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Zhong X, Peddada N, Moresco JJ, Wang J, Jiang Y, Rios JJ, Moresco EMY, Choi JH, Beutler B. Viable mutations of mouse midnolin suppress B cell malignancies. J Exp Med 2024; 221:e20232132. [PMID: 38625151 DOI: 10.1084/jem.20232132] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/18/2023] [Revised: 02/20/2024] [Accepted: 03/28/2024] [Indexed: 04/17/2024] Open
Abstract
In a genetic screen, we identified two viable missense alleles of the essential gene Midnolin (Midn) that were associated with reductions in peripheral B cells. Causation was confirmed in mice with targeted deletion of four of six MIDN protein isoforms. MIDN was expressed predominantly in lymphocytes where it augmented proteasome activity. We showed that purified MIDN directly stimulated 26S proteasome activity in vitro in a manner dependent on the ubiquitin-like domain and a C-terminal region. MIDN-deficient B cells displayed aberrant activation of the IRE-1/XBP-1 pathway of the unfolded protein response. Partial or complete MIDN deficiency strongly suppressed Eμ-Myc-driven B cell leukemia and the antiapoptotic effects of Eμ-BCL2 on B cells in vivo and induced death of Sp2/0 hybridoma cells in vitro, but only partially impaired normal lymphocyte development. Thus, MIDN is required for proteasome activity in support of normal lymphopoiesis and is essential for malignant B cell proliferation over a broad range of differentiation states.
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Affiliation(s)
- Xue Zhong
- Center for the Genetics of Host Defense, University of Texas Southwestern Medical Center , Dallas, TX, USA
| | - Nagesh Peddada
- Center for the Genetics of Host Defense, University of Texas Southwestern Medical Center , Dallas, TX, USA
| | - James J Moresco
- Center for the Genetics of Host Defense, University of Texas Southwestern Medical Center , Dallas, TX, USA
| | - Jianhui Wang
- Center for the Genetics of Host Defense, University of Texas Southwestern Medical Center , Dallas, TX, USA
| | - Yiao Jiang
- Center for the Genetics of Host Defense, University of Texas Southwestern Medical Center , Dallas, TX, USA
| | - Jonathan J Rios
- Center for Pediatric Bone Biology and Translational Research, Scottish Rite for Children , Dallas, TX, USA
- McDermott Center for Human Growth and Development, University of Texas Southwestern Medical Center , Dallas, TX, USA
- Department of Pediatrics, University of Texas Southwestern Medical Center, Dallas, TX, USA
- Department of Orthopaedic Surgery, University of Texas Southwestern Medical Center, Dallas, TX, USA
| | - Eva Marie Y Moresco
- Center for the Genetics of Host Defense, University of Texas Southwestern Medical Center , Dallas, TX, USA
| | - Jin Huk Choi
- Center for the Genetics of Host Defense, University of Texas Southwestern Medical Center , Dallas, TX, USA
| | - Bruce Beutler
- Center for the Genetics of Host Defense, University of Texas Southwestern Medical Center , Dallas, TX, USA
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2
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Jurkovic CM, Raisch J, Tran S, Nguyen HD, Lévesque D, Scott MS, Campos EI, Boisvert FM. Replisome proximal protein associations and dynamic proteomic changes at stalled replication forks. Mol Cell Proteomics 2024:100767. [PMID: 38615877 DOI: 10.1016/j.mcpro.2024.100767] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/16/2023] [Revised: 03/19/2024] [Accepted: 04/11/2024] [Indexed: 04/16/2024] Open
Abstract
DNA replication is a fundamental cellular process that ensures the transfer of genetic information during cell division. Genome duplication takes place in S phase and requires a dynamic and highly coordinated recruitment of multiple proteins at replication forks. Various genotoxic stressors lead to fork instability and collapse, hence the need for DNA repair pathways. By identifying the multitude of protein interactions implicated in those events we can better grasp the complex and dynamic molecular mechanisms that facilitate DNA replication and repair. Proximity-dependent biotin identification (BioID) was used to identify associations with 17 proteins within four core replication components, namely the CDC45/MCM2-7/GINS (CMG) helicase that unwinds DNA, the DNA polymerases, replication protein A subunits, and histone chaperones needed to disassemble and reassemble chromatin. We further investigated the impact of genotoxic stress on these interactions. This analysis revealed a vast proximity associations network with 108 nuclear proteins further modulated in the presence of hydroxyurea; 45 being enriched and 63 depleted. Interestingly, hydroxyurea treatment also caused a redistribution of associations with eleven interactors, meaning that the replisome is dynamically reorganized when stressed. The analysis identified several poorly characterized proteins, thereby uncovering new putative players in the cellular response to DNA replication arrest. It also provides a new comprehensive proteomic framework to understand how cells respond to obstacles during DNA replication.
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Affiliation(s)
- Carla-Marie Jurkovic
- Department of Immunology and Cell Biology, Faculty of Medicine and Health Sciences, Université de Sherbrooke
| | - Jennifer Raisch
- Department of Immunology and Cell Biology, Faculty of Medicine and Health Sciences, Université de Sherbrooke
| | - Stephanie Tran
- Genetics & Genome Biology program, The Hospital for Sick Children, and Department of Molecular Biology, University of Toronto
| | - Hoang Dong Nguyen
- Department of Biochemistry and Functional Genomics, Faculty of Medicine and Health Sciences, Université de Sherbrooke
| | - Dominique Lévesque
- Department of Immunology and Cell Biology, Faculty of Medicine and Health Sciences, Université de Sherbrooke
| | - Michelle S Scott
- Department of Biochemistry and Functional Genomics, Faculty of Medicine and Health Sciences, Université de Sherbrooke
| | - Eric I Campos
- Genetics & Genome Biology program, The Hospital for Sick Children, and Department of Molecular Biology, University of Toronto.
| | - François-Michel Boisvert
- Department of Immunology and Cell Biology, Faculty of Medicine and Health Sciences, Université de Sherbrooke.
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3
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Prasasya RD, Caldwell BA, Liu Z, Wu S, Leu NA, Fowler JM, Cincotta SA, Laird DJ, Kohli RM, Bartolomei MS. Iterative oxidation by TET1 is required for reprogramming of imprinting control regions and patterning of mouse sperm hypomethylated regions. Dev Cell 2024:S1534-5807(24)00144-8. [PMID: 38569549 DOI: 10.1016/j.devcel.2024.02.012] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/15/2023] [Revised: 12/07/2023] [Accepted: 02/29/2024] [Indexed: 04/05/2024]
Abstract
Ten-eleven translocation (TET) enzymes iteratively oxidize 5-methylcytosine (5mC) to generate 5-hydroxymethylcytosine (5hmC), 5-formylcytosine, and 5-carboxylcytosine to facilitate active genome demethylation. Whether these bases are required to promote replication-coupled dilution or activate base excision repair during mammalian germline reprogramming remains unresolved due to the inability to decouple TET activities. Here, we generated two mouse lines expressing catalytically inactive TET1 (Tet1-HxD) and TET1 that stalls oxidation at 5hmC (Tet1-V). Tet1 knockout and catalytic mutant primordial germ cells (PGCs) fail to erase methylation at select imprinting control regions and promoters of meiosis-associated genes, validating the requirement for the iterative oxidation of 5mC for complete germline reprogramming. TET1V and TET1HxD rescue most hypermethylation of Tet1-/- sperm, suggesting the role of TET1 beyond its oxidative capability. We additionally identify a broader class of hypermethylated regions in Tet1 mutant mouse sperm that depend on TET oxidation for reprogramming. Our study demonstrates the link between TET1-mediated germline reprogramming and sperm methylome patterning.
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Affiliation(s)
- Rexxi D Prasasya
- Department of Cell and Developmental Biology, Perelman School of Medicine, University of Pennsylvania, Philadelphia, PA 19104, USA
| | - Blake A Caldwell
- Department of Cell and Developmental Biology, Perelman School of Medicine, University of Pennsylvania, Philadelphia, PA 19104, USA
| | - Zhengfeng Liu
- Department of Cell and Developmental Biology, Perelman School of Medicine, University of Pennsylvania, Philadelphia, PA 19104, USA
| | - Songze Wu
- Department of Cell and Developmental Biology, Perelman School of Medicine, University of Pennsylvania, Philadelphia, PA 19104, USA
| | - N Adrian Leu
- Department of Biomedical Sciences, Center for Animal Transgenesis and Germ Cell Research, University of Pennsylvania School of Veterinary Medicine, Philadelphia, PA 19104, USA
| | - Johanna M Fowler
- Department of Medicine, Perelman School of Medicine, University of Pennsylvania, Philadelphia, PA 19104, USA
| | - Steven A Cincotta
- Department of Obstetrics, Gynecology and Reproductive Science, Center for Reproductive Sciences, Eli and Edythe Broad Center for Regenerative Medicine and Stem Cell Research, University of California, San Francisco, San Francisco, CA 84143, USA
| | - Diana J Laird
- Department of Obstetrics, Gynecology and Reproductive Science, Center for Reproductive Sciences, Eli and Edythe Broad Center for Regenerative Medicine and Stem Cell Research, University of California, San Francisco, San Francisco, CA 84143, USA
| | - Rahul M Kohli
- Department of Medicine, Perelman School of Medicine, University of Pennsylvania, Philadelphia, PA 19104, USA; Penn Epigenetics Institute, University of Pennsylvania, Philadelphia, PA 19104, USA.
| | - Marisa S Bartolomei
- Department of Cell and Developmental Biology, Perelman School of Medicine, University of Pennsylvania, Philadelphia, PA 19104, USA; Penn Epigenetics Institute, University of Pennsylvania, Philadelphia, PA 19104, USA.
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Fernandez A, Hoq MR, Hallinan GI, Li D, Bharath SR, Vago FS, Zhang X, Ozcan KA, Newell KL, Garringer HJ, Jiang W, Ghetti B, Vidal R. Cryo-EM structures of amyloid-β and tau filaments in Down syndrome. Nat Struct Mol Biol 2024:10.1038/s41594-024-01252-3. [PMID: 38553642 DOI: 10.1038/s41594-024-01252-3] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/11/2023] [Accepted: 02/09/2024] [Indexed: 04/10/2024]
Abstract
Adult individuals with Down syndrome (DS) develop Alzheimer disease (AD). Whether there is a difference between AD in DS and AD regarding the structure of amyloid-β (Aβ) and tau filaments is unknown. Here we report the structure of Aβ and tau filaments from two DS brains. We found two Aβ40 filaments (types IIIa and IIIb) that differ from those previously reported in sporadic AD and two types of Aβ42 filaments (I and II) identical to those found in sporadic and familial AD. Tau filaments (paired helical filaments and straight filaments) were identical to those in AD, supporting the notion of a common mechanism through which amyloids trigger aggregation of tau. This knowledge is important for understanding AD in DS and assessing whether adults with DS could be included in AD clinical trials.
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Affiliation(s)
- Anllely Fernandez
- Department of Pathology and Laboratory Medicine, Indiana University School of Medicine, Indianapolis, IN, USA
| | - Md Rejaul Hoq
- Department of Biological Sciences, Markey Center for Structural Biology, Purdue University, West Lafayette, IN, USA
| | - Grace I Hallinan
- Department of Pathology and Laboratory Medicine, Indiana University School of Medicine, Indianapolis, IN, USA
| | - Daoyi Li
- Department of Biological Sciences, Markey Center for Structural Biology, Purdue University, West Lafayette, IN, USA
| | - Sakshibeedu R Bharath
- Department of Biological Sciences, Markey Center for Structural Biology, Purdue University, West Lafayette, IN, USA
| | - Frank S Vago
- Department of Biological Sciences, Markey Center for Structural Biology, Purdue University, West Lafayette, IN, USA
| | - Xiaoqi Zhang
- Department of Biological Sciences, Markey Center for Structural Biology, Purdue University, West Lafayette, IN, USA
| | - Kadir A Ozcan
- Department of Biological Sciences, Markey Center for Structural Biology, Purdue University, West Lafayette, IN, USA
| | - Kathy L Newell
- Department of Pathology and Laboratory Medicine, Indiana University School of Medicine, Indianapolis, IN, USA
| | - Holly J Garringer
- Department of Pathology and Laboratory Medicine, Indiana University School of Medicine, Indianapolis, IN, USA
| | - Wen Jiang
- Department of Biological Sciences, Markey Center for Structural Biology, Purdue University, West Lafayette, IN, USA.
| | - Bernardino Ghetti
- Department of Pathology and Laboratory Medicine, Indiana University School of Medicine, Indianapolis, IN, USA.
| | - Ruben Vidal
- Department of Pathology and Laboratory Medicine, Indiana University School of Medicine, Indianapolis, IN, USA.
- Stark Neurosciences Research Institute, Indiana University School of Medicine, Indianapolis, IN, USA.
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5
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Chomiak AA, Tiedemann RL, Liu Y, Kong X, Cui Y, Wiseman AK, Thurlow KE, Cornett EM, Topper MJ, Baylin SB, Rothbart SB. Select EZH2 inhibitors enhance viral mimicry effects of DNMT inhibition through a mechanism involving NFAT:AP-1 signaling. Sci Adv 2024; 10:eadk4423. [PMID: 38536911 PMCID: PMC10971413 DOI: 10.1126/sciadv.adk4423] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Subscribe] [Scholar Register] [Received: 08/25/2023] [Accepted: 02/21/2024] [Indexed: 04/05/2024]
Abstract
DNA methyltransferase inhibitor (DNMTi) efficacy in solid tumors is limited. Colon cancer cells exposed to DNMTi accumulate lysine-27 trimethylation on histone H3 (H3K27me3). We propose this Enhancer of Zeste Homolog 2 (EZH2)-dependent repressive modification limits DNMTi efficacy. Here, we show that low-dose DNMTi treatment sensitizes colon cancer cells to select EZH2 inhibitors (EZH2is). Integrative epigenomic analysis reveals that DNMTi-induced H3K27me3 accumulates at genomic regions poised with EZH2. Notably, combined EZH2i and DNMTi alters the epigenomic landscape to transcriptionally up-regulate the calcium-induced nuclear factor of activated T cells (NFAT):activating protein 1 (AP-1) signaling pathway. Blocking this pathway limits transcriptional activating effects of these drugs, including transposable element and innate immune response gene expression involved in viral defense. Analysis of primary human colon cancer specimens reveals positive correlations between DNMTi-, innate immune response-, and calcium signaling-associated transcription profiles. Collectively, we show that compensatory EZH2 activity limits DNMTi efficacy in colon cancer and link NFAT:AP-1 signaling to epigenetic therapy-induced viral mimicry.
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Affiliation(s)
- Alison A. Chomiak
- Department of Epigenetics, Van Andel Institute, Grand Rapids, MI 49503, USA
| | | | - Yanqing Liu
- Department of Epigenetics, Van Andel Institute, Grand Rapids, MI 49503, USA
| | - Xiangqian Kong
- Department of Oncology, the Sidney Kimmel Comprehensive Cancer Center at Johns Hopkins, The Johns Hopkins University School of Medicine, Baltimore, MD 21287, USA
| | - Ying Cui
- Department of Oncology, the Sidney Kimmel Comprehensive Cancer Center at Johns Hopkins, The Johns Hopkins University School of Medicine, Baltimore, MD 21287, USA
| | - Ashley K. Wiseman
- Department of Epigenetics, Van Andel Institute, Grand Rapids, MI 49503, USA
| | - Kate E. Thurlow
- Department of Epigenetics, Van Andel Institute, Grand Rapids, MI 49503, USA
| | - Evan M. Cornett
- Department of Biochemistry and Molecular Biology, Indiana University School of Medicine, Indiana University, Indianapolis, IN 46202, USA
| | - Michael J. Topper
- Department of Oncology, the Sidney Kimmel Comprehensive Cancer Center at Johns Hopkins, The Johns Hopkins University School of Medicine, Baltimore, MD 21287, USA
| | - Stephen B. Baylin
- Department of Oncology, the Sidney Kimmel Comprehensive Cancer Center at Johns Hopkins, The Johns Hopkins University School of Medicine, Baltimore, MD 21287, USA
| | - Scott B. Rothbart
- Department of Epigenetics, Van Andel Institute, Grand Rapids, MI 49503, USA
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6
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Jauhiainen S, Onyeogaziri FC, Lazzaroni F, Conze LL, Laakkonen JP, Laham-Karam N, Laakso A, Niemelä M, Rezai Jahromi B, Magnusson PU. Proteomics on human cerebral cavernous malformations reveals novel biomarkers in neurovascular dysfunction for the disease pathology. Biochim Biophys Acta Mol Basis Dis 2024; 1870:167139. [PMID: 38537685 DOI: 10.1016/j.bbadis.2024.167139] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/17/2023] [Revised: 03/20/2024] [Accepted: 03/21/2024] [Indexed: 04/16/2024]
Abstract
BACKGROUND Cerebral cavernous malformation (CCM) is a disease associated with an elevated risk of focal neurological deficits, seizures, and hemorrhagic stroke. The disease has an inflammatory profile and improved knowledge of CCM pathology mechanisms and exploration of candidate biomarkers will enable new non-invasive treatments. METHODS We analyzed protein signatures in human CCM tissue samples by using a highly specific and sensitive multiplexing technique, proximity extension assay. FINDINGS Data analysis revealed CCM specific proteins involved in endothelial dysfunction/inflammation/activation, leukocyte infiltration/chemotaxis, hemostasis, extracellular matrix dysfunction, astrocyte and microglial cell activation. Biomarker expression profiles matched bleeding status, especially with higher levels of inflammatory markers and activated astrocytes in ruptured than non-ruptured samples, some of these biomarkers are secreted into blood or urine. Furthermore, analysis was also done in a spatially resolving manner by separating the lesion area from the surrounding brain tissue. Our spatial studies revealed that although appearing histologically normal, the CCM border areas were pathological when compared to control brain tissues. Moreover, the functional relevance of CD93, ICAM-1 and MMP9, markers related to endothelial cell activation and extracellular matrix was validated by a murine pre-clinical CCM model. INTERPRETATION Here we present a novel strategy for proteomics analysis on human CCMs, offering a possibility for high-throughput protein screening acquiring data on the local environment in the brain. Our data presented here describe CCM relevant brain proteins and specifically those which are secreted can serve the need of circulating CCM biomarkers to predict cavernoma's risk of bleeding.
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Affiliation(s)
- Suvi Jauhiainen
- Department of Immunology, Genetics and Pathology, Uppsala University, Uppsala, Sweden; A.I. Virtanen Institute for Molecular Sciences, University of Eastern Finland, Kuopio, Finland
| | - Favour C Onyeogaziri
- Department of Immunology, Genetics and Pathology, Uppsala University, Uppsala, Sweden
| | - Francesca Lazzaroni
- Hematology Unit, Fondazione IRCCS Ca' Granda Ospedale Maggiore Policlinico, Milan, Italy
| | - Lei Liu Conze
- Department of Immunology, Genetics and Pathology, Uppsala University, Uppsala, Sweden
| | - Johanna P Laakkonen
- A.I. Virtanen Institute for Molecular Sciences, University of Eastern Finland, Kuopio, Finland
| | - Nihay Laham-Karam
- A.I. Virtanen Institute for Molecular Sciences, University of Eastern Finland, Kuopio, Finland
| | - Aki Laakso
- Department of Neurosurgery, University of Helsinki and Helsinki University Hospital, Helsinki, Finland
| | - Mika Niemelä
- Department of Neurosurgery, University of Helsinki and Helsinki University Hospital, Helsinki, Finland
| | - Behnam Rezai Jahromi
- Department of Neurosurgery, University of Helsinki and Helsinki University Hospital, Helsinki, Finland
| | - Peetra U Magnusson
- Department of Immunology, Genetics and Pathology, Uppsala University, Uppsala, Sweden.
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7
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Zhang W, Sun S, Zhu W, Meng D, Hu W, Yang S, Gao M, Yao P, Wang Y, Wang Q, Ji J. Birinapant Reshapes the Tumor Immunopeptidome and Enhances Antigen Presentation. Int J Mol Sci 2024; 25:3660. [PMID: 38612472 PMCID: PMC11011986 DOI: 10.3390/ijms25073660] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/05/2024] [Revised: 03/18/2024] [Accepted: 03/20/2024] [Indexed: 04/14/2024] Open
Abstract
Birinapant, an antagonist of the inhibitor of apoptosis proteins, upregulates MHCs in tumor cells and displays a better tumoricidal effect when used in combination with immune checkpoint inhibitors, indicating that Birinapant may affect the antigen presentation pathway; however, the mechanism remains elusive. Based on high-resolution mass spectrometry and in vitro and in vivo models, we adopted integrated genomics, proteomics, and immunopeptidomics strategies to study the mechanism underlying the regulation of tumor immunity by Birinapant from the perspective of antigen presentation. Firstly, in HT29 and MCF7 cells, Birinapant increased the number and abundance of immunopeptides and source proteins. Secondly, a greater number of cancer/testis antigen peptides with increased abundance and more neoantigens were identified following Birinapant treatment. Moreover, we demonstrate the existence and immunogenicity of a neoantigen derived from insertion/deletion mutation. Thirdly, in HT29 cell-derived xenograft models, Birinapant administration also reshaped the immunopeptidome, and the tumor exhibited better immunogenicity. These data suggest that Birinapant can reshape the tumor immunopeptidome with respect to quality and quantity, which improves the presentation of CTA peptides and neoantigens, thus enhancing the immunogenicity of tumor cells. Such changes may be vital to the effectiveness of combination therapy, which can be further transferred to the clinic or aid in the development of new immunotherapeutic strategies to improve the anti-tumor immune response.
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Affiliation(s)
- Weiyan Zhang
- State Key Laboratory of Protein and Plant Gene Research, School of Life Sciences, Peking University, Beijing 100871, China; (W.Z.)
| | - Shenghuan Sun
- Bakar Computational Health Sciences Institute, University of California, San Francisco, CA 94143, USA;
| | - Wenyuan Zhu
- State Key Laboratory of Protein and Plant Gene Research, School of Life Sciences, Peking University, Beijing 100871, China; (W.Z.)
| | - Delan Meng
- State Key Laboratory of Protein and Plant Gene Research, School of Life Sciences, Peking University, Beijing 100871, China; (W.Z.)
| | - Weiyi Hu
- State Key Laboratory of Protein and Plant Gene Research, School of Life Sciences, Peking University, Beijing 100871, China; (W.Z.)
| | - Siqi Yang
- State Key Laboratory of Protein and Plant Gene Research, School of Life Sciences, Peking University, Beijing 100871, China; (W.Z.)
| | - Mingjie Gao
- State Key Laboratory of Protein and Plant Gene Research, School of Life Sciences, Peking University, Beijing 100871, China; (W.Z.)
| | - Pengju Yao
- State Key Laboratory of Protein and Plant Gene Research, School of Life Sciences, Peking University, Beijing 100871, China; (W.Z.)
| | - Yuhao Wang
- State Key Laboratory of Protein and Plant Gene Research, School of Life Sciences, Peking University, Beijing 100871, China; (W.Z.)
| | - Qingsong Wang
- State Key Laboratory of Protein and Plant Gene Research, School of Life Sciences, Peking University, Beijing 100871, China; (W.Z.)
| | - Jianguo Ji
- State Key Laboratory of Protein and Plant Gene Research, School of Life Sciences, Peking University, Beijing 100871, China; (W.Z.)
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8
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Ciordia S, Santos FM, Dias JML, Lamas JR, Paradela A, Alvarez-Sola G, Ávila MA, Corrales F. Refinement of paramagnetic bead-based digestion protocol for automatic sample preparation using an artificial neural network. Talanta 2024; 274:125988. [PMID: 38569368 DOI: 10.1016/j.talanta.2024.125988] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/25/2024] [Revised: 03/19/2024] [Accepted: 03/22/2024] [Indexed: 04/05/2024]
Abstract
Despite technological advances in the proteomics field, sample preparation still represents the main bottleneck in mass spectrometry (MS) analysis. Bead-based protein aggregation techniques have recently emerged as an efficient, reproducible, and high-throughput alternative for protein extraction and digestion. Here, a refined paramagnetic bead-based digestion protocol is described for Opentrons® OT-2 platform (OT-2) as a versatile, reproducible, and affordable alternative for the automatic sample preparation for MS analysis. For this purpose, an artificial neural network (ANN) was applied to maximize the number of peptides without missed cleavages identified in HeLa extract by combining factors such as the quantity (μg) of trypsin/Lys-C and beads (MagReSyn® Amine), % (w/v) SDS, % (v/v) acetonitrile, and time of digestion (h). ANN model predicted the optimal conditions for the digestion of 50 μg of HeLa extract, pointing to the use of 2.5% (w/v) SDS and 300 μg of beads for sample preparation and long-term digestion (16h) with 0.15 μg Lys-C and 2.5 μg trypsin (≈1:17 ratio). Based on the results of the ANN model, the manual protocol was automated in OT-2. The performance of the automatic protocol was evaluated with different sample types, including human plasma, Arabidopsis thaliana leaves, Escherichia coli cells, and mouse tissue cortex, showing great reproducibility and low sample-to-sample variability in all cases. In addition, we tested the performance of this method in the preparation of a challenging biological fluid such as rat bile, a proximal fluid that is rich in bile salts, bilirubin, cholesterol, and fatty acids, among other MS interferents. Compared to other protocols described in the literature for the extraction and digestion of bile proteins, the method described here allowed identify 385 unique proteins, thus contributing to improving the coverage of the bile proteome.
