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González C, Martínez‐Sánchez L, Clemente P, Toivonen JM, Arredondo JJ, Fernández‐Moreno MÁ, Carrodeguas JA. Dysfunction of Drosophila mitochondrial carrier homolog (Mtch) alters apoptosis and disturbs development. FEBS Open Bio 2024; 14:276-289. [PMID: 38013241 PMCID: PMC10839352 DOI: 10.1002/2211-5463.13742] [Citation(s) in RCA: 1] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/23/2023] [Revised: 10/27/2023] [Accepted: 11/24/2023] [Indexed: 11/29/2023] Open
Abstract
Mitochondrial carrier homologs 1 (MTCH1) and 2 (MTCH2) are orphan members of the mitochondrial transporter family SLC25. Human MTCH1 is also known as presenilin 1-associated protein, PSAP. MTCH2 is a receptor for tBid and is related to lipid metabolism. Both proteins have been recently described as protein insertases of the outer mitochondrial membrane. We have depleted Mtch in Drosophila and show here that mutant flies are unable to complete development, showing an excess of apoptosis during pupation; this observation was confirmed by RNAi in Schneider cells. These findings are contrary to what has been described in humans. We discuss the implications in view of recent reports concerning the function of these proteins.
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Affiliation(s)
- Cristina González
- Departamento de Bioquímica & Instituto de Investigaciones Biomédicas “Alberto Sols”The Autonomous University of Madrid‐Consejo Superior de Investigaciones CientíficasSpain
| | - Lidia Martínez‐Sánchez
- Departamento de Bioquímica & Instituto de Investigaciones Biomédicas “Alberto Sols”The Autonomous University of Madrid‐Consejo Superior de Investigaciones CientíficasSpain
| | - Paula Clemente
- Departamento de Bioquímica & Instituto de Investigaciones Biomédicas “Alberto Sols”The Autonomous University of Madrid‐Consejo Superior de Investigaciones CientíficasSpain
| | - Janne Markus Toivonen
- LAGENBIO, Departamento de Anatomía, Embriología y Genética Animal, Facultad de Veterinaria, Instituto Agroalimentario de Aragón (IA2)Universidad de ZaragozaSpain
- IIS AragónZaragozaSpain
- Centro de Investigación Biomédica en Red de Enfermedades Neurodegenerativas (CIBERNED)MadridSpain
| | - Juan José Arredondo
- Departamento de Bioquímica & Instituto de Investigaciones Biomédicas “Alberto Sols”The Autonomous University of Madrid‐Consejo Superior de Investigaciones CientíficasSpain
| | - Miguel Ángel Fernández‐Moreno
- Centro de Investigación Biomédica en Red en Enfermedades Raras (CIBERER)Facultad de Medicina, UAMMadridSpain
- Departamento de Bioquímica & Instituto de Investigaciones Biomédicas Sols‐MorrealeThe Autonomous University of Madrid‐Consejo Superior de Investigaciones CientíficasMadridSpain
| | - José Alberto Carrodeguas
- IIS AragónZaragozaSpain
- Institute for Biocomputation and Physics of Complex Systems (BIFI)University of ZaragozaSpain
- Department of Biochemistry and Molecular and Cellular Biology, School of SciencesUniversity of ZaragozaSpain
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2
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Rasam S, Lin Q, Shen S, Straubinger RM, Qu J. Highly Reproducible Quantitative Proteomics Analysis of Pancreatic Cancer Cells Reveals Proteome-Level Effects of a Novel Combination Drug Therapy That Induces Cancer Cell Death via Metabolic Remodeling and Activation of the Extrinsic Apoptosis Pathway. J Proteome Res 2023; 22:3780-3792. [PMID: 37906173 DOI: 10.1021/acs.jproteome.3c00463] [Citation(s) in RCA: 2] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/02/2023]
Abstract
Pancreatic cancer patients have poor survival rates and are frequently treated using gemcitabine (Gem). However, initial tumor sensitivity often gives way to rapid development of resistance. Gem-based drug combinations are employed to increase efficacy and mitigate resistance, but our understanding of molecular-level drug interactions, which could assist in the development of more effective therapeutic regimens, is limited. Global quantitative proteomic analysis could provide novel mechanistic insights into drug combination interactions, but it is challenging to achieve high-quality quantitative proteomics analysis of the large sample sets that are typically required for drug combination studies. Here, we investigated molecular-level temporal interactions of Gem with BGJ398 (infigratinib), a recently approved pan-FGFR inhibitor, in multiple treatment groups (N = 42 samples) using IonStar, a robust large-scale proteomics method that employs well-controlled, ultrahigh-resolution MS1 quantification. A total of 5514 proteins in the sample set were quantified without missing data, requiring >2 unique peptides/protein, <1% protein false discovery rate (FDR), <0.1% peptide FDR, and CV < 10%. Functional analysis of the differentially altered proteins revealed drug-dysregulated processes such as metabolism, apoptosis, and antigen presentation pathways. These changes were validated experimentally using Seahorse metabolic assays and immunoassays. Overall, in-depth analysis of large-scale proteomics data provided novel insights into possible mechanisms by which FGFR inhibitors complement and enhance Gem activity in pancreatic cancers.
