Intracellular Localization of the BCL-2 Family Member BOK and Functional Implications
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Download.Cse.Ucsc.Edu/ Early Age of Onset (~2.5 Years) of This PRA Form in Goldenpath/Canfam2/Database/) Using Standard Settings
Kropatsch et al. Canine Genetics and Epidemiology (2016) 3:7 DOI 10.1186/s40575-016-0037-x RESEARCH Open Access A large deletion in RPGR causes XLPRA in Weimaraner dogs Regina Kropatsch1*, Denis A. Akkad1, Matthias Frank2, Carsten Rosenhagen3, Janine Altmüller4,5, Peter Nürnberg4,6,7, Jörg T. Epplen1,8 and Gabriele Dekomien1 Abstract Background: Progressive retinal atrophy (PRA) belongs to a group of inherited retinal disorders associated with gradual vision impairment due to degeneration of retinal photoreceptors in various dog breeds. PRA is highly heterogeneous, with autosomal dominant, recessive or X-linked modes of inheritance. In this study we used exome sequencing to investigate the molecular genetic basis of a new type of PRA, which occurred spontaneously in a litter of German short-hair Weimaraner dogs. Results: Whole exome sequencing in two PRA-affected Weimaraner dogs identified a large deletion comprising the first four exons of the X-linked retinitis pigmentosa GTPase regulator (RPGR) gene known to be involved in human retinitis pigmentosa and canine PRA. Screening of 16 individuals in the corresponding pedigree of short-hair Weimaraners by qPCR, verified the deletion in hemizygous or heterozygous state in one male and six female dogs, respectively. The mutation was absent in 88 additional unrelated Weimaraners. The deletion was not detectable in the parents of one older female which transmitted the mutation to her offspring, indicating that the RPGR deletion represents a de novo mutation concerning only recent generations of the Weimaraner breed in Germany. Conclusion: Our results demonstrate the value of an existing DNA biobank combined with exome sequencing to identify the underlying genetic cause of a spontaneously occurring inherited disease. -
Analysis of Trans Esnps Infers Regulatory Network Architecture
Analysis of trans eSNPs infers regulatory network architecture Anat Kreimer Submitted in partial fulfillment of the requirements for the degree of Doctor of Philosophy in the Graduate School of Arts and Sciences COLUMBIA UNIVERSITY 2014 © 2014 Anat Kreimer All rights reserved ABSTRACT Analysis of trans eSNPs infers regulatory network architecture Anat Kreimer eSNPs are genetic variants associated with transcript expression levels. The characteristics of such variants highlight their importance and present a unique opportunity for studying gene regulation. eSNPs affect most genes and their cell type specificity can shed light on different processes that are activated in each cell. They can identify functional variants by connecting SNPs that are implicated in disease to a molecular mechanism. Examining eSNPs that are associated with distal genes can provide insights regarding the inference of regulatory networks but also presents challenges due to the high statistical burden of multiple testing. Such association studies allow: simultaneous investigation of many gene expression phenotypes without assuming any prior knowledge and identification of unknown regulators of gene expression while uncovering directionality. This thesis will focus on such distal eSNPs to map regulatory interactions between different loci and expose the architecture of the regulatory network defined by such interactions. We develop novel computational approaches and apply them to genetics-genomics data in human. We go beyond pairwise interactions to define network motifs, including regulatory modules and bi-fan structures, showing them to be prevalent in real data and exposing distinct attributes of such arrangements. We project eSNP associations onto a protein-protein interaction network to expose topological properties of eSNPs and their targets and highlight different modes of distal regulation. -