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Affiliation(s)
- Sergio Ciordia
- Functional Proteomics Laboratory, Centro Nacional de Biotecnología, CSIC, Calle Darwin 3, Campus de Cantoblanco, 28049, Madrid, Spain
| | - Fátima Milhano Santos
- Functional Proteomics Laboratory, Centro Nacional de Biotecnología, CSIC, Calle Darwin 3, Campus de Cantoblanco, 28049, Madrid, Spain
| | - João M L Dias
- Department of Medical Genetics, University of Cambridge, Cambridge, United Kingdom; Early Cancer Institute, University of Cambridge, Cambridge, United Kingdom
| | - José Ramón Lamas
- Functional Proteomics Laboratory, Centro Nacional de Biotecnología, CSIC, Calle Darwin 3, Campus de Cantoblanco, 28049, Madrid, Spain
| | - Alberto Paradela
- Functional Proteomics Laboratory, Centro Nacional de Biotecnología, CSIC, Calle Darwin 3, Campus de Cantoblanco, 28049, Madrid, Spain
| | - Gloria Alvarez-Sola
- Hepatology Laboratory, Solid Tumors Program, Center for Applied Medical Research (CIMA), University of Navarra, 31008, Pamplona, Spain; National Institute for the Study of Liver and Gastrointestinal Diseases (CIBERehd, Carlos III Health Institute), 28029, Madrid, Spain; IdiSNA, Navarra Institute for Health Research, 31008, Pamplona, Spain
| | - Matías A Ávila
- Hepatology Laboratory, Solid Tumors Program, Center for Applied Medical Research (CIMA), University of Navarra, 31008, Pamplona, Spain; National Institute for the Study of Liver and Gastrointestinal Diseases (CIBERehd, Carlos III Health Institute), 28029, Madrid, Spain; IdiSNA, Navarra Institute for Health Research, 31008, Pamplona, Spain
| | - Fernando Corrales
- Functional Proteomics Laboratory, Centro Nacional de Biotecnología, CSIC, Calle Darwin 3, Campus de Cantoblanco, 28049, Madrid, Spain.
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9
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Paul S, McCourt PM, Le LTM, Ryu J, Czaja W, Bode AM, Contreras-Galindo R, Dong Z. Fyn-mediated phosphorylation of Menin disrupts telomere maintenance in stem cells. bioRxiv 2024:2023.10.04.560876. [PMID: 37873235 PMCID: PMC10592958 DOI: 10.1101/2023.10.04.560876] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 10/25/2023]
Abstract
Telomeres protect chromosome ends and determine the replication potential of dividing cells. The canonical telomere sequence TTAGGG is synthesized by telomerase holoenzyme, which maintains telomere length in proliferative stem cells. Although the core components of telomerase are well-defined, mechanisms of telomerase regulation are still under investigation. We report a novel role for the Src family kinase Fyn, which disrupts telomere maintenance in stem cells by phosphorylating the scaffold protein Menin. We found that Fyn knockdown prevented telomere erosion in human and mouse stem cells, validating the results with four telomere measurement techniques. We show that Fyn phosphorylates Menin at tyrosine 603 (Y603), which increases Menin's SUMO1 modification, C-terminal stability, and importantly, its association with the telomerase RNA component (TR). Using mass spectrometry, immunoprecipitation, and immunofluorescence experiments we found that SUMO1-Menin decreases TR's association with telomerase subunit Dyskerin, suggesting that Fyn's phosphorylation of Menin induces telomerase subunit mislocalization and may compromise telomerase function at telomeres. Importantly, we find that Fyn inhibition reduces accelerated telomere shortening in human iPSCs harboring mutations for dyskeratosis congenita.
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Affiliation(s)
- Souren Paul
- The Hormel Institute, University of Minnesota, 801 16th Avenue NE, Austin, MN 55912, USA
| | - Preston M. McCourt
- The Hormel Institute, University of Minnesota, 801 16th Avenue NE, Austin, MN 55912, USA
| | - Le Thi My Le
- The Hormel Institute, University of Minnesota, 801 16th Avenue NE, Austin, MN 55912, USA
| | - Joohyun Ryu
- The Hormel Institute, University of Minnesota, 801 16th Avenue NE, Austin, MN 55912, USA
- Department of Laboratory Medicine and Pathology, University of Minnesota School of Medicine, Minneapolis, MN, USA
| | - Wioletta Czaja
- The Hormel Institute, University of Minnesota, 801 16th Avenue NE, Austin, MN 55912, USA
- Department of Genetics, University of Alabama, Birmingham, AL 35294, USA
| | - Ann M. Bode
- The Hormel Institute, University of Minnesota, 801 16th Avenue NE, Austin, MN 55912, USA
| | - Rafael Contreras-Galindo
- The Hormel Institute, University of Minnesota, 801 16th Avenue NE, Austin, MN 55912, USA
- Department of Genetics, University of Alabama, Birmingham, AL 35294, USA
| | - Zigang Dong
- Department of Pathophysiology, School of Basic Medical Sciences, College of Medicine, Zhengzhou University, Henan, China 450001
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10
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Emerson FJ, Chiu C, Lin LY, Riedel CG, Zhu M, Lee SS. The chromatin factors SET-26 and HCF-1 oppose the histone deacetylase HDA-1 in longevity and gene regulation in C. elegans. Nat Commun 2024; 15:2320. [PMID: 38485937 PMCID: PMC10940595 DOI: 10.1038/s41467-024-46510-6] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/01/2023] [Accepted: 02/28/2024] [Indexed: 03/18/2024] Open
Abstract
SET-26, HCF-1, and HDA-1 are highly conserved chromatin factors with key roles in development and aging. Here we present mechanistic insights into how these factors regulate gene expression and modulate longevity in C. elegans. We show that SET-26 and HCF-1 cooperate to regulate a common set of genes, and both antagonize the histone deacetylase HDA-1 to limit longevity. HCF-1 localization at chromatin is largely dependent on functional SET-26, whereas SET-26 is only minorly affected by loss of HCF-1, suggesting that SET-26 could recruit HCF-1 to chromatin. HDA-1 opposes SET-26 and HCF-1 on the regulation of a subset of their common target genes and in longevity. Our findings suggest that SET-26, HCF-1, and HDA-1 comprise a mechanism to fine-tune gene expression and longevity and likely have important implications for the mechanistic understanding of how these factors function in diverse organisms, particularly in aging biology.
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Affiliation(s)
- Felicity J Emerson
- Department of Molecular Biology and Genetics, Cornell University, Ithaca, NY, USA
| | - Caitlin Chiu
- Department of Molecular Biology and Genetics, Cornell University, Ithaca, NY, USA
| | - Laura Y Lin
- Department of Molecular Biology and Genetics, Cornell University, Ithaca, NY, USA
| | - Christian G Riedel
- Department of Biosciences and Nutrition, Karolinska Institutet, Huddinge, Sweden
| | - Ming Zhu
- National Institute of Biological Sciences, Beijing, China
| | - Siu Sylvia Lee
- Department of Molecular Biology and Genetics, Cornell University, Ithaca, NY, USA.
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11
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Mitsi V, Ruiz A, Polizu C, Farzinpour Z, Ramakrishnan A, Serafini RA, Parise EM, Floodstrand M, Sial OK, Gaspari S, Tang CY, Nestler EJ, Schmidt EF, Shen L, Zachariou V. RGS4 Actions in Mouse Prefrontal Cortex Modulate Behavioral and Transcriptomic Responses to Chronic Stress and Ketamine. Mol Pharmacol 2024; 105:272-285. [PMID: 38351270 PMCID: PMC10949159 DOI: 10.1124/molpharm.123.000753] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/06/2023] [Accepted: 01/16/2024] [Indexed: 03/16/2024] Open
Abstract
The signal transduction protein, regulator of G protein signaling 4 (RGS4), plays a prominent role in physiologic and pharmacological responses by controlling multiple intracellular pathways. Our earlier work identified the dynamic but distinct roles of RGS4 in the efficacy of monoamine-targeting versus fast-acting antidepressants. Using a modified chronic variable stress (CVS) paradigm in mice, we demonstrate that stress-induced behavioral abnormalities are associated with the downregulation of RGS4 in the medial prefrontal cortex (mPFC). Knockout of RGS4 (RGS4KO) increases susceptibility to CVS, as mutant mice develop behavioral abnormalities as early as 2 weeks after CVS resting-state functional magnetic resonance imaging I (rs-fMRI) experiments indicate that stress susceptibility in RGS4KO mice is associated with changes in connectivity between the mediodorsal thalamus (MD-THL) and the mPFC. Notably, RGS4KO also paradoxically enhances the antidepressant efficacy of ketamine in the CVS paradigm. RNA-sequencing analysis of naive and CVS samples obtained from mPFC reveals that RGS4KO triggers unique gene expression signatures and affects several intracellular pathways associated with human major depressive disorder. Our analysis suggests that ketamine treatment in the RGS4KO group triggers changes in pathways implicated in synaptic activity and responses to stress, including pathways associated with axonal guidance and myelination. Overall, we show that reducing RGS4 activity triggers unique gene expression adaptations that contribute to chronic stress disorders and that RGS4 is a negative modulator of ketamine actions. SIGNIFICANCE STATEMENT: Chronic stress promotes robust maladaptation in the brain, but the exact intracellular pathways contributing to stress vulnerability and mood disorders have not been thoroughly investigated. In this study, the authors used murine models of chronic stress and multiple methodologies to demonstrate the critical role of the signal transduction modulator regulator of G protein signaling 4 in the medial prefrontal cortex in vulnerability to chronic stress and the efficacy of the fast-acting antidepressant ketamine.
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Affiliation(s)
- Vasiliki Mitsi
- Nash Family Department of Neuroscience and Friedman Brain Institute (V.M., A.Ru., C.P., A.Ra., R.A.S., E.M.P. M.F., S.G., E.J.N., L.S.) and BioMedical Engineering and Imaging Institute (C.Y.T.), Icahn School of Medicine at Mount Sinai, New York, New York; University of Crete, Department of Basic Sciences, Crete, Greece (V.M.); Department of Pharmacology, Physiology & Biophysics, Boston University Chobanian and Avedisian School of Medicine, Boston, Massachusetts (Z.F., R.A.S., V.Z.); Department of Psychology, Texas A&M University, College Station, Texas (O.K.S.); and Laboratory of Molecular Biology, Rockefeller University, New York, New York (E.F.S.)
| | - Anne Ruiz
- Nash Family Department of Neuroscience and Friedman Brain Institute (V.M., A.Ru., C.P., A.Ra., R.A.S., E.M.P. M.F., S.G., E.J.N., L.S.) and BioMedical Engineering and Imaging Institute (C.Y.T.), Icahn School of Medicine at Mount Sinai, New York, New York; University of Crete, Department of Basic Sciences, Crete, Greece (V.M.); Department of Pharmacology, Physiology & Biophysics, Boston University Chobanian and Avedisian School of Medicine, Boston, Massachusetts (Z.F., R.A.S., V.Z.); Department of Psychology, Texas A&M University, College Station, Texas (O.K.S.); and Laboratory of Molecular Biology, Rockefeller University, New York, New York (E.F.S.)
| | - Claire Polizu
- Nash Family Department of Neuroscience and Friedman Brain Institute (V.M., A.Ru., C.P., A.Ra., R.A.S., E.M.P. M.F., S.G., E.J.N., L.S.) and BioMedical Engineering and Imaging Institute (C.Y.T.), Icahn School of Medicine at Mount Sinai, New York, New York; University of Crete, Department of Basic Sciences, Crete, Greece (V.M.); Department of Pharmacology, Physiology & Biophysics, Boston University Chobanian and Avedisian School of Medicine, Boston, Massachusetts (Z.F., R.A.S., V.Z.); Department of Psychology, Texas A&M University, College Station, Texas (O.K.S.); and Laboratory of Molecular Biology, Rockefeller University, New York, New York (E.F.S.)
| | - Zahra Farzinpour
- Nash Family Department of Neuroscience and Friedman Brain Institute (V.M., A.Ru., C.P., A.Ra., R.A.S., E.M.P. M.F., S.G., E.J.N., L.S.) and BioMedical Engineering and Imaging Institute (C.Y.T.), Icahn School of Medicine at Mount Sinai, New York, New York; University of Crete, Department of Basic Sciences, Crete, Greece (V.M.); Department of Pharmacology, Physiology & Biophysics, Boston University Chobanian and Avedisian School of Medicine, Boston, Massachusetts (Z.F., R.A.S., V.Z.); Department of Psychology, Texas A&M University, College Station, Texas (O.K.S.); and Laboratory of Molecular Biology, Rockefeller University, New York, New York (E.F.S.)
| | - Aarthi Ramakrishnan
- Nash Family Department of Neuroscience and Friedman Brain Institute (V.M., A.Ru., C.P., A.Ra., R.A.S., E.M.P. M.F., S.G., E.J.N., L.S.) and BioMedical Engineering and Imaging Institute (C.Y.T.), Icahn School of Medicine at Mount Sinai, New York, New York; University of Crete, Department of Basic Sciences, Crete, Greece (V.M.); Department of Pharmacology, Physiology & Biophysics, Boston University Chobanian and Avedisian School of Medicine, Boston, Massachusetts (Z.F., R.A.S., V.Z.); Department of Psychology, Texas A&M University, College Station, Texas (O.K.S.); and Laboratory of Molecular Biology, Rockefeller University, New York, New York (E.F.S.)
| | - Randal A Serafini
- Nash Family Department of Neuroscience and Friedman Brain Institute (V.M., A.Ru., C.P., A.Ra., R.A.S., E.M.P. M.F., S.G., E.J.N., L.S.) and BioMedical Engineering and Imaging Institute (C.Y.T.), Icahn School of Medicine at Mount Sinai, New York, New York; University of Crete, Department of Basic Sciences, Crete, Greece (V.M.); Department of Pharmacology, Physiology & Biophysics, Boston University Chobanian and Avedisian School of Medicine, Boston, Massachusetts (Z.F., R.A.S., V.Z.); Department of Psychology, Texas A&M University, College Station, Texas (O.K.S.); and Laboratory of Molecular Biology, Rockefeller University, New York, New York (E.F.S.)
| | - Eric M Parise
- Nash Family Department of Neuroscience and Friedman Brain Institute (V.M., A.Ru., C.P., A.Ra., R.A.S., E.M.P. M.F., S.G., E.J.N., L.S.) and BioMedical Engineering and Imaging Institute (C.Y.T.), Icahn School of Medicine at Mount Sinai, New York, New York; University of Crete, Department of Basic Sciences, Crete, Greece (V.M.); Department of Pharmacology, Physiology & Biophysics, Boston University Chobanian and Avedisian School of Medicine, Boston, Massachusetts (Z.F., R.A.S., V.Z.); Department of Psychology, Texas A&M University, College Station, Texas (O.K.S.); and Laboratory of Molecular Biology, Rockefeller University, New York, New York (E.F.S.)
| | - Madeline Floodstrand
- Nash Family Department of Neuroscience and Friedman Brain Institute (V.M., A.Ru., C.P., A.Ra., R.A.S., E.M.P. M.F., S.G., E.J.N., L.S.) and BioMedical Engineering and Imaging Institute (C.Y.T.), Icahn School of Medicine at Mount Sinai, New York, New York; University of Crete, Department of Basic Sciences, Crete, Greece (V.M.); Department of Pharmacology, Physiology & Biophysics, Boston University Chobanian and Avedisian School of Medicine, Boston, Massachusetts (Z.F., R.A.S., V.Z.); Department of Psychology, Texas A&M University, College Station, Texas (O.K.S.); and Laboratory of Molecular Biology, Rockefeller University, New York, New York (E.F.S.)
| | - Omar K Sial
- Nash Family Department of Neuroscience and Friedman Brain Institute (V.M., A.Ru., C.P., A.Ra., R.A.S., E.M.P. M.F., S.G., E.J.N., L.S.) and BioMedical Engineering and Imaging Institute (C.Y.T.), Icahn School of Medicine at Mount Sinai, New York, New York; University of Crete, Department of Basic Sciences, Crete, Greece (V.M.); Department of Pharmacology, Physiology & Biophysics, Boston University Chobanian and Avedisian School of Medicine, Boston, Massachusetts (Z.F., R.A.S., V.Z.); Department of Psychology, Texas A&M University, College Station, Texas (O.K.S.); and Laboratory of Molecular Biology, Rockefeller University, New York, New York (E.F.S.)
| | - Sevasti Gaspari
- Nash Family Department of Neuroscience and Friedman Brain Institute (V.M., A.Ru., C.P., A.Ra., R.A.S., E.M.P. M.F., S.G., E.J.N., L.S.) and BioMedical Engineering and Imaging Institute (C.Y.T.), Icahn School of Medicine at Mount Sinai, New York, New York; University of Crete, Department of Basic Sciences, Crete, Greece (V.M.); Department of Pharmacology, Physiology & Biophysics, Boston University Chobanian and Avedisian School of Medicine, Boston, Massachusetts (Z.F., R.A.S., V.Z.); Department of Psychology, Texas A&M University, College Station, Texas (O.K.S.); and Laboratory of Molecular Biology, Rockefeller University, New York, New York (E.F.S.)
| | - Cheuk Y Tang
- Nash Family Department of Neuroscience and Friedman Brain Institute (V.M., A.Ru., C.P., A.Ra., R.A.S., E.M.P. M.F., S.G., E.J.N., L.S.) and BioMedical Engineering and Imaging Institute (C.Y.T.), Icahn School of Medicine at Mount Sinai, New York, New York; University of Crete, Department of Basic Sciences, Crete, Greece (V.M.); Department of Pharmacology, Physiology & Biophysics, Boston University Chobanian and Avedisian School of Medicine, Boston, Massachusetts (Z.F., R.A.S., V.Z.); Department of Psychology, Texas A&M University, College Station, Texas (O.K.S.); and Laboratory of Molecular Biology, Rockefeller University, New York, New York (E.F.S.)
| | - Eric J Nestler
- Nash Family Department of Neuroscience and Friedman Brain Institute (V.M., A.Ru., C.P., A.Ra., R.A.S., E.M.P. M.F., S.G., E.J.N., L.S.) and BioMedical Engineering and Imaging Institute (C.Y.T.), Icahn School of Medicine at Mount Sinai, New York, New York; University of Crete, Department of Basic Sciences, Crete, Greece (V.M.); Department of Pharmacology, Physiology & Biophysics, Boston University Chobanian and Avedisian School of Medicine, Boston, Massachusetts (Z.F., R.A.S., V.Z.); Department of Psychology, Texas A&M University, College Station, Texas (O.K.S.); and Laboratory of Molecular Biology, Rockefeller University, New York, New York (E.F.S.)
| | - Eric F Schmidt
- Nash Family Department of Neuroscience and Friedman Brain Institute (V.M., A.Ru., C.P., A.Ra., R.A.S., E.M.P. M.F., S.G., E.J.N., L.S.) and BioMedical Engineering and Imaging Institute (C.Y.T.), Icahn School of Medicine at Mount Sinai, New York, New York; University of Crete, Department of Basic Sciences, Crete, Greece (V.M.); Department of Pharmacology, Physiology & Biophysics, Boston University Chobanian and Avedisian School of Medicine, Boston, Massachusetts (Z.F., R.A.S., V.Z.); Department of Psychology, Texas A&M University, College Station, Texas (O.K.S.); and Laboratory of Molecular Biology, Rockefeller University, New York, New York (E.F.S.)
| | - Li Shen
- Nash Family Department of Neuroscience and Friedman Brain Institute (V.M., A.Ru., C.P., A.Ra., R.A.S., E.M.P. M.F., S.G., E.J.N., L.S.) and BioMedical Engineering and Imaging Institute (C.Y.T.), Icahn School of Medicine at Mount Sinai, New York, New York; University of Crete, Department of Basic Sciences, Crete, Greece (V.M.); Department of Pharmacology, Physiology & Biophysics, Boston University Chobanian and Avedisian School of Medicine, Boston, Massachusetts (Z.F., R.A.S., V.Z.); Department of Psychology, Texas A&M University, College Station, Texas (O.K.S.); and Laboratory of Molecular Biology, Rockefeller University, New York, New York (E.F.S.)
| | - Venetia Zachariou
- Nash Family Department of Neuroscience and Friedman Brain Institute (V.M., A.Ru., C.P., A.Ra., R.A.S., E.M.P. M.F., S.G., E.J.N., L.S.) and BioMedical Engineering and Imaging Institute (C.Y.T.), Icahn School of Medicine at Mount Sinai, New York, New York; University of Crete, Department of Basic Sciences, Crete, Greece (V.M.); Department of Pharmacology, Physiology & Biophysics, Boston University Chobanian and Avedisian School of Medicine, Boston, Massachusetts (Z.F., R.A.S., V.Z.); Department of Psychology, Texas A&M University, College Station, Texas (O.K.S.); and Laboratory of Molecular Biology, Rockefeller University, New York, New York (E.F.S.)
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12
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Mathies LD, Kim AC, Soukup EM, Thomas AE, Bettinger JC. PBRM-1/PBAF-regulated genes in a multipotent progenitor in Caenorhabditis elegans. G3 (Bethesda) 2024; 14:jkad297. [PMID: 38150396 PMCID: PMC10917506 DOI: 10.1093/g3journal/jkad297] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 10/15/2023] [Revised: 12/13/2023] [Accepted: 12/20/2023] [Indexed: 12/29/2023]
Abstract
The Caenorhabditis elegans somatic gonadal precursors (SGPs) are multipotent progenitors that generate all somatic cells of the adult reproductive system. The 2 SGPs originate in the mesodermal layer and are born through a division that produces one SGP and one head mesodermal cell (hmc). One hmc terminally differentiates, and the other dies by programmed cell death. The polybromo-associated BAF (PBAF) chromatin remodeling complex promotes the multipotent SGP fate. The complete loss of PBAF causes lethality, so we used a combination of Cre/lox recombination and GFP nanobody-directed protein degradation to eliminate PBRM-1, the signature subunit of the PBAF complex, from 83 mesodermal cells, including SGPs, body muscles, and the hmc. We used RNA sequencing to identify genes acting downstream of PBAF in these cells and identified 1,955 transcripts that were significantly differentially expressed between pbrm-1(-) and pbrm-1(+) in the mesoderm of L1 larvae. We found that genes involved in muscle cell function were overrepresented; most of these genes had lower expression in the absence of PBRM-1, suggesting that PBAF promotes muscle differentiation. Among the differentially expressed genes were 125 that are normally expressed at higher levels in SGP vs hmc and positively regulated by pbrm-1 and 53 that are normally expressed at higher levels in hmc vs SGP and are negatively regulated by pbrm-1; these are candidate regulators of the SGP/hmc fate decision. We validated one candidate gene using a fluorescent reporter; the hsp-12.3 reporter was derepressed in SGPs in pbrm-1 mutants, suggesting that hsp-12.3 expression is normally repressed by pbrm-1 in SGPs.
