these tags -- to explain how the cell's degradative organelles, called autophagosomes, target sick mitochondria, explained Dr. Levine, who holds the Charles Cameron Sprague Distinguished Chair in Biomedical Science. (Autophagosomes are double-membraned vesicles that contain cellular material to be degraded in the process called autophagy.) But UT Southwestern scientists, working with human and mouse cells, discovered that a receptor on an inner mitochondrial membrane actually is more important in guiding these autophagosomes to their prey. In the study, researchers found that a protein called prohibitin 2 (PHB2) resides on the inner membrane of mitochondria, but is exposed when an ailing mitochondrion's outer membrane ruptures. Once the break occurs, the protein LC3, which rides on an autophagosome's exterior like a lookout, is drawn to the PHB2. The LC3 protein then attaches to PHB2, and the autophagosome carries its doomed cargo to a lysosome - yet another organelle found within cells - that acts like a tiny stomach, with enzymes to break down cell waste. The study's finding that PHB2 is crucial in targeting mitochondria for autophagic degradation is new, said Dr. Levine. However, she said, previous research had linked the presence of PHB2 to prevention of cancer, aging effects, neurodegeneration, and inflammation. So, given these beneficial health effects, it makes sense that a key action of PHB2 is to help rid cells of damaging mitochondria that contribute to such disease processes, she said. "By understanding how cells get rid of damaged mitochondria that contribute to cancer, neurodegenerative diseases, and aging, we may be able to develop treatments to prevent those processes," Dr. Levine said. The study also found that PHB2 is necessary for the routine elimination of paternal mitochondrial DNA in developing embryos, leaving only mitochondrial DNA from the mother. This work was done in roundworms, but a recent study performed elsewhere using mouse models demonstrated that mitophagy is also used to remove paternal mitochondria in mammalian embryos, said Dr. Wei-Chung "Daniel" Chiang, a postdoctoral researcher at UT Southwestern and co-first author of the study. Usually, only maternal mitochondrial DNA is passed to offspring, Dr. Levine said. For unknown reasons, the continued presence of paternal mitochondrial DNA signals genetic or health problems in the progeny. In yet another finding, the UTSW research shows that - despite scientists' greater focus on the Parkin protein's role in supporting autophagy -- PHB2 is required for Parkin to work.


Sumpter R.,Center for Autophagy Research | Sirasanagandla S.,Center for Autophagy Research | Fernandez A.F.,Center for Autophagy Research | Fernandez A.F.,University of Oviedo | And 13 more authors.
Cell | Year: 2016

Summary Fanconi anemia (FA) pathway genes are important tumor suppressors whose best-characterized function is repair of damaged nuclear DNA. Here, we describe an essential role for FA genes in two forms of selective autophagy. Genetic deletion of Fancc blocks the autophagic clearance of viruses (virophagy) and increases susceptibility to lethal viral encephalitis. Fanconi anemia complementation group C (FANCC) protein interacts with Parkin, is required in vitro and in vivo for clearance of damaged mitochondria, and decreases mitochondrial reactive oxygen species (ROS) production and inflammasome activation. The mitophagy function of FANCC is genetically distinct from its role in genomic DNA damage repair. Moreover, additional genes in the FA pathway, including FANCA, FANCF, FANCL, FANCD2, BRCA1, and BRCA2, are required for mitophagy. Thus, members of the FA pathway represent a previously undescribed class of selective autophagy genes that function in immunity and organellar homeostasis. These findings have implications for understanding the pathogenesis of FA and cancers associated with mutations in FA genes. © 2016 Elsevier Inc.


Dong X.,Center for Autophagy Research | Feng P.,Southwestern Medical Center
Journal of Visualized Experiments | Year: 2011