Profiling of Transcripts and Proteins Modulated by the E7 Oncogene in the Lung Tissue of E7-Tg Mice by the Omics Approach
MOLECULAR MEDICINE REPORTS 2: 129-137, 2009 129 Profiling of transcripts and proteins modulated by the E7 oncogene in the lung tissue of E7-Tg mice by the omics approach EUNJIN KIM1*, JEONGWOO KANG1,3*, MINCHUL CHO1, SOJUNG LEE1, EUNHEE SEO1, HEESOOK CHOI1, YUMI KIM1, JUNGHEE KIM1, KUM YONG KANG2, KWANG PYO KIM2, JAEYONG HAN3, YHUNYHONG SHEEN4, YOUNG NA YUM5, SUE-NIE PARK5 and DO-YOUNG YOON1 Departments of 1Bioscience and Biotechnology, and 2Molecular Biotechnology, Konkuk University, Hwayang-dong 1, Gwangjin-gu, Seoul 143-701; 3Laboratory of Animal Genetic Engineering, Department of Food and Animal Biotechnology, Seoul National University, Seoul 151-742; 4School of Pharmacy, Ewha Womans University, Seoul 120-750; 5Korea Food and Drug Administration, #194 Tongil-ro, Eunpyung-gu, Seoul 122-704, Korea Received August 18, 2008; Accepted November 10, 2008 DOI: 10.3892/mmr_00000073 Abstract. The E6 and E7 oncoproteins of human papilloma suggest that the E7 oncogene modulates the expression levels virus (HPV) type 16 have been known to cooperatively induce of cell cycle-related (cyclin B1, cyclin E2) and cell adhesion- the immortalization and transformation of primary keratino- and migration-related (actinin ·1, CD166) factors, which may cytes. We established an E7 transgenic mouse model to play important roles in cellular transformation in cancer. In screen HPV-related biomakers using the omics approach. addition, the solubilization of the rigid intermediate filament The methods used to identify HPV-modulated factors were network by specific proteolysis mediated via up-regulating genomics analysis by microarray using the Affymetrix 430 gelsolin and down-regulating cofilin-1, as well as increased 2.0 array to screen E7-modulated genes, and proteomics levels of endoplasmic reticulum protein calnexin with chap- analysis using nano-LC-ESI-MS/MS to screen E7-modulated erone functions, might also be involved in E7-lung epithelial proteins with the lung tissue of E7 transgenic mice. -
Calreticulin—Multifunctional Chaperone in Immunogenic Cell Death: Potential Significance As a Prognostic Biomarker in Ovarian
cells Review Calreticulin—Multifunctional Chaperone in Immunogenic Cell Death: Potential Significance as a Prognostic Biomarker in Ovarian Cancer Patients Michal Kielbik *, Izabela Szulc-Kielbik and Magdalena Klink Institute of Medical Biology, Polish Academy of Sciences, 106 Lodowa Str., 93-232 Lodz, Poland; [email protected] (I.S.-K.); [email protected] (M.K.) * Correspondence: [email protected]; Tel.: +48-42-27-23-636 Abstract: Immunogenic cell death (ICD) is a type of death, which has the hallmarks of necroptosis and apoptosis, and is best characterized in malignant diseases. Chemotherapeutics, radiotherapy and photodynamic therapy induce intracellular stress response pathways in tumor cells, leading to a secretion of various factors belonging to a family of damage-associated molecular patterns molecules, capable of inducing the adaptive immune response. One of them is calreticulin (CRT), an endoplasmic reticulum-associated chaperone. Its presence on the surface of dying tumor cells serves as an “eat me” signal for antigen presenting cells (APC). Engulfment of tumor cells by APCs results in the presentation of tumor’s antigens to cytotoxic T-cells and production of cytokines/chemokines, which activate immune cells responsible for tumor cells killing. Thus, the development of ICD and the expression of CRT can help standard therapy to eradicate tumor cells. Here, we review the physiological functions of CRT and its involvement in the ICD appearance in malignant dis- ease. Moreover, we also focus on the ability of various anti-cancer drugs to induce expression of surface CRT on ovarian cancer cells. The second aim of this work is to discuss and summarize the prognostic/predictive value of CRT in ovarian cancer patients. -
Is BOK Required for Apoptosis Induced by Endoplasmic Reticulum Stress?