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Affiliation(s)
- Laura D Mathies
- Department of Pharmacology and Toxicology, Virginia Commonwealth University, Richmond, VA 23298, USA
| | - Andrew C Kim
- Department of Pharmacology and Toxicology, Virginia Commonwealth University, Richmond, VA 23298, USA
| | - Evan M Soukup
- Department of Pharmacology and Toxicology, Virginia Commonwealth University, Richmond, VA 23298, USA
| | - Alan’da E Thomas
- Department of Pharmacology and Toxicology, Virginia Commonwealth University, Richmond, VA 23298, USA
| | - Jill C Bettinger
- Department of Pharmacology and Toxicology, Virginia Commonwealth University, Richmond, VA 23298, USA
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13
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Fülle JB, de Almeida RA, Lawless C, Stockdale L, Yanes B, Lane EB, Garrod DR, Ballestrem C. Proximity Mapping of Desmosomes Reveals a Striking Shift in Their Molecular Neighborhood Associated With Maturation. Mol Cell Proteomics 2024; 23:100735. [PMID: 38342409 PMCID: PMC10943070 DOI: 10.1016/j.mcpro.2024.100735] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/04/2023] [Revised: 01/29/2024] [Accepted: 02/08/2024] [Indexed: 02/13/2024] Open
Abstract
Desmosomes are multiprotein adhesion complexes that link intermediate filaments to the plasma membrane, ensuring the mechanical integrity of cells across tissues, but how they participate in the wider signaling network to exert their full function is unclear. To investigate this, we carried out protein proximity mapping using biotinylation (BioID). The combined interactomes of the essential desmosomal proteins desmocollin 2a, plakoglobin, and plakophilin 2a (Pkp2a) in Madin-Darby canine kidney epithelial cells were mapped and their differences and commonalities characterized as desmosome matured from Ca2+ dependence to the mature, Ca2+-independent, hyper-adhesive state, which predominates in tissues. Results suggest that individual desmosomal proteins have distinct roles in connecting to cellular signaling pathways and that these roles alter substantially when cells change their adhesion state. The data provide further support for a dualistic concept of desmosomes in which the properties of Pkp2a differ from those of the other, more stable proteins. This body of data provides an invaluable resource for the analysis of desmosome function.
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Affiliation(s)
- Judith B Fülle
- Wellcome Trust Centre for Cell-Matrix Research, University of Manchester, Manchester, UK
| | | | - Craig Lawless
- Wellcome Trust Centre for Cell-Matrix Research, University of Manchester, Manchester, UK
| | - Liam Stockdale
- Wellcome Trust Centre for Cell-Matrix Research, University of Manchester, Manchester, UK
| | - Bian Yanes
- Wellcome Trust Centre for Cell-Matrix Research, University of Manchester, Manchester, UK
| | - E Birgitte Lane
- Skin Research Institute of Singapore, Agency of Science Technology and Research (A∗STAR), Singapore, Singapore
| | - David R Garrod
- Wellcome Trust Centre for Cell-Matrix Research, University of Manchester, Manchester, UK.
| | - Christoph Ballestrem
- Wellcome Trust Centre for Cell-Matrix Research, University of Manchester, Manchester, UK.
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14
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Taniguchi R, Moriya Y, Dohmae N, Suzuki T, Nakahara K, Kubota S, Takasugi N, Uehara T. Attenuation of protein arginine dimethylation via S-nitrosylation of protein arginine methyltransferase 1. J Pharmacol Sci 2024; 154:209-217. [PMID: 38395522 DOI: 10.1016/j.jphs.2023.12.012] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/01/2023] [Revised: 12/14/2023] [Accepted: 12/27/2023] [Indexed: 02/25/2024] Open
Abstract
Upregulation of nitric oxide (NO) production contributes to the pathogenesis of numerous diseases via S-nitrosylation, a post-translational modification of proteins. This process occurs due to the oxidative reaction between NO and a cysteine thiol group; however, the extent of this reaction remains unknown. S-Nitrosylation of PRMT1, a major asymmetric arginine methyltransferase of histones and numerous RNA metabolic proteins, was induced by NO donor treatment. We found that nitrosative stress leads to S-nitrosylation of cysteine 119, located near the active site, and attenuates the enzymatic activity of PRMT1. Interestingly, RNA sequencing analysis revealed similarities in the changes in expression elicited by NO and PRMT1 inhibitors or knockdown. A comprehensive search for PRMT1 substrates using the proximity-dependent biotin identification method highlighted many known and new substrates, including RNA-metabolizing enzymes. To validate this result, we selected the RNA helicase DDX3 and demonstrated that arginine methylation of DDX3 is induced by PRMT1 and attenuated by NO treatment. Our results suggest the existence of a novel regulatory system associated with transcription and RNA metabolism via protein S-nitrosylation.
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Affiliation(s)
- Rikako Taniguchi
- Department of Medicinal Pharmacology, Graduate School of Medicine, Dentistry and Pharmaceutical Sciences, Okayama University, Okayama, Japan
| | - Yuto Moriya
- Department of Medicinal Pharmacology, Graduate School of Medicine, Dentistry and Pharmaceutical Sciences, Okayama University, Okayama, Japan
| | - Naoshi Dohmae
- Biomolecular Characterization Unit, Technology Platform Division, RIKEN Center for Sustainable Resource Science, Wako, Saitama, Japan
| | - Takehiro Suzuki
- Biomolecular Characterization Unit, Technology Platform Division, RIKEN Center for Sustainable Resource Science, Wako, Saitama, Japan
| | - Kengo Nakahara
- Department of Medicinal Pharmacology, Graduate School of Medicine, Dentistry and Pharmaceutical Sciences, Okayama University, Okayama, Japan
| | - Sho Kubota
- Department of Medicinal Pharmacology, Graduate School of Medicine, Dentistry and Pharmaceutical Sciences, Okayama University, Okayama, Japan
| | - Nobumasa Takasugi
- Department of Medicinal Pharmacology, Graduate School of Medicine, Dentistry and Pharmaceutical Sciences, Okayama University, Okayama, Japan
| | - Takashi Uehara
- Department of Medicinal Pharmacology, Graduate School of Medicine, Dentistry and Pharmaceutical Sciences, Okayama University, Okayama, Japan.
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15
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Niu B, Pang J, Lundholm N, Liang C, Teng ST, Zheng Q, Guo X, Li Y. A Pseudo-nitzschia metabarcoding approach with a calibrated ITS1 reference sequence database applied in the Taiwan Strait. Harmful Algae 2024; 133:102602. [PMID: 38485439 DOI: 10.1016/j.hal.2024.102602] [Citation(s) in RCA: 1] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 06/19/2023] [Revised: 01/28/2024] [Accepted: 02/05/2024] [Indexed: 03/19/2024]
Abstract
Pseudo-nitzschia is a cosmopolitan phytoplankton genus of which some species can form blooms and produce the neurotoxin domoic acid (DA). Identification of Pseudo-nitzschia is generally based on field material or strains followed by morphological and/or molecular characterization. However, this process is time-consuming and laborious, and can not obtain a relatively complete and reliable profile of the Pseudo-nitzschia community, because species with low abundance in the field or potentially unavailable for culturing may easily be overlooked. In the present study, specific ITS primer sets were designed and evaluated using in silico matching. The primer set ITS-84F/456R involving the complete ITS1 region was found optimal. Based on matching with a Pseudo-nitzschia ITS1 reference sequence database carefully-calibrated in this study, a metabarcoding approach using annotated amplicon sequence variants (ASV) was applied in the Taiwan Strait of the East China Sea during two cruises in the spring and summer of 2019. In total, 48 Pseudo-nitzschia species/phylotypes including 36 known and 12 novel were uncovered, and verified by haplotype networks, ITS2 secondary structure comparisons and divergence analyses. Correlation analyses revealed that temperature was a key factor affecting the seasonal variation of the Pseudo-nitzschia community. This study provides an overview of the Pseudo-nitzschia community in the Taiwan Strait, with new insights into the diversity. The developed metabarcoding approach may be used elsewhere as a standard reference for accurate annotation of Pseudo-nitzschia.
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Affiliation(s)
- Biaobiao Niu
- Guangdong Provincial Key Laboratory of Biotechnology for Plant Development, Guangzhou Key Laboratory of Subtropical Biodiversity and Biomonitoring, College of Life Science, South China Normal University, West 55 of Zhongshan Avenue, Guangzhou 510631, China
| | - Jinxiu Pang
- Guangdong Provincial Key Laboratory of Biotechnology for Plant Development, Guangzhou Key Laboratory of Subtropical Biodiversity and Biomonitoring, College of Life Science, South China Normal University, West 55 of Zhongshan Avenue, Guangzhou 510631, China
| | - Nina Lundholm
- Natural History Museum of Denmark, University of Copenhagen, Øster Farimagsgade 5, 1353 Copenhagen K, Denmark
| | - Cuiwen Liang
- Guangdong Provincial Key Laboratory of Biotechnology for Plant Development, Guangzhou Key Laboratory of Subtropical Biodiversity and Biomonitoring, College of Life Science, South China Normal University, West 55 of Zhongshan Avenue, Guangzhou 510631, China
| | - Sing Tung Teng
- Faculty of Resource Science and Technology, Universiti Malaysia Sarawak, Kota Samarahan 94300, Sarawak, Malaysia
| | - Qixiang Zheng
- Guangdong Provincial Key Laboratory of Biotechnology for Plant Development, Guangzhou Key Laboratory of Subtropical Biodiversity and Biomonitoring, College of Life Science, South China Normal University, West 55 of Zhongshan Avenue, Guangzhou 510631, China
| | - Xin Guo
- Guangdong Provincial Key Laboratory of Biotechnology for Plant Development, Guangzhou Key Laboratory of Subtropical Biodiversity and Biomonitoring, College of Life Science, South China Normal University, West 55 of Zhongshan Avenue, Guangzhou 510631, China
| | - Yang Li
- Guangdong Provincial Key Laboratory of Biotechnology for Plant Development, Guangzhou Key Laboratory of Subtropical Biodiversity and Biomonitoring, College of Life Science, South China Normal University, West 55 of Zhongshan Avenue, Guangzhou 510631, China.
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16
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Rossi IV, de Almeida RF, Sabatke B, de Godoy LMF, Ramirez MI. Trypanosoma cruzi interaction with host tissues modulate the composition of large extracellular vesicles. Sci Rep 2024; 14:5000. [PMID: 38424216 PMCID: PMC10904747 DOI: 10.1038/s41598-024-55302-3] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/20/2023] [Accepted: 02/22/2024] [Indexed: 03/02/2024] Open
Abstract
Trypanosoma cruzi is the protozoan that causes Chagas disease (CD), an endemic parasitosis in Latin America distributed around the globe. If CD is not treated in acute phase, the parasite remains silent for years in the host's tissues in a chronic form, which may progress to cardiac, digestive or neurological manifestations. Recently, studies indicated that the gastrointestinal tract represents an important reservoir for T. cruzi in the chronic phase. During interaction T. cruzi and host cells release extracellular vesicles (EVs) that modulates the immune system and infection, but the dynamics of secretion of host and parasite molecules through these EVs is not understood. Now, we used two cell lines: mouse myoblast cell line C2C12, and human intestinal epithelial cell line Caco-2to simulate the environments found by the parasite in the host. We isolated large EVs (LEVs) from the interaction of T. cruzi CL Brener and Dm28c/C2C12 and Caco-2 cells upon 2 and 24 h of infection. Our data showed that at two hours there is a strong cellular response mediated by EVs, both in the number, variety and enrichment/targeting of proteins found in LEVs for diverse functions. Qualitative and quantitative analysis showed that proteins exported in LEVs of C2C12 and Caco-2 have different patterns. We found a predominance of host proteins at early infection. The parasite-host cell interaction induces a switch in the functionality of proteins carried by LEVs and a heterogeneous response depending on the tissues analyzed. Protein-protein interaction analysis showed that cytoplasmic and mitochondrial homologues of the same parasite protein, tryparedoxin peroxidase, were differentially packaged in LEVs, also impacting the interacting molecule of this protein in the host. These data provide new evidence that the interaction with T. cruzi leads to a rapid tissue response through the release of LEVs, reflecting the enrichment of some proteins that could modulate the infection environment.
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Affiliation(s)
- Izadora Volpato Rossi
- Programa de Pós-graduação em Microbiologia, Parasitologia e Patologia, Universidade Federal do Paraná, Curitiba, Paraná, Brazil
- EVAHPI Research Group, Laboratório de Biologia Celular, Instituto Carlos Chagas, Fundação Oswaldo Cruz, Curitiba, Paraná, Brazil
| | - Rafael Fogaça de Almeida
- Laboratório de Biologia Molecular e Sistêmica de Tripanossomatídeos, Instituto Carlos Chagas, Fundação Oswaldo Cruz, Curitiba, Paraná, Brazil
| | - Bruna Sabatke
- Programa de Pós-graduação em Microbiologia, Parasitologia e Patologia, Universidade Federal do Paraná, Curitiba, Paraná, Brazil
- EVAHPI Research Group, Laboratório de Biologia Celular, Instituto Carlos Chagas, Fundação Oswaldo Cruz, Curitiba, Paraná, Brazil
| | - Lyris Martins Franco de Godoy
- Laboratório de Biologia Molecular e Sistêmica de Tripanossomatídeos, Instituto Carlos Chagas, Fundação Oswaldo Cruz, Curitiba, Paraná, Brazil
| | - Marcel Ivan Ramirez
- EVAHPI Research Group, Laboratório de Biologia Celular, Instituto Carlos Chagas, Fundação Oswaldo Cruz, Curitiba, Paraná, Brazil.
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Flores-Concha M, Gómez LA, Soto-Shara R, Molina RE, Coloma-Rivero RF, Montero DA, Ferrari Í, Oñate Á. Brucella abortus triggers the differential expression of immunomodulatory lncRNAs in infected murine macrophages. Front Immunol 2024; 15:1352306. [PMID: 38464511 PMCID: PMC10921354 DOI: 10.3389/fimmu.2024.1352306] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/07/2023] [Accepted: 01/30/2024] [Indexed: 03/12/2024] Open
Abstract
Introduction The lncRNAs (long non-coding RNAs) are the most diverse group of non-coding RNAs and are involved in most biological processes including the immune response. While some of them have been recognized for their influence on the regulation of inflammatory activity, little is known in the context of infection by Brucella abortus, a pathogen that presents significant challenges due to its ability to manipulate and evade the host immune system. This study focuses on characterize the expression profile of LincRNA-cox2, Lethe, lincRNA-EPS, Malat1 and Gas5 during infection of macrophages by B. abortus. Methods Using public raw RNA-seq datasets we constructed for a lncRNA expression profile in macrophages Brucella-infected. In addition, from public RNA-seq raw datasets of RAW264.7 cells infected with B. abortus we constructed a transcriptomic profile of lncRNAs in order to know the expression of the five immunomodulating lncRNAs studied here at 8 and 24 h post-infection. Finally, we performed in vitro infection assays in RAW264.7 cells and peritoneal macrophages to detect by qPCR changes in the expression of these lncRNAs at first 12 hours post infection, a key stage in the infection cycle where Brucella modulates the immune response to survive. Results Our results demonstrate that infection of macrophages with Brucella abortus, induces significant changes in the expression of LincRNA-Cox2, Lethe, LincRNA-EPS, Gas5, and Malat1. Discussion The change in the expression profile of these immunomodulatory lncRNAs in response to infection, suggest a potential involvement in the immune evasion strategy employed by Brucella to facilitate its intracellular survival.
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Affiliation(s)
| | | | | | | | | | | | | | - Ángel Oñate
- Laboratory of Molecular Immunology, Department of Microbiology, Universidad de Concepción, Concepción, Chile
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18
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Dhakal A, Salim C, Skelly M, Amichan Y, Lamm AT, Hundley HA. ADARs regulate cuticle collagen expression and promote survival to pathogen infection. BMC Biol 2024; 22:37. [PMID: 38360623 PMCID: PMC10870475 DOI: 10.1186/s12915-024-01840-1] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/05/2023] [Accepted: 02/02/2024] [Indexed: 02/17/2024] Open
Abstract
BACKGROUND In all organisms, the innate immune system defends against pathogens through basal expression of molecules that provide critical barriers to invasion and inducible expression of effectors that combat infection. The adenosine deaminase that act on RNA (ADAR) family of RNA-binding proteins has been reported to influence innate immunity in metazoans. However, studies on the susceptibility of ADAR mutant animals to infection are largely lacking. RESULTS Here, by analyzing adr-1 and adr-2 null mutants in well-established slow-killing assays, we find that both Caenorhabditis elegans ADARs are important for organismal survival to gram-negative and gram-positive bacteria, all of which are pathogenic to humans. Furthermore, our high-throughput sequencing and genetic analysis reveal that ADR-1 and ADR-2 function in the same pathway to regulate collagen expression. Consistent with this finding, our scanning electron microscopy studies indicate adr-1;adr-2 mutant animals also have altered cuticle morphology prior to pathogen exposure. CONCLUSIONS Our data uncover a critical role of the C. elegans ADAR family of RNA-binding proteins in promoting cuticular collagen expression, which represents a new post-transcriptional regulatory node that influences the extracellular matrix. In addition, we provide the first evidence that ADAR mutant animals have altered susceptibility to infection with several opportunistic human pathogens, suggesting a broader role of ADARs in altering physical barriers to infection to influence innate immunity.
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Affiliation(s)
- Alfa Dhakal
- Cell, Molecular and Cancer Biology Graduate Program, Indiana University School of Medicine-Bloomington, Bloomington, IN, 47405, USA
| | - Chinnu Salim
- Department of Biology, Indiana University, Bloomington, IN, 47405, USA
| | - Mary Skelly
- Department of Biology, Indiana University, Bloomington, IN, 47405, USA
| | - Yarden Amichan
- Faculty of Biology, Technion Institute of Technology, Haifa, Israel
| | - Ayelet T Lamm
- Faculty of Biology, Technion Institute of Technology, Haifa, Israel
| | - Heather A Hundley
- Department of Biology, Indiana University, Bloomington, IN, 47405, USA.
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19
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Forsyth KS, Toothacre NE, Jiwrajka N, Driscoll AM, Shallberg LA, Cunningham-Rundles C, Barmettler S, Farmer J, Verbsky J, Routes J, Beiting DP, Romberg N, May MJ, Anguera MC. NF-κB Signaling is Required for X-Chromosome Inactivation Maintenance Following T cell Activation. bioRxiv 2024:2024.02.08.579505. [PMID: 38405871 PMCID: PMC10888971 DOI: 10.1101/2024.02.08.579505] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Abstract] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 02/27/2024]
Abstract
X Chromosome Inactivation (XCI) is a female-specific process which balances X-linked gene dosage between sexes. Unstimulated T cells lack cytological enrichment of Xist RNA and heterochromatic modifications on the inactive X chromosome (Xi), and these modifications become enriched at the Xi after cell stimulation. Here, we examined allele-specific gene expression and the epigenomic profiles of the Xi following T cell stimulation. We found that the Xi in unstimulated T cells is largely dosage compensated and is enriched with the repressive H3K27me3 modification, but not the H2AK119-ubiquitin (Ub) mark, even at promoters of XCI escape genes. Upon CD3/CD28-mediated T cell stimulation, the Xi accumulates H2AK119-Ub and H3K27me3 across the Xi. Next, we examined the T cell signaling pathways responsible for Xist RNA localization to the Xi and found that T cell receptor (TCR) engagement, specifically NF-κB signaling downstream of TCR, is required. Disruption of NF-κB signaling, using inhibitors or genetic deletions, in mice and patients with immunodeficiencies prevents Xist/XIST RNA accumulation at the Xi and alters expression of some X-linked genes. Our findings reveal a novel connection between NF-κB signaling pathways which impact XCI maintenance in female T cells.
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20
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Begni V, Marizzoni M, Creutzberg KC, Silipo DM, Papp M, Cattaneo A, Riva MA. Transcriptomic analyses of rats exposed to chronic mild stress: Modulation by chronic treatment with the antipsychotic drug lurasidone. Prog Neuropsychopharmacol Biol Psychiatry 2024; 129:110885. [PMID: 37865392 DOI: 10.1016/j.pnpbp.2023.110885] [Citation(s) in RCA: 1] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Received: 07/04/2023] [Revised: 10/09/2023] [Accepted: 10/18/2023] [Indexed: 10/23/2023]
Abstract
Exposure to stressful experiences accounts for almost half of the risk for mental disorders. Hence, stress-induced alterations represent a key target for pharmacological interventions aimed at restoring brain function in affected individuals. We have previously demonstrated that lurasidone, a multi-receptor antipsychotic drug approved for the treatment of schizophrenia and bipolar depression, can normalize the functional and molecular impairments induced by stress exposure, representing a valuable tool for the treatment of stress-induced mental illnesses. However, the mechanisms that may contribute to the therapeutic effects of lurasidone are still poorly understood. Here, we performed a transcriptomic analysis on the prefrontal cortex (PFC) of adult male rats exposed to the chronic mild stress (CMS) paradigm and we investigated the impact of chronic lurasidone treatment on such changes. We found that CMS exposure leads to an anhedonic phenotype associated with a down-regulation of different pathways associated to neuronal guidance and synaptic plasticity within the PFC. Interestingly, a significant part of these alterations (around 25%) were counteracted by lurasidone treatment. In summary, we provided new insights on the transcriptional changes relevant for the therapeutic intervention with lurasidone, which may ultimately promote resilience.
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Affiliation(s)
- Veronica Begni
- Department of Pharmacological and Biomolecular Sciences, University of Milan, Via Balzaretti 9, 20133 Milan, Italy
| | - Moira Marizzoni
- Biological Psychiatry Unit, IRCCS Istituto Centro San Giovanni di Dio Fatebenefratelli, Via Pilastroni 4, 25125 Brescia, Italy; Lab of Neuroimaging and Alzheimer's Epidemiology, IRCCS Istituto Centro San Giovanni di Dio Fatebenefratelli, Via Pilastroni 4, 25125 Brescia, Italy
| | - Kerstin Camile Creutzberg
- Department of Pharmacological and Biomolecular Sciences, University of Milan, Via Balzaretti 9, 20133 Milan, Italy
| | - Diana Morena Silipo
- Department of Pharmacological and Biomolecular Sciences, University of Milan, Via Balzaretti 9, 20133 Milan, Italy
| | - Mariusz Papp
- Institute of Pharmacology and Polish Academy of Sciences, Smętna Street 12, Kraków 31-343, Poland
| | - Annamaria Cattaneo
- Department of Pharmacological and Biomolecular Sciences, University of Milan, Via Balzaretti 9, 20133 Milan, Italy; Biological Psychiatry Unit, IRCCS Istituto Centro San Giovanni di Dio Fatebenefratelli, Via Pilastroni 4, 25125 Brescia, Italy
| | - Marco Andrea Riva
- Department of Pharmacological and Biomolecular Sciences, University of Milan, Via Balzaretti 9, 20133 Milan, Italy; Biological Psychiatry Unit, IRCCS Istituto Centro San Giovanni di Dio Fatebenefratelli, Via Pilastroni 4, 25125 Brescia, Italy.
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21
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Rebak AS, Hendriks IA, Elsborg JD, Buch-Larsen SC, Nielsen CH, Terslev L, Kirsch R, Damgaard D, Doncheva NT, Lennartsson C, Rykær M, Jensen LJ, Christophorou MA, Nielsen ML. A quantitative and site-specific atlas of the citrullinome reveals widespread existence of citrullination and insights into PADI4 substrates. Nat Struct Mol Biol 2024:10.1038/s41594-024-01214-9. [PMID: 38321148 DOI: 10.1038/s41594-024-01214-9] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/22/2022] [Accepted: 01/04/2024] [Indexed: 02/08/2024]
Abstract
Despite the importance of citrullination in physiology and disease, global identification of citrullinated proteins, and the precise targeted sites, has remained challenging. Here we employed quantitative-mass-spectrometry-based proteomics to generate a comprehensive atlas of citrullination sites within the HL60 leukemia cell line following differentiation into neutrophil-like cells. We identified 14,056 citrullination sites within 4,008 proteins and quantified their regulation upon inhibition of the citrullinating enzyme PADI4. With this resource, we provide quantitative and site-specific information on thousands of PADI4 substrates, including signature histone marks and transcriptional regulators. Additionally, using peptide microarrays, we demonstrate the potential clinical relevance of certain identified sites, through distinct reactivities of antibodies contained in synovial fluid from anti-CCP-positive and anti-CCP-negative people with rheumatoid arthritis. Collectively, we describe the human citrullinome at a systems-wide level, provide a resource for understanding citrullination at the mechanistic level and link the identified targeted sites to rheumatoid arthritis.