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Affiliation(s)
- Sailee Rasam
- Department of Biochemistry, University at Buffalo, Buffalo, New York 14260, United States
- New York State Center of Excellence in Bioinformatics and Life Sciences, 701 Ellicott Street, Buffalo, New York 14203, United States
| | - Qingxiang Lin
- Department of Pharmaceutical Sciences, University at Buffalo, Buffalo, New York 14260, United States
- Department of Cell Stress Biology, Roswell Park Comprehensive Cancer Center, Elm and Carlton Streets, Buffalo, New York 14203, United States
| | - Shichen Shen
- New York State Center of Excellence in Bioinformatics and Life Sciences, 701 Ellicott Street, Buffalo, New York 14203, United States
| | - Robert M Straubinger
- New York State Center of Excellence in Bioinformatics and Life Sciences, 701 Ellicott Street, Buffalo, New York 14203, United States
- Department of Pharmaceutical Sciences, University at Buffalo, Buffalo, New York 14260, United States
- Department of Cell Stress Biology, Roswell Park Comprehensive Cancer Center, Elm and Carlton Streets, Buffalo, New York 14203, United States
| | - Jun Qu
- Department of Biochemistry, University at Buffalo, Buffalo, New York 14260, United States
- New York State Center of Excellence in Bioinformatics and Life Sciences, 701 Ellicott Street, Buffalo, New York 14203, United States
- Department of Pharmaceutical Sciences, University at Buffalo, Buffalo, New York 14260, United States
- Department of Cell Stress Biology, Roswell Park Comprehensive Cancer Center, Elm and Carlton Streets, Buffalo, New York 14203, United States
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In Vitro Study of Ineffective Erythropoiesis in Thalassemia: Diverse Intrinsic Pathophysiological Features of Erythroid Cells Derived from Various Thalassemia Syndromes. J Clin Med 2022; 11:jcm11185356. [PMID: 36143003 PMCID: PMC9504363 DOI: 10.3390/jcm11185356] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/16/2022] [Revised: 08/30/2022] [Accepted: 09/06/2022] [Indexed: 11/16/2022] Open
Abstract
Defective hemoglobin production and ineffective erythropoiesis contribute to the pathophysiology of thalassemia syndromes. Previous studies in the field of erythropoiesis mainly focused on the severe forms of thalassemia, such as β-thalassemia major, while mechanisms underlying the pathogenesis of other thalassemia syndromes remain largely unexplored. The current study aimed to investigate the intrinsic pathophysiological properties of erythroid cells derived from the most common forms of thalassemia diseases, including α-thalassemia (hemoglobin H and hemoglobin H-Constant Spring diseases) and β-thalassemia (homozygous β0-thalassemia and β0-thalassemia/hemoglobin E diseases), under an identical in vitro erythroid culture system. Cell proliferation capacity, differentiation velocity, cell death, as well as globin synthesis and the expression levels of erythropoiesis modifying factors were determined. Accelerated expansion was found in erythroblast cells derived from all types of thalassemia, with the highest degree in β0-thalassemia/hemoglobin E. Likewise, all types of thalassemia showed limited erythroid cell differentiation, but each of them manifested varying degrees of erythroid maturation arrest corresponding with the clinical severity. Robust induction of HSP70 transcripts, an erythroid maturation-related factor, was found in both α- and β-thalassemia erythroid cells. Increased cell death was distinctly present only in homozygous β0-thalassemia erythroblasts and associated with the up-regulation of pro-apoptotic (Caspase 9, BAD, and MTCH1) genes and down-regulation of the anti-apoptotic BCL-XL gene.
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Zhang J, Zhao ZJ, Fu X, Niu H, Hu C, Dong Y, Cui MZ, Zhang F, Zeng L, Xu X. Proapoptotic Mitochondrial Carrier Homolog Protein PSAP Mediates Death Receptor 6 Induced Apoptosis. J Alzheimers Dis 2021; 74:1097-1106. [PMID: 32144986 DOI: 10.3233/jad-191086] [Citation(s) in RCA: 6] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/15/2022]
Abstract
Presenilin-associated protein (PSAP) was originally identified as a mitochondrial proapoptotic protein. To further explore the apoptotic pathway that involves PSAP, our yeast two-hybrid screen revealed that PSAP interacts with a death receptor, DR6. DR6 is a relatively less common member of the death receptor family and has been shown to mediate the neurotoxicity of amyloid-β, mutant SOD1, and prion proteins and has also been implicated in the regulation of immune cell proliferation and differentiation. Our previous study showed that DR6 induces apoptosis via a unique mitochondria-dependent pathway different from the conventional death receptor-mediated extrinsic apoptotic pathways. Thus, the interaction of DR6 with PSAP established a direct molecular link between DR6 and mitochondrial apoptotic pathway. We investigated the possible role of PSAP in DR6-induced apoptosis. Interestingly, it was discovered that knockdown of PSAP strongly inhibited DR6-induced apoptosis. To further elucidate the mechanism by which PSAP mediates DR6-induced mitochondria-dependent apoptosis, our data demonstrated that knockdown of PSAP blocked DR6-induced Bax translocation and cytochrome c release from the mitochondria. Moreover, it was found that both PSAP and DR6 form complexes with Bax, but at different subcellular locations. The DR6-Bax complex was detected in the cytosolic fraction while the PSAP-Bax complex was detected in the mitochondrial fraction. The observation that knockdown of DR6 significantly reduced the amount of PSAP-Bax complex detected in mitochondria suggests a possibility that DR6-bound Bax is transferred to PSAP upon interaction with PSAP at the mitochondria, leading to cytochrome c release and eventually apoptosis.
