99901
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Epigenetics Identifier screens reveal regulators of chromatin acylation and limited specificity of acylation antibodies. Sci Rep 2021; 11:12795. [PMID: 34140538 PMCID: PMC8211816 DOI: 10.1038/s41598-021-91359-0] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/06/2020] [Accepted: 05/20/2021] [Indexed: 11/15/2022] Open
Abstract
The collection of known posttranslational modifications (PTMs) has expanded rapidly with the identification of various non-acetyl histone lysine acylations, such as crotonylation, succinylation and butyrylation, yet their regulation is still not fully understood. Through an unbiased chromatin immunoprecipitation (ChIP)-based approach called Epigenetics-IDentifier (Epi-ID), we aimed to identify regulators of crotonylation, succinylation and butyrylation in thousands of yeast mutants simultaneously. However, highly correlative results led us to further investigate the specificity of the pan-K-acyl antibodies used in our Epi-ID studies. This revealed cross-reactivity and lack of specificity of pan-K-acyl antibodies in various assays. Our findings suggest that the antibodies might recognize histone acetylation in vivo, in addition to histone acylation, due to the vast overabundance of acetylation compared to other acylation modifications in cells. Consequently, our Epi-ID screen mostly identified factors affecting histone acetylation, including known (e.g. GCN5, HDA1, and HDA2) and unanticipated (MET7, MTF1, CLB3, and RAD26) factors, expanding the repertoire of acetylation regulators. Antibody-independent follow-up experiments on the Gcn5-Ada2-Ada3 (ADA) complex revealed that, in addition to acetylation and crotonylation, ADA has the ability to butyrylate histones. Thus, our Epi-ID screens revealed limits of using pan-K-acyl antibodies in epigenetics research, expanded the repertoire of regulators of histone acetylation, and attributed butyrylation activity to the ADA complex.
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99902
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Logeswaran D, Li Y, Podlevsky JD, Chen JJL. Monophyletic Origin and Divergent Evolution of Animal Telomerase RNA. Mol Biol Evol 2021; 38:215-228. [PMID: 32770221 PMCID: PMC8480181 DOI: 10.1093/molbev/msaa203] [Citation(s) in RCA: 13] [Impact Index Per Article: 4.3] [Reference Citation Analysis] [Abstract] [Key Words] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/20/2022] Open
Abstract
Telomerase RNA (TR) is a noncoding RNA essential for the function of telomerase ribonucleoprotein. TRs from vertebrates, fungi, ciliates, and plants exhibit extreme diversity in size, sequence, secondary structure, and biogenesis pathway. However, the evolutionary pathways leading to such unusual diversity among eukaryotic kingdoms remain elusive. Within the metazoan kingdom, the study of TR has been limited to vertebrates and echinoderms. To understand the origin and evolution of TR across the animal kingdom, we employed a phylogeny-guided, structure-based bioinformatics approach to identify 82 novel TRs from eight previously unexplored metazoan phyla, including the basal-branching sponges. Synthetic TRs from two representative species, a hemichordate and a mollusk, reconstitute active telomerase in vitro with their corresponding telomerase reverse transcriptase components, confirming that they are authentic TRs. Comparative analysis shows that three functional domains, template-pseudoknot (T-PK), CR4/5, and box H/ACA, are conserved between vertebrate and the basal metazoan lineages, indicating a monophyletic origin of the animal TRs with a snoRNA-related biogenesis mechanism. Nonetheless, TRs along separate animal lineages evolved with divergent structural elements in the T-PK and CR4/5 domains. For example, TRs from echinoderms and protostomes lack the canonical CR4/5 and have independently evolved functionally equivalent domains with different secondary structures. In the T-PK domain, a P1.1 stem common in most metazoan clades defines the template boundary, which is replaced by a P1-defined boundary in vertebrates. This study provides unprecedented insight into the divergent evolution of detailed TR secondary structures across broad metazoan lineages, revealing ancestral and later-diversified elements.