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Affiliation(s)
- Alexandra S Rebak
- Proteomics Program, Novo Nordisk Foundation Center for Protein Research, Faculty of Health and Medical Sciences, University of Copenhagen, Copenhagen, Denmark
| | - Ivo A Hendriks
- Proteomics Program, Novo Nordisk Foundation Center for Protein Research, Faculty of Health and Medical Sciences, University of Copenhagen, Copenhagen, Denmark
| | - Jonas D Elsborg
- Proteomics Program, Novo Nordisk Foundation Center for Protein Research, Faculty of Health and Medical Sciences, University of Copenhagen, Copenhagen, Denmark
| | - Sara C Buch-Larsen
- Proteomics Program, Novo Nordisk Foundation Center for Protein Research, Faculty of Health and Medical Sciences, University of Copenhagen, Copenhagen, Denmark
| | - Claus H Nielsen
- Institute for Inflammation Research, Center for Rheumatology and Spine Diseases, Rigshospitalet, Copenhagen University Hospital, Copenhagen, Denmark
| | - Lene Terslev
- Copenhagen Center for Arthritis Research, Center for Rheumatology and Spine Diseases, Rigshospitalet, Copenhagen University Hospital, Copenhagen, Denmark
| | - Rebecca Kirsch
- Disease Systems Biology Program, Novo Nordisk Foundation Center for Protein Research, Faculty of Health and Medical Sciences, University of Copenhagen, Copenhagen, Denmark
| | - Dres Damgaard
- Institute for Inflammation Research, Center for Rheumatology and Spine Diseases, Rigshospitalet, Copenhagen University Hospital, Copenhagen, Denmark
| | - Nadezhda T Doncheva
- Disease Systems Biology Program, Novo Nordisk Foundation Center for Protein Research, Faculty of Health and Medical Sciences, University of Copenhagen, Copenhagen, Denmark
| | - Caroline Lennartsson
- Proteomics Program, Novo Nordisk Foundation Center for Protein Research, Faculty of Health and Medical Sciences, University of Copenhagen, Copenhagen, Denmark
| | - Martin Rykær
- Proteomics Program, Novo Nordisk Foundation Center for Protein Research, Faculty of Health and Medical Sciences, University of Copenhagen, Copenhagen, Denmark
| | - Lars J Jensen
- Disease Systems Biology Program, Novo Nordisk Foundation Center for Protein Research, Faculty of Health and Medical Sciences, University of Copenhagen, Copenhagen, Denmark
| | | | - Michael L Nielsen
- Proteomics Program, Novo Nordisk Foundation Center for Protein Research, Faculty of Health and Medical Sciences, University of Copenhagen, Copenhagen, Denmark.
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22
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Bayne EF, Buck KM, Towler AG, Zhu Y, Pergande MR, Zhou T, Price S, Rossler KJ, Morales-Tirado V, Lloyd S, Wang F, He Y, Tian Y, Ge Y. High-Throughput Extracellular Matrix Proteomics of Human Lungs Enabled by Photocleavable Surfactant and diaPASEF. J Proteome Res 2024. [PMID: 38315831 DOI: 10.1021/acs.jproteome.3c00532] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 02/07/2024]
Abstract
The extracellular matrix (ECM) is a complex assembly of proteins that provide interstitial scaffolding and elastic recoil for human lungs. The pulmonary extracellular matrix is increasingly recognized as an independent bioactive entity, by creating biochemical and mechanical signals that influence disease pathogenesis, making it an attractive therapeutic target. However, the pulmonary ECM proteome ("matrisome") remains challenging to analyze by mass spectrometry due to its inherent biophysical properties and relatively low abundance. Here, we introduce a strategy designed for rapid and efficient characterization of the human pulmonary ECM using the photocleavable surfactant Azo. We coupled this approach with trapped ion mobility MS with diaPASEF to maximize the depth of matrisome coverage. Using this strategy, we identify nearly 400 unique matrisome proteins with excellent reproducibility that are known to be important in lung biology, including key core matrisome proteins.
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Affiliation(s)
- Elizabeth F Bayne
- Department of Chemistry, University of Wisconsin-Madison, Madison, Wisconsin 53706, United States
| | - Kevin M Buck
- Department of Chemistry, University of Wisconsin-Madison, Madison, Wisconsin 53706, United States
| | - Anna G Towler
- Department of Chemistry, University of Wisconsin-Madison, Madison, Wisconsin 53706, United States
| | - Yanlong Zhu
- Department of Cell and Regenerative Biology, University of Wisconsin-Madison, Madison, Wisconsin 53705, United States
- Human Proteomics Program, School of Medicine and Public Health, University of Wisconsin-Madison, Madison, Wisconsin 53705, United States
| | - Melissa R Pergande
- Department of Cell and Regenerative Biology, University of Wisconsin-Madison, Madison, Wisconsin 53705, United States
- Human Proteomics Program, School of Medicine and Public Health, University of Wisconsin-Madison, Madison, Wisconsin 53705, United States
| | - Tianhua Zhou
- Department of Medicine, University of Wisconsin-Madison, Madison, Wisconsin 53705, United States
| | - Scott Price
- Department of Medicine, University of Wisconsin-Madison, Madison, Wisconsin 53705, United States
| | - Kalina J Rossler
- Department of Cell and Regenerative Biology, University of Wisconsin-Madison, Madison, Wisconsin 53705, United States
- Molecular and Cellular Pharmacology Training Program, University of Wisconsin-Madison, Madison, Wisconsin 53705, United States
| | - Vanessa Morales-Tirado
- Discovery Immunology, Pharmacology and Pathology, AbbVie Bioresearch Center, Worcester, Massachusetts 01605, United States
| | - Sarah Lloyd
- Discovery Immunology, Pharmacology and Pathology, AbbVie, Inc., North Chicago, Illinois 60064, United States
| | - Fei Wang
- Quantitative Translational & ADME Science, AbbVie Bioresearch Center, Worcester, Massachusetts 01605, United States
| | - Yupeng He
- Discovery Immunology, Pharmacology and Pathology, AbbVie, Inc., North Chicago, Illinois 60064, United States
| | - Yu Tian
- Quantitative Translational & ADME Science, AbbVie Bioresearch Center, Worcester, Massachusetts 01605, United States
| | - Ying Ge
- Department of Chemistry, University of Wisconsin-Madison, Madison, Wisconsin 53706, United States
- Department of Cell and Regenerative Biology, University of Wisconsin-Madison, Madison, Wisconsin 53705, United States
- Human Proteomics Program, School of Medicine and Public Health, University of Wisconsin-Madison, Madison, Wisconsin 53705, United States
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23
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Yousef A, Yousef M, Zeineddine MA, More A, Fanaeian M, Chowdhury S, Knafl M, Edelkamp P, Ito I, Gu Y, Pattalachinti V, Naini ZA, Zeineddine FA, Peterson J, Alfaro K, Foo WC, Jin J, Bhutiani N, Higbie V, Scally CP, Kee B, Kopetz S, Goldstein D, Strach M, Williamson A, Aziz O, Barriuso J, Uppal A, White MG, Helmink B, Fournier KF, Raghav KP, Taggart MW, Overman MJ, Shen JP. Serum Tumor Markers and Outcomes in Patients With Appendiceal Adenocarcinoma. JAMA Netw Open 2024; 7:e240260. [PMID: 38416491 PMCID: PMC10902735 DOI: 10.1001/jamanetworkopen.2024.0260] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Received: 09/07/2023] [Accepted: 01/02/2024] [Indexed: 02/29/2024] Open
Abstract
Importance Serum tumor markers carcinoembryonic antigen (CEA), carbohydrate antigen 19-9 (CA19-9), and cancer antigen 125 (CA125) have been useful in the management of gastrointestinal and gynecological cancers; however, there is limited information regarding their utility in patients with appendiceal adenocarcinoma. Objective To assess the association of serum tumor markers (CEA, CA19-9, and CA125) with clinical outcomes and pathologic and molecular features in patients with appendiceal adenocarcinoma. Design, Setting, and Participants This is a retrospective cohort study at a single tertiary care comprehensive cancer center. The median (IQR) follow-up time was 52 (21-101) months. Software was used to query the MD Anderson internal patient database to identify patients with a diagnosis of appendiceal adenocarcinoma and at least 1 tumor marker measured at MD Anderson between March 2016 and May 2023. Data were analyzed from January to December 2023. Main Outcomes and Measures Association of serum tumor markers with survival in patients with appendiceal adenocarcinoma. Cox proportional hazards regression analyses were also performed to assess associations between clinical factors (serum tumor marker levels, demographics, and patient and disease characteristics) and patient outcomes (overall survival). Results A total of 1338 patients with appendiceal adenocarcinoma were included, with a median (range) age at diagnosis of 56.5 (22.3-89.6) years. The majority of the patients had metastatic disease (1080 patients [80.7%]). CEA was elevated in 742 of the patients tested (56%), while CA19-9 and CA125 were elevated in 381 patients (34%) and 312 patients (27%), respectively. Individually, elevation of CEA, CA19-9, or CA125 were associated with worse 5-year survival; elevated vs normal was 81% vs 95% for CEA (hazard ratio [HR], 4.0; 95% CI, 2.9-5.6), 84% vs 92% for CA19-9 (HR, 2.2; 95% CI, 1.4-3.4), and 69% vs 93% for CA125 (HR, 4.6; 95% CI, 2.7-7.8) (P < .001 for all). Quantitative evaluation of tumor markers was associated with outcomes. Patients with highly elevated (top 10th percentile) CEA, CA19-9, or CA125 had markedly worse survival, with 5-year survival rates of 59% for CEA (HR, 9.8; 95% CI, 5.3-18.0), 64% for CA19-9 (HR, 6.0; 95% CI, 3.0-11.7), and 57% for CA125 (HR, 7.6; 95% CI, 3.5-16.5) (P < .001 for all). Although metastatic tumors had higher levels of all tumor markers, when restricting survival analysis to 1080 patients with metastatic disease, elevated CEA, CA19-9, or CA125 were all still associated worse survival (HR for CEA, 3.4; 95% CI, 2.5-4.8; P < .001; HR for CA19-9, 1.8; 95% CI, 1.2-2.7; P = .002; and HR for CA125, 3.9; 95% CI, 2.4-6.4; P < .001). Interestingly, tumor grade was not associated with CEA or CA19-9 level, while CA-125 was slightly higher in high-grade tumors relative to low-grade tumors (mean value, 18.3 vs 15.0; difference, 3.3; 95% CI, 0.9-3.7; P < .001). Multivariable analysis identified an incremental increase in the risk of death with an increase in the number of elevated tumor markers, with an 11-fold increased risk of death in patients with all 3 tumor markers elevated relative to those with none elevated. Somatic mutations in KRAS and GNAS were associated with significantly higher levels of CEA and CA19-9. Conclusions and Relevance In this retrospective study of serum tumor markers in patients with appendiceal adenocarcinoma, CEA, CA19-9, and CA125 were associated with overall survival in appendiceal adenocarcinoma. Given their value, all 3 biomarkers should be included in the initial workup of patients with a diagnosis of appendiceal adenocarcinoma.
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Affiliation(s)
- Abdelrahman Yousef
- Department of Gastrointestinal Medical Oncology, University of Texas MD Anderson Cancer Center, Houston
| | - Mahmoud Yousef
- Department of Gastrointestinal Medical Oncology, University of Texas MD Anderson Cancer Center, Houston
| | - Mohammad A. Zeineddine
- Department of Gastrointestinal Medical Oncology, University of Texas MD Anderson Cancer Center, Houston
| | - Aditya More
- Department of Gastrointestinal Medical Oncology, University of Texas MD Anderson Cancer Center, Houston
| | - Mohammad Fanaeian
- Department of Gastrointestinal Medical Oncology, University of Texas MD Anderson Cancer Center, Houston
| | - Saikat Chowdhury
- Department of Gastrointestinal Medical Oncology, University of Texas MD Anderson Cancer Center, Houston
| | - Mark Knafl
- Department of Genomic Medicine, University of Texas MD Anderson Cancer Center, Houston
| | - Paul Edelkamp
- Department of Data Engineering and Analytics, University of Texas MD Anderson Cancer Center, Houston
| | - Ichiaki Ito
- Department of Gastrointestinal Medical Oncology, University of Texas MD Anderson Cancer Center, Houston
| | - Yue Gu
- Department of Gastrointestinal Medical Oncology, University of Texas MD Anderson Cancer Center, Houston
| | - Vinay Pattalachinti
- Department of Gastrointestinal Medical Oncology, University of Texas MD Anderson Cancer Center, Houston
| | - Zahra Alavi Naini
- Department of Gastrointestinal Medical Oncology, University of Texas MD Anderson Cancer Center, Houston
| | - Fadl A. Zeineddine
- Department of Internal Medicine, Houston Methodist Hospital, Houston, Texas
| | - Jennifer Peterson
- Department of Gastrointestinal Medical Oncology, University of Texas MD Anderson Cancer Center, Houston
| | - Kristin Alfaro
- Department of Gastrointestinal Medical Oncology, University of Texas MD Anderson Cancer Center, Houston
| | - Wai Chin Foo
- Department of Pathology, University of Texas MD Anderson Cancer Center, Houston
| | - Jeff Jin
- Department of Enterprise Development and Integration, University of Texas MD Anderson Cancer Center, Houston
| | - Neal Bhutiani
- Department of Colon and Rectal Surgery, University of Texas MD Anderson Cancer Center, Houston
| | - Victoria Higbie
- Department of Gastrointestinal Medical Oncology, University of Texas MD Anderson Cancer Center, Houston
| | - Christopher P. Scally
- Department of Surgical Oncology, University of Texas MD Anderson Cancer Center, Houston
| | - Bryan Kee
- Department of Gastrointestinal Medical Oncology, University of Texas MD Anderson Cancer Center, Houston
| | - Scott Kopetz
- Department of Gastrointestinal Medical Oncology, University of Texas MD Anderson Cancer Center, Houston
| | | | - Madeleine Strach
- Colorectal and Peritoneal Oncology Centre, The Christie NHS Foundation Trust, Manchester, United Kingdom
- Division of Cancer Sciences, Faculty of Biology, Medicine and Health, School of Medical Sciences, University of Manchester, Manchester, United Kingdom
- Faculty of Medicine and Health, The University of Sydney, Darlington, Victoria, Australia
| | - Andrew Williamson
- Department of Medical Oncology, The Christie National Health Service Foundation Trust, Manchester, United Kingdom
| | - Omer Aziz
- Colorectal and Peritoneal Oncology Centre, The Christie NHS Foundation Trust, Manchester, United Kingdom
- Division of Cancer Sciences, Faculty of Biology, Medicine and Health, School of Medical Sciences, University of Manchester, Manchester, United Kingdom
| | - Jorge Barriuso
- Colorectal and Peritoneal Oncology Centre, The Christie NHS Foundation Trust, Manchester, United Kingdom
- Division of Cancer Sciences, Faculty of Biology, Medicine and Health, School of Medical Sciences, University of Manchester, Manchester, United Kingdom
| | - Abhineet Uppal
- Department of Colon and Rectal Surgery, University of Texas MD Anderson Cancer Center, Houston
| | - Michael G. White
- Department of Colon and Rectal Surgery, University of Texas MD Anderson Cancer Center, Houston
| | - Beth Helmink
- Department of Surgical Oncology, University of Texas MD Anderson Cancer Center, Houston
| | - Keith F. Fournier
- Department of Surgical Oncology, University of Texas MD Anderson Cancer Center, Houston
| | - Kanwal P. Raghav
- Department of Gastrointestinal Medical Oncology, University of Texas MD Anderson Cancer Center, Houston
| | - Melissa W. Taggart
- Department of Pathology, University of Texas MD Anderson Cancer Center, Houston
| | - Michael J. Overman
- Department of Gastrointestinal Medical Oncology, University of Texas MD Anderson Cancer Center, Houston
| | - John Paul Shen
- Department of Gastrointestinal Medical Oncology, University of Texas MD Anderson Cancer Center, Houston
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24
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Chen S, Phillips CM. HRDE-2 drives small RNA specificity for the nuclear Argonaute protein HRDE-1. Nat Commun 2024; 15:957. [PMID: 38302462 PMCID: PMC10834429 DOI: 10.1038/s41467-024-45245-8] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/23/2023] [Accepted: 01/18/2024] [Indexed: 02/03/2024] Open
Abstract
RNA interference (RNAi) is a conserved gene silencing process that exists in diverse organisms to protect genome integrity and regulate gene expression. In C. elegans, the majority of RNAi pathway proteins localize to perinuclear, phase-separated germ granules, which are comprised of sub-domains referred to as P granules, Mutator foci, Z granules, and SIMR foci. However, the protein components and function of the newly discovered SIMR foci are unknown. Here we demonstrate that HRDE-2 localizes to SIMR foci and interacts with the germline nuclear Argonaute HRDE-1 in its small RNA unbound state. In the absence of HRDE-2, HRDE-1 exclusively loads CSR-class 22G-RNAs rather than WAGO-class 22G-RNAs, resulting in inappropriate H3K9me3 deposition on CSR-target genes. Thus, our study demonstrates that the recruitment of unloaded HRDE-1 to germ granules, mediated by HRDE-2, is critical to ensure that the correct small RNAs are used to guide nuclear RNA silencing in the C. elegans germline.
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Affiliation(s)
- Shihui Chen
- Department of Biological Sciences, University of Southern California, Los Angeles, CA, 90089, USA
| | - Carolyn M Phillips
- Department of Biological Sciences, University of Southern California, Los Angeles, CA, 90089, USA.
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25
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Ciceri G, Baggiolini A, Cho HS, Kshirsagar M, Benito-Kwiecinski S, Walsh RM, Aromolaran KA, Gonzalez-Hernandez AJ, Munguba H, Koo SY, Xu N, Sevilla KJ, Goldstein PA, Levitz J, Leslie CS, Koche RP, Studer L. An epigenetic barrier sets the timing of human neuronal maturation. Nature 2024; 626:881-890. [PMID: 38297124 PMCID: PMC10881400 DOI: 10.1038/s41586-023-06984-8] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/17/2022] [Accepted: 12/15/2023] [Indexed: 02/02/2024]
Abstract
The pace of human brain development is highly protracted compared with most other species1-7. The maturation of cortical neurons is particularly slow, taking months to years to develop adult functions3-5. Remarkably, such protracted timing is retained in cortical neurons derived from human pluripotent stem cells (hPSCs) during in vitro differentiation or upon transplantation into the mouse brain4,8,9. Those findings suggest the presence of a cell-intrinsic clock setting the pace of neuronal maturation, although the molecular nature of this clock remains unknown. Here we identify an epigenetic developmental programme that sets the timing of human neuronal maturation. First, we developed a hPSC-based approach to synchronize the birth of cortical neurons in vitro which enabled us to define an atlas of morphological, functional and molecular maturation. We observed a slow unfolding of maturation programmes, limited by the retention of specific epigenetic factors. Loss of function of several of those factors in cortical neurons enables precocious maturation. Transient inhibition of EZH2, EHMT1 and EHMT2 or DOT1L, at progenitor stage primes newly born neurons to rapidly acquire mature properties upon differentiation. Thus our findings reveal that the rate at which human neurons mature is set well before neurogenesis through the establishment of an epigenetic barrier in progenitor cells. Mechanistically, this barrier holds transcriptional maturation programmes in a poised state that is gradually released to ensure the prolonged timeline of human cortical neuron maturation.
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Affiliation(s)
- Gabriele Ciceri
- The Center for Stem Cell Biology and Developmental Biology Program, Memorial Sloan Kettering Cancer Center, New York, NY, USA.
| | - Arianna Baggiolini
- The Center for Stem Cell Biology and Developmental Biology Program, Memorial Sloan Kettering Cancer Center, New York, NY, USA
- Institute of Oncology Research (IOR), Bellinzona Institutes of Science (BIOS+), Bellinzona, Switzerland
- Faculty of Biomedical Sciences, Università della Svizzera Italiana, Lugano, Switzerland
| | - Hyein S Cho
- The Center for Stem Cell Biology and Developmental Biology Program, Memorial Sloan Kettering Cancer Center, New York, NY, USA
- Computational Biology Program, Memorial Sloan Kettering Cancer Center, New York, NY, USA
| | - Meghana Kshirsagar
- Computational Biology Program, Memorial Sloan Kettering Cancer Center, New York, NY, USA
- Microsoft AI for Good Research, Redmond, WA, USA
| | - Silvia Benito-Kwiecinski
- The Center for Stem Cell Biology and Developmental Biology Program, Memorial Sloan Kettering Cancer Center, New York, NY, USA
| | - Ryan M Walsh
- The Center for Stem Cell Biology and Developmental Biology Program, Memorial Sloan Kettering Cancer Center, New York, NY, USA
| | | | | | - Hermany Munguba
- Department of Biochemistry, Weill Cornell Medicine, New York, NY, USA
| | - So Yeon Koo
- The Center for Stem Cell Biology and Developmental Biology Program, Memorial Sloan Kettering Cancer Center, New York, NY, USA
- Weill Cornell Neuroscience PhD Program, New York, NY, USA
| | - Nan Xu
- The Center for Stem Cell Biology and Developmental Biology Program, Memorial Sloan Kettering Cancer Center, New York, NY, USA
- Louis V. Gerstner Jr Graduate School of Biomedical Sciences, Memorial Sloan Kettering Cancer Center, New York, NY, USA
| | - Kaylin J Sevilla
- The Center for Stem Cell Biology and Developmental Biology Program, Memorial Sloan Kettering Cancer Center, New York, NY, USA
| | - Peter A Goldstein
- Department of Anesthesiology, Weill Cornell Medicine, New York, NY, USA
| | - Joshua Levitz
- Department of Biochemistry, Weill Cornell Medicine, New York, NY, USA
| | - Christina S Leslie
- Computational Biology Program, Memorial Sloan Kettering Cancer Center, New York, NY, USA
| | - Richard P Koche
- Center for Epigenetics Research, Memorial Sloan Kettering Cancer Center, New York, NY, USA
| | - Lorenz Studer
- The Center for Stem Cell Biology and Developmental Biology Program, Memorial Sloan Kettering Cancer Center, New York, NY, USA.
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26
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Chauhan PS, Benninghoff AD, Favor OK, Wagner JG, Lewandowski RP, Rajasinghe LD, Li QZ, Harkema JR, Pestka JJ. Dietary docosahexaenoic acid supplementation inhibits acute pulmonary transcriptional and autoantibody responses to a single crystalline silica exposure in lupus-prone mice. Front Immunol 2024; 15:1275265. [PMID: 38361937 PMCID: PMC10867581 DOI: 10.3389/fimmu.2024.1275265] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/09/2023] [Accepted: 01/08/2024] [Indexed: 02/17/2024] Open
Abstract
Introduction Workplace exposure to respirable crystalline silica (cSiO2) has been epidemiologically linked to lupus. Consistent with this, repeated subchronic intranasal cSiO2 instillation in lupus-prone NZBWF1 mice induces inflammation-/autoimmune-related gene expression, ectopic lymphoid tissue (ELT), autoantibody (AAb) production in the lung within 5 to 13 wk followed systemic AAb increases and accelerated onset and progression of glomerulonephritis within 13 to 17 wk. Interestingly, dietary docosahexaenoic acid (DHA) supplementation suppresses these pathologic effects, but the underlying molecular mechanisms remain unclear. Methods This study aimed to test the hypothesis that dietary DHA supplementation impacts acute transcriptional and autoantibody responses in the lungs of female NZBWF1 mice 1 and 4 wk after a single high-dose cSiO2 challenge. Groups of mice were initially fed a control (Con) diet or a DHA-containing diet (10 g/kg). Cohorts of Con- and DHA-fed were subjected to a single intranasal instillation of 2.5 mg cSiO2 in a saline vehicle (Veh), while a Con-fed cohort was instilled with Veh only. At 1 and 4 wk post-instillation (PI), we compared cSiO2's effects on innate-/autoimmune-related gene expression and autoantibody (AAb) in lavage fluid/lungs of Con- and DHA-fed mice and related these findings to inflammatory cell profiles, histopathology, cell death, and cytokine/chemokine production. Results DHA partially alleviated cSiO2-induced alterations in total immune cell and lymphocyte counts in lung lavage fluid. cSiO2-triggered dead cell accumulation and levels of inflammation-associated cytokines and IFN-stimulated chemokines were more pronounced in Con-fed mice than DHA-fed mice. Targeted multiplex transcriptome analysis revealed substantial upregulation of genes associated with autoimmune pathways in Con-fed mice in response to cSiO2 that were suppressed in DHA-fed mice. Pathway analysis indicated that DHA inhibited cSiO2 induction of proinflammatory and IFN-regulated gene networks, affecting key upstream regulators (e.g., TNFα, IL-1β, IFNAR, and IFNγ). Finally, cSiO2-triggered AAb responses were suppressed in DHA-fed mice. Discussion Taken together, DHA mitigated cSiO2-induced upregulation of pathways associated with proinflammatory and IFN-regulated gene responses within 1 wk and reduced AAb responses by 4 wk. These findings suggest that the acute short-term model employed here holds substantial promise for efficient elucidation of the molecular mechanisms through which omega-3 PUFAs exert protective effects against cSiO2-induced autoimmunity.