LETTER Is BOK required for apoptosis induced by endoplasmic reticulum stress? LETTER Yuniel Fernandez-Marreroa, Francine Keb,c, Nohemy Echeverrya,1, Philippe Bouilletb,c, Daniel Bachmanna, Andreas Strasserb,c, and Thomas Kaufmanna,2 The B-cell lymphoma 2 (BCL-2)-related ovarian killer comparable Chop levels). Given the critical role of BIM (BOK) shares sequence homology with the proapo- in ER stress-induced apoptosis, this reduction of Bim ptotic BCL-2 family members BAX and BAK. However, may fully account for the reported resistance to ER −/− Bok cells are not protected from classic apoptotic stress. It is unclear whether this reduction of Bim is par- triggers and evidence for a proapoptotic role of BOK ticular to these SV40 MEFs, which are prone to line-to- is derived mostly from overexpression studies (1). BOK line variations within the one genotype, or whether this localizes preferentially to the endoplasmic reticulum is also seen in primary cells (e.g., primary MEFs, which (ER) membrane, where it interacts with IP3-receptors were used for some experiments) from these mice. Im- −/− (2, 3). Using cells from their newly generated Bok portantly, we did not observe significant changes in Bim −/− mouse strain, Carpio et al. propose that BOK is a crit- levels in SV40 MEFs or tissues from our Bok mice (Fig. ical inducer of BAX/BAK-dependent apoptosis in re- 1A). Overall, our analysis of SV40 MEFs, primary MEFs, sponse to ER stress (4). This proposal is in contrast to myeloid progenitors, mast cells, and primary neutrophils our earlier report, in which we showed that loss of BOK did not support a proapoptotic role of BOK downstream did not confer resistance toward ER stress in several of ER stress (2) (Fig. -
BCL-2 Family Proteins: Changing Partners in the Dance Towards Death
Cell Death and Differentiation (2018) 25, 65–80 OPEN Official journal of the Cell Death Differentiation Association www.nature.com/cdd Review BCL-2 family proteins: changing partners in the dance towards death Justin Kale1, Elizabeth J Osterlund1,2 and David W Andrews*,1,2,3 The BCL-2 family of proteins controls cell death primarily by direct binding interactions that regulate mitochondrial outer membrane permeabilization (MOMP) leading to the irreversible release of intermembrane space proteins, subsequent caspase activation and apoptosis. The affinities and relative abundance of the BCL-2 family proteins dictate the predominate interactions between anti-apoptotic and pro-apoptotic BCL-2 family proteins that regulate MOMP. We highlight the core mechanisms of BCL-2 family regulation of MOMP with an emphasis on how the interactions between the BCL-2 family proteins govern cell fate. We address the critical importance of both the concentration and affinities of BCL-2 family proteins and show how differences in either can greatly change the outcome. Further, we explain the importance of using full-length BCL-2 family proteins (versus truncated versions or peptides) to parse out the core mechanisms of MOMP regulation by the BCL-2 family. Finally, we discuss how post- translational modifications and differing intracellular localizations alter the mechanisms of apoptosis regulation by BCL-2 family proteins. Successful therapeutic intervention of MOMP regulation in human disease requires an understanding of the factors that mediate the major binding interactions between BCL-2 family proteins in cells. Cell Death and Differentiation (2018) 25, 65–80; doi:10.1038/cdd.2017.186; published online 17 November 2017 The membrane plays an active role in most BCL-2 family interactions by changing the affinities and local relative abundance of these proteins. -
A Selective ER-Phagy Exerts Procollagen Quality Control Via a Calnexin-FAM134B Complex