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Affiliation(s)
- Jingtian Zhang
- Edmond H. Fischer Signal Transduction Laboratory, College of Life Sciences, Jilin University, Changchun, China
| | - Zhizhuang Joe Zhao
- Edmond H. Fischer Signal Transduction Laboratory, College of Life Sciences, Jilin University, Changchun, China.,Department of Pathology, University of Oklahoma Health Sciences Center, Oklahoma City, OK, USA
| | - Xueqi Fu
- Edmond H. Fischer Signal Transduction Laboratory, College of Life Sciences, Jilin University, Changchun, China
| | - Han Niu
- Edmond H. Fischer Signal Transduction Laboratory, College of Life Sciences, Jilin University, Changchun, China
| | - Chen Hu
- School of Life Sciences and Technology, Tongji University, Shanghai, China
| | - Yunzhou Dong
- Vascular Biology Program, Boston Children's Hospital, Harvard Medical School, Boston, MA, USA
| | - Mei-Zhen Cui
- Department of Biology, College of Arts and Sciences, University of Texas of the Permian Basin, Odessa, TX, USA
| | - Fuqiang Zhang
- Scientific Research Centre of China-Japan Union Hospital, Jilin University, Changchun, China
| | - Linlin Zeng
- Edmond H. Fischer Signal Transduction Laboratory, College of Life Sciences, Jilin University, Changchun, China
| | - Xuemin Xu
- Department of Biology, College of Arts and Sciences, University of Texas of the Permian Basin, Odessa, TX, USA
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5
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Böhme I, Schönherr R, Eberle J, Bosserhoff AK. Membrane Transporters and Channels in Melanoma. Rev Physiol Biochem Pharmacol 2020; 181:269-374. [PMID: 32737752 DOI: 10.1007/112_2020_17] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/12/2022]
Abstract
Recent research has revealed that ion channels and transporters can be important players in tumor development, progression, and therapy resistance in melanoma. For example, members of the ABC family were shown to support cancer stemness-like features in melanoma cells, while several members of the TRP channel family were reported to act as tumor suppressors.Also, many transporter proteins support tumor cell viability and thus suppress apoptosis induction by anticancer therapy. Due to the high number of ion channels and transporters and the resulting high complexity of the field, progress in understanding is often focused on single molecules and is in total rather slow. In this review, we aim at giving an overview about a broad subset of ion transporters, also illustrating some aspects of the field, which have not been addressed in detail in melanoma. In context with the other chapters in this special issue on "Transportome Malfunctions in the Cancer Spectrum," a comparison between melanoma and these tumors will be possible.
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Affiliation(s)
- Ines Böhme
- Institute of Biochemistry, Emil Fischer Center, Friedrich-Alexander-University of Erlangen-Nürnberg, Erlangen, Germany
| | - Roland Schönherr
- Institute of Biochemistry and Biophysics, Friedrich Schiller University Jena and Jena University Hospital, Jena, Germany
| | - Jürgen Eberle
- Department of Dermatology, Venerology and Allergology, Skin Cancer Center Charité, University Medical Center Charité, Berlin, Germany
| | - Anja Katrin Bosserhoff
- Institute of Biochemistry, Emil Fischer Center, Friedrich-Alexander-University of Erlangen-Nürnberg, Erlangen, Germany. .,Comprehensive Cancer Center (CCC) Erlangen-EMN, Erlangen, Germany.
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Kumar N, Mishra B, Mehmood A, Athar M, Mukhtar MS. Integrative Network Biology Framework Elucidates Molecular Mechanisms of SARS-CoV-2 Pathogenesis. SSRN 2020:3581857. [PMID: 32714115 PMCID: PMC7366800 DOI: 10.2139/ssrn.3581857] [Citation(s) in RCA: 5] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 04/21/2020] [Revised: 05/07/2020] [Indexed: 01/02/2023]
Abstract
COVID-19 (Coronavirus disease 2019) is a respiratory illness caused by severe acute respiratory syndrome coronavirus 2 (SARS-CoV-2). While the pathophysiology of this deadly virus is complex and largely unknown, we employ a network biology-fueled approach and integrate multiomics data pertaining to lung epithelial cells-specific co-expression network and human interactome to generate Calu-3-specific human-SARS-CoV-2 Interactome (CSI). Topological clustering and pathway enrichment analysis show that SARS-CoV-2 target central nodes of host-viral network that participate in core functional pathways. Network centrality analyses discover 28 high-value SARS-CoV-2 targets, which are possibly involved in viral entry, proliferation and survival to establish infection and facilitate disease progression. Our probabilistic modeling framework elucidates critical regulatory circuitry and molecular events pertinent to COVID-19, particularly the host modifying responses and cytokine storm. Overall, our network centric analyses reveal novel molecular components, uncover structural and functional modules, and provide molecular insights into SARS-CoV-2 pathogenicity that may foster effective therapeutic design. Funding: This work was supported by the National Science Foundation (IOS-1557796) to M.S.M., and U54 ES 030246 from NIH/NIEHS to M. A. Conflict of Interest: The authors declare no competing interests. The authors also declare no financial interests.