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Affiliation(s)
- Preeti S. Chauhan
- Department of Food Science and Human Nutrition, Michigan State University, East Lansing, MI, United States
- Institute for Integrative Toxicology, Michigan State University, East Lansing, MI, United States
| | - Abby D. Benninghoff
- Department of Animal, Dairy and Veterinary Sciences, Utah State University, Logan, UT, United States
| | - Olivia K. Favor
- Institute for Integrative Toxicology, Michigan State University, East Lansing, MI, United States
- Department of Microbiology, Genetics, and Immunology, Michigan State University, East Lansing, MI, United States
- Department of Pharmacology and Toxicology, Michigan State University, East Lansing, MI, United States
| | - James G. Wagner
- Institute for Integrative Toxicology, Michigan State University, East Lansing, MI, United States
- Department of Pathobiology and Diagnostic Investigation, Michigan State University, East Lansing, MI, United States
| | - Ryan P. Lewandowski
- Department of Pathobiology and Diagnostic Investigation, Michigan State University, East Lansing, MI, United States
| | - Lichchavi D. Rajasinghe
- Department of Food Science and Human Nutrition, Michigan State University, East Lansing, MI, United States
- Institute for Integrative Toxicology, Michigan State University, East Lansing, MI, United States
| | | | - Jack R. Harkema
- Department of Animal, Dairy and Veterinary Sciences, Utah State University, Logan, UT, United States
- Department of Pharmacology and Toxicology, Michigan State University, East Lansing, MI, United States
- Department of Pathobiology and Diagnostic Investigation, Michigan State University, East Lansing, MI, United States
| | - James J. Pestka
- Institute for Integrative Toxicology, Michigan State University, East Lansing, MI, United States
- Department of Animal, Dairy and Veterinary Sciences, Utah State University, Logan, UT, United States
- Department of Microbiology, Genetics, and Immunology, Michigan State University, East Lansing, MI, United States
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Hofford RS, Meckel KR, Wiser EJ, Wang W, Sens JP, Kim M, Godino A, Lam TT, Kiraly DD. Microbiome Depletion Increases Fentanyl Self-Administration and Alters the Striatal Proteome Through Short-Chain Fatty Acids. eNeuro 2024; 11:11/2/ENEURO.0388-23.2023. [PMID: 38164564 PMCID: PMC10875718 DOI: 10.1523/eneuro.0388-23.2023] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/05/2023] [Revised: 11/10/2023] [Accepted: 11/13/2023] [Indexed: 01/03/2024] Open
Abstract
Opioid use disorder (OUD) is a public health crisis currently being exacerbated by increased rates of use and overdose of synthetic opioids, primarily fentanyl. Therefore, the identification of novel biomarkers and treatment strategies to reduce problematic fentanyl use and relapse to fentanyl taking is critical. In recent years, there has been a growing body of work demonstrating that the gut microbiome can serve as a potent modulator of the behavioral and transcriptional responses to both stimulants and opioids. Here, we advance this work to define how manipulations of the microbiome drive fentanyl intake and fentanyl-seeking in a translationally relevant drug self-administration model. Depletion of the microbiome of male rats with broad spectrum antibiotics leads to increased drug administration on increased fixed ratio, progressive ratio, and drug seeking after abstinence. Utilizing 16S sequencing of microbiome contents from these animals, specific populations of bacteria from the gut microbiome correlate closely with levels of drug taking. Additionally, global proteomic analysis of the nucleus accumbens following microbiome manipulation and fentanyl administration to define how microbiome status alters the functional proteomic landscape in this key limbic substructure. These data demonstrate that an altered microbiome leads to marked changes in the synaptic proteome in response to repeated fentanyl treatment. Finally, behavioral effects of microbiome depletion are reversible by upplementation of the microbiome derived short-chain fatty acid metabolites. Taken together, these findings establish clear relevance for gut-brain signaling in models of OUD and lay foundations for further translational work in this space.
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Affiliation(s)
- Rebecca S Hofford
- Department of Translational Neuroscience, Wake Forest School of Medicine, Winston-Salem, NC 27101
- Department of Psychiatry, Icahn School of Medicine at Mount Sinai, NewYork, NY 10029
- Friedman Brain Institute, Icahn School of Medicine at Mount Sinai, NewYork, NY 10029
| | - Katherine R Meckel
- Friedman Brain Institute, Icahn School of Medicine at Mount Sinai, NewYork, NY 10029
- Nash Family Department of Neuroscience, Icahn School of Medicine at Mount Sinai, NewYork, NY 10029
| | - Elizabeth J Wiser
- Department of Translational Neuroscience, Wake Forest School of Medicine, Winston-Salem, NC 27101
| | - Weiwei Wang
- Keck MS & Proteomics Resource, Yale University School of Medicine, New Haven, CT 06520
| | - Jonathon P Sens
- Department of Translational Neuroscience, Wake Forest School of Medicine, Winston-Salem, NC 27101
| | - Michelle Kim
- Friedman Brain Institute, Icahn School of Medicine at Mount Sinai, NewYork, NY 10029
- Nash Family Department of Neuroscience, Icahn School of Medicine at Mount Sinai, NewYork, NY 10029
| | - Arthur Godino
- Friedman Brain Institute, Icahn School of Medicine at Mount Sinai, NewYork, NY 10029
- Nash Family Department of Neuroscience, Icahn School of Medicine at Mount Sinai, NewYork, NY 10029
| | - TuKiet T Lam
- Keck MS & Proteomics Resource, Yale University School of Medicine, New Haven, CT 06520
- Yale/NIDA Neuroproteomics Center, Yale University School of Medicine, New Haven, CT 06520
- Department of Molecular Biophysics and Biochemistry, Yale University School of Medicine, New Haven, CT 06520
| | - Drew D Kiraly
- Department of Translational Neuroscience, Wake Forest School of Medicine, Winston-Salem, NC 27101
- Department of Psychiatry, Icahn School of Medicine at Mount Sinai, NewYork, NY 10029
- Friedman Brain Institute, Icahn School of Medicine at Mount Sinai, NewYork, NY 10029
- Nash Family Department of Neuroscience, Icahn School of Medicine at Mount Sinai, NewYork, NY 10029
- Department of Psychiatry, Atrium Health Wake Forest Baptist, Winston-Salem, NC 27101
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28
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Zeng Z, Wijnands LM, Boeren S, Smid EJ, Notebaart RA, Abee T. Impact of vitamin B 12 on rhamnose metabolism, stress defense and in-vitro virulence of Listeria monocytogenes. Int J Food Microbiol 2024; 410:110486. [PMID: 37992553 DOI: 10.1016/j.ijfoodmicro.2023.110486] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/03/2023] [Revised: 07/05/2023] [Accepted: 11/11/2023] [Indexed: 11/24/2023]
Abstract
Listeria monocytogenes is a facultative anaerobe which can cause a severe food-borne infection known as listeriosis. L. monocytogenes is capable of utilizing various nutrient sources including rhamnose, a naturally occurring deoxy sugar abundant in foods. L. monocytogenes can degrade rhamnose into lactate, acetate and 1,2-propanediol. Our previous study showed that addition of vitamin B12 stimulated anaerobic growth of L. monocytogenes on rhamnose due to the activation of bacterial microcompartments for 1,2-propanediol utilization (pdu BMC) with concomitant production of propionate and propanol. Notably, anaerobic 1,2-propanediol metabolism has been linked to virulence of enteric pathogens including Salmonella spp. and L. monocytogenes. In this study we investigated the impact of B12 and BMC activation on i) aerobic and anerobic growth of L. monocytogenes on rhamnose and ii) the level of virulence. We observed B12-induced pdu BMC activation and growth stimulation only in anaerobically grown cells. Comparative Caco-2 virulence assays showed that these pdu BMC-induced cells have significantly higher translocation efficiency compared to non-induced cells (anaerobic growth without B12; aerobic growth with or without B12), while adhesion and invasion capacity is similar for all cells. Comparative proteome analysis showed specific and overlapping responses linked to metabolic shifts, activation of stress defense proteins and virulence factors, with RNA polymerase sigma factor SigL, teichoic acid export ATP-binding protein TagH, DNA repair and protection proteins, RadA and DPS, and glutathione synthase GshAB, previously linked to activation of virulence response in L. monocytogenes, uniquely upregulated in anaerobically rhamnose grown pdu-induced cells. Our results shed light on possible effects of B12 on L. monocytogenes competitive fitness and virulence activation when utilizing rhamnose in anaerobic conditions encountered during transmission and the human intestine.
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Affiliation(s)
- Zhe Zeng
- Food Microbiology, Wageningen University and Research, Wageningen, the Netherlands
| | - Lucas M Wijnands
- National Institute of Public Health and the Environment, Bilthoven, the Netherlands
| | - Sjef Boeren
- Laboratory of Biochemistry, Wageningen University and Research, Wageningen, the Netherlands
| | - Eddy J Smid
- Food Microbiology, Wageningen University and Research, Wageningen, the Netherlands
| | - Richard A Notebaart
- Food Microbiology, Wageningen University and Research, Wageningen, the Netherlands
| | - Tjakko Abee
- Food Microbiology, Wageningen University and Research, Wageningen, the Netherlands.
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Xu W, Billon C, Li H, Wilderman A, Qi L, Graves A, Rideb JRDC, Zhao Y, Hayes M, Yu K, Losby M, Hampton CS, Adeyemi CM, Hong SJ, Nasiotis E, Fu C, Oh TG, Fan W, Downes M, Welch RD, Evans RM, Milosavljevic A, Walker JK, Jensen BC, Pei L, Burris T, Zhang L. Novel Pan-ERR Agonists Ameliorate Heart Failure Through Enhancing Cardiac Fatty Acid Metabolism and Mitochondrial Function. Circulation 2024; 149:227-250. [PMID: 37961903 PMCID: PMC10842599 DOI: 10.1161/circulationaha.123.066542] [Citation(s) in RCA: 1] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Received: 08/09/2023] [Accepted: 10/20/2023] [Indexed: 11/15/2023]
Abstract
BACKGROUND Cardiac metabolic dysfunction is a hallmark of heart failure (HF). Estrogen-related receptors ERRα and ERRγ are essential regulators of cardiac metabolism. Therefore, activation of ERR could be a potential therapeutic intervention for HF. However, in vivo studies demonstrating the potential usefulness of ERR agonist for HF treatment are lacking, because compounds with pharmacokinetics appropriate for in vivo use have not been available. METHODS Using a structure-based design approach, we designed and synthesized 2 structurally distinct pan-ERR agonists, SLU-PP-332 and SLU-PP-915. We investigated the effect of ERR agonist on cardiac function in a pressure overload-induced HF model in vivo. We conducted comprehensive functional, multi-omics (RNA sequencing and metabolomics studies), and genetic dependency studies both in vivo and in vitro to dissect the molecular mechanism, ERR isoform dependency, and target specificity. RESULTS Both SLU-PP-332 and SLU-PP-915 significantly improved ejection fraction, ameliorated fibrosis, and increased survival associated with pressure overload-induced HF without affecting cardiac hypertrophy. A broad spectrum of metabolic genes was transcriptionally activated by ERR agonists, particularly genes involved in fatty acid metabolism and mitochondrial function. Metabolomics analysis showed substantial normalization of metabolic profiles in fatty acid/lipid and tricarboxylic acid/oxidative phosphorylation metabolites in the mouse heart with 6-week pressure overload. ERR agonists increase mitochondria oxidative capacity and fatty acid use in vitro and in vivo. Using both in vitro and in vivo genetic dependency experiments, we show that ERRγ is the main mediator of ERR agonism-induced transcriptional regulation and cardioprotection and definitively demonstrated target specificity. ERR agonism also led to downregulation of cell cycle and development pathways, which was partially mediated by E2F1 in cardiomyocytes. CONCLUSIONS ERR agonists maintain oxidative metabolism, which confers cardiac protection against pressure overload-induced HF in vivo. Our results provide direct pharmacologic evidence supporting the further development of ERR agonists as novel HF therapeutics.
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Affiliation(s)
- Weiyi Xu
- Department of Molecular & Human Genetics, Baylor College of Medicine, Houston, TX (W.X., H.L., A.W., L.Q., A.G., J.R.D.C.R., Y.Z., K.Y., M.L., E.N., A.M., L.Z.)
| | - Cyrielle Billon
- Department of Pharmaceutical and Administrative Sciences, University of Health Sciences and Pharmacy, St Louis, MO (C.B., M.H., T.B.)
- Center for Clinical Pharmacology, St Louis College of Pharmacy, Washington University School of Medicine, St Louis, MO (C.B., M.H., T.B.)
| | - Hui Li
- Department of Molecular & Human Genetics, Baylor College of Medicine, Houston, TX (W.X., H.L., A.W., L.Q., A.G., J.R.D.C.R., Y.Z., K.Y., M.L., E.N., A.M., L.Z.)
| | - Andrea Wilderman
- Department of Molecular & Human Genetics, Baylor College of Medicine, Houston, TX (W.X., H.L., A.W., L.Q., A.G., J.R.D.C.R., Y.Z., K.Y., M.L., E.N., A.M., L.Z.)
| | - Lei Qi
- Department of Molecular & Human Genetics, Baylor College of Medicine, Houston, TX (W.X., H.L., A.W., L.Q., A.G., J.R.D.C.R., Y.Z., K.Y., M.L., E.N., A.M., L.Z.)
| | - Andrea Graves
- Department of Molecular & Human Genetics, Baylor College of Medicine, Houston, TX (W.X., H.L., A.W., L.Q., A.G., J.R.D.C.R., Y.Z., K.Y., M.L., E.N., A.M., L.Z.)
| | - Jernie Rae Dela Cruz Rideb
- Department of Molecular & Human Genetics, Baylor College of Medicine, Houston, TX (W.X., H.L., A.W., L.Q., A.G., J.R.D.C.R., Y.Z., K.Y., M.L., E.N., A.M., L.Z.)
| | - Yuanbiao Zhao
- Department of Molecular & Human Genetics, Baylor College of Medicine, Houston, TX (W.X., H.L., A.W., L.Q., A.G., J.R.D.C.R., Y.Z., K.Y., M.L., E.N., A.M., L.Z.)
| | - Matthew Hayes
- Department of Pharmaceutical and Administrative Sciences, University of Health Sciences and Pharmacy, St Louis, MO (C.B., M.H., T.B.)
- Center for Clinical Pharmacology, St Louis College of Pharmacy, Washington University School of Medicine, St Louis, MO (C.B., M.H., T.B.)
| | - Keyang Yu
- Department of Molecular & Human Genetics, Baylor College of Medicine, Houston, TX (W.X., H.L., A.W., L.Q., A.G., J.R.D.C.R., Y.Z., K.Y., M.L., E.N., A.M., L.Z.)
| | - McKenna Losby
- Department of Molecular & Human Genetics, Baylor College of Medicine, Houston, TX (W.X., H.L., A.W., L.Q., A.G., J.R.D.C.R., Y.Z., K.Y., M.L., E.N., A.M., L.Z.)
| | - Carissa S Hampton
- Department of Pharmacology and Physiology, St Louis University School of Medicine, MO (C.S.H., C.M.A., J.K.W.)
| | - Christiana M Adeyemi
- Department of Pharmacology and Physiology, St Louis University School of Medicine, MO (C.S.H., C.M.A., J.K.W.)
| | - Seok Jae Hong
- McAllister Heart Institute (S.J.H., B.C.J.), University of North Carolina, Chapel Hill
| | - Eleni Nasiotis
- Department of Molecular & Human Genetics, Baylor College of Medicine, Houston, TX (W.X., H.L., A.W., L.Q., A.G., J.R.D.C.R., Y.Z., K.Y., M.L., E.N., A.M., L.Z.)
| | - Chen Fu
- Department of Psychiatry, University of Massachusetts Chan Medical School, Worcester, MA (C.F.)
- University Hospitals Cleveland Medical Center, OH (C.F.)
| | - Tae Gyu Oh
- Howard Hughes Medical Institute, Salk Institute for Biological Studies, La Jolla, CA (T.G.O., W.F., M.D., R.M.E.)
| | - Weiwei Fan
- Howard Hughes Medical Institute, Salk Institute for Biological Studies, La Jolla, CA (T.G.O., W.F., M.D., R.M.E.)
| | - Michael Downes
- Howard Hughes Medical Institute, Salk Institute for Biological Studies, La Jolla, CA (T.G.O., W.F., M.D., R.M.E.)
| | - Ryan D Welch
- Biology and Chemistry Department, Blackburn College, Carlinville, IL (R.D.W.)
| | - Ronald M Evans
- Howard Hughes Medical Institute, Salk Institute for Biological Studies, La Jolla, CA (T.G.O., W.F., M.D., R.M.E.)
| | - Aleksandar Milosavljevic
- Department of Molecular & Human Genetics, Baylor College of Medicine, Houston, TX (W.X., H.L., A.W., L.Q., A.G., J.R.D.C.R., Y.Z., K.Y., M.L., E.N., A.M., L.Z.)
| | - John K Walker
- Department of Pharmacology and Physiology, St Louis University School of Medicine, MO (C.S.H., C.M.A., J.K.W.)
| | - Brian C Jensen
- McAllister Heart Institute (S.J.H., B.C.J.), University of North Carolina, Chapel Hill
- Department of Medicine, Division of Cardiology (B.C.J.), University of North Carolina, Chapel Hill
| | - Liming Pei
- Department of Pathology and Laboratory Medicine, Children's Hospital of Philadelphia, and University of Pennsylvania, Philadelphia (L.P.)
| | - Thomas Burris
- Department of Pharmaceutical and Administrative Sciences, University of Health Sciences and Pharmacy, St Louis, MO (C.B., M.H., T.B.)
- Center for Clinical Pharmacology, St Louis College of Pharmacy, Washington University School of Medicine, St Louis, MO (C.B., M.H., T.B.)
| | - Lilei Zhang
- Department of Molecular & Human Genetics, Baylor College of Medicine, Houston, TX (W.X., H.L., A.W., L.Q., A.G., J.R.D.C.R., Y.Z., K.Y., M.L., E.N., A.M., L.Z.)
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30
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Deschner F, Risch T, Baier C, Schlüter D, Herrmann J, Müller R. Nitroxoline resistance is associated with significant fitness loss and diminishes in vivo virulence of Escherichia coli. Microbiol Spectr 2024; 12:e0307923. [PMID: 38063385 PMCID: PMC10782962 DOI: 10.1128/spectrum.03079-23] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/11/2023] [Accepted: 11/14/2023] [Indexed: 01/13/2024] Open
Abstract
IMPORTANCE Antimicrobial resistance (AMR) poses a global threat and requires the exploration of underestimated treatment options. Nitroxoline, an effective broad-spectrum antibiotic, does not suffer from high resistance rates in the clinics but surprisingly, it is not heavily used yet. Our findings provide compelling evidence that Nitroxoline resistance renders bacteria unable to cause an infection in vivo, thereby reinvigorating the potential of Nitroxoline in combating AMR.
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Affiliation(s)
- Felix Deschner
- Microbial Natural Products, Helmholtz Institute for Pharmaceutical Research Saarland (HIPS), Helmholtz Centre for Infection Research (HZI) and Department of Pharmacy Saarland University, Saarbrücken, Germany
- German Centre for Infection Research (DZIF), Braunschweig, Germany
| | - Timo Risch
- Microbial Natural Products, Helmholtz Institute for Pharmaceutical Research Saarland (HIPS), Helmholtz Centre for Infection Research (HZI) and Department of Pharmacy Saarland University, Saarbrücken, Germany
- German Centre for Infection Research (DZIF), Braunschweig, Germany
| | - Claas Baier
- Institute for Medical Microbiology and Hospital Epidemiology, Hannover Medical School (MHH), Hannover, Germany
| | - Dirk Schlüter
- German Centre for Infection Research (DZIF), Braunschweig, Germany
- Institute for Medical Microbiology and Hospital Epidemiology, Hannover Medical School (MHH), Hannover, Germany
| | - Jennifer Herrmann
- Microbial Natural Products, Helmholtz Institute for Pharmaceutical Research Saarland (HIPS), Helmholtz Centre for Infection Research (HZI) and Department of Pharmacy Saarland University, Saarbrücken, Germany
- German Centre for Infection Research (DZIF), Braunschweig, Germany
| | - Rolf Müller
- Microbial Natural Products, Helmholtz Institute for Pharmaceutical Research Saarland (HIPS), Helmholtz Centre for Infection Research (HZI) and Department of Pharmacy Saarland University, Saarbrücken, Germany
- German Centre for Infection Research (DZIF), Braunschweig, Germany
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Gómez-Brandón M, Beesigamukama D, Probst M, Klammsteiner T, Zhou Y, Zhu YG, Mbi Tanga C. Garden fruit chafer (Pachnoda sinuata L.) accelerates recycling and bioremediation of animal waste. Waste Manag 2024; 173:131-140. [PMID: 37989012 DOI: 10.1016/j.wasman.2023.11.019] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 05/09/2023] [Revised: 10/26/2023] [Accepted: 11/16/2023] [Indexed: 11/23/2023]
Abstract
Bioconversion of livestock wastes using insect larvae represents an emerging and effective strategy for waste management. However, knowledge on the role of the garden fruit chafer (Pachnoda sinuataL.) in waste recycling and influence on the diversity ofmicrobial community infrass fertilizeris limited. Here, we determined whether and to what extent the conversion of cattle dung into insect frass fertilizer byP. sinuatainfluences the frass' microbial community and its associated antibiotic resistance genes abundance. Pachnoda sinuata larvae were used to valorise cattle dung into frass fertilizer; samples were collected weekly to determine the composition of bacteria and fungi, and antibiotic resistant genes using molecular tools. Results revealed that bioconversion of cattle dung byP. sinuatalarvae significantly increased the richness of beneficial bacteria in the frass fertilizer by 2.5-folds within 28 days, but fungal richness did not vary during the study. Treatment of cattle dung withP. sinuatalarvae caused 2 - 3-folds decrease in the genes conferring resistance to commonly used antibiotics such as aminoglycoside, diaminopyrimidine, multidrug, sulfonamide and tetracycline within 14 days. Furthermore, the recycling cattle dung using considerably reduced the abundance of mobile genetic elements known to play critical roles in the horizontal transfer of antibiotic resistance genes between organisms. This studyhighlights the efficiency ofsaprohytic insects in recycling animal manure and suppressing manure-borne pathogens in the organic fertilizer products, opening new market opportunities for innovative and safe bio-based products and achieving efficient resource utilization in a circular and green economy.
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Affiliation(s)
- María Gómez-Brandón
- Grupo de Ecología Animal (GEA), University of Vigo, Vigo 36310, Galicia, Spain
| | - Dennis Beesigamukama
- International Centre of Insect Physiology and Ecology, P. O. Box 30772-00100, Nairobi, Kenya
| | - Maraike Probst
- Universität Innsbruck, Department of Microbiology, Technikerstraβe 25d, Innsbruck, A-6020, Austria
| | - Thomas Klammsteiner
- Universität Innsbruck, Department of Microbiology, Technikerstraβe 25d, Innsbruck, A-6020, Austria; Universität Innsbruck, Department of Ecology, Technikerstraße 25, Innsbruck, A-6020, Austria
| | - YanYan Zhou
- Key Lab of Urban Environment and Health, Institute of Urban Environment, Chinese Academy of Sciences, Xiamen, 361021 China
| | - Yong-Guan Zhu
- Key Lab of Urban Environment and Health, Institute of Urban Environment, Chinese Academy of Sciences, Xiamen, 361021 China; State Key Laboratory of Urban and Regional Ecology, Research Center for Eco-Environmental Sciences, Chinese Academy of Sciences, Beijing 100085, China
| | - Chrysantus Mbi Tanga
- International Centre of Insect Physiology and Ecology, P. O. Box 30772-00100, Nairobi, Kenya.