Article A selective ER-phagy exerts procollagen quality control via a Calnexin-FAM134B complex Alison Forrester1,†, Chiara De Leonibus1,†, Paolo Grumati2,†, Elisa Fasana3,†, Marilina Piemontese1, Leopoldo Staiano1, Ilaria Fregno3,4, Andrea Raimondi5, Alessandro Marazza3,6, Gemma Bruno1, Maria Iavazzo1, Daniela Intartaglia1, Marta Seczynska2, Eelco van Anken7, Ivan Conte1, Maria Antonietta De Matteis1,8, Ivan Dikic2,9,* , Maurizio Molinari3,10,** & Carmine Settembre1,11,*** Abstract The EMBO Journal (2019) 38:e99847 Autophagy is a cytosolic quality control process that recognizes substrates through receptor-mediated mechanisms. Procollagens, Introduction the most abundant gene products in Metazoa, are synthesized in the endoplasmic reticulum (ER), and a fraction that fails to attain Macroautophagy (hereafter referred to as autophagy) is a homeostatic the native structure is cleared by autophagy. However, how auto- catabolic process devoted to the sequestration of cytoplasmic material phagy selectively recognizes misfolded procollagens in the ER in double-membrane vesicles (autophagic vesicles, AVs) that eventu- lumen is still unknown. We performed siRNA interference, CRISPR- ally fuse with lysosomes where cargo is degraded (Mizushima, 2011). Cas9 or knockout-mediated gene deletion of candidate autophagy Autophagy is essential to maintain tissue homeostasis and counter- and ER proteins in collagen producing cells. We found that the ER- acts both the onset and progression of many disease conditions, such resident lectin chaperone Calnexin (CANX) and the ER-phagy as ageing, neurodegeneration and cancer (Levine et al, 2015). receptor FAM134B are required for autophagy-mediated quality Substrates can be selectively delivered to AVs through receptor- control of endogenous procollagens. Mechanistically, CANX acts as mediated processes. Autophagy receptors harbour a LC3 or GABARAP co-receptor that recognizes ER luminal misfolded procollagens and interaction motif (LIR or GIM, respectively) that facilitate binding of interacts with the ER-phagy receptor FAM134B. -
Detection of Pro Angiogenic and Inflammatory Biomarkers in Patients With
www.nature.com/scientificreports OPEN Detection of pro angiogenic and infammatory biomarkers in patients with CKD Diana Jalal1,2,3*, Bridget Sanford4, Brandon Renner5, Patrick Ten Eyck6, Jennifer Laskowski5, James Cooper5, Mingyao Sun1, Yousef Zakharia7, Douglas Spitz7,9, Ayotunde Dokun8, Massimo Attanasio1, Kenneth Jones10 & Joshua M. Thurman5 Cardiovascular disease (CVD) is the most common cause of death in patients with native and post-transplant chronic kidney disease (CKD). To identify new biomarkers of vascular injury and infammation, we analyzed the proteome of plasma and circulating extracellular vesicles (EVs) in native and post-transplant CKD patients utilizing an aptamer-based assay. Proteins of angiogenesis were signifcantly higher in native and post-transplant CKD patients versus healthy controls. Ingenuity pathway analysis (IPA) indicated Ephrin receptor signaling, serine biosynthesis, and transforming growth factor-β as the top pathways activated in both CKD groups. Pro-infammatory proteins were signifcantly higher only in the EVs of native CKD patients. IPA indicated acute phase response signaling, insulin-like growth factor-1, tumor necrosis factor-α, and interleukin-6 pathway activation. These data indicate that pathways of angiogenesis and infammation are activated in CKD patients’ plasma and EVs, respectively. The pathways common in both native and post-transplant CKD may signal similar mechanisms of CVD. Approximately one in 10 individuals has chronic kidney disease (CKD) rendering CKD one of the most common diseases worldwide1. CKD is associated with a high burden of morbidity in the form of end stage kidney disease (ESKD) requiring dialysis or transplantation 2. Furthermore, patients with CKD are at signifcantly increased risk of death from cardiovascular disease (CVD)3,4. -