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Affiliation(s)
- Nilesh Kumar
- Department of Biology, 464 Campbell Hall, 1300 University Boulevard, University of Alabama at Birmingham, Alabama 35294, USA
| | - Bharat Mishra
- Department of Biology, 464 Campbell Hall, 1300 University Boulevard, University of Alabama at Birmingham, Alabama 35294, USA
| | - Adeel Mehmood
- Department of Biology, 464 Campbell Hall, 1300 University Boulevard, University of Alabama at Birmingham, Alabama 35294, USA
- Department of Computer Science, University of Alabama at Birmingham, 1402 10th Ave. S. , Birmingham, AL 35294, USA
| | - Mohammad Athar
- Department of Dermatology, School of Medicine, University of Alabama at Birmingham, Alabama 35294, USA
| | - M. Shahid Mukhtar
- Department of Biology, 464 Campbell Hall, 1300 University Boulevard, University of Alabama at Birmingham, Alabama 35294, USA
- Nutrition Obesity Research Center, 1675 University Blvd, University of Alabama at Birmingham, Birmingham, AL 35294, USA
- Department of Surgery, 1808 7th Ave S, University of Alabama at Birmingham, Birmingham, AL 35294, USA
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7
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Rojas-Charry L, Calero-Martinez S, Morganti C, Morciano G, Park K, Hagel C, Marciniak SJ, Glatzel M, Pinton P, Sepulveda-Falla D. Susceptibility to cellular stress in PS1 mutant N2a cells is associated with mitochondrial defects and altered calcium homeostasis. Sci Rep 2020; 10:6455. [PMID: 32296078 PMCID: PMC7160112 DOI: 10.1038/s41598-020-63254-7] [Citation(s) in RCA: 6] [Impact Index Per Article: 1.5] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/08/2019] [Accepted: 03/27/2020] [Indexed: 12/16/2022] Open
Abstract
Presenilin 1 (PS1) mutations are the most common cause of familial Alzheimer's disease (FAD). PS1 also plays a role in cellular processes such as calcium homeostasis and autophagy. We hypothesized that mutant presenilins increase cellular vulnerability to stress. We stably expressed human PS1, mutant PS1E280A and mutant PS1Δ9 in mouse neuroblastoma N2a cells. We examined early signs of stress in different conditions: endoplasmic reticulum (ER) stress, calcium overload, oxidative stress, and Aβ 1-42 oligomers toxicity. Additionally, we induced autophagy via serum starvation. PS1 mutations did not have an effect in ER stress but PS1E280A mutation affected autophagy. PS1 overexpression influenced calcium homeostasis and generated mitochondrial calcium overload modifying mitochondrial function. However, the opening of the mitochondrial permeability transition pore (MPTP) was affected in PS1 mutants, being accelerated in PS1E280A and inhibited in PS1Δ9 cells. Altered autophagy in PS1E280A cells was neither modified by inhibition of γ-secretase, nor by ER calcium retention. MPTP opening was directly regulated by γ-secretase inhibitors independent on organelle calcium modulation, suggesting a novel direct role for PS1 and γ-secretase in mitochondrial stress. We identified intrinsic cellular vulnerability to stress in PS1 mutants associated simultaneously with both, autophagic and mitochondrial function, independent of Aβ pathology.
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Affiliation(s)
- Liliana Rojas-Charry
- Institute of Neuropathology, University Medical Center Hamburg-Eppendorf, Hamburg, Germany
| | - Sergio Calero-Martinez
- Institute of Neuropathology, University Medical Center Hamburg-Eppendorf, Hamburg, Germany
| | - Claudia Morganti
- Department of Morphology, Surgery and Experimental Medicine, Section of Pathology, Oncology and Experimental Biology, University of Ferrara, 44121, Ferrara, Italy
| | - Giampaolo Morciano
- Department of Morphology, Surgery and Experimental Medicine, Section of Pathology, Oncology and Experimental Biology, University of Ferrara, 44121, Ferrara, Italy
| | - Kyungeun Park
- Institute of Neuropathology, University Medical Center Hamburg-Eppendorf, Hamburg, Germany
| | - Christian Hagel
- Institute of Neuropathology, University Medical Center Hamburg-Eppendorf, Hamburg, Germany
| | - Stefan J Marciniak
- Cambridge Institute for Medical Research (CIMR), University of Cambridge, Cambridge, UK
| | - Markus Glatzel
- Institute of Neuropathology, University Medical Center Hamburg-Eppendorf, Hamburg, Germany
| | - Paolo Pinton
- Department of Morphology, Surgery and Experimental Medicine, Section of Pathology, Oncology and Experimental Biology, University of Ferrara, 44121, Ferrara, Italy
| | - Diego Sepulveda-Falla
- Institute of Neuropathology, University Medical Center Hamburg-Eppendorf, Hamburg, Germany.
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Shawn, the Drosophila Homolog of SLC25A39/40, Is a Mitochondrial Carrier That Promotes Neuronal Survival. J Neurosci 2016; 36:1914-29. [PMID: 26865615 DOI: 10.1523/jneurosci.3432-15.2016] [Citation(s) in RCA: 24] [Impact Index Per Article: 3.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/20/2022] Open
Abstract
UNLABELLED Mitochondria play an important role in the regulation of neurotransmission, and mitochondrial impairment is a key event in neurodegeneration. Cells rely on mitochondrial carrier proteins of the SLC25 family to shuttle ions, cofactors, and metabolites necessary for enzymatic reactions. Mutations in these carriers often result in rare but severe pathologies in the brain, and some of the genes, including SLC25A39 and SLC25A40, reside in susceptibility loci of severe forms of epilepsy. However, the role of most of these carriers has not been investigated in neurons in vivo. We identified shawn, the Drosophila homolog of SLC25A39 and SLC25A40, in a genetic screen to identify genes involved in neuronal function. Shawn localizes to mitochondria, and missense mutations result in an accumulation of reactive oxygen species, mitochondrial dysfunction, and neurodegeneration. Shawn regulates metal homeostasis, and we found in shawn mutants increased levels of manganese, calcium, and mitochondrial free iron. Mitochondrial mutants often cannot maintain synaptic transmission under demanding conditions, but shawn mutants do, and they also do not display endocytic defects. In contrast, shawn mutants harbor a significant increase in neurotransmitter release. Our work provides the first functional annotation of these essential mitochondrial carriers in the nervous system, and the results suggest that metal imbalances and mitochondrial dysfunction may contribute to defects in synaptic transmission and neuronal survival. SIGNIFICANCE STATEMENT We describe for the first time the role of the mitochondrial carrier Shawn/SLC25A39/SLC25A40 in the nervous system. In humans, these genes reside in susceptibility loci for epilepsy, and, in flies, we observe neuronal defects related to mitochondrial dysfunction and metal homeostasis defects. Interestingly, shawn mutants also harbor increased neurotransmitter release and neurodegeneration. Our data suggest a connection between maintaining a correct metal balance and mitochondrial function to regulate neuronal survival and neurotransmitter release.