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Maddalon A, Pierzchalski A, Krause JL, Bauer M, Finckh S, Brack W, Zenclussen AC, Marinovich M, Corsini E, Krauss M, Herberth G. Impact of chemical mixtures from wastewater treatment plant effluents on human immune cell activation: An effect-based analysis. Sci Total Environ 2024; 906:167495. [PMID: 37804965 DOI: 10.1016/j.scitotenv.2023.167495] [Citation(s) in RCA: 1] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 08/23/2023] [Revised: 09/27/2023] [Accepted: 09/28/2023] [Indexed: 10/09/2023]
Abstract
BACKGROUND Humans are exposed to many different chemicals on a daily basis, mostly as chemical mixtures, usually from food, consumer products and the environment. Wastewater treatment plant effluent contains mixtures of chemicals that have been discarded or excreted by humans and not removed by water treatment. These effluents contribute directly to water pollution, they are used in agriculture and may affect human health. The possible effect of such chemical mixtures on the immune system has not been characterized. OBJECTIVE The aim of this study was to investigate the effect of extracts obtained from four European wastewater treatment plant effluents on human primary immune cell activation. METHODS Immune cells were exposed to the effluent extracts and modulation of cell activation was performed by multi-parameter flow cytometry. Messenger-RNA (mRNA) expression of genes related to immune system and hormone receptors was measured by RT-PCR. RESULTS The exposure of immune cells to these extracts, containing 339 detected chemicals, significantly reduced the activation of human lymphocytes, mainly affecting T helper and mucosal-associated invariant T cells. In addition, basophil activation was also altered upon mixture exposure. Concerning mRNA expression, we observed that 12 transcripts were down-regulated by at least one extract while 11 were up-regulated. Correlation analyses between the analyzed immune parameters and the concentration of chemicals in the WWTP extracts, highlighted the most immunomodulatory chemicals. DISCUSSION Our results suggest that the mixture of chemicals present in the effluents of wastewater treatment plants could be considered as immunosuppressive, due to their ability to interfere with the activation of immune cells, a process of utmost importance for the functionality of the immune system. The combined approach of immune effect-based analysis and chemical content analysis used in our study provides a useful tool for investigating the effect of environmental mixtures on the human immune response.
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Affiliation(s)
- Ambra Maddalon
- Laboratory of Toxicology, Department of Pharmacological and Biomolecular Sciences 'Rodolfo Paoletti', Università degli Studi di Milano, Via Balzaretti 9, 20133 Milan, Italy
| | - Arkadiusz Pierzchalski
- Department of Environmental Immunology, Helmholtz Centre for Environmental Research - UFZ, Leipzig, Germany
| | - Jannike Lea Krause
- Schwiete Laboratory for Microbiota and Inflammation, German Rheumatism Research (DRFZ), Centre-a Leibniz Institute, Berlin, Germany
| | - Mario Bauer
- Department of Environmental Immunology, Helmholtz Centre for Environmental Research - UFZ, Leipzig, Germany
| | - Saskia Finckh
- Department of Effect-Directed Analysis, Helmholtz Centre for Environmental Research - UFZ, Leipzig, Germany
| | - Werner Brack
- Department of Effect-Directed Analysis, Helmholtz Centre for Environmental Research - UFZ, Leipzig, Germany; Department of Evolutionary Ecology and Environmental Toxicology, Faculty of Biological Sciences, Goethe University Frankfurt, Frankfurt/Main, Germany
| | - Ana C Zenclussen
- Department of Environmental Immunology, Helmholtz Centre for Environmental Research - UFZ, Leipzig, Germany; Perinatal Immunology Research Group, Medical Faculty, Saxonian Incubator for Clinical Translation (SIKT), University of Leipzig, Germany
| | - Marina Marinovich
- Laboratory of Toxicology, Department of Pharmacological and Biomolecular Sciences 'Rodolfo Paoletti', Università degli Studi di Milano, Via Balzaretti 9, 20133 Milan, Italy
| | - Emanuela Corsini
- Laboratory of Toxicology, Department of Pharmacological and Biomolecular Sciences 'Rodolfo Paoletti', Università degli Studi di Milano, Via Balzaretti 9, 20133 Milan, Italy
| | - Martin Krauss
- Department of Effect-Directed Analysis, Helmholtz Centre for Environmental Research - UFZ, Leipzig, Germany
| | - Gunda Herberth
- Department of Environmental Immunology, Helmholtz Centre for Environmental Research - UFZ, Leipzig, Germany.
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El Hindi K, Brachtendorf S, Hartel JC, Renné C, Birod K, Schilling K, Labocha S, Thomas D, Ferreirós N, Hahnefeld L, Dorochow E, Del Turco D, Deller T, Scholich K, Fuhrmann DC, Weigert A, Brüne B, Geisslinger G, Wittig I, Link KH, Grösch S. Hypoxia induced deregulation of sphingolipids in colon cancer is a prognostic marker for patient outcome. Biochim Biophys Acta Mol Basis Dis 2024; 1870:166906. [PMID: 37802156 DOI: 10.1016/j.bbadis.2023.166906] [Citation(s) in RCA: 1] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/29/2023] [Revised: 09/26/2023] [Accepted: 09/27/2023] [Indexed: 10/08/2023]
Abstract
Sphingolipids are important for the physicochemical properties of cellular membranes and deregulated in tumors. In human colon cancer tissue ceramide synthase (CerS) 4 and CerS5 are reduced which correlates with a reduced survival probability of late-stage colon cancer patients. Both enzymes are reduced after hypoxia in advanced colorectal cancer (CRC) cells (HCT-116, SW620) but not in non-metastatic CRC cells (SW480, Caco-2). Downregulation of CerS4 or CerS5 in advanced CRC cells enhanced tumor formation in nude mice and organoid growth in vitro. This was accompanied by an enhanced proliferation rate and metabolic changes leading to a shift towards the Warburg effect. In contrast, CerS4 or CerS5 depletion in Caco-2 cells reduced tumor growth in vivo. Lipidomic and proteomic analysis of membrane fractions revealed significant changes in tumor-promoting cellular pathways and cellular transporters. This study identifies CerS4 and CerS5 as prognostic markers for advanced colon cancer patients and provides a comprehensive overview about the associated cellular metabolic changes. We propose that the expression level of CerS4 and CerS5 in colon tumors could serve as a basis for decision-making for personalized treatment of advanced colon cancer patients. Trial registration: The study was accredited by the study board of the Deutsche Krebsgesellschaft (Registration No: St-D203, 2017/06/30, retrospectively registered).
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Affiliation(s)
- Khadija El Hindi
- Goethe-University Frankfurt, Institute of Clinical Pharmacology, Faculty of Medicine, Theodor Stern Kai 7, 60590 Frankfurt, Germany
| | - Sebastian Brachtendorf
- Goethe-University Frankfurt, Institute of Clinical Pharmacology, Faculty of Medicine, Theodor Stern Kai 7, 60590 Frankfurt, Germany
| | - Jennifer C Hartel
- Goethe-University Frankfurt, Institute of Clinical Pharmacology, Faculty of Medicine, Theodor Stern Kai 7, 60590 Frankfurt, Germany; Goethe-University Frankfurt, Department of Life Sciences, 60590 Frankfurt, Germany
| | - Christoph Renné
- Institute of Pathology and Cytology, Group Practice Wiesbaden, Germany
| | - Kerstin Birod
- Goethe-University Frankfurt, Institute of Clinical Pharmacology, Faculty of Medicine, Theodor Stern Kai 7, 60590 Frankfurt, Germany
| | - Karin Schilling
- Goethe-University Frankfurt, Institute of Clinical Pharmacology, Faculty of Medicine, Theodor Stern Kai 7, 60590 Frankfurt, Germany
| | - Sandra Labocha
- Goethe-University Frankfurt, Institute of Clinical Pharmacology, Faculty of Medicine, Theodor Stern Kai 7, 60590 Frankfurt, Germany
| | - Dominique Thomas
- Goethe-University Frankfurt, Institute of Clinical Pharmacology, Faculty of Medicine, Theodor Stern Kai 7, 60590 Frankfurt, Germany; Fraunhofer Institute for Translational Medicine and Pharmacology ITMP, Theodor-Stern-Kai 7, 60596 Frankfurt am Main, Germany; Fraunhofer Cluster of Excellence for Immune-Mediated Diseases CIMD, Theodor-Stern-Kai 7, 60596 Frankfurt am Main, Germany
| | - Nerea Ferreirós
- Goethe-University Frankfurt, Institute of Clinical Pharmacology, Faculty of Medicine, Theodor Stern Kai 7, 60590 Frankfurt, Germany
| | - Lisa Hahnefeld
- Goethe-University Frankfurt, Institute of Clinical Pharmacology, Faculty of Medicine, Theodor Stern Kai 7, 60590 Frankfurt, Germany; Fraunhofer Institute for Translational Medicine and Pharmacology ITMP, Theodor-Stern-Kai 7, 60596 Frankfurt am Main, Germany; Fraunhofer Cluster of Excellence for Immune-Mediated Diseases CIMD, Theodor-Stern-Kai 7, 60596 Frankfurt am Main, Germany
| | - Erika Dorochow
- Goethe-University Frankfurt, Institute of Clinical Pharmacology, Faculty of Medicine, Theodor Stern Kai 7, 60590 Frankfurt, Germany
| | - Domenico Del Turco
- Goethe-University Frankfurt, Institute of Clinical Neuroanatomy, Dr. Senckenberg Anatomy, Faculty of Medicine, Theodor Stern Kai 7, 60596 Frankfurt am Main, Germany
| | - Thomas Deller
- Goethe-University Frankfurt, Institute of Clinical Neuroanatomy, Dr. Senckenberg Anatomy, Faculty of Medicine, Theodor Stern Kai 7, 60596 Frankfurt am Main, Germany
| | - Klaus Scholich
- Goethe-University Frankfurt, Institute of Clinical Pharmacology, Faculty of Medicine, Theodor Stern Kai 7, 60590 Frankfurt, Germany; Fraunhofer Institute for Translational Medicine and Pharmacology ITMP, Theodor-Stern-Kai 7, 60596 Frankfurt am Main, Germany
| | - Dominik C Fuhrmann
- Goethe-University Frankfurt, Institute of Biochemistry I, Faculty of Medicine, Theodor-Stern-Kai 7, 60596 Frankfurt, Germany
| | - Andreas Weigert
- Goethe-University Frankfurt, Institute of Biochemistry I, Faculty of Medicine, Theodor-Stern-Kai 7, 60596 Frankfurt, Germany
| | - Bernhard Brüne
- Goethe-University Frankfurt, Institute of Biochemistry I, Faculty of Medicine, Theodor-Stern-Kai 7, 60596 Frankfurt, Germany
| | - Gerd Geisslinger
- Goethe-University Frankfurt, Institute of Clinical Pharmacology, Faculty of Medicine, Theodor Stern Kai 7, 60590 Frankfurt, Germany; Fraunhofer Institute for Translational Medicine and Pharmacology ITMP, Theodor-Stern-Kai 7, 60596 Frankfurt am Main, Germany; Fraunhofer Cluster of Excellence for Immune-Mediated Diseases CIMD, Theodor-Stern-Kai 7, 60596 Frankfurt am Main, Germany
| | - Ilka Wittig
- Goethe-University Frankfurt, Functional Proteomics, Institute of Cardiovascular Physiology, Faculty of Medicine, Frankfurt am Main, Germany
| | - Karl-Heinrich Link
- Asklepios Tumor Center (ATC) and Surgical Center, Asklepios Paulinen Klinik, Wiesbaden 65197, Germany
| | - Sabine Grösch
- Goethe-University Frankfurt, Institute of Clinical Pharmacology, Faculty of Medicine, Theodor Stern Kai 7, 60590 Frankfurt, Germany; Fraunhofer Institute for Translational Medicine and Pharmacology ITMP, Theodor-Stern-Kai 7, 60596 Frankfurt am Main, Germany.
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Selheim F, Aasebø E, Bruserud Ø, Hernandez-Valladares M. High Mitochondrial Protein Expression as a Potential Predictor of Relapse Risk in Acute Myeloid Leukemia Patients with the Monocytic FAB Subtypes M4 and M5. Cancers (Basel) 2023; 16:8. [PMID: 38201437 PMCID: PMC10778527 DOI: 10.3390/cancers16010008] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/24/2023] [Revised: 12/08/2023] [Accepted: 12/12/2023] [Indexed: 01/12/2024] Open
Abstract
AML is a highly aggressive and heterogeneous form of hematological cancer. Proteomics-based stratification of patients into more refined subgroups may contribute to a more precise characterization of the patient-derived AML cells. Here, we reanalyzed liquid chromatography-tandem mass spectrometry (LC-MS/MS) generated proteomic and phosphoproteomic data from 26 FAB-M4/M5 patients. The patients achieved complete hematological remission after induction therapy. Twelve of them later developed chemoresistant relapse (RELAPSE), and 14 patients were relapse-free (REL_FREE) long-term survivors. We considered not only the RELAPSE and REL_FREE characteristics but also integrated the French-American-British (FAB) classification, along with considering the presence of nucleophosmin 1 (NPM1) mutation and cytogenetically normal AML. We found a significant number of differentially enriched proteins (911) and phosphoproteins (257) between the various FAB subtypes in RELAPSE patients. Patients with the myeloblastic M1/M2 subtype showed higher levels of RNA processing-related routes and lower levels of signaling related to terms like translation and degranulation when compared with the M4/M5 subtype. Moreover, we found that a high abundance of proteins associated with mitochondrial translation and oxidative phosphorylation, particularly observed in the RELAPSE M4/M5 NPM1 mutated subgroup, distinguishes relapsing from non-relapsing AML patient cells with the FAB subtype M4/M5. Thus, the discovery of subtype-specific biomarkers through proteomic profiling may complement the existing classification system for AML and potentially aid in selecting personalized treatment strategies for individual patients.
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Affiliation(s)
- Frode Selheim
- Proteomics Unit of University of Bergen (PROBE), University of Bergen, Jonas Lies vei 91, 5009 Bergen, Norway
| | - Elise Aasebø
- Acute Leukemia Research Group, Department of Clinical Science, University of Bergen, Jonas Lies vei 91, 5009 Bergen, Norway; (E.A.); (Ø.B.)
| | - Øystein Bruserud
- Acute Leukemia Research Group, Department of Clinical Science, University of Bergen, Jonas Lies vei 91, 5009 Bergen, Norway; (E.A.); (Ø.B.)
- Section for Hematology, Department of Medicine, Haukeland University Hospital, 5009 Bergen, Norway
| | - Maria Hernandez-Valladares
- Proteomics Unit of University of Bergen (PROBE), University of Bergen, Jonas Lies vei 91, 5009 Bergen, Norway
- Department of Physical Chemistry, Institute of Biotechnology, Excellence Unit in Chemistry Applied to Biomedicine and Environment, School of Sciences, University of Granada, Campus Fuentenueva s/n, 18071 Granada, Spain
- Instituto de Investigación Biosanitaria ibs.GRANADA, 18012 Granada, Spain
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Zhang X, Bradford B, Baweja S, Tan T, Lee HW, Jose CC, Kim N, Katari M, Cuddapah S. Nickel-induced transcriptional memory in lung epithelial cells promotes interferon signaling upon nicotine exposure. Toxicol Appl Pharmacol 2023; 481:116753. [PMID: 37951547 DOI: 10.1016/j.taap.2023.116753] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/12/2023] [Revised: 11/06/2023] [Accepted: 11/07/2023] [Indexed: 11/14/2023]
Abstract
Exposure to nickel, an environmental respiratory toxicant, is associated with lung diseases including asthma, pulmonary fibrosis, bronchitis and cancers. Our previous studies have shown that a majority of the nickel-induced transcriptional changes are persistent and do not reverse even after the termination of exposure. This suggested transcriptional memory, wherein the cell 'remembers' past nickel exposure. Transcriptional memory, due to which the cells respond more robustly to a previously encountered stimulus has been identified in a number of organisms. Therefore, transcriptional memory has been described as an adaptive mechanism. However, transcriptional memory caused by environmental toxicant exposures has not been well investigated. Moreover, how the transcriptional memory caused by an environmental toxicant might influence the outcome of exposure to a second toxicant has not been explored. In this study, we investigated whether nickel-induced transcriptional memory influences the outcome of the cell's response to a second respiratory toxicant, nicotine. Nicotine, an addictive compound in tobacco, is associated with the development of chronic lung diseases including chronic obstructive pulmonary disease (COPD) and pulmonary fibrosis. Our results show that nicotine exposure upregulated a subset of genes only in the cells previously exposed to nickel. Furthermore, our analyses indicate robust activation of interferon (IFN) signaling in these cells. IFN signaling is a driver of inflammation, which is associated with many chronic lung diseases. Therefore, our results suggest that nicotine exposure of lung cells that retain the transcriptional memory of previous nickel exposure could result in increased susceptibility to developing chronic inflammatory lung diseases.
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Affiliation(s)
- Xiaoru Zhang
- Division of Environmental Medicine, Department of Medicine, New York University Grossman School of Medicine, New York, NY 10010, USA
| | - Beatrix Bradford
- Division of Environmental Medicine, Department of Medicine, New York University Grossman School of Medicine, New York, NY 10010, USA
| | - Sahdev Baweja
- Division of Environmental Medicine, Department of Medicine, New York University Grossman School of Medicine, New York, NY 10010, USA; Center for Genomics and Systems Biology, Department of Biology, New York University, New York, NY 10003, USA
| | - Taotao Tan
- Center for Genomics and Systems Biology, Department of Biology, New York University, New York, NY 10003, USA
| | - Hyun-Wook Lee
- Division of Environmental Medicine, Department of Medicine, New York University Grossman School of Medicine, New York, NY 10010, USA
| | - Cynthia C Jose
- Division of Environmental Medicine, Department of Medicine, New York University Grossman School of Medicine, New York, NY 10010, USA
| | - Nicholas Kim
- Division of Environmental Medicine, Department of Medicine, New York University Grossman School of Medicine, New York, NY 10010, USA
| | - Manpreet Katari
- Center for Genomics and Systems Biology, Department of Biology, New York University, New York, NY 10003, USA.
| | - Suresh Cuddapah
- Division of Environmental Medicine, Department of Medicine, New York University Grossman School of Medicine, New York, NY 10010, USA.
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Wilcox NS, Yarovinsky TO, Pandya P, Ramgolam VS, Moro A, Wu Y, Nicoli S, Hirschi KK, Bender JR. Distinct hypoxia-induced translational profiles of embryonic and adult-derived macrophages. iScience 2023; 26:107985. [PMID: 38047075 PMCID: PMC10690575 DOI: 10.1016/j.isci.2023.107985] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/20/2021] [Revised: 07/21/2023] [Accepted: 09/15/2023] [Indexed: 12/05/2023] Open
Abstract
Tissue resident macrophages are largely of embryonic (fetal liver) origin and long-lived, while bone marrow-derived macrophages (BMDM) are recruited following an acute perturbation, such as hypoxia in the setting of myocardial ischemia. Prior transcriptome analyses identified BMDM and fetal liver-derived macrophage (FLDM) differences at the RNA expression level. Posttranscriptional regulation determining mRNA stability and translation rate may override transcriptional signals in response to hypoxia. We profiled differentially regulated BMDM and FLDM transcripts in response to hypoxia at the level of mRNA translation. Using a translating ribosome affinity purification (TRAP) assay and RNA-seq, we identified non-overlapping transcripts with increased translation rate in BMDM (Ly6e, vimentin, PF4) and FLDM (Ccl7, Ccl2) after hypoxia. We further identified hypoxia-induced transcripts within these subsets that are regulated by the RNA-binding protein HuR. These findings define translational differences in macrophage subset gene expression programs, highlighting potential therapeutic targets in ischemic myocardium.
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Affiliation(s)
- Nicholas S. Wilcox
- Department of Internal Medicine, Section of Cardiovascular Medicine, Yale Cardiovascular Research Center, New Haven, CT USA
- Department of Immunobiology, and Yale University School of Medicine, New Haven, CT 06511, USA
| | - Timur O. Yarovinsky
- Department of Internal Medicine, Section of Cardiovascular Medicine, Yale Cardiovascular Research Center, New Haven, CT USA
- Department of Immunobiology, and Yale University School of Medicine, New Haven, CT 06511, USA
| | - Prakruti Pandya
- Department of Internal Medicine, Section of Cardiovascular Medicine, Yale Cardiovascular Research Center, New Haven, CT USA
- Department of Immunobiology, and Yale University School of Medicine, New Haven, CT 06511, USA
| | - Vinod S. Ramgolam
- Department of Internal Medicine, Section of Cardiovascular Medicine, Yale Cardiovascular Research Center, New Haven, CT USA
- Department of Immunobiology, and Yale University School of Medicine, New Haven, CT 06511, USA
| | - Albertomaria Moro
- Department of Internal Medicine, Section of Cardiovascular Medicine, Yale Cardiovascular Research Center, New Haven, CT USA
- Department of Genetics, Yale University School of Medicine, New Haven, CT 06511, USA
| | - Yinyu Wu
- Department of Internal Medicine, Section of Cardiovascular Medicine, Yale Cardiovascular Research Center, New Haven, CT USA
- Department of Genetics, Yale University School of Medicine, New Haven, CT 06511, USA
| | - Stefania Nicoli
- Department of Internal Medicine, Section of Cardiovascular Medicine, Yale Cardiovascular Research Center, New Haven, CT USA
- Department of Genetics, Yale University School of Medicine, New Haven, CT 06511, USA
| | - Karen K. Hirschi
- Department of Internal Medicine, Section of Cardiovascular Medicine, Yale Cardiovascular Research Center, New Haven, CT USA
- Department of Genetics, Yale University School of Medicine, New Haven, CT 06511, USA
| | - Jeffrey R. Bender
- Department of Internal Medicine, Section of Cardiovascular Medicine, Yale Cardiovascular Research Center, New Haven, CT USA
- Department of Immunobiology, and Yale University School of Medicine, New Haven, CT 06511, USA
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37
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Goyon V, Besse‐Patin A, Zunino R, Ignatenko O, Nguyen M, Coyaud É, Lee JM, Nguyen BN, Raught B, McBride HM. MAPL loss dysregulates bile and liver metabolism in mice. EMBO Rep 2023; 24:e57972. [PMID: 37962001 PMCID: PMC10702803 DOI: 10.15252/embr.202357972] [Citation(s) in RCA: 1] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/10/2023] [Revised: 10/10/2023] [Accepted: 10/17/2023] [Indexed: 11/15/2023] Open
Abstract
Mitochondrial and peroxisomal anchored protein ligase (MAPL) is a dual ubiquitin and small ubiquitin-like modifier (SUMO) ligase with roles in mitochondrial quality control, cell death and inflammation in cultured cells. Here, we show that MAPL function in the organismal context converges on metabolic control, as knockout mice are viable, insulin-sensitive, and protected from diet-induced obesity. MAPL loss leads to liver-specific activation of the integrated stress response, inducing secretion of stress hormone FGF21. MAPL knockout mice develop fully penetrant spontaneous hepatocellular carcinoma. Mechanistically, the peroxisomal bile acid transporter ABCD3 is a primary MAPL interacting partner and SUMOylated in a MAPL-dependent manner. MAPL knockout leads to increased bile acid production coupled with defective regulatory feedback in liver in vivo and in isolated primary hepatocytes, suggesting cell-autonomous function. Together, our findings establish MAPL function as a regulator of bile acid synthesis whose loss leads to the disruption of bile acid feedback mechanisms. The consequences of MAPL loss in liver, along with evidence of tumor suppression through regulation of cell survival pathways, ultimately lead to hepatocellular carcinogenesis.