In response to viral infection, a host develops various defensive responses, such as activating innate immune signaling pathways that lead to antiviral cytokine production. In order to colonize the host, viruses are obligate to evade host antiviral responses and manipulate signaling pathways. Unraveling the host-virus interaction will shed light on the development of novel therapeutic strategies against viral infection. Murine γHV68 is closely related to human oncogenic Kaposi's sarcoma-associated herpesvirus and Epsten-Barr virus. γHV68 infection in laboratory mice provides a tractable small animal model to examine the entire course of host responses and viral infection in vivo, which are not available for human herpesviruses. In this protocol, we present a panel of methods for phenotypic characterization and molecular dissection of host signaling components in γHV68 lytic replication both in vivo and ex vivo. The availability of genetically modified mouse strains permits the interrogation of the roles of host signaling pathways during γHV68 acute infection in vivo. Additionally, mouse embryonic fibroblasts (MEFs) isolated from these deficient mouse strains can be used to further dissect roles of these molecules during γHV68 lytic replication ex vivo. Using virological and molecular biology assays, we can pinpoint the molecular mechanism of host-virus interactions and identify host and viral genes essential for viral lytic replication. Finally, a bacterial artificial chromosome (BAC) system facilitates the introduction of mutations into the viral factor(s) that specifically interrupt the host-virus interaction. Recombinant γHV68 carrying these mutations can be used to recapitulate the phenotypes of γHV68 lytic replication in MEFs deficient in key host signaling components. This protocol offers an excellent strategy to interrogate host-pathogen interaction at multiple levels of intervention in vivo and ex vivo. Recently, we have discovered that γHV68 usurps an innate immune signaling pathway to promote viral lytic replication. Specifically, γHV68 de novo infection activates the immune kinase IKKβ and activated IKKβ phosphorylates the master viral transcription factor, replication and transactivator (RTA), to promote viral transcriptional activation. In doing so, γHV68 efficiently couples its transcriptional activation to host innate immune activation, thereby facilitating viral transcription and lytic replication. This study provides an excellent example that can be applied to other viruses to interrogate host-virus interaction. © 2011 Creative Commons Attribution License.


Wei Y.,Center for Autophagy Research | Wei Y.,Howard Hughes Medical Institute | An Z.,Center for Autophagy Research | Zou Z.,Center for Autophagy Research | And 9 more authors.
eLife | Year: 2015

Autophagy is a fundamental adaptive response to amino acid starvation orchestrated by conserved gene products, the autophagy (ATG) proteins. However, the cellular cues that activate the function of ATG proteins during amino acid starvation are incompletely understood. Here we show that two related stress-responsive kinases, members of the p38 mitogen-activated protein kinase (MAPK) signaling pathway MAPKAPK2 (MK2) and MAPKAPK3 (MK3), positively regulate starvation-induced autophagy by phosphorylating an essential ATG protein, Beclin 1, at serine 90, and that this phosphorylation site is essential for the tumor suppressor function of Beclin 1. Moreover, MK2/MK3-dependent Beclin 1 phosphorylation (and starvation-induced autophagy) is blocked in vitro and in vivo by BCL2, a negative regulator of Beclin 1. Together, these findings reveal MK2/MK3 as crucial stress-responsive kinases that promote autophagy through Beclin 1 S90 phosphorylation, and identify the blockade of MK2/3-dependent Beclin 1 S90 phosphorylation as a mechanism by which BCL2 inhibits the autophagy function of Beclin 1. © Copyright Wei et al.


PubMed | Hannover Medical School, Center for Autophagy Research, Southwestern Medical Center and North Dakota State University
Type: | Journal: eLife | Year: 2015

Autophagy is a fundamental adaptive response to amino acid starvation orchestrated by conserved gene products, the autophagy (ATG) proteins. However, the cellular cues that activate the function of ATG proteins during amino acid starvation are incompletely understood. Here we show that two related stress-responsive kinases, members of the p38 mitogen-activated protein kinase (MAPK) signaling pathway MAPKAPK2 (MK2) and MAPKAPK3 (MK3), positively regulate starvation-induced autophagy by phosphorylating an essential ATG protein, Beclin 1, at serine 90, and that this phosphorylation site is essential for the tumor suppressor function of Beclin 1. Moreover, MK2/MK3-dependent Beclin 1 phosphorylation (and starvation-induced autophagy) is blocked in vitro and in vivo by BCL2, a negative regulator of Beclin 1. Together, these findings reveal MK2/MK3 as crucial stress-responsive kinases that promote autophagy through Beclin 1 S90 phosphorylation, and identify the blockade of MK2/3-dependent Beclin 1 S90 phosphorylation as a mechanism by which BCL2 inhibits the autophagy function of Beclin 1.


Levine B.,Center for Autophagy Research | Levine B.,Howard Hughes Medical Institute | Packer M.,University of Texas Southwestern Medical Center | Codogno P.,University of Paris Descartes
Journal of Clinical Investigation | Year: 2015

Defects in autophagy have been linked to a wide range of medical illnesses, including cancer as well as infectious, neurodegenerative, inflammatory, and metabolic diseases. These observations have led to the hypothesis that autophagy inducers may prevent or treat certain clinical conditions. Lifestyle and nutritional factors, such as exercise and caloric restriction, may exert their known health benefits through the autophagy pathway. Several currently available FDA-approved drugs have been shown to enhance autophagy, and this autophagy-enhancing action may be repurposed for use in novel clinical indications. The development of new drugs that are designed to be more selective inducers of autophagy function in target organs is expected to maximize clinical benefits while minimizing toxicity. This Review summarizes the rationale and current approaches for developing autophagy inducers in medicine, the factors to be considered in defining disease targets for such therapy, and the potential benefits of such treatment for human health.