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Affiliation(s)
| | - Yang Li
- School of Molecular Sciences, Arizona State University, Tempe, AZ
| | | | - Julian J-L Chen
- School of Molecular Sciences, Arizona State University, Tempe, AZ
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99903
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Kuhl H, Frankl-Vilches C, Bakker A, Mayr G, Nikolaus G, Boerno ST, Klages S, Timmermann B, Gahr M. An Unbiased Molecular Approach Using 3'-UTRs Resolves the Avian Family-Level Tree of Life. Mol Biol Evol 2021; 38:108-127. [PMID: 32781465 PMCID: PMC7783168 DOI: 10.1093/molbev/msaa191] [Citation(s) in RCA: 59] [Impact Index Per Article: 19.7] [Reference Citation Analysis] [Abstract] [Key Words] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/20/2023] Open
Abstract
Presumably, due to a rapid early diversification, major parts of the higher-level phylogeny of birds are still resolved controversially in different analyses or are considered unresolvable. To address this problem, we produced an avian tree of life, which includes molecular sequences of one or several species of ∼90% of the currently recognized family-level taxa (429 species, 379 genera) including all 106 family-level taxa of the nonpasserines and 115 of the passerines (Passeriformes). The unconstrained analyses of noncoding 3-prime untranslated region (3′-UTR) sequences and those of coding sequences yielded different trees. In contrast to the coding sequences, the 3′-UTR sequences resulted in a well-resolved and stable tree topology. The 3′-UTR contained, unexpectedly, transcription factor binding motifs that were specific for different higher-level taxa. In this tree, grebes and flamingos are the sister clade of all other Neoaves, which are subdivided into five major clades. All nonpasserine taxa were placed with robust statistical support including the long-time enigmatic hoatzin (Opisthocomiformes), which was found being the sister taxon of the Caprimulgiformes. The comparatively late radiation of family-level clades of the songbirds (oscine Passeriformes) contrasts with the attenuated diversification of nonpasseriform taxa since the early Miocene. This correlates with the evolution of vocal production learning, an important speciation factor, which is ancestral for songbirds and evolved convergent only in hummingbirds and parrots. As 3′-UTR-based phylotranscriptomics resolved the avian family-level tree of life, we suggest that this procedure will also resolve the all-species avian tree of life
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Affiliation(s)
- Heiner Kuhl
- Department of Behavioural Neurobiology, Max Planck Institute for Ornithology, Seewiesen, Germany.,Max Planck Institute for Molecular Genetics, Sequencing Core Facility, Berlin, Germany.,Department of Ecophysiology and Aquaculture, Leibniz-Institute of Freshwater Ecology and Inland Fisheries, Berlin, Germany
| | - Carolina Frankl-Vilches
- Department of Behavioural Neurobiology, Max Planck Institute for Ornithology, Seewiesen, Germany
| | - Antje Bakker
- Department of Behavioural Neurobiology, Max Planck Institute for Ornithology, Seewiesen, Germany
| | - Gerald Mayr
- Ornithological Section, Senckenberg Research Institute, Frankfurt am Main, Germany
| | - Gerhard Nikolaus
- Department of Behavioural Neurobiology, Max Planck Institute for Ornithology, Seewiesen, Germany
| | - Stefan T Boerno
- Max Planck Institute for Molecular Genetics, Sequencing Core Facility, Berlin, Germany
| | - Sven Klages
- Max Planck Institute for Molecular Genetics, Sequencing Core Facility, Berlin, Germany
| | - Bernd Timmermann
- Max Planck Institute for Molecular Genetics, Sequencing Core Facility, Berlin, Germany
| | - Manfred Gahr
- Department of Behavioural Neurobiology, Max Planck Institute for Ornithology, Seewiesen, Germany
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99904