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Affiliation(s)
- Vanessa Goyon
- Montreal Neurological InstituteMcGill UniversityMontrealQCCanada
| | | | - Rodolfo Zunino
- Montreal Neurological InstituteMcGill UniversityMontrealQCCanada
| | - Olesia Ignatenko
- Montreal Neurological InstituteMcGill UniversityMontrealQCCanada
| | - Mai Nguyen
- Montreal Neurological InstituteMcGill UniversityMontrealQCCanada
| | - Étienne Coyaud
- Princess Margaret Cancer CentreUniversity Health NetworkTorontoONCanada
- Department of Medical BiophysicsUniversity of TorontoTorontoONCanada
| | - Jonathan M Lee
- Biochemistry, Microbiology & ImmunologyUniversity of OttawaOttawaONCanada
| | - Bich N Nguyen
- Department of Pathology and Cell BiologyUniversity of MontrealMontrealQCCanada
- University of Montreal Health NetworkMontrealQCCanada
| | - Brian Raught
- Princess Margaret Cancer CentreUniversity Health NetworkTorontoONCanada
- Department of Medical BiophysicsUniversity of TorontoTorontoONCanada
| | - Heidi M McBride
- Montreal Neurological InstituteMcGill UniversityMontrealQCCanada
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Tian X, Teo WFA, Wee WY, Yang Y, Ahmed H, Jakubovics NS, Choo SW, Tan GYA. Genome characterization and taxonomy of Actinomyces acetigenes sp. nov., and Actinomyces stomatis sp. nov., previously isolated from the human oral cavity. BMC Genomics 2023; 24:734. [PMID: 38049764 PMCID: PMC10696680 DOI: 10.1186/s12864-023-09831-2] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/30/2023] [Accepted: 11/22/2023] [Indexed: 12/06/2023] Open
Abstract
BACKGROUND Actinomyces strains are commonly found as part of the normal microflora on human tissue surfaces, including the oropharynx, gastrointestinal tract, and female genital tract. Understanding the diversity and characterization of Actinomyces species is crucial for human health, as they play an important role in dental plaque formation and biofilm-related infections. Two Actinomyces strains ATCC 49340 T and ATCC 51655 T have been utilized in various studies, but their accurate species classification and description remain unresolved. RESULTS To investigate the genomic properties and taxonomic status of these strains, we employed both 16S rRNA Sanger sequencing and whole-genome sequencing using the Illumina HiSeq X Ten platform with PE151 (paired-end) sequencing. Our analyses revealed that the draft genome of Actinomyces acetigenes ATCC 49340 T was 3.27 Mbp with a 68.0% GC content, and Actinomyces stomatis ATCC 51655 T has a genome size of 3.08 Mbp with a 68.1% GC content. Multi-locus (atpA, rpoB, pgi, metG, gltA, gyrA, and core genome SNPs) sequence analysis supported the phylogenetic placement of strains ATCC 51655 T and ATCC 49340 T as independent lineages. Digital DNA-DNA hybridization (dDDH), average nucleotide identity (ANI), and average amino acid identity (AAI) analyses indicated that both strains represented novel Actinomyces species, with values below the threshold for species demarcation (70% dDDH, 95% ANI and AAI). Pangenome analysis identified 5,731 gene clusters with strains ATCC 49340 T and ATCC 51655 T possessing 1,515 and 1,518 unique gene clusters, respectively. Additionally, genomic islands (GIs) prediction uncovered 24 putative GIs in strain ATCC 49340 T and 16 in strain ATCC 51655 T, contributing to their genetic diversity and potential adaptive capabilities. Pathogenicity analysis highlighted the potential human pathogenicity risk associated with both strains, with several virulence-associated factors identified. CRISPR-Cas analysis exposed the presence of CRISPR and Cas genes in both strains, indicating these strains might evolve a robust defense mechanism against them. CONCLUSION This study supports the classification of strains ATCC 49340 T and ATCC 51655 T as novel species within the Actinomyces, in which the name Actinomyces acetigenes sp. nov. (type strain ATCC 49340 T = VPI D163E-3 T = CCUG 34286 T = CCUG 35339 T) and Actinomyces stomatis sp. nov. (type strain ATCC 51655 T = PK606T = CCUG 33930 T) are proposed.
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Affiliation(s)
- Xuechen Tian
- Institute of Biological Sciences, Faculty of Science, Universiti Malaya, 50603, Kuala Lumpur, Malaysia
| | - Wee Fei Aaron Teo
- Institute of Biological Sciences, Faculty of Science, Universiti Malaya, 50603, Kuala Lumpur, Malaysia
- Centre for Research in Biotechnology for Agriculture, Universiti Malaya, 50603, Kuala Lumpur, Malaysia
| | - Wei Yee Wee
- School of Science, Monash University Malaysia, Jalan Lagoon Selatan, Bandar Sunway, Subang Jaya, Selangor, 46150, Malaysia
| | - Yixin Yang
- College of Science, Mathematics and Technology, Wenzhou-Kean University, 88 Daxue Road, Ouhai, Wenzhou, Zhejiang Province, 325060, China
- Wenzhou Municipal Key Laboratory for Applied Biomedical and Biopharmaceutical Informatics, Wenzhou-Kean University, 88 Daxue Road, Ouhai, Wenzhou, Zhejiang Province, 325060, China
- Zhejiang Bioinformatics International Science and Technology Cooperation Center, Wenzhou-Kean University, 88 Daxue Road, Ouhai, Wenzhou, Zhejiang Province, 325060, China
| | - Halah Ahmed
- School of Dental Sciences, Faculty of Medical Sciences, Newcastle University, Framlington Place, Newcastle Upon Tyne, NE2 4BW, UK
| | - Nicholas S Jakubovics
- School of Dental Sciences, Faculty of Medical Sciences, Newcastle University, Framlington Place, Newcastle Upon Tyne, NE2 4BW, UK.
| | - Siew Woh Choo
- College of Science, Mathematics and Technology, Wenzhou-Kean University, 88 Daxue Road, Ouhai, Wenzhou, Zhejiang Province, 325060, China.
- Wenzhou Municipal Key Laboratory for Applied Biomedical and Biopharmaceutical Informatics, Wenzhou-Kean University, 88 Daxue Road, Ouhai, Wenzhou, Zhejiang Province, 325060, China.
- Zhejiang Bioinformatics International Science and Technology Cooperation Center, Wenzhou-Kean University, 88 Daxue Road, Ouhai, Wenzhou, Zhejiang Province, 325060, China.
| | - Geok Yuan Annie Tan
- Institute of Biological Sciences, Faculty of Science, Universiti Malaya, 50603, Kuala Lumpur, Malaysia.
- Centre for Research in Biotechnology for Agriculture, Universiti Malaya, 50603, Kuala Lumpur, Malaysia.
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Moreno-Paz M, dos Santos Severino RS, Sánchez-García L, Manchado JM, García-Villadangos M, Aguirre J, Fernández-Martínez MA, Carrizo D, Kobayashi L, Dave A, Warren-Rhodes K, Davila A, Stoker CR, Glass B, Parro V. Life Detection and Microbial Biomarker Profiling with Signs of Life Detector-Life Detector Chip During a Mars Drilling Simulation Campaign in the Hyperarid Core of the Atacama Desert. Astrobiology 2023; 23:1259-1283. [PMID: 37930382 PMCID: PMC10825288 DOI: 10.1089/ast.2021.0174] [Citation(s) in RCA: 2] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 10/26/2021] [Accepted: 07/02/2023] [Indexed: 11/07/2023]
Abstract
The low organic matter content in the hyperarid core of the Atacama Desert, together with abrupt temperature shifts and high ultraviolet radiation at its surface, makes this region one of the best terrestrial analogs of Mars and one of the best scenarios for testing instrumentation devoted to in situ planetary exploration. We have operated remotely and autonomously the SOLID-LDChip (Signs of Life Detector-Life Detector Chip), an antibody microarray-based sensor instrument, as part of a rover payload during the 2019 NASA Atacama Rover Astrobiology Drilling Studies (ARADS) Mars drilling simulation campaign. A robotic arm collected drilled cuttings down to 80 cm depth and loaded SOLID to process and assay them with LDChip for searching for molecular biomarkers. A remote science team received and analyzed telemetry data and LDChip results. The data revealed the presence of microbial markers from Proteobacteria, Acidobacteria, Bacteroidetes, Actinobacteria, Firmicutes, and Cyanobacteria to be relatively more abundant in the middle layer (40-50 cm). In addition, the detection of several proteins from nitrogen metabolism indicates a pivotal role in the system. These findings were corroborated and complemented on "returned samples" to the lab by a comprehensive analysis that included DNA sequencing, metaproteomics, and a metabolic reconstruction of the sampled area. Altogether, the results describe a relatively complex microbial community with members capable of nitrogen fixation and denitrification, sulfur oxidation and reduction, or triggering oxidative stress responses, among other traits. This remote operation demonstrated the high maturity of SOLID-LDChip as a powerful tool for remote in situ life detection for future missions in the Solar System.
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Affiliation(s)
- Mercedes Moreno-Paz
- Department of Molecular Evolution, Centro de Astrobiología (CAB), INTA-CSIC, Madrid, Spain
| | - Rita Sofia dos Santos Severino
- Department of Molecular Evolution, Centro de Astrobiología (CAB), INTA-CSIC, Madrid, Spain
- Departament of Física y Matemáticas y de Automática, University of Alcalá de Henares (UAH), Madrid, Spain
| | - Laura Sánchez-García
- Department of Molecular Evolution, Centro de Astrobiología (CAB), INTA-CSIC, Madrid, Spain
| | - Juan Manuel Manchado
- Department of Molecular Evolution, Centro de Astrobiología (CAB), INTA-CSIC, Madrid, Spain
| | | | - Jacobo Aguirre
- Department of Molecular Evolution, Centro de Astrobiología (CAB), INTA-CSIC, Madrid, Spain
| | - Miguel Angel Fernández-Martínez
- Department of Molecular Evolution, Centro de Astrobiología (CAB), INTA-CSIC, Madrid, Spain
- Department of Natural Resource Sciences, McGill University, Québec, Canada
| | - Daniel Carrizo
- Department of Molecular Evolution, Centro de Astrobiología (CAB), INTA-CSIC, Madrid, Spain
| | - Linda Kobayashi
- Space Science Division and Astrobiology Division, NASA Ames Research Center, Moffett Field, California, USA
| | - Arwen Dave
- Space Science Division and Astrobiology Division, NASA Ames Research Center, Moffett Field, California, USA
| | - Kim Warren-Rhodes
- Space Science Division and Astrobiology Division, NASA Ames Research Center, Moffett Field, California, USA
- Carl Sagan Center, SETI Institute, Mountain View, California, USA
| | - Alfonso Davila
- Space Science Division and Astrobiology Division, NASA Ames Research Center, Moffett Field, California, USA
| | - Carol R. Stoker
- Space Science Division and Astrobiology Division, NASA Ames Research Center, Moffett Field, California, USA
| | - Brian Glass
- Space Science Division and Astrobiology Division, NASA Ames Research Center, Moffett Field, California, USA
| | - Víctor Parro
- Department of Molecular Evolution, Centro de Astrobiología (CAB), INTA-CSIC, Madrid, Spain
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Aisagbonhi O, Bui T, Nasamran CA, St Louis H, Pizzo D, Meads M, Mulholland M, Magallanes C, Lamale-Smith L, Laurent LC, Morey R, Jacobs MB, Fisch KM, Horii M. High placental expression of FLT1, LEP, PHYHIP and IL3RA - In persons of African ancestry with severe preeclampsia. Placenta 2023; 144:13-22. [PMID: 37949031 PMCID: PMC10843761 DOI: 10.1016/j.placenta.2023.10.008] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Received: 07/05/2023] [Revised: 10/13/2023] [Accepted: 10/16/2023] [Indexed: 11/12/2023]
Abstract
INTRODUCTION Mortality from preeclampsia (PE) and PE-associated morbidities are 3-to 5-fold higher in persons of African ancestry than in those of Asian and European ancestries. METHODS To elucidate placental contribution to worse PE outcomes in African ancestry pregnancies, we performed bulk RNA sequencing on 50 placentas from persons with severe PE (sPE) of African (n = 9), Asian (n = 18) and European (n = 23) ancestries and 73 normotensive controls of African (n = 10), Asian (n = 15) and European (n = 48) ancestries. RESULTS Previously described canonical preeclampsia genes, involved in metabolism and hypoxia/angiogenesis including: LEP, HK2, FSTL3, FLT1, ENG, TMEM45A, ARHGEF4 and HTRA1 were upregulated sPE versus normotensive placentas across ancestries. LTF, NPR3 and PHYHIP were higher in African vs. Asian ancestry sPE placentas. Allograft rejection/adaptive immune response genes were upregulated in placentas from African but not in Asian or European ancestry sPE patients; IL3RA was of particular interest because the patient with the highest placental IL3RA expression, a person of African ancestry with sPE, developed postpartum cardiomyopathy, and was the only patient out of 123, that developed this condition. Interestingly, the sPE patients with the highest IL3RA expression among persons of Asian and European ancestries developed unexplained tachycardia peripartum, necessitating echocardiography in the European ancestry patient. The association between elevated placental IL3RA levels and unexplained tachycardia or peripartum cardiomyopathy was found to be significant in the 50 sPE patients (p = .0005). DISCUSSION High placental upregulation of both canonical preeclampsia and allograft rejection/adaptive immune response genes may contribute to worse PE outcomes in African ancestry sPE patients.
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Affiliation(s)
- Omonigho Aisagbonhi
- Department of Pathology, University of California, San Diego, La Jolla, CA, USA; Center for Perinatal Discovery, University of California, San Diego, La Jolla, CA, USA.
| | - Tony Bui
- Department of Pathology, University of California, San Diego, La Jolla, CA, USA; Center for Perinatal Discovery, University of California, San Diego, La Jolla, CA, USA; Sanford Consortium for Regenerative Medicine, University of California, San Diego, La Jolla, CA, USA
| | - Chanond A Nasamran
- Center for Computational Biology and Bioinformatics, University of California, San Diego, La Jolla, CA, USA
| | - Hailee St Louis
- Department of Pathology, University of California, San Diego, La Jolla, CA, USA
| | - Donald Pizzo
- Department of Pathology, University of California, San Diego, La Jolla, CA, USA
| | - Morgan Meads
- Department of Pathology, University of California, San Diego, La Jolla, CA, USA; Center for Perinatal Discovery, University of California, San Diego, La Jolla, CA, USA; Sanford Consortium for Regenerative Medicine, University of California, San Diego, La Jolla, CA, USA
| | - Megan Mulholland
- Department of Pathology, University of California, San Diego, La Jolla, CA, USA; Center for Perinatal Discovery, University of California, San Diego, La Jolla, CA, USA; Sanford Consortium for Regenerative Medicine, University of California, San Diego, La Jolla, CA, USA
| | - Celestine Magallanes
- Department of Obstetrics, Gynecology and Reproductive Sciences, University of California, San Diego, La Jolla, CA, USA
| | - Leah Lamale-Smith
- Department of Obstetrics, Gynecology and Reproductive Sciences, University of California, San Diego, La Jolla, CA, USA
| | - Louise C Laurent
- Department of Obstetrics, Gynecology and Reproductive Sciences, University of California, San Diego, La Jolla, CA, USA
| | - Robert Morey
- Department of Pathology, University of California, San Diego, La Jolla, CA, USA; Sanford Consortium for Regenerative Medicine, University of California, San Diego, La Jolla, CA, USA
| | - Marni B Jacobs
- Center for Perinatal Discovery, University of California, San Diego, La Jolla, CA, USA; Department of Obstetrics, Gynecology and Reproductive Sciences, University of California, San Diego, La Jolla, CA, USA
| | - Kathleen M Fisch
- Center for Perinatal Discovery, University of California, San Diego, La Jolla, CA, USA; Sanford Consortium for Regenerative Medicine, University of California, San Diego, La Jolla, CA, USA; Center for Computational Biology and Bioinformatics, University of California, San Diego, La Jolla, CA, USA; Department of Obstetrics, Gynecology and Reproductive Sciences, University of California, San Diego, La Jolla, CA, USA
| | - Mariko Horii
- Department of Pathology, University of California, San Diego, La Jolla, CA, USA; Center for Perinatal Discovery, University of California, San Diego, La Jolla, CA, USA; Sanford Consortium for Regenerative Medicine, University of California, San Diego, La Jolla, CA, USA
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Liu Z, Gao J, Li C, Xu L, Lv X, Deng H, Gao Y, Wang H, Li H, Wang Z. Application of QSAR models for acute toxicity of tetrazole compounds administrated orally and intraperitoneally in rat and mouse. Toxicology 2023; 500:153679. [PMID: 38042272 DOI: 10.1016/j.tox.2023.153679] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/07/2023] [Revised: 11/10/2023] [Accepted: 11/20/2023] [Indexed: 12/04/2023]
Abstract
Tetrazoles and their derivatives possess various biological activities, such as antibacterial, anti-fungal, and other activities. However, these compounds may induce specific cumulative and toxic effects in living organisms. Therefore, quantitative structure-activity relationship (QSAR) models were constructed to study the acute oral toxicity of tetrazoles in rats and mice. The toxicity data of 111 tetrazole compounds were collected using the ChemIDplus, ChEMBL and ECHA databases as response variables, while the PaDEL-descriptor generated the 2D descriptors as independent variables. The models were developed and validated following the OECD guidelines by the DTC-QSAR tool. Three QSAR models were successfully established for the oral routes of rat and mouse and the intraperitoneal route of mouse, respectively. The scatter plots showed high consistency between the training and test data sets. All the models successfully met the external and internal validation criteria. Most of the descriptors kept in the final models exhibited positive correlations with toxicity, whereas only 6 descriptors exhibited negative associations. Several chemicals were identified as response or structural outliers, based on the standardized residuals and leverage values. In conclusion, the findings of this investigation demonstrate that the proposed QSAR models hold promise in forecasting the acute toxicity of recently developed or synthesized tetrazole compounds, thereby mitigating potential risks to human health and the environment.
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Affiliation(s)
- Zhiyong Liu
- Toxicology Research Center, Xi'an Key Laboratory of Toxicology and Biological effect, Institute for Hygiene of Ordnance Industry, Xi'an, Shaanxi 710065, China.
| | - Junhong Gao
- Toxicology Research Center, Xi'an Key Laboratory of Toxicology and Biological effect, Institute for Hygiene of Ordnance Industry, Xi'an, Shaanxi 710065, China.
| | - Cunzhi Li
- Toxicology Research Center, Xi'an Key Laboratory of Toxicology and Biological effect, Institute for Hygiene of Ordnance Industry, Xi'an, Shaanxi 710065, China
| | - Lihong Xu
- Department of Infectious Disease Supervision, Xi'an Health Supervision Institute, Xi'an, Shaanxi 710018, China
| | - Xiaoqiang Lv
- Toxicology Research Center, Xi'an Key Laboratory of Toxicology and Biological effect, Institute for Hygiene of Ordnance Industry, Xi'an, Shaanxi 710065, China
| | - Hui Deng
- Toxicology Research Center, Xi'an Key Laboratory of Toxicology and Biological effect, Institute for Hygiene of Ordnance Industry, Xi'an, Shaanxi 710065, China
| | - Yongchao Gao
- Toxicology Research Center, Xi'an Key Laboratory of Toxicology and Biological effect, Institute for Hygiene of Ordnance Industry, Xi'an, Shaanxi 710065, China
| | - Hong Wang
- Toxicology Research Center, Xi'an Key Laboratory of Toxicology and Biological effect, Institute for Hygiene of Ordnance Industry, Xi'an, Shaanxi 710065, China
| | - Huan Li
- Toxicology Research Center, Xi'an Key Laboratory of Toxicology and Biological effect, Institute for Hygiene of Ordnance Industry, Xi'an, Shaanxi 710065, China
| | - Zhigang Wang
- Toxicology Research Center, Xi'an Key Laboratory of Toxicology and Biological effect, Institute for Hygiene of Ordnance Industry, Xi'an, Shaanxi 710065, China
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Yang Q, Loureiro ZY, Desai A, DeSouza T, Li K, Wang H, Nicoloro SM, Solivan-Rivera J, Corvera S. Regulation of lipolysis by 14-3-3 proteins on human adipocyte lipid droplets. PNAS Nexus 2023; 2:pgad420. [PMID: 38130664 PMCID: PMC10733194 DOI: 10.1093/pnasnexus/pgad420] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Grants] [Track Full Text] [Figures] [Subscribe] [Scholar Register] [Received: 05/15/2023] [Accepted: 11/17/2023] [Indexed: 12/23/2023]
Abstract
Adipocyte lipid droplets (LDs) play a crucial role in systemic lipid metabolism by storing and releasing lipids to meet the organism's energy needs. Hormonal signals such as catecholamines and insulin act on adipocyte LDs, and impaired responsiveness to these signals can lead to uncontrolled lipolysis, lipotoxicity, and metabolic disease. To investigate the mechanisms that control LD function in human adipocytes, we applied proximity labeling mediated by enhanced ascorbate peroxidase (APEX2) to identify the interactome of PLIN1 in adipocytes differentiated from human mesenchymal progenitor cells. We identified 70 proteins that interact specifically with PLIN1, including PNPLA2 and LIPE, which are the primary effectors of regulated triglyceride hydrolysis, and 4 members of the 14-3-3 protein family (YWHAB, YWHAE, YWHAZ, and YWHAG), which are known to regulate diverse signaling pathways. Functional studies showed that YWHAB is required for maximum cyclic adenosine monophosphate (cAMP)-stimulated lipolysis, as its CRISPR-Cas9-mediated knockout mitigates lipolysis through a mechanism independent of insulin signaling. These findings reveal a new regulatory mechanism operating in human adipocytes that can impact lipolysis and potentially systemic metabolism.
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Affiliation(s)
- Qin Yang
- Program in Molecular Medicine, University of Massachusetts Chan Medical School, Worcester, MA 01605, USA
- Morningside Graduate School of Biomedical Sciences, University of Massachusetts Chan Medical School, Worcester MA 01605, USA
| | - Zinger Yang Loureiro
- Program in Molecular Medicine, University of Massachusetts Chan Medical School, Worcester, MA 01605, USA
- Morningside Graduate School of Biomedical Sciences, University of Massachusetts Chan Medical School, Worcester MA 01605, USA
| | - Anand Desai
- Program in Molecular Medicine, University of Massachusetts Chan Medical School, Worcester, MA 01605, USA
| | - Tiffany DeSouza
- Program in Molecular Medicine, University of Massachusetts Chan Medical School, Worcester, MA 01605, USA
| | - Kaida Li
- Program in Molecular Medicine, University of Massachusetts Chan Medical School, Worcester, MA 01605, USA
| | - Hui Wang
- Program in Molecular Medicine, University of Massachusetts Chan Medical School, Worcester, MA 01605, USA
| | - Sarah M Nicoloro
- Program in Molecular Medicine, University of Massachusetts Chan Medical School, Worcester, MA 01605, USA
| | - Javier Solivan-Rivera
- Program in Molecular Medicine, University of Massachusetts Chan Medical School, Worcester, MA 01605, USA
| | - Silvia Corvera
- Program in Molecular Medicine, University of Massachusetts Chan Medical School, Worcester, MA 01605, USA
- Diabetes Center of Excellence, University of Massachusetts Chan Medical School, Worcester, MA 01605, USA
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Zhong X, Peddada N, Wang J, Moresco JJ, Zhan X, Shelton JM, SoRelle JA, Keller K, Lazaro DR, Moresco EMY, Choi JH, Beutler B. OVOL2 sustains postnatal thymic epithelial cell identity. Nat Commun 2023; 14:7786. [PMID: 38012144 PMCID: PMC10682436 DOI: 10.1038/s41467-023-43456-z] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/13/2023] [Accepted: 11/09/2023] [Indexed: 11/29/2023] Open
Abstract
Distinct pathways and molecules may support embryonic versus postnatal thymic epithelial cell (TEC) development and maintenance. Here, we identify a mechanism by which TEC numbers and function are maintained postnatally. A viable missense allele (C120Y) of Ovol2, expressed ubiquitously or specifically in TECs, results in lymphopenia, in which T cell development is compromised by loss of medullary TECs and dysfunction of cortical TECs. We show that the epithelial identity of TECs is aberrantly subverted towards a mesenchymal state in OVOL2-deficient mice. We demonstrate that OVOL2 inhibits the epigenetic regulatory BRAF-HDAC complex, specifically disrupting RCOR1-LSD1 interaction. This causes inhibition of LSD1-mediated H3K4me2 demethylation, resulting in chromatin accessibility and transcriptional activation of epithelial genes. Thus, OVOL2 controls the epigenetic landscape of TECs to enforce TEC identity. The identification of a non-redundant postnatal mechanism for TEC maintenance offers an entry point to understanding thymic involution, which normally begins in early adulthood.
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Affiliation(s)
- Xue Zhong
- Center for the Genetics of Host Defense, University of Texas Southwestern Medical Center, Dallas, TX, 75390-8505, USA
| | - Nagesh Peddada
- Center for the Genetics of Host Defense, University of Texas Southwestern Medical Center, Dallas, TX, 75390-8505, USA
| | - Jianhui Wang
- Center for the Genetics of Host Defense, University of Texas Southwestern Medical Center, Dallas, TX, 75390-8505, USA
| | - James J Moresco
- Center for the Genetics of Host Defense, University of Texas Southwestern Medical Center, Dallas, TX, 75390-8505, USA
| | - Xiaowei Zhan
- Center for the Genetics of Host Defense, University of Texas Southwestern Medical Center, Dallas, TX, 75390-8505, USA
- Department of Population and Data Sciences, Quantitative Biomedical Research Center, University of Texas Southwestern Medical Center, Dallas, TX, 75390-8821, USA
| | - John M Shelton
- Intermal Medicine-Histopathology Core, University of Texas Southwestern Medical Center, Dallas, TX, 75390-8573, USA
| | - Jeffrey A SoRelle
- Department of Pathology, University of Texas Southwestern Medical Center, Dallas, TX, 75390-9072, USA
- Department of Pediatrics, University of Texas Southwestern Medical Center, Dallas, TX, 75390-9063, USA
| | - Katie Keller
- Center for the Genetics of Host Defense, University of Texas Southwestern Medical Center, Dallas, TX, 75390-8505, USA
| | - Danielle Renee Lazaro
- Center for the Genetics of Host Defense, University of Texas Southwestern Medical Center, Dallas, TX, 75390-8505, USA
| | - Eva Marie Y Moresco
- Center for the Genetics of Host Defense, University of Texas Southwestern Medical Center, Dallas, TX, 75390-8505, USA
| | - Jin Huk Choi
- Center for the Genetics of Host Defense, University of Texas Southwestern Medical Center, Dallas, TX, 75390-8505, USA.
| | - Bruce Beutler
- Center for the Genetics of Host Defense, University of Texas Southwestern Medical Center, Dallas, TX, 75390-8505, USA.