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Garg NJ, Soman KV, Zago MP, Koo SJ, Spratt H, Stafford S, Blell ZN, Gupta S, Nuñez Burgos J, Barrientos N, Brasier AR, Wiktorowicz JE. Changes in Proteome Profile of Peripheral Blood Mononuclear Cells in Chronic Chagas Disease. PLoS Negl Trop Dis 2016; 10:e0004490. [PMID: 26919708 PMCID: PMC4769231 DOI: 10.1371/journal.pntd.0004490] [Citation(s) in RCA: 17] [Impact Index Per Article: 2.1] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/25/2015] [Accepted: 02/03/2016] [Indexed: 12/15/2022] Open
Abstract
Trypanosoma cruzi (Tc) infection causes chagasic cardiomyopathy; however, why 30-40% of the patients develop clinical disease is not known. To discover the pathomechanisms in disease progression, we obtained the proteome signature of peripheral blood mononuclear cells (PBMCs) of normal healthy controls (N/H, n = 30) and subjects that were seropositive for Tc-specific antibodies, but were clinically asymptomatic (C/A, n = 25) or clinically symptomatic (C/S, n = 28) with cardiac involvement and left ventricular dysfunction. Protein samples were labeled with BODIPY FL-maleimide (dynamic range: > 4 orders of magnitude, detection limit: 5 f-mol) and resolved by two-dimensional gel electrophoresis (2D-GE). After normalizing the gel images, protein spots that exhibited differential abundance in any of the two groups were analyzed by mass spectrometry, and searched against UniProt human database for protein identification. We found 213 and 199 protein spots (fold change: |≥ 1.5|, p< 0.05) were differentially abundant in C/A and C/S individuals, respectively, with respect to N/H controls. Ingenuity Pathway Analysis (IPA) of PBMCs proteome dataset identified an increase in disorganization of cytoskeletal assembly and recruitment/activation and migration of immune cells in all chagasic subjects, though the invasion capacity of cells was decreased in C/S individuals. IPA predicted with high probability a decline in cell survival and free radical scavenging capacity in C/S (but not C/A) subjects. The MYC/SP1 transcription factors that regulate hypoxia and oxidative/inflammatory stress were predicted to be key targets in the context of control of Chagas disease severity. Further, MARS-modeling identified a panel of proteins that had >93% prediction success in classifying infected individuals with no disease and those with cardiac involvement and LV dysfunction. In conclusion, we have identified molecular pathways and a panel of proteins that could aid in detecting seropositive individuals at risk of developing cardiomyopathy.
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Affiliation(s)
- Nisha Jain Garg
- Department of Microbiology and Immunology, University of Texas Medical Branch (UTMB), Galveston, Texas, United States of America
- Department of Pathology, UTMB, Galveston, Texas, United States of America
- Faculty of the Institute for Human Infections and Immunity, and Sealy Center for Vaccine Development, UTMB, Galveston, Texas, United States of America
| | - Kizhake V. Soman
- Department of Biochemistry and Molecular Biology, and the Sealy Center for Molecular Medicine, UTMB, Galveston, Texas, United States of America
| | - Maria P. Zago
- Instituto de Patología Experimental, CONICET-UNSa, Salta, Argentina
| | - Sue-Jie Koo
- Department of Pathology, UTMB, Galveston, Texas, United States of America
| | - Heidi Spratt
- Department of Preventive Medicine and Community Health, UTMB, Galveston, Texas, United States of America
- Institute for Translational Sciences, UTMB, Galveston, Texas, United States of America
| | - Susan Stafford
- Department of Biochemistry and Molecular Biology, and the Sealy Center for Molecular Medicine, UTMB, Galveston, Texas, United States of America
| | - Zinzi N. Blell
- Department of Microbiology and Immunology, University of Texas Medical Branch (UTMB), Galveston, Texas, United States of America
| | - Shivali Gupta
- Department of Microbiology and Immunology, University of Texas Medical Branch (UTMB), Galveston, Texas, United States of America
| | | | | | - Allan R. Brasier
- Institute for Translational Sciences, UTMB, Galveston, Texas, United States of America
- Department of Internal Medicine, UTMB, Galveston, Texas, United States of America
| | - John E. Wiktorowicz
- Department of Biochemistry and Molecular Biology, and the Sealy Center for Molecular Medicine, UTMB, Galveston, Texas, United States of America
- Institute for Translational Sciences, UTMB, Galveston, Texas, United States of America
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10
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Nelo-Bazán MA, Latorre P, Bolado-Carrancio A, Pérez-Campo FM, Echenique-Robba P, Rodríguez-Rey JC, Carrodeguas JA. Early growth response 1 (EGR-1) is a transcriptional regulator of mitochondrial carrier homolog 1 (MTCH 1)/presenilin 1-associated protein (PSAP). Gene 2015; 578:52-62. [PMID: 26692143 DOI: 10.1016/j.gene.2015.12.014] [Citation(s) in RCA: 6] [Impact Index Per Article: 0.7] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/18/2014] [Revised: 11/26/2015] [Accepted: 12/07/2015] [Indexed: 01/25/2023]