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Giesel FL, Kratochwil C, Schlittenhardt J, Dendl K, Eiber M, Staudinger F, Kessler L, Fendler WP, Lindner T, Koerber SA, Cardinale J, Sennung D, Roehrich M, Debus J, Sathekge M, Haberkorn U, Calais J, Serfling S, Buck AL. Head-to-head intra-individual comparison of biodistribution and tumor uptake of 68Ga-FAPI and 18F-FDG PET/CT in cancer patients. Eur J Nucl Med Mol Imaging 2021; 48:4377-4385. [PMID: 34137945 PMCID: PMC8566651 DOI: 10.1007/s00259-021-05307-1] [Citation(s) in RCA: 101] [Impact Index Per Article: 33.7] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/11/2021] [Accepted: 03/08/2021] [Indexed: 02/06/2023]
Abstract
Purpose FAPI ligands (fibroblast activation protein inhibitor), a novel class of radiotracers for PET/CT imaging, demonstrated in previous studies rapid and high tumor uptake. The purpose of this study is the head-to-head intra-individual comparison of 68Ga-FAPI versus standard-of-care 18F-FDG in PET/CT in organ biodistribution and tumor uptake in patients with various cancers. Material and Methods This international retrospective multicenter analysis included PET/CT data from 71 patients from 6 centers who underwent both 68Ga-FAPI and 18F-FDG PET/CT within a median time interval of 10 days (range 1–89 days). Volumes of interest (VOIs) were manually drawn in normal organs and tumor lesions to quantify tracer uptake by SUVmax and SUVmean. Furthermore, tumor-to-background ratios (TBR) were generated (SUVmax tumor/ SUVmax organ). Results A total of 71 patients were studied of, which 28 were female and 43 male (median age 60). In 41 of 71 patients, the primary tumor was present. Forty-three of 71 patients exhibited 162 metastatic lesions. 68Ga-FAPI uptake in primary tumors and metastases was comparable to 18F-FDG in most cases. The SUVmax was significantly lower for 68Ga-FAPI than 18F-FDG in background tissues such as the brain, oral mucosa, myocardium, blood pool, liver, pancreas, and colon. Thus, 68Ga-FAPI TBRs were significantly higher than 18F-FDG TBRs in some sites, including liver and bone metastases. Conclusion Quantitative tumor uptake is comparable between 68Ga-FAPI and 18F-FDG, but lower background uptake in most normal organs results in equal or higher TBRs for 68Ga-FAPI. Thus, 68Ga-FAPI PET/CT may yield improved diagnostic information in various cancers and especially in tumor locations with high physiological 18F-FDG uptake. Supplementary Information The online version contains supplementary material available at 10.1007/s00259-021-05307-1.
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Affiliation(s)
- Frederik L Giesel
- Department of Nuclear Medicine, University Hospital Duesseldorf, Duesseldorf, Germany. .,Department of Nuclear Medicine, University Hospital Heidelberg, INF 400, 69120, Heidelberg, Germany.
| | - Clemens Kratochwil
- Department of Nuclear Medicine, University Hospital Heidelberg, INF 400, 69120, Heidelberg, Germany
| | - Joel Schlittenhardt
- Department of Nuclear Medicine, University Hospital Heidelberg, INF 400, 69120, Heidelberg, Germany
| | - Katharina Dendl
- Department of Nuclear Medicine, University Hospital Heidelberg, INF 400, 69120, Heidelberg, Germany
| | - Matthias Eiber
- Department of Nuclear Medicine, Klinikum rechts der Isar, Technical University of Munich, Munich, Germany
| | - Fabian Staudinger
- Department of Nuclear Medicine, University Hospital Heidelberg, INF 400, 69120, Heidelberg, Germany
| | - Lukas Kessler
- Department of Nuclear Medicine, University of Duisburg-Essen and German Cancer Consortium (DKTK)-University Hospital Essen, Essen, Germany
| | - Wolfgang P Fendler
- Department of Nuclear Medicine, University of Duisburg-Essen and German Cancer Consortium (DKTK)-University Hospital Essen, Essen, Germany
| | - Thomas Lindner
- Department of Nuclear Medicine, University Hospital Heidelberg, INF 400, 69120, Heidelberg, Germany
| | - Stefan A Koerber