Genetic, Cytogenetic and Physical Refinement of the Autosomal Recessive CMT Linked to 5Q31ð Q33: Exclusion of Candidate Genes I
European Journal of Human Genetics (1999) 7, 849–859 © 1999 Stockton Press All rights reserved 1018–4813/99 $15.00 t http://www.stockton-press.co.uk/ejhg ARTICLE Genetic, cytogenetic and physical refinement of the autosomal recessive CMT linked to 5q31–q33: exclusion of candidate genes including EGR1 Ang`ele Guilbot1, Nicole Ravis´e1, Ahmed Bouhouche6, Philippe Coullin4, Nazha Birouk6, Thierry Maisonobe3, Thierry Kuntzer7, Christophe Vial8, Djamel Grid5, Alexis Brice1,2 and Eric LeGuern1,2 1INSERM U289, 2F´ed´eration de Neurologie and 3Laboratoire de Neuropathologie R Escourolle, Hˆopital de la Salpˆetri`ere, Paris 4Laboratoire de cytog´en´etique, Villejuif 5G´en´ethon, Evry, France 6Service de Neurologie, Hˆopital des Sp´ecialit´es, Rabat, Morocco 7Service de Neurologie, Centre Hospitalier Universitaire Vaudois, Lausanne, Switzerland 8Service D’EMG et de pathologie neuromusculaire, Hˆopital neurologique Pierre Wertheimer, Lyon, France Charcot-Marie-Tooth disease is an heterogeneous group of inherited peripheral motor and sensory neuropathies with several modes of inheritance: autosomal dominant, X-linked and autosomal recessive. By homozygosity mapping, we have identified, in the 5q23–q33 region, a third locus responsible for an autosomal recessive form of demyelinating CMT. Haplotype reconstruction and determination of the minimal region of homozygosity restricted the candidate region to a 4 cM interval. A physical map of the candidate region was established by screening YACs for microsatellites used for genetic analysis. Combined genetic, cytogenetic and physical mapping restricted the locus to a less than 2 Mb interval on chromosome 5q32. Seventeen consanguineous families with demyelinating ARCMT of various origins were screened for linkage to 5q31–q33. -
Anoctamin 1 (Tmem16a) Ca -Activated Chloride Channel Stoichiometrically Interacts with an Ezrin–Radixin–Moesin Network
Anoctamin 1 (Tmem16A) Ca2+-activated chloride channel stoichiometrically interacts with an ezrin–radixin–moesin network Patricia Perez-Cornejoa,1, Avanti Gokhaleb,1, Charity Duranb,1, Yuanyuan Cuib, Qinghuan Xiaob, H. Criss Hartzellb,2, and Victor Faundezb,2 aPhysiology Department, School of Medicine, Universidad Autónoma de San Luis Potosí, San Luis Potosí, SLP 78210, Mexico; and bDepartment of Cell Biology, Emory University School of Medicine, Atlanta, GA 30322 Edited by David E. Clapham, Howard Hughes Medical Institute, Children’s Hospital Boston, Boston, MA, and approved May 9, 2012 (received for review January 4, 2012) The newly discovered Ca2+-activated Cl− channel (CaCC), Anocta- approach to identify Ano1-interacting proteins. We find that min 1 (Ano1 or TMEM16A), has been implicated in vital physiolog- Ano1 forms a complex with two high stochiometry interactomes. ical functions including epithelial fluid secretion, gut motility, and One protein network is centered on the signaling/scaffolding smooth muscle tone. Overexpression of Ano1 in HEK cells or Xen- actin-binding regulatory proteins ezrin, radixin, moesin, and opus oocytes is sufficient to generate Ca2+-activated Cl− currents, RhoA. The ezrin–radixin–moesin (ERM) proteins organize the but the details of channel composition and the regulatory factors cortical cytoskeleton by linking actin to the plasma membrane that control channel biology are incompletely understood. We and coordinate cell signaling events by scaffolding signaling used a highly sensitive quantitative SILAC proteomics approach molecules (19). The other major interactome is centered on the to obtain insights into stoichiometric protein networks associated SNARE and SM proteins VAMP3, syntaxins 2 and -4, and the with the Ano1 channel. -