Abstract
Attempts to elucidate the cellular function of MTCH1 (mitochondrial carrier homolog 1) have not yet rendered a clear insight into the function of this outer mitochondrial membrane protein. Classical biochemical and cell biology approaches have not produced the expected outcome. In vitro experiments have indicated a likely role in the regulation of cell death by apoptosis, and its reported interaction with presenilin 1 suggests a role in the cellular pathways in which this membrane protease participates, nevertheless in vivo data are missing. In an attempt to identify cellular pathways in which this protein might participate, we have studied its promoter looking for transcriptional regulators. We have identified several putative binding sites for EGR-1 (Early growth response 1; a protein involved in growth, proliferation and differentiation), in the proximal region of the MTCH1 promoter. Chromatin immunoprecipitation showed an enrichment of these sequences in genomic DNA bound to EGR-1 and transient overexpression of EGR-1 in cultured HEK293T cells induces an increase of endogenous MTCH1 levels. We also show that MTCH1 levels increase in response to treatment of cells with doxorubicin, an apoptosis inducer through DNA damage. The endogenous levels of MTCH1 decrease when EGR-1 levels are lowered by RNA interference. Our results indicate that EGR-1 is a transcriptional regulator of MTCH1 and give some clues about the cellular processes in which MTCH1 might participate.
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Affiliation(s)
- María Alejandra Nelo-Bazán
- Institute for Biocomputation and Physics of Complex Systems, University of Zaragoza, Zaragoza, Spain; Department of Biochemistry and Molecular and Cellular Biology, University of Zaragoza, Zaragoza, Spain.
| | - Pedro Latorre
- Institute for Biocomputation and Physics of Complex Systems, University of Zaragoza, Zaragoza, Spain; Department of Animal Production and Food Science and Technology, University of Zaragoza, Spain.
| | | | - Flor M Pérez-Campo
- Department of Internal Medicine, Hospital U. Marqués de Valdecilla-IDIVAL University of Cantabria, 39008 Santander, Cantabria, Spain.
| | - Pablo Echenique-Robba
- Institute for Biocomputation and Physics of Complex Systems, University of Zaragoza, Zaragoza, Spain; Instituto de Química Física Rocasolano, CSIC, Madrid, Spain; Zaragoza Scientific Center for Advanced Modeling (ZCAM), Universidad de Zaragoza, Spain; Departamento de Física Teórica, Universidad de Zaragoza, Spain; Unidad Asociada IQFR-BIFI, Madrid-Zaragoza, Spain.
| | | | - José Alberto Carrodeguas
- Institute for Biocomputation and Physics of Complex Systems, University of Zaragoza, Zaragoza, Spain; Department of Biochemistry and Molecular and Cellular Biology, University of Zaragoza, Zaragoza, Spain; Unidad Asociada IQFR-BIFI, Madrid-Zaragoza, Spain.
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Zeng L, Hu C, Zhang F, Xu DC, Cui MZ, Xu X. Cellular FLICE-like Inhibitory Protein (c-FLIP) and PS1-associated Protein (PSAP) Mediate Presenilin 1-induced γ-Secretase-dependent and -independent Apoptosis, Respectively. J Biol Chem 2015; 290:18269-80. [PMID: 26025363 DOI: 10.1074/jbc.m115.640177] [Citation(s) in RCA: 12] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/21/2015] [Indexed: 12/21/2022] Open
Abstract
Presenilin 1 (PS1) has been implicated in apoptosis; however, its mechanism remains elusive. We report that PS1-induced apoptosis was associated with cellular FLICE-like inhibitory protein (c-FLIP) turnover and that γ-secretase inhibitor blocked c-FLIP turnover and also partially blocked PS1-induced apoptosis. A complete inhibition of PS1-induced apoptosis was achieved by knockdown of PS1-associated protein (PSAP), a mitochondrial proapoptotic protein that forms a complex with Bax upon induction of apoptosis, in the presence of γ-secretase inhibitor. PS1-induced apoptosis was partially inhibited by knockdown of caspase-8, Fas-associated protein with death domain (FADD), or Bid. However, knockdown of Bax or overexpression of Bcl-2 resulted in complete inhibition of PS1-induced apoptosis. These data suggest that PS1 induces apoptosis through two pathways: the γ-secretase-dependent pathway mediated by turnover of c-FLIP and the γ-secretase-independent pathway mediated by PSAP-Bax complex formation. These two pathways converge on Bax to activate mitochondria-dependent apoptosis. These findings provide new insight into the mechanisms by which PS1 is involved in apoptosis and the mechanism by which PS1 exerts its pathogenic effects. In addition, our results suggest that PS2 induces apoptosis through a pathway that is different from that of PS1.