- National Center for Tumor diseases (NCT), Heidelberg, Germany.,Clinical Cooperation Unit Radiation Oncology, German Cancer Research Center (DKFZ), Im Neuenheimer Feld 280, 69120, Heidelberg, Germany.,Heidelberg Institute of Radiation Oncology (HIRO), Im Neuenheimer Feld 400, 69120, Heidelberg, Germany.,Department of Radiation Oncology, University Hospital Heidelberg, Im Neuenheimer Feld 400, 69120, Heidelberg, Germany
| | - Jens Cardinale
- Department of Nuclear Medicine, University Hospital Heidelberg, INF 400, 69120, Heidelberg, Germany
| | - David Sennung
- Ahmanson Translational Theranostics Division, Department of Molecular and Medical Pharmacology, University of California at Los Angeles, Los Angeles, CA, USA
| | - Manuel Roehrich
- Department of Nuclear Medicine, University Hospital Heidelberg, INF 400, 69120, Heidelberg, Germany
| | - Juergen Debus
- National Center for Tumor diseases (NCT), Heidelberg, Germany.,Clinical Cooperation Unit Radiation Oncology, German Cancer Research Center (DKFZ), Im Neuenheimer Feld 280, 69120, Heidelberg, Germany.,Heidelberg Institute of Radiation Oncology (HIRO), Im Neuenheimer Feld 400, 69120, Heidelberg, Germany.,Department of Radiation Oncology, University Hospital Heidelberg, Im Neuenheimer Feld 400, 69120, Heidelberg, Germany.,Heidelberg Ion-Beam Therapy Center (HIT), Im Neuenheimer Feld 450, 69120, Heidelberg, Germany
| | - Mike Sathekge
- Department of Nuclear Medicine, University of Pretoria and Steve Biko Academic Hospital, Pretoria, South Africa
| | - Uwe Haberkorn
- Department of Nuclear Medicine, University Hospital Heidelberg, INF 400, 69120, Heidelberg, Germany.,Clinical Cooperation Unit Nuclear Medicine, German Cancer Research Center (DKFZ), Heidelberg, Germany.,Translational Lung Research Center Heidelberg (TLRC), German Center for Lung Research (DZL), Heidelberg, Germany
| | - Jeremie Calais
- Ahmanson Translational Theranostics Division, Department of Molecular and Medical Pharmacology, University of California at Los Angeles, Los Angeles, CA, USA
| | - Sebastian Serfling
- Department of Nuclear Medicine, University Hospital Würzburg, Würzburg, Germany
| | - Andreas L Buck
- Department of Nuclear Medicine, University Hospital Würzburg, Würzburg, Germany.,Comprehensive Cancer Center Mainfranken, 97080, Wuerzburg, Germany
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99905
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Rtt105 promotes high-fidelity DNA replication and repair by regulating the single-stranded DNA-binding factor RPA. Proc Natl Acad Sci U S A 2021; 118:2106393118. [PMID: 34140406 DOI: 10.1073/pnas.2106393118] [Citation(s) in RCA: 9] [Impact Index Per Article: 3.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/13/2022] Open
Abstract
Single-stranded DNA (ssDNA) covered with the heterotrimeric Replication Protein A (RPA) complex is a central intermediate of DNA replication and repair. How RPA is regulated to ensure the fidelity of DNA replication and repair remains poorly understood. Yeast Rtt105 is an RPA-interacting protein required for RPA nuclear import and efficient ssDNA binding. Here, we describe an important role of Rtt105 in high-fidelity DNA replication and recombination and demonstrate that these functions of Rtt105 primarily depend on its regulation of RPA. The deletion of RTT105 causes elevated spontaneous DNA mutations with large duplications or deletions mediated by microhomologies. Rtt105 is recruited to DNA double-stranded break (DSB) ends where it promotes RPA assembly and homologous recombination repair by gene conversion or break-induced replication. In contrast, Rtt105 attenuates DSB repair by the mutagenic single-strand annealing or alternative end joining pathway. Thus, Rtt105-mediated regulation of RPA promotes high-fidelity replication and recombination while suppressing repair by deleterious pathways. Finally, we show that the human RPA-interacting protein hRIP-α, a putative functional homolog of Rtt105, also stimulates RPA assembly on ssDNA, suggesting the conservation of an Rtt105-mediated mechanism.