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Jadeja S, Kupcik R, Fabrik I, Sklenářová H, Lenčo J. A stationary phase with a positively charged surface allows for minimizing formic acid concentration in the mobile phase, enhancing electrospray ionization in LC-MS proteomic experiments. Analyst 2023; 148:5980-5990. [PMID: 37870390 DOI: 10.1039/d3an01508d] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 10/24/2023]
Abstract
The default choice of mobile phase acidifier for bottom-up LC-MS proteomic analyses is 0.10% formic acid because of its decent acidity, decent ion pairing ability, and low suppression of electrospray ionization. In recent years, state-of-the-art columns have been designed specifically to provide efficient separation even when using an MS-friendly mobile phase of low ionic strength. Despite this, no attempts have been made to improve the sensitivity of the MS-based analytical methods by reducing the amount of formic acid in the mobile phase. In this study, we evaluated the effect of reduced formic acid concentration in the mobile phase on the chromatographic behavior and MS response of peptides when separated using columns packed with a C18 stationary phase with a positively charged surface. Using 0.01% formic acid in the mobile phase maintained excellent chromatographic performance and increased MS signal response compared to the standard of 0.10%. The enhanced MS response translated to about 50% improved peptide identifications depending on the complexity and amount of sample injected. The increased retention of peptides at a reduced formic acid concentration was directly proportional to the number of acidic residues in the peptide sequence. The study was carried out by covering a spectrum of protein samples with varied complexity using analytical flow, micro-, and nanoflow regimes to expand the applicability in routine practice.
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Affiliation(s)
- Siddharth Jadeja
- Department of Analytical Chemistry, Faculty of Pharmacy in Hradec Králové, Charles University, Heyrovského 1203/8, 500 03 Hradec Králové, Czech Republic.
| | - Rudolf Kupcik
- Biomedical Research Centre, University Hospital Hradec Králové, Sokolská 581, 500 05 Hradec Králové, Czech Republic
| | - Ivo Fabrik
- Biomedical Research Centre, University Hospital Hradec Králové, Sokolská 581, 500 05 Hradec Králové, Czech Republic
| | - Hana Sklenářová
- Department of Analytical Chemistry, Faculty of Pharmacy in Hradec Králové, Charles University, Heyrovského 1203/8, 500 03 Hradec Králové, Czech Republic.
| | - Juraj Lenčo
- Department of Analytical Chemistry, Faculty of Pharmacy in Hradec Králové, Charles University, Heyrovského 1203/8, 500 03 Hradec Králové, Czech Republic.
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Hoenisch Gravel N, Nelde A, Bauer J, Mühlenbruch L, Schroeder SM, Neidert MC, Scheid J, Lemke S, Dubbelaar ML, Wacker M, Dengler A, Klein R, Mauz PS, Löwenheim H, Hauri-Hohl M, Martin R, Hennenlotter J, Stenzl A, Heitmann JS, Salih HR, Rammensee HG, Walz JS. TOF IMS mass spectrometry-based immunopeptidomics refines tumor antigen identification. Nat Commun 2023; 14:7472. [PMID: 37978195 PMCID: PMC10656517 DOI: 10.1038/s41467-023-42692-7] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/12/2023] [Accepted: 10/18/2023] [Indexed: 11/19/2023] Open
Abstract
T cell recognition of human leukocyte antigen (HLA)-presented tumor-associated peptides is central for cancer immune surveillance. Mass spectrometry (MS)-based immunopeptidomics represents the only unbiased method for the direct identification and characterization of naturally presented tumor-associated peptides, a key prerequisite for the development of T cell-based immunotherapies. This study reports on the implementation of ion mobility separation-based time-of-flight (TOFIMS) MS for next-generation immunopeptidomics, enabling high-speed and sensitive detection of HLA-presented peptides. Applying TOFIMS-based immunopeptidomics, a novel extensive benignTOFIMS dataset was generated from 94 primary benign samples of solid tissue and hematological origin, which enabled the expansion of benign reference immunopeptidome databases with > 150,000 HLA-presented peptides, the refinement of previously described tumor antigens, as well as the identification of frequently presented self antigens and not yet described tumor antigens comprising low abundant mutation-derived neoepitopes that might serve as targets for future cancer immunotherapy development.
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Affiliation(s)
- Naomi Hoenisch Gravel
- Department of Peptide-based Immunotherapy, University and University Hospital Tübingen, Tübingen, Germany
- Institute for Cell Biology, Department of Immunology, University of Tübingen, Tübingen, Germany
- Cluster of Excellence iFIT (EXC2180) "Image-Guided and Functionally Instructed Tumor Therapies", University of Tübingen, Tübingen, Germany
| | - Annika Nelde
- Department of Peptide-based Immunotherapy, University and University Hospital Tübingen, Tübingen, Germany
- Institute for Cell Biology, Department of Immunology, University of Tübingen, Tübingen, Germany
- Cluster of Excellence iFIT (EXC2180) "Image-Guided and Functionally Instructed Tumor Therapies", University of Tübingen, Tübingen, Germany
| | - Jens Bauer
- Department of Peptide-based Immunotherapy, University and University Hospital Tübingen, Tübingen, Germany
- Institute for Cell Biology, Department of Immunology, University of Tübingen, Tübingen, Germany
- Cluster of Excellence iFIT (EXC2180) "Image-Guided and Functionally Instructed Tumor Therapies", University of Tübingen, Tübingen, Germany
| | - Lena Mühlenbruch
- Department of Peptide-based Immunotherapy, University and University Hospital Tübingen, Tübingen, Germany
- Institute for Cell Biology, Department of Immunology, University of Tübingen, Tübingen, Germany
- Cluster of Excellence iFIT (EXC2180) "Image-Guided and Functionally Instructed Tumor Therapies", University of Tübingen, Tübingen, Germany
- German Cancer Consortium (DKTK) and German Cancer Research Center (DKFZ), partner site Tübingen, Tübingen, Germany
| | - Sarah M Schroeder
- Department of Peptide-based Immunotherapy, University and University Hospital Tübingen, Tübingen, Germany
- Institute for Cell Biology, Department of Immunology, University of Tübingen, Tübingen, Germany
- Department of Otorhinolaryngology, Head and Neck Surgery, University of Tübingen, Tübingen, Germany
| | - Marian C Neidert
- Neuroscience Center Zürich (ZNZ), University of Zürich and ETH Zürich, Zürich, Switzerland
- Clinical Neuroscience Center and Department of Neurosurgery, University Hospital and University of Zurich, Zürich, Switzerland
- Department of Neurosurgery, Cantonal Hospital St. Gallen, Zürich, Switzerland
| | - Jonas Scheid
- Department of Peptide-based Immunotherapy, University and University Hospital Tübingen, Tübingen, Germany
- Institute for Cell Biology, Department of Immunology, University of Tübingen, Tübingen, Germany
- Cluster of Excellence iFIT (EXC2180) "Image-Guided and Functionally Instructed Tumor Therapies", University of Tübingen, Tübingen, Germany
- Quantitative Biology Center (QBIC), University of Tübingen, Tübingen, Germany
| | - Steffen Lemke
- Department of Peptide-based Immunotherapy, University and University Hospital Tübingen, Tübingen, Germany
- Institute for Cell Biology, Department of Immunology, University of Tübingen, Tübingen, Germany
- Cluster of Excellence iFIT (EXC2180) "Image-Guided and Functionally Instructed Tumor Therapies", University of Tübingen, Tübingen, Germany
- Quantitative Biology Center (QBIC), University of Tübingen, Tübingen, Germany
| | - Marissa L Dubbelaar
- Department of Peptide-based Immunotherapy, University and University Hospital Tübingen, Tübingen, Germany
- Institute for Cell Biology, Department of Immunology, University of Tübingen, Tübingen, Germany
- Cluster of Excellence iFIT (EXC2180) "Image-Guided and Functionally Instructed Tumor Therapies", University of Tübingen, Tübingen, Germany
- Quantitative Biology Center (QBIC), University of Tübingen, Tübingen, Germany
| | - Marcel Wacker
- Department of Peptide-based Immunotherapy, University and University Hospital Tübingen, Tübingen, Germany
- Institute for Cell Biology, Department of Immunology, University of Tübingen, Tübingen, Germany
- Cluster of Excellence iFIT (EXC2180) "Image-Guided and Functionally Instructed Tumor Therapies", University of Tübingen, Tübingen, Germany
| | - Anna Dengler
- Department of Peptide-based Immunotherapy, University and University Hospital Tübingen, Tübingen, Germany
- Institute for Cell Biology, Department of Immunology, University of Tübingen, Tübingen, Germany
- Cluster of Excellence iFIT (EXC2180) "Image-Guided and Functionally Instructed Tumor Therapies", University of Tübingen, Tübingen, Germany
| | - Reinhild Klein
- Department of Hematology, Oncology, Clinical Immunology and Rheumatology, University Hospital Tübingen, Tübingen, Germany
| | - Paul-Stefan Mauz
- Department of Otorhinolaryngology, Head and Neck Surgery, University of Tübingen, Tübingen, Germany
| | - Hubert Löwenheim
- Department of Otorhinolaryngology, Head and Neck Surgery, University of Tübingen, Tübingen, Germany
| | - Mathias Hauri-Hohl
- Pediatric Stem Cell Transplantation, University Children's Hospital Zürich, Zürich, Switzerland
| | - Roland Martin
- Neuroimmunology and MS Research, Neurology Clinic, University and University Hospital Zürich, Zürich, Switzerland
| | - Jörg Hennenlotter
- Department of Urology, University Hospital Tübingen, Tübingen, Germany
| | - Arnulf Stenzl
- Department of Urology, University Hospital Tübingen, Tübingen, Germany
| | - Jonas S Heitmann
- Cluster of Excellence iFIT (EXC2180) "Image-Guided and Functionally Instructed Tumor Therapies", University of Tübingen, Tübingen, Germany
- Clinical Collaboration Unit Translational Immunology, German Cancer Consortium (DKTK), Department of Internal Medicine, University Hospital Tübingen, Tübingen, Germany
| | - Helmut R Salih
- Cluster of Excellence iFIT (EXC2180) "Image-Guided and Functionally Instructed Tumor Therapies", University of Tübingen, Tübingen, Germany
- German Cancer Consortium (DKTK) and German Cancer Research Center (DKFZ), partner site Tübingen, Tübingen, Germany
- Clinical Collaboration Unit Translational Immunology, German Cancer Consortium (DKTK), Department of Internal Medicine, University Hospital Tübingen, Tübingen, Germany
| | - Hans-Georg Rammensee
- Institute for Cell Biology, Department of Immunology, University of Tübingen, Tübingen, Germany
- Cluster of Excellence iFIT (EXC2180) "Image-Guided and Functionally Instructed Tumor Therapies", University of Tübingen, Tübingen, Germany
- German Cancer Consortium (DKTK) and German Cancer Research Center (DKFZ), partner site Tübingen, Tübingen, Germany
| | - Juliane S Walz
- Department of Peptide-based Immunotherapy, University and University Hospital Tübingen, Tübingen, Germany.
- Institute for Cell Biology, Department of Immunology, University of Tübingen, Tübingen, Germany.
- Cluster of Excellence iFIT (EXC2180) "Image-Guided and Functionally Instructed Tumor Therapies", University of Tübingen, Tübingen, Germany.
- Clinical Collaboration Unit Translational Immunology, German Cancer Consortium (DKTK), Department of Internal Medicine, University Hospital Tübingen, Tübingen, Germany.
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Gleichman AJ, Kawaguchi R, Sofroniew MV, Carmichael ST. A toolbox of astrocyte-specific, serotype-independent adeno-associated viral vectors using microRNA targeting sequences. Nat Commun 2023; 14:7426. [PMID: 37973910 PMCID: PMC10654773 DOI: 10.1038/s41467-023-42746-w] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/28/2023] [Accepted: 10/17/2023] [Indexed: 11/19/2023] Open
Abstract
Astrocytes, one of the most prevalent cell types in the central nervous system (CNS), are critically involved in neural function. Genetically manipulating astrocytes is an essential tool in understanding and affecting their roles. Adeno-associated viruses (AAVs) enable rapid genetic manipulation; however, astrocyte specificity of AAVs can be limited, with high off-target expression in neurons and sparsely in endothelial cells. Here, we report the development of a cassette of four copies of six miRNA targeting sequences (4x6T) which triggers transgene degradation specifically in neurons and endothelial cells. In combination with the GfaABC1D promoter, 4x6T increases astrocytic specificity of Cre with a viral reporter from <50% to >99% in multiple serotypes in mice, and confers astrocyte specificity in multiple recombinases and reporters. We also present empty vectors to add 4x6T to other cargo, independently and in Cre/Dre-dependent forms. This toolbox of AAVs allows rapid manipulation of astrocytes throughout the CNS, is compatible with different AAV serotypes, and demonstrates the efficacy of using multiplexed miRNA targeting sequences to decrease expression in multiple off-target cell populations simultaneously.
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Affiliation(s)
- Amy J Gleichman
- Department of Neurology, David Geffen School of Medicine at University of California-Los Angeles, Los Angeles, CA, USA
| | - Riki Kawaguchi
- Center for Neurobehavioral Genetics, Semel Institute for Neuroscience and Human Behavior, University of California Los Angeles, Los Angeles, CA, USA
| | - Michael V Sofroniew
- Department of Neurobiology, University of California-Los Angeles, Los Angeles, CA, USA
| | - S Thomas Carmichael
- Department of Neurology, David Geffen School of Medicine at University of California-Los Angeles, Los Angeles, CA, USA.
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Xu Y, Miller CP, Xue J, Zheng Y, Warren EH, Tykodi SS, Akilesh S. Single cell atlas of kidney cancer endothelial cells reveals distinct expression profiles and phenotypes. Res Sq 2023:rs.3.rs-3558517. [PMID: 37986984 PMCID: PMC10659545 DOI: 10.21203/rs.3.rs-3558517/v1] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 11/22/2023]
Abstract
Background Tumor endothelial cells (TECs) represent the primary interface between the tumor microenvironment and circulating immune cells, however their phenotypes are incompletely understood in highly vascularized clear cell renal cell carcinoma (ccRCC). Methods We purified tumor and matched normal endothelial cells (NECs) from ccRCC specimens and performed single-cell RNA-sequencing to create a reference-quality atlas available as a searchable web resource for gene expression patterns. We established paired primary TECs and NECs cultures for ex vivo functional testing. Results TECs from multiple donors shared a common phenotype with increased expression of pathways related to extracellular matrix regulation, cell-cell communication, and insulin-like growth factor signaling that was conserved in comparison to hepatocellular carcinoma associated TECs, suggesting convergent TEC phenotypes between unrelated tumors. Cultured TECs stably maintained a core program of differentially regulated genes, were inherently resistant to apoptosis after vascular endothelial growth factor removal and displayed increased adhesiveness to subsets of immune cells including regulatory T-cells. Conclusions Our studies delineate unique functional and phenotypic properties of TECs, which may provide insights into their interactions with available and emerging therapies. Functional phenotypes of cultured TECs suggest potential mechanisms of resistance to both antiangiogenic and immune-based therapies.
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48
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Xu H, Akinyemi IA, Haley J, McIntosh MT, Bhaduri-McIntosh S. ATM, KAP1 and the Epstein-Barr virus polymerase processivity factor direct traffic at the intersection of transcription and replication. Nucleic Acids Res 2023; 51:11104-11122. [PMID: 37852757 PMCID: PMC10639065 DOI: 10.1093/nar/gkad823] [Citation(s) in RCA: 1] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/06/2023] [Revised: 09/09/2023] [Accepted: 09/20/2023] [Indexed: 10/20/2023] Open
Abstract
The timing of transcription and replication must be carefully regulated for heavily-transcribed genomes of double-stranded DNA viruses: transcription of immediate early/early genes must decline as replication ramps up from the same genome-ensuring efficient and timely replication of viral genomes followed by their packaging by structural proteins. To understand how the prototypic DNA virus Epstein-Barr virus tackles the logistical challenge of switching from transcription to DNA replication, we examined the proteome at viral replication forks. Specifically, to transition from transcription, the viral DNA polymerase-processivity factor EA-D is SUMOylated by the epigenetic regulator and E3 SUMO-ligase KAP1/TRIM28. KAP1's SUMO2-ligase function is triggered by phosphorylation via the PI3K-related kinase ATM and the RNA polymerase II-associated helicase RECQ5 at the transcription machinery. SUMO2-EA-D then recruits the histone loader CAF1 and the methyltransferase SETDB1 to silence the parental genome via H3K9 methylation, prioritizing replication. Thus, a key viral protein and host DNA repair, epigenetic and transcription-replication interference pathways orchestrate the handover from transcription-to-replication, a fundamental feature of DNA viruses.
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Affiliation(s)
- Huanzhou Xu
- Division of Infectious Diseases, Department of Pediatrics, University of Florida, Gainesville, FL 32610, USA
| | - Ibukun A Akinyemi
- Child Health Research Institute, Department of Pediatrics, University of Florida, Gainesville, FL 32610, USA
| | - John Haley
- Department of Pathology and Stony Brook Proteomics Center, Stony Brook University, Stony Brook, NY 11794, USA
| | - Michael T McIntosh
- Child Health Research Institute, Department of Pediatrics, University of Florida, Gainesville, FL 32610, USA
- Department of Molecular Genetics and Microbiology, University of Florida, Gainesville, FL 32610, USA
| | - Sumita Bhaduri-McIntosh
- Division of Infectious Diseases, Department of Pediatrics, University of Florida, Gainesville, FL 32610, USA
- Department of Molecular Genetics and Microbiology, University of Florida, Gainesville, FL 32610, USA
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49
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Olayinka JT, Nagarkar A, Ma DJ, Wong NB, Romasco A, Piedra-Mora C, Wrijil L, David CN, Gardner HL, Robinson NA, Hughes KL, Barton B, London CA, Almela RM, Richmond JM. Cathepsin W, T-cell receptor-associated transmembrane adapter 1, lymphotactin and killer cell lectin like receptor K1 are sensitive and specific RNA biomarkers of canine epitheliotropic lymphoma. Front Vet Sci 2023; 10:1225764. [PMID: 38026637 PMCID: PMC10654980 DOI: 10.3389/fvets.2023.1225764] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Grants] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/19/2023] [Accepted: 10/18/2023] [Indexed: 12/01/2023] Open
Abstract
Cutaneous T-cell lymphoma (CTCL) is an uncommon type of lymphoma involving malignant skin-resident or skin-homing T cells. Canine epitheliotropic lymphoma (EL) is the most common form of CTCL in dogs, and it also spontaneously arises from T lymphocytes in the mucosa and skin. Clinically, it can be difficult to distinguish early-stage CTCLs apart from other forms of benign interface dermatitis (ID) in both dogs and people. Our objective was to identify novel biomarkers that can distinguish EL from other forms of ID, and perform comparative transcriptomics of human CTCL and canine EL. Here, we present a retrospective gene expression study that employed archival tissue from biorepositories. We analyzed a discovery cohort of 6 canines and a validation cohort of 8 canines with EL which occurred spontaneously in client-owned companion dogs. We performed comparative targeted transcriptomics studies using NanoString to assess 160 genes from lesional skin biopsies from the discovery cohort and 800 genes from the validation cohort to identify any significant differences that may reflect oncogenesis and immunopathogenesis. We further sought to determine if gene expression in EL and CTCL are conserved across humans and canines by comparing our data to previously published human datasets. Similar chemokine profiles were observed in dog EL and human CTCL, and analyses were performed to validate potential biomarkers and drivers of disease. In dogs, we found enrichment of T cell gene signatures, with upregulation of IFNG, TNF, PRF1, IL15, CD244, CXCL10, and CCL5 in EL in dogs compared to healthy controls. Importantly, CTSW, TRAT1 and KLRK1 distinguished EL from all other forms of interface dermatitis we studied, providing much-needed biomarkers for the veterinary field. XCL1/XCL2 were also highly specific of EL in our validation cohort. Future studies exploring the oncogenesis of spontaneous lymphomas in companion animals will expand our understanding of these disorders. Biomarkers may be useful for predicting disease prognosis and treatment responses. We plan to use our data to inform future development of targeted therapies, as well as for repurposing drugs for both veterinary and human medicine.
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Affiliation(s)
- Jadesola Temitope Olayinka
- Department of Dermatology, UMass Chan Medical School, Worcester, MA, United States
- SUNY Downstate School of Medicine, New York, NY, United States
| | - Akanksha Nagarkar
- Department of Dermatology, UMass Chan Medical School, Worcester, MA, United States
| | - Diana Junyue Ma
- Department of Dermatology, UMass Chan Medical School, Worcester, MA, United States
| | - Neil B. Wong
- Department of Dermatology, UMass Chan Medical School, Worcester, MA, United States
| | - Andrew Romasco
- Department of Dermatology, UMass Chan Medical School, Worcester, MA, United States
| | - Cesar Piedra-Mora
- Pathology Department, Tufts Cummings School of Veterinary Medicine, North Grafton, MA, United States
| | - Linda Wrijil
- Pathology Department, Tufts Cummings School of Veterinary Medicine, North Grafton, MA, United States
| | | | - Heather L. Gardner
- Department of Clinical Sciences, Tufts Cummings School of Veterinary Medicine, North Grafton, MA, United States
| | - Nicholas A. Robinson
- Pathology Department, Tufts Cummings School of Veterinary Medicine, North Grafton, MA, United States
| | - Kelly L. Hughes
- Department of Microbiology, Immunology and Pathology, Colorado State University Veterinary Diagnostic Laboratory, Fort Collins, CO, United States
| | - Bruce Barton
- Department of Population and Quantitative Health Sciences, UMass Chan Medical School, Worcester, MA, United States
| | - Cheryl A. London
- Department of Clinical Sciences, Tufts Cummings School of Veterinary Medicine, North Grafton, MA, United States
| | - Ramón M. Almela
- Department of Clinical Sciences, Tufts Cummings School of Veterinary Medicine, North Grafton, MA, United States
| | - Jillian M. Richmond
- Department of Dermatology, UMass Chan Medical School, Worcester, MA, United States
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50
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Rogers MF, Marshall OJ, Secombe J. KDM5-mediated activation of genes required for mitochondrial biology is necessary for viability in Drosophila. Development 2023; 150:dev202024. [PMID: 37800333 PMCID: PMC10651110 DOI: 10.1242/dev.202024] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/20/2023] [Accepted: 09/29/2023] [Indexed: 10/07/2023]
Abstract
Histone-modifying proteins play important roles in the precise regulation of the transcriptional programs that coordinate development. KDM5 family proteins interact with chromatin through demethylation of H3K4me3 as well as demethylase-independent mechanisms that remain less understood. To gain fundamental insights into the transcriptional activities of KDM5 proteins, we examined the essential roles of the single Drosophila Kdm5 ortholog during development. KDM5 performs crucial functions in the larval neuroendocrine prothoracic gland, providing a model to study its role in regulating key gene expression programs. Integrating genome binding and transcriptomic data, we identify that KDM5 regulates the expression of genes required for the function and maintenance of mitochondria, and we find that loss of KDM5 causes morphological changes to mitochondria. This is key to the developmental functions of KDM5, as expression of the mitochondrial biogenesis transcription factor Ets97D, homolog of GABPα, is able to suppress the altered mitochondrial morphology as well as the lethality of Kdm5 null animals. Together, these data establish KDM5-mediated cellular functions that are important for normal development and could contribute to KDM5-linked disorders when dysregulated.
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Affiliation(s)
- Michael F. Rogers
- Department of Genetics, Albert Einstein College of Medicine, Bronx, NY 10461, USA
| | - Owen J. Marshall
- Menzies Institute for Medical Research, University of Tasmania, Hobart TAS 7000, Australia
| | - Julie Secombe
- Department of Genetics, Albert Einstein College of Medicine, Bronx, NY 10461, USA
- Dominick P. Purpura Department of Neuroscience, Albert Einstein College of Medicine, Bronx, NY 10461, USA
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