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Affiliation(s)
- Linlin Zeng
- From the Department of Biomedical and Diagnostic Sciences, College of Veterinary Medicine, and
| | - Chen Hu
- From the Department of Biomedical and Diagnostic Sciences, College of Veterinary Medicine, and the Department of Comparative and Experimental Medicine, University of Tennessee, Knoxville, Tennessee 37996 and
| | - Fuqiang Zhang
- From the Department of Biomedical and Diagnostic Sciences, College of Veterinary Medicine, and
| | - Daniel C Xu
- the Department of Molecular Biology, Princeton University, Princeton, New Jersey 08544
| | - Mei-Zhen Cui
- From the Department of Biomedical and Diagnostic Sciences, College of Veterinary Medicine, and
| | - Xuemin Xu
- From the Department of Biomedical and Diagnostic Sciences, College of Veterinary Medicine, and
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12
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Li H, Li X, Smerin SE, Zhang L, Jia M, Xing G, Su YA, Wen J, Benedek D, Ursano R. Mitochondrial Gene Expression Profiles and Metabolic Pathways in the Amygdala Associated with Exaggerated Fear in an Animal Model of PTSD. Front Neurol 2014; 5:164. [PMID: 25295026 PMCID: PMC4172054 DOI: 10.3389/fneur.2014.00164] [Citation(s) in RCA: 17] [Impact Index Per Article: 1.7] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/03/2013] [Accepted: 08/15/2014] [Indexed: 12/19/2022] Open
Abstract
The metabolic mechanisms underlying the development of exaggerated fear in post-traumatic stress disorder (PTSD) are not well defined. In the present study, alteration in the expression of genes associated with mitochondrial function in the amygdala of an animal model of PTSD was determined. Amygdala tissue samples were excised from 10 non-stressed control rats and 10 stressed rats, 14 days post-stress treatment. Total RNA was isolated, cDNA was synthesized, and gene expression levels were determined using a cDNA microarray. During the development of the exaggerated fear associated with PTSD, 48 genes were found to be significantly upregulated and 37 were significantly downregulated in the amygdala complex based on stringent criteria (p < 0.01). Ingenuity pathway analysis revealed up- or downregulation in the amygdala complex of four signaling networks – one associated with inflammatory and apoptotic pathways, one with immune mediators and metabolism, one with transcriptional factors, and one with chromatin remodeling. Thus, informatics of a neuronal gene array allowed us to determine the expression profile of mitochondrial genes in the amygdala complex of an animal model of PTSD. The result is a further understanding of the metabolic and neuronal signaling mechanisms associated with delayed and exaggerated fear.
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Affiliation(s)
- He Li
- Department of Psychiatry, Center for the Study of Traumatic Stress, Uniformed Services University of the Health Sciences , Bethesda, MD , USA
| | - Xin Li
- Department of Biostatistics, Bioinformatics, and Biomathematics, Georgetown University Medical Center , Washington, DC , USA
| | - Stanley E Smerin
- Department of Psychiatry, Center for the Study of Traumatic Stress, Uniformed Services University of the Health Sciences , Bethesda, MD , USA
| | - Lei Zhang
- Department of Psychiatry, Center for the Study of Traumatic Stress, Uniformed Services University of the Health Sciences , Bethesda, MD , USA
| | - Min Jia
- Department of Psychiatry, Center for the Study of Traumatic Stress, Uniformed Services University of the Health Sciences , Bethesda, MD , USA
| | - Guoqiang Xing
- Department of Psychiatry, Center for the Study of Traumatic Stress, Uniformed Services University of the Health Sciences , Bethesda, MD , USA
| | - Yan A Su
- Department of Gene and Protein Biomarkers, GenProMarkers , Rockville, MD , USA
| | - Jillian Wen
- Department of Psychiatry, Center for the Study of Traumatic Stress, Uniformed Services University of the Health Sciences , Bethesda, MD , USA
| | - David Benedek
- Department of Psychiatry, Center for the Study of Traumatic Stress, Uniformed Services University of the Health Sciences , Bethesda, MD , USA
| | - Robert Ursano
- Department of Psychiatry, Center for the Study of Traumatic Stress, Uniformed Services University of the Health Sciences , Bethesda, MD , USA
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13
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Abstract
The mitochondrion relies on compartmentalization of certain enzymes, ions and metabolites for the sake of efficient metabolism. In order to fulfil its activities, a myriad of carriers are properly expressed, targeted and folded in the inner mitochondrial membrane. Among these carriers, the six-transmembrane-helix mitochondrial SLC25 (solute carrier family 25) proteins facilitate transport of solutes with disparate chemical identities across the inner mitochondrial membrane. Although their proper function replenishes building blocks needed for metabolic reactions, dysfunctional SLC25 proteins are involved in pathological states. It is the purpose of the present review to cover the current knowledge on the role of SLC25 transporters in health and disease.
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14
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Echenique-Robba P, Nelo-Bazán MA, Carrodeguas JA. Reducing the standard deviation in multiple-assay experiments where the variation matters but the absolute value does not. PLoS One 2013; 8:e78205. [PMID: 24205158 PMCID: PMC3813515 DOI: 10.1371/journal.pone.0078205] [Citation(s) in RCA: 5] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/01/2013] [Accepted: 09/10/2013] [Indexed: 11/18/2022] Open
Abstract
When the value of a quantity x for a number of systems (cells, molecules, people, chunks of metal, DNA vectors, so on) is measured and the aim is to replicate the whole set again for different trials or assays, despite the efforts for a near-equal design, scientists might often obtain quite different measurements. As a consequence, some systems' averages present standard deviations that are too large to render statistically significant results. This work presents a novel correction method of a very low mathematical and numerical complexity that can reduce the standard deviation of such results and increase their statistical significance. Two conditions are to be met: the inter-system variations of x matter while its absolute value does not, and a similar tendency in the values of x must be present in the different assays (or in other words, the results corresponding to different assays must present a high linear correlation). We demonstrate the improvements this method offers with a cell biology experiment, but it can definitely be applied to any problem that conforms to the described structure and requirements and in any quantitative scientific field that deals with data subject to uncertainty.