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99906
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Ekstrom TL, Pathoulas NM, Huehls AM, Kanakkanthara A, Karnitz LM. VLX600 Disrupts Homologous Recombination and Synergizes with PARP Inhibitors and Cisplatin by Inhibiting Histone Lysine Demethylases. Mol Cancer Ther 2021; 20:1561-1571. [PMID: 34224364 DOI: 10.1158/1535-7163.mct-20-1099] [Citation(s) in RCA: 7] [Impact Index Per Article: 2.3] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/18/2020] [Revised: 02/23/2021] [Accepted: 05/27/2021] [Indexed: 11/16/2022]
Abstract
Tumors with defective homologous recombination (HR) DNA repair are more sensitive to chemotherapies that induce lesions repaired by HR as well as PARP inhibitors (PARPis). However, these therapies have limited activity in HR-proficient cells. Accordingly, agents that disrupt HR may be a means to augment the activities of these therapies in HR-proficient tumors. Here we show that VLX600, a small molecule that has been in a phase I clinical trial, disrupts HR and synergizes with PARPis and platinum compounds in ovarian cancer cells. We further found that VLX600 and other iron chelators disrupt HR, in part, by inhibiting iron-dependent histone lysine demethylases (KDM) family members, thus blocking recruitment of HR repair proteins, including RAD51, to double-strand DNA breaks. Collectively, these findings suggest that pharmacologically targeting KDM family members with VLX600 may be a potential novel strategy to therapeutically induce HR defects in ovarian cancers and correspondingly sensitize them to platinum agents and PARPis, two standard-of-care therapies for ovarian cancer.
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Affiliation(s)
- Thomas L Ekstrom
- Division of Oncology Research, Mayo Clinic College of Medicine, Mayo Clinic, Rochester, Minnesota
| | - Nicholas M Pathoulas
- Division of Oncology Research, Mayo Clinic College of Medicine, Mayo Clinic, Rochester, Minnesota
| | - Amelia M Huehls
- Division of Oncology Research, Mayo Clinic College of Medicine, Mayo Clinic, Rochester, Minnesota
| | - Arun Kanakkanthara
- Division of Oncology Research, Mayo Clinic College of Medicine, Mayo Clinic, Rochester, Minnesota. .,Department of Molecular Pharmacology and Experimental Therapeutics, Mayo Clinic College of Medicine, Mayo Clinic, Rochester, Minnesota
| | - Larry M Karnitz
- Division of Oncology Research, Mayo Clinic College of Medicine, Mayo Clinic, Rochester, Minnesota. .,Department of Molecular Pharmacology and Experimental Therapeutics, Mayo Clinic College of Medicine, Mayo Clinic, Rochester, Minnesota
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99907
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Nikolettos K, Damaskos C, Garmpis N, Nikolettos N. BRCA 1, 2 mutation and earlier menopause. Could BRCA 1, 2 be used as predictor of menopause? Minerva Obstet Gynecol 2021; 74:165-170. [PMID: 34137566 DOI: 10.23736/s2724-606x.21.04813-2] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/08/2022]
Abstract
Many studies have shown that BRCA mutation is not only related to cancer but also to ovarian aging. Studies in both human and mice oocytes have shown that Double-strand breaks (DSBs) accumulate with age. Genome-wide association studies (GWAS) have found 44 genetic loci that are related to variations when a female is about to have menopause. BRCA1 is involved in these 44 loci that are associated with the age of menopause. This review has gathered all results of literature search about the association between BRCA genes and early menopause. The majority of the articles found that women with BRCA mutation have earlier menopause compared to non-carriers. In conclusion, in the near future BRCA1,2 genes could be used as predictive biomarkers of menopause.