Dong X.,Center for Autophagy Research
Journal of visualized experiments : JoVE | Year: 2011

In response to viral infection, a host develops various defensive responses, such as activating innate immune signaling pathways that lead to antiviral cytokine production. In order to colonize the host, viruses are obligate to evade host antiviral responses and manipulate signaling pathways. Unraveling the host-virus interaction will shed light on the development of novel therapeutic strategies against viral infection. Murine γHV68 is closely related to human oncogenic Kaposi's sarcoma-associated herpesvirus and Epsten-Barr virus. γHV68 infection in laboratory mice provides a tractable small animal model to examine the entire course of host responses and viral infection in vivo, which are not available for human herpesviruses. In this protocol, we present a panel of methods for phenotypic characterization and molecular dissection of host signaling components in γHV68 lytic replication both in vivo and ex vivo. The availability of genetically modified mouse strains permits the interrogation of the roles of host signaling pathways during γHV68 acute infection in vivo. Additionally, mouse embryonic fibroblasts (MEFs) isolated from these deficient mouse strains can be used to further dissect roles of these molecules during γHV68 lytic replication ex vivo. Using virological and molecular biology assays, we can pinpoint the molecular mechanism of host-virus interactions and identify host and viral genes essential for viral lytic replication. Finally, a bacterial artificial chromosome (BAC) system facilitates the introduction of mutations into the viral factor(s) that specifically interrupt the host-virus interaction. Recombinant γHV68 carrying these mutations can be used to recapitulate the phenotypes of γHV68 lytic replication in MEFs deficient in key host signaling components. This protocol offers an excellent strategy to interrogate host-pathogen interaction at multiple levels of intervention in vivo and ex vivo. Recently, we have discovered that γHV68 usurps an innate immune signaling pathway to promote viral lytic replication. Specifically, γHV68 de novo infection activates the immune kinase IKKβ and activated IKKβ phosphorylates the master viral transcription factor, replication and transactivator (RTA), to promote viral transcriptional activation. In doing so, γHV68 efficiently couples its transcriptional activation to host innate immune activation, thereby facilitating viral transcription and lytic replication. This study provides an excellent example that can be applied to other viruses to interrogate host-virus interaction.


PubMed | Center for Autophagy Research
Type: | Journal: Journal of visualized experiments : JoVE | Year: 2011

In response to viral infection, a host develops various defensive responses, such as activating innate immune signaling pathways that lead to antiviral cytokine production. In order to colonize the host, viruses are obligate to evade host antiviral responses and manipulate signaling pathways. Unraveling the host-virus interaction will shed light on the development of novel therapeutic strategies against viral infection. Murine HV68 is closely related to human oncogenic Kaposis sarcoma-associated herpesvirus and Epsten-Barr virus. HV68 infection in laboratory mice provides a tractable small animal model to examine the entire course of host responses and viral infection in vivo, which are not available for human herpesviruses. In this protocol, we present a panel of methods for phenotypic characterization and molecular dissection of host signaling components in HV68 lytic replication both in vivo and ex vivo. The availability of genetically modified mouse strains permits the interrogation of the roles of host signaling pathways during HV68 acute infection in vivo. Additionally, mouse embryonic fibroblasts (MEFs) isolated from these deficient mouse strains can be used to further dissect roles of these molecules during HV68 lytic replication ex vivo. Using virological and molecular biology assays, we can pinpoint the molecular mechanism of host-virus interactions and identify host and viral genes essential for viral lytic replication. Finally, a bacterial artificial chromosome (BAC) system facilitates the introduction of mutations into the viral factor(s) that specifically interrupt the host-virus interaction. Recombinant HV68 carrying these mutations can be used to recapitulate the phenotypes of HV68 lytic replication in MEFs deficient in key host signaling components. This protocol offers an excellent strategy to interrogate host-pathogen interaction at multiple levels of intervention in vivo and ex vivo. Recently, we have discovered that HV68 usurps an innate immune signaling pathway to promote viral lytic replication. Specifically, HV68 de novo infection activates the immune kinase IKK and activated IKK phosphorylates the master viral transcription factor, replication and transactivator (RTA), to promote viral transcriptional activation. In doing so, HV68 efficiently couples its transcriptional activation to host innate immune activation, thereby facilitating viral transcription and lytic replication. This study provides an excellent example that can be applied to other viruses to interrogate host-virus interaction.

Loading Center for Autophagy Research collaborators
Loading Center for Autophagy Research collaborators