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Affiliation(s)
- Pablo Echenique-Robba
- Instituto de Química Física Rocasolano, Consejo Superior de Investigaciones Científicas, Madrid, Spain
- Instituto de Biocomputación y Física de Sistemas Complejos, Universidad de Zaragoza, Zaragoza, Spain
- Zaragoza Scientific Center for Advanced Modeling, Universidad de Zaragoza, Zaragoza, Spain
- Departamento de Fsica Teórica, Universidad de Zaragoza, Zaragoza, Spain
- Unidad Asociada IQFR-BIFI, Madrid-Zaragoza, Spain
- * E-mail:
| | - María Alejandra Nelo-Bazán
- Instituto de Biocomputación y Física de Sistemas Complejos, Universidad de Zaragoza, Zaragoza, Spain
- Fundación Gran Mariscal de Ayacucho (Fundayacucho), La Urbina, Venezuela
- Departamento de Bioqumica y Biología Molecular y Celular, Universidad de Zaragoza, Zaragoza, Spain
| | - José A. Carrodeguas
- Instituto de Biocomputación y Física de Sistemas Complejos, Universidad de Zaragoza, Zaragoza, Spain
- Unidad Asociada IQFR-BIFI, Madrid-Zaragoza, Spain
- Departamento de Bioqumica y Biología Molecular y Celular, Universidad de Zaragoza, Zaragoza, Spain
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15
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Generation of a genome scale lentiviral vector library for EF1α promoter-driven expression of human ORFs and identification of human genes affecting viral titer. PLoS One 2012; 7:e51733. [PMID: 23251614 PMCID: PMC3520899 DOI: 10.1371/journal.pone.0051733] [Citation(s) in RCA: 19] [Impact Index Per Article: 1.6] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/06/2012] [Accepted: 11/06/2012] [Indexed: 01/12/2023] Open
Abstract
The bottleneck in elucidating gene function through high-throughput gain-of-function genome screening is the limited availability of comprehensive libraries for gene overexpression. Lentiviral vectors are the most versatile and widely used vehicles for gene expression in mammalian cells. Lentiviral supernatant libraries for genome screening are commonly generated in the HEK293T cell line, yet very little is known about the effect of introduced sequences on the produced viral titer, which we have shown to be gene dependent. We have generated an arrayed lentiviral vector library for the expression of 17,030 human proteins by using the GATEWAY® cloning system to transfer ORFs from the Mammalian Gene Collection into an EF1alpha promoter-dependent lentiviral expression vector. This promoter was chosen instead of the more potent and widely used CMV promoter, because it is less prone to silencing and provides more stable long term expression. The arrayed lentiviral clones were used to generate viral supernatant by packaging in the HEK293T cell line. The efficiency of transfection and virus production was estimated by measuring the fluorescence of IRES driven GFP, co-expressed with the ORFs. More than 90% of cloned ORFs produced sufficient virus for downstream screening applications. We identified genes which consistently produced very high or very low viral titer. Supernatants from select clones that were either high or low virus producers were tested on a range of cell lines. Some of the low virus producers, including two previously uncharacterized proteins were cytotoxic to HEK293T cells. The library we have constructed presents a powerful resource for high-throughput gain-of-function screening of the human genome and drug-target discovery. Identification of human genes that affect lentivirus production may lead to improved technology for gene expression using lentiviral vectors.
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16
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Ospina A, Lagunas-Martínez A, Pardo J, Carrodeguas JA. Protein oligomerization mediated by the transmembrane carboxyl terminal domain of Bcl-XL. FEBS Lett 2011; 585:2935-42. [PMID: 21856303 PMCID: PMC7164028 DOI: 10.1016/j.febslet.2011.08.012] [Citation(s) in RCA: 10] [Impact Index Per Article: 0.8] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/09/2010] [Revised: 07/28/2011] [Accepted: 08/09/2011] [Indexed: 12/22/2022]
Abstract
Bcl-XL is a pro-survival member of the Bcl-2 family that can be found in the outer mitochondrial membrane and in soluble cytosolic homodimers. Bcl-XL can bind pro-apoptotic members of this family preventing them from activating the execution phase of apoptosis. Bcl-XL has been shown to homodimerize in different ways, although most binding and structural assays have been carried out in the absence of its carboxyl terminal transmembrane domain. We show here that this domain can by itself direct protein oligomerization, which could be related to its previously reported role in mitochondrial morphology alterations and apoptosis inhibition. Structured summary of protein interactions Vamp2 physically interacts with Vamp2 by blue native page (View interaction) Vamp2 physically interacts with Vamp2 by cross-linking study (View interaction) Bcl-Xl physically interacts with Bcl-Xl by blue native page (View interaction) Bcl-Xl physically interacts with Bcl-Xl by cross-linking study (View interaction)
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Affiliation(s)
- Angélica Ospina
- Institute for Biocomputation and Physics of Complex Systems, Edificio I+D, University of Zaragoza, Zaragoza, Spain
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