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Affiliation(s)
| | - Christos Damaskos
- Renal Transplantation Unit, Laiko General Hospital, Athens, Greece.,N.S. Christeas Laboratory of Experimental Surgery and Surgical Research, Medical School, National and Kapodistrian University of Athens, Athens, Greece
| | - Nikolaos Garmpis
- N.S. Christeas Laboratory of Experimental Surgery and Surgical Research, Medical School, National and Kapodistrian University of Athens, Athens, Greece.,Second Department of Propedeutic Surgery, Laiko General Hospital, Medical School, National and Kapodistrian University of Athens, Athens, Greece
| | - Nikos Nikolettos
- Obstetric and Gynecologic Clinic, Medical School, Democritus University of Thrace, Alexandroupolis, Greece
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99908
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Shiraishi R, Kawauchi D. Epigenetic regulation in medulloblastoma pathogenesis revealed by genetically engineered mouse models. Cancer Sci 2021; 112:2948-2957. [PMID: 34050694 PMCID: PMC8353939 DOI: 10.1111/cas.14990] [Citation(s) in RCA: 3] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/07/2021] [Revised: 05/16/2021] [Accepted: 05/18/2021] [Indexed: 12/11/2022] Open
Abstract
Medulloblastoma is the most common malignant cerebellar tumor in children. Recent technological advances in multilayered ’omics data analysis have revealed 4 molecular subgroups of medulloblastoma (Wingless/int, Sonic hedgehog, Group3, and Group4). (Epi)genomic and transcriptomic profiling on human primary medulloblastomas has shown distinct oncogenic drivers and cellular origin(s) across the subgroups. Despite tremendous efforts to identify the molecular signals driving tumorigenesis, few of the identified targets were druggable; therefore, a further understanding of the etiology of tumors is required to establish effective molecular‐targeted therapies. Chromatin regulators are frequently mutated in medulloblastoma, prompting us to investigate epigenetic changes and the accompanying activation of oncogenic signaling during tumorigenesis. For this purpose, we have used germline and non‐germline genetically engineered mice to model human medulloblastoma and to conduct useful, molecularly targeted, preclinical studies. This review discusses the biological implications of chromatin regulator mutations during medulloblastoma pathogenesis, based on recent in vivo animal studies.
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Affiliation(s)
- Ryo Shiraishi
- Department of Biochemistry and Cellular Biology, National Center of Neurology and Psychiatry (NCNP), Tokyo, Japan.,Department of NCNP Brain Physiology and Pathology, Graduate School of Medical and Dental Sciences, Tokyo Medical and Dental University, Tokyo, Japan
| | - Daisuke Kawauchi
- Department of Biochemistry and Cellular Biology, National Center of Neurology and Psychiatry (NCNP), Tokyo, Japan
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99909
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Puri D, Ponniah K, Biswas K, Basu A, Dey S, Lundquist EA, Ghosh-Roy A. Wnt signaling establishes the microtubule polarity in neurons through regulation of Kinesin-13. J Cell Biol 2021; 220:212396. [PMID: 34137792 DOI: 10.1083/jcb.202005080] [Citation(s) in RCA: 7] [Impact Index Per Article: 2.3] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/23/2023] Open
Abstract
Neuronal polarization is facilitated by the formation of axons with parallel arrays of plus-end-out and dendrites with the nonuniform orientation of microtubules. In C. elegans, the posterior lateral microtubule (PLM) neuron is bipolar with its two processes growing along the anterior-posterior axis under the guidance of Wnt signaling. Here we found that loss of the Kinesin-13 family microtubule-depolymerizing enzyme KLP-7 led to the ectopic extension of axon-like processes from the PLM cell body. Live imaging of the microtubules and axonal transport revealed mixed polarity of the microtubules in the short posterior process, which is dependent on both KLP-7 and the minus-end binding protein PTRN-1. KLP-7 is positively regulated in the posterior process by planar cell polarity components of Wnt involving rho-1/rock to induce mixed polarity of microtubules, whereas it is negatively regulated in the anterior process by the unc-73/ced-10 cascade to establish a uniform microtubule polarity. Our work elucidates how evolutionarily conserved Wnt signaling establishes the microtubule polarity in neurons through Kinesin-13.
