Non-Apoptotic Functions of BCL-2 Family Proteins
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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. -
Amyloid Β-Peptide Increases Mitochondria-Endoplasmic
cells Article Amyloid β-Peptide Increases Mitochondria-Endoplasmic Reticulum Contact Altering Mitochondrial Function and Autophagosome Formation in Alzheimer’s Disease-Related Models Nuno Santos Leal 1,*, Giacomo Dentoni 1 , Bernadette Schreiner 1 , Luana Naia 1, Antonio Piras 1, Caroline Graff 1, Antonio Cattaneo 2, Giovanni Meli 2 , Maho Hamasaki 3, Per Nilsson 1 and Maria Ankarcrona 1,* 1 Division of Neurogeriatrics, Department of Neurobiology, Care Science and Society, Karolinska Institutet, BioClinicum J9:20, Visionsgatan 4, 171 64 Solna, Sweden; [email protected] (G.D.); [email protected] (B.S.); [email protected] (L.N.); [email protected] (A.P.); caroline.graff@ki.se (C.G.); [email protected] (P.N.) 2 European Brain Research Institute (EBRI), Viale Regina Elena 295, 00161 Roma, Italy; [email protected] (A.C.); [email protected] (G.M.) 3 Department of Genetics, Graduate School of Medicine, Osaka University, 2-2 Yamadaoka, Suita, Osaka 565-0871, Japan; [email protected] * Correspondence: [email protected] (N.S.L.); [email protected] (M.A.); Tel.: +44-122-333-4390 (N.S.L.); +46-852-483-577 (M.A.) Received: 23 October 2020; Accepted: 25 November 2020; Published: 28 November 2020 Abstract: Recent findings have shown that the connectivity and crosstalk between mitochondria and the endoplasmic reticulum (ER) at mitochondria–ER contact sites (MERCS) are altered in Alzheimer’s disease (AD) and in AD-related models. MERCS have been related to the initial steps of autophagosome formation as well as regulation of mitochondrial function. Here, the interplay between MERCS, mitochondria ultrastructure and function and autophagy were evaluated in different AD animal models with increased levels of Aβ as well as in primary neurons derived from these animals. -
The Mitochondrial Kinase PINK1 in Diabetic Kidney Disease
International Journal of Molecular Sciences Review The Mitochondrial Kinase PINK1 in Diabetic Kidney Disease Chunling Huang * , Ji Bian , Qinghua Cao, Xin-Ming Chen and Carol A. Pollock * Kolling Institute, Sydney Medical School, Royal North Shore Hospital, University of Sydney, St. Leonards, NSW 2065, Australia; [email protected] (J.B.); [email protected] (Q.C.); [email protected] (X.-M.C.) * Correspondence: [email protected] (C.H.); [email protected] (C.A.P.); Tel.: +61-2-9926-4784 (C.H.); +61-2-9926-4652 (C.A.P.) Abstract: Mitochondria are critical organelles that play a key role in cellular metabolism, survival, and homeostasis. Mitochondrial dysfunction has been implicated in the pathogenesis of diabetic kidney disease. The function of mitochondria is critically regulated by several mitochondrial protein kinases, including the phosphatase and tensin homolog (PTEN)-induced kinase 1 (PINK1). The focus of PINK1 research has been centered on neuronal diseases. Recent studies have revealed a close link between PINK1 and many other diseases including kidney diseases. This review will provide a concise summary of PINK1 and its regulation of mitochondrial function in health and disease. The physiological role of PINK1 in the major cells involved in diabetic kidney disease including proximal tubular cells and podocytes will also be summarized. Collectively, these studies suggested that targeting PINK1 may offer a promising alternative for the treatment of diabetic kidney disease. Keywords: PINK1; diabetic kidney disease; mitochondria; mitochondria quality control; mitophagy Citation: Huang, C.; Bian, J.; Cao, Q.; 1. Introduction Chen, X.-M.; Pollock, C.A. -
Apoptosis in the Resolution of Systemic Inflammation
Apoptosis in the Resolution of Systemic Inflammation J. c. Marshall and R. W. G. Watson Introduction Admission to a contemporary leU is precipitated by a heterogeneous group of dis ease processes, yet the final common pathway to death is strikingly similar [I). Fully 80% of all leu deaths occur in association with the multiple organ dysfunction syn drome (MODS) [2), a poorly understood process characterized by the development of progressive physiologic dysfunction in organ systems initially unaffected by the primary disease process. Activation of a host inflammatory response by infection, injury, or ischemia, invariably proceeds the development of MODS [3). The proxi mate causes of organ injury are not bacterial products, but the same endogenous host-derived mediators of inflammation that are responsible for containing an in fectious challenge and initiating the process of tissue repair. MODS can be concep tualized as the consequence of an overly activated or inappropriately prolonged systemic inflammatory response, therefore an understanding of the mechanisms underlying the resolution of inflammation is important to the development of clini cal strategies to prevent the syndrome. The Resolution of Inflammation Mechanisms As important to the host as the ability to activate an efficient response to an exoge nous threat, is the ability to terminate that response once the threat has passed. Both humoral and cellular counter-inflammatory mechanisms have been identified. Monocyte-mediated non-specific responses are regulated through autocrine and paracrine pathways involving the release of counter-inflammatory mediators such as lL-IO [4) or lL-lra [5) that restore the cell to a resting state. For the neutrophil, however, the expression of an inflammatory response results both in the extravasa tion of large numbers of cells into an inflammatory focus, and in the activation of these cells for antimicrobial activity. -