Profiling of Transcripts and Proteins Modulated by the E7 Oncogene in the Lung Tissue of E7-Tg Mice by the Omics Approach
MOLECULAR MEDICINE REPORTS 2: 129-137, 2009 129 Profiling of transcripts and proteins modulated by the E7 oncogene in the lung tissue of E7-Tg mice by the omics approach EUNJIN KIM1*, JEONGWOO KANG1,3*, MINCHUL CHO1, SOJUNG LEE1, EUNHEE SEO1, HEESOOK CHOI1, YUMI KIM1, JUNGHEE KIM1, KUM YONG KANG2, KWANG PYO KIM2, JAEYONG HAN3, YHUNYHONG SHEEN4, YOUNG NA YUM5, SUE-NIE PARK5 and DO-YOUNG YOON1 Departments of 1Bioscience and Biotechnology, and 2Molecular Biotechnology, Konkuk University, Hwayang-dong 1, Gwangjin-gu, Seoul 143-701; 3Laboratory of Animal Genetic Engineering, Department of Food and Animal Biotechnology, Seoul National University, Seoul 151-742; 4School of Pharmacy, Ewha Womans University, Seoul 120-750; 5Korea Food and Drug Administration, #194 Tongil-ro, Eunpyung-gu, Seoul 122-704, Korea Received August 18, 2008; Accepted November 10, 2008 DOI: 10.3892/mmr_00000073 Abstract. The E6 and E7 oncoproteins of human papilloma suggest that the E7 oncogene modulates the expression levels virus (HPV) type 16 have been known to cooperatively induce of cell cycle-related (cyclin B1, cyclin E2) and cell adhesion- the immortalization and transformation of primary keratino- and migration-related (actinin ·1, CD166) factors, which may cytes. We established an E7 transgenic mouse model to play important roles in cellular transformation in cancer. In screen HPV-related biomakers using the omics approach. addition, the solubilization of the rigid intermediate filament The methods used to identify HPV-modulated factors were network by specific proteolysis mediated via up-regulating genomics analysis by microarray using the Affymetrix 430 gelsolin and down-regulating cofilin-1, as well as increased 2.0 array to screen E7-modulated genes, and proteomics levels of endoplasmic reticulum protein calnexin with chap- analysis using nano-LC-ESI-MS/MS to screen E7-modulated erone functions, might also be involved in E7-lung epithelial proteins with the lung tissue of E7 transgenic mice. -
Transcriptomic Landscape of Breast Cancers Through Mrna Sequencing Jeyanthy Eswaran George Washington University
Himmelfarb Health Sciences Library, The George Washington University Health Sciences Research Commons Biochemistry and Molecular Medicine Faculty Biochemistry and Molecular Medicine Publications 2-14-2012 Transcriptomic landscape of breast cancers through mRNA sequencing Jeyanthy Eswaran George Washington University Dinesh Cyanam George Washington University Prakriti Mudvari George Washington University Sirigiri Divijendra Natha Reddy George Washington University Suresh Pakala George Washington University See next page for additional authors Follow this and additional works at: http://hsrc.himmelfarb.gwu.edu/smhs_biochem_facpubs Part of the Biochemistry, Biophysics, and Structural Biology Commons Recommended Citation Eswaran, J., Cyanam, D., Mudvari, P., Reddy, S., Pakala, S., Nair, S., Florea, L., & Fuqua, S. (2012). Transcriptomic landscape of breast cancers through mrna sequencing. Scientific Reports, 2, 264. This Journal Article is brought to you for free and open access by the Biochemistry and Molecular Medicine at Health Sciences Research Commons. It has been accepted for inclusion in Biochemistry and Molecular Medicine Faculty Publications by an authorized administrator of Health Sciences Research Commons. For more information, please contact [email protected]. Authors Jeyanthy Eswaran, Dinesh Cyanam, Prakriti Mudvari, Sirigiri Divijendra Natha Reddy, Suresh Pakala, Sujit S. Nair, Liliana Florea, Suzanne A.W. Fuqua, Sucheta Godbole, and Rakesh Kumar This journal article is available at Health Sciences Research Commons: http://hsrc.himmelfarb.gwu.edu/smhs_biochem_facpubs/3