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. -
2328.Full.Pdf
Altered interplay between endoplasmic reticulum and mitochondria in Charcot–Marie–Tooth type 2A neuropathy Nathalie Bernard-Marissala,b,1, Gerben van Hamerenc, Manisha Junejad,e, Christophe Pellegrinof, Lauri Louhivuorig, Luca Bartesaghih,i, Cylia Rochata, Omar El Mansoura, Jean-Jacques Médardh,i, Marie Croisierj, Catherine Maclachlanj, Olivier Poirotk, Per Uhléng, Vincent Timmermand,e, Nicolas Tricaudc, Bernard L. Schneidera,1,2, and Roman Chrasth,i,1,2 aBrain Mind Institute, École Polytechnique Fédérale de Lausanne, 1015 Lausanne, Switzerland; bMarseille Medical Genetics, INSERM, Aix-Marseille Univ, 13385 Marseille, France; cINSERM U1051, Institut des Neurosciences de Montpellier, Université de Montpellier, 34295 Montpellier, France; dPeripheral Neuropathy Research Group, Department of Biomedical Sciences, University of Antwerp, 2610 Antwerp, Belgium; eInstitute Born Bunge, 2610 Antwerp, Belgium; fInstitut de Neurobiologie de la Méditerranée, INSERM, Aix-Marseille Univ, 13009 Marseille, France; gDepartment of Medical Biochemistry and Biophysics, Karolinska Institutet, 17177 Stockholm, Sweden; hDepartment of Neuroscience, Karolinska Institutet, 17177 Stockholm, Sweden; iDepartment of Clinical Neuroscience, Karolinska Institutet, 17177 Stockholm, Sweden; jCentre of Interdisciplinary Electron Microscopy, École Polytechnique Fédérale de Lausanne, 1015 Lausanne, Switzerland; and kDepartment of Medical Genetics, University of Lausanne, 1005 Lausanne, Switzerland Edited by Stephen T. Warren, Emory University School of Medicine, Atlanta, GA, and approved December 14, 2018 (received for review June 26, 2018) Mutations in the MFN2 gene encoding Mitofusin 2 lead to the axons (8). However, the long-term progression of the disease and development of Charcot–Marie–Tooth type 2A (CMT2A), a domi- the mechanisms underlying motor and/or sensory dysfunction nant axonal form of peripheral neuropathy. Mitofusin 2 is local- have not been fully characterized in this model. -
The Nature of Programmed Cell Death
Biological Theory https://doi.org/10.1007/s13752-018-0311-0 ORIGINAL ARTICLE The Nature of Programmed Cell Death Pierre M. Durand1 · Grant Ramsey2 Received: 14 March 2018 / Accepted: 10 October 2018 © Konrad Lorenz Institute for Evolution and Cognition Research 2018 Abstract In multicellular organisms, cells are frequently programmed to die. This makes good sense: cells that fail to, or are no longer playing important roles are eliminated. From the cell’s perspective, this also makes sense, since somatic cells in multicel- lular organisms require the cooperation of clonal relatives. In unicellular organisms, however, programmed cell death (PCD) poses a difficult and unresolved evolutionary problem. The empirical evidence for PCD in diverse microbial taxa has spurred debates about what precisely PCD means in the case of unicellular organisms (how it should be defined). In this article, we survey the concepts of PCD in the literature and the selective pressures associated with its evolution. We show that defini- tions of PCD have been almost entirely mechanistic and fail to separate questions concerning what PCD fundamentally is from questions about the kinds of mechanisms that realize PCD. We conclude that an evolutionary definition is best able to distinguish PCD from closely related phenomena. Specifically, we define “true” PCD as an adaptation for death triggered by abiotic or biotic environmental stresses. True PCD is thus not only an evolutionary product but must also have been a target of selection. Apparent PCD resulting from pleiotropy, genetic drift, or trade-offs is not true PCD. We call this “ersatz PCD.” Keywords Adaptation · Aging · Apoptosis · Price equation · Programmed cell death · Selection · Unicellular organisms Introduction in animal ontogeny, was made explicit several decades later (Glücksmann 1951; Lockshin and Williams 1964). -
Snapshot: BCL-2 Proteins J
SnapShot: BCL-2 Proteins J. Marie Hardwick and Richard J. Youle Johns Hopkins, Baltimore, MD 21205, USA and NIH/NINDS, Bethesda, MD 20892, USA 404 Cell 138, July 24, 2009 ©2009 Elsevier Inc. DOI 10.1016/j.cell.2009.07.003 See online version for legend and references. SnapShot: BCL-2 Proteins J. Marie Hardwick and Richard J. Youle Johns Hopkins, Baltimore, MD 21205, USA and NIH/NINDS, Bethesda, MD 20892, USA BCL-2 family proteins regulate apoptotic cell death. BCL-2 proteins localize to intracellular membranes such as endoplasmic reticulum and mitochondria, and some fam- ily members translocate from the cytoplasm to mitochondria following a cell death stimulus. The prototypical family member Bcl-2 was originally identified at chromo- some translocation breakpoints in human follicular lymphoma and was subsequently shown to promote tumorigenesis by inhibiting cell death rather than by promoting cell-cycle progression. BCL-2 family proteins have traditionally been classified according to their function and their BCL-2 homology (BH) motifs. The general categories include multidomain antiapoptotic proteins (BH1-BH4), multidomain proapoptotic proteins (BH1-BH3), and proapoptotic BH3-only proteins (see Table 1). In the traditional view, anti-death BCL-2 family members in healthy cells hold pro-death BCL-2 family members in check. Upon receiving a death stimulus, BH3-only proteins inactivate the protective BCL-2 proteins, forcing them to release their pro-death partners. These pro-death BCL-2 family proteins homo-oligomerize to create pores in the mitochondrial outer membrane, resulting in cytochrome c release into the cytoplasm, which leads to caspase activation and cell death. -
Odorant Receptors: Regulation, Signaling, and Expression Michele Lynn Rankin Louisiana State University and Agricultural and Mechanical College, [email protected]
Louisiana State University LSU Digital Commons LSU Doctoral Dissertations Graduate School 2002 Odorant receptors: regulation, signaling, and expression Michele Lynn Rankin Louisiana State University and Agricultural and Mechanical College, [email protected] Follow this and additional works at: https://digitalcommons.lsu.edu/gradschool_dissertations Recommended Citation Rankin, Michele Lynn, "Odorant receptors: regulation, signaling, and expression" (2002). LSU Doctoral Dissertations. 540. https://digitalcommons.lsu.edu/gradschool_dissertations/540 This Dissertation is brought to you for free and open access by the Graduate School at LSU Digital Commons. It has been accepted for inclusion in LSU Doctoral Dissertations by an authorized graduate school editor of LSU Digital Commons. For more information, please [email protected]. ODORANT RECEPTORS: REGULATION, SIGNALING, AND EXPRESSION A Dissertation Submitted to the Graduate Faculty of the Louisiana State University and Agricultural and Mechanical College in partial fulfillment of the requirements for the degree of Doctor of Philosophy In The Department of Biological Sciences By Michele L. Rankin B.S., Louisiana State University, 1990 M.S., Louisiana State University, 1997 August 2002 ACKNOWLEDGMENTS I would like to thank several people who participated in my successfully completing the requirements for the Ph.D. degree. I thank Dr. Richard Bruch for giving me the opportunity to work in his laboratory and guiding me along during the degree program. I am very thankful for the support and generosity of my advisory committee consisting of Dr. John Caprio, Dr. Evanna Gleason, and Dr. Jaqueline Stephens. At one time or another, I performed experiments in each of their laboratories and include that work in this dissertation. -
Systematic Reconstruction of Autism Biology with Multi-Level Whole
bioRxiv preprint doi: https://doi.org/10.1101/052878; this version posted May 11, 2016. The copyright holder for this preprint (which was not certified by peer review) is the author/funder, who has granted bioRxiv a license to display the preprint in perpetuity. It is made available under aCC-BY-ND 4.0 International license. 1 Systematic Reconstruction of Autism Biology with Multi-Level 2 Whole Exome Analysis 3 4 Weijun Luo1,2*, Chaolin Zhang3, Cory R. Brouwer1,2 5 1Department of Bioinformatics and Genomics, UNC Charlotte, Charlotte, NC 28223 6 2UNC Charlotte Bioinformatics Service Division, North Carolina Research Campus, 7 Kannapolis, NC 28081 8 3Department of Systems Biology, Department of Biochemistry and Molecular 9 Biophysics, Center for Motor Neuron Biology and Disease, Columbia University, New 10 York, New York 10032, USA 11 *Correspondence: [email protected] 12 13 14 Abstract 15 Whole exome/genome studies on autism spectrum disorder (ASD) identified thousands of 16 variants, yet not a coherent and systematic disease mechanism. We conduct novel 17 integrated analyses across multiple levels on ASD exomes. These mutations do not recur 18 or replicate at variant level, but significantly and increasingly so at gene and pathway 19 level. Genetic association reveals a novel gene+pathway dual-hit model, better explaining 20 ASD risk than the well-accepted mutation burden model. 21 In multiple analyses with independent datasets, hundreds of variants or genes consistently 22 converge to several canonical pathways. Unlike the reported gene groups or networks, 23 these pathways define novel, relevant, recurrent and systematic ASD biology. At sub- 24 pathway level, most variants disrupt the pathway-related gene functions, and multiple 25 interacting variants spotlight key modules, e.g.