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Affiliation(s)
- Dharmendra Puri
- Department of Cellular and Molecular Neuroscience, National Brain Research Centre, Manesar, Gurgaon, Haryana, India
| | - Keerthana Ponniah
- Department of Cellular and Molecular Neuroscience, National Brain Research Centre, Manesar, Gurgaon, Haryana, India
| | - Kasturi Biswas
- Department of Cellular and Molecular Neuroscience, National Brain Research Centre, Manesar, Gurgaon, Haryana, India
| | - Atrayee Basu
- Department of Cellular and Molecular Neuroscience, National Brain Research Centre, Manesar, Gurgaon, Haryana, India
| | - Swagata Dey
- Department of Cellular and Molecular Neuroscience, National Brain Research Centre, Manesar, Gurgaon, Haryana, India
| | - Erik A Lundquist
- Department of Molecular Biosciences, University of Kansas, Lawrence, KS
| | - Anindya Ghosh-Roy
- Department of Cellular and Molecular Neuroscience, National Brain Research Centre, Manesar, Gurgaon, Haryana, India
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99910
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Bernstock JD, Hoffman SE, Chen JA, Gupta S, Kappel AD, Smith TR, Chiocca EA. The Current Landscape of Oncolytic Herpes Simplex Viruses as Novel Therapies for Brain Malignancies. Viruses 2021; 13:v13061158. [PMID: 34204248 PMCID: PMC8234451 DOI: 10.3390/v13061158] [Citation(s) in RCA: 11] [Impact Index Per Article: 3.7] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/19/2021] [Revised: 06/09/2021] [Accepted: 06/12/2021] [Indexed: 01/02/2023] Open
Abstract
Despite advances in surgical resection and chemoradiation, high-grade brain tumors continue to be associated with significant morbidity/mortality. Novel therapeutic strategies and approaches are, therefore, desperately needed for patients and their families. Given the success experienced in treating multiple other forms of cancer, immunotherapy and, in particular, immunovirotherapy are at the forefront amongst novel therapeutic strategies that are currently under investigation for incurable brain tumors. Accordingly, herein, we provide a focused mini review of pertinent oncolytic herpes viruses (oHSV) that are being investigated in clinical trials.
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Affiliation(s)
- Joshua D. Bernstock
- Department of Neurosurgery, Brigham and Women’s Hospital, Harvard Medical School, Boston, MA 02115, USA; (J.D.B.); (S.E.H.); (J.A.C.); (S.G.); (A.D.K.); (T.R.S.)
| | - Samantha E. Hoffman
- Department of Neurosurgery, Brigham and Women’s Hospital, Harvard Medical School, Boston, MA 02115, USA; (J.D.B.); (S.E.H.); (J.A.C.); (S.G.); (A.D.K.); (T.R.S.)
- Harvard-MIT MD-PhD Program, Harvard Medical School, Boston, MA 02115, USA
| | - Jason A. Chen
- Department of Neurosurgery, Brigham and Women’s Hospital, Harvard Medical School, Boston, MA 02115, USA; (J.D.B.); (S.E.H.); (J.A.C.); (S.G.); (A.D.K.); (T.R.S.)
| | - Saksham Gupta
- Department of Neurosurgery, Brigham and Women’s Hospital, Harvard Medical School, Boston, MA 02115, USA; (J.D.B.); (S.E.H.); (J.A.C.); (S.G.); (A.D.K.); (T.R.S.)
| | - Ari D. Kappel
- Department of Neurosurgery, Brigham and Women’s Hospital, Harvard Medical School, Boston, MA 02115, USA; (J.D.B.); (S.E.H.); (J.A.C.); (S.G.); (A.D.K.); (T.R.S.)
| | - Timothy R. Smith
- Department of Neurosurgery, Brigham and Women’s Hospital, Harvard Medical School, Boston, MA 02115, USA; (J.D.B.); (S.E.H.); (J.A.C.); (S.G.); (A.D.K.); (T.R.S.)
- Computational Neuroscience Outcomes Center, Brigham & Women’s Hospital, Harvard Medical School, Boston, MA 02115, USA
| | - E. Antonio Chiocca
- Department of Neurosurgery, Brigham and Women’s Hospital, Harvard Medical School, Boston, MA 02115, USA; (J.D.B.); (S.E.H.); (J.A.C.); (S.G.); (A.D.K.); (T.R.S.)
- Correspondence:
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99911
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Reid BM, Vyas S, Chen Z, Chen A, Kanetsky PA, Permuth JB, Sellers TA, Saglam O. Morphologic and molecular correlates of EZH2 as a predictor of platinum resistance in high-grade ovarian serous carcinoma. BMC Cancer 2021; 21:714. [PMID: 34140011 PMCID: PMC8212453 DOI: 10.1186/s12885-021-08413-3] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/15/2021] [Accepted: 05/21/2021] [Indexed: 12/12/2022] Open
Abstract
BACKGROUND Enhancer of zesta homologue 2 (EZH2) is an essential component of polycomb repressive complex 2 (PRC2) that contributes to tumor progression and chemo-resistance. The aim of this study was to comprehensively assess the prognostic value of EZH2 across the morphologic and molecular spectra of high-grade serous ovarian carcinoma (HGSOC) by utilizing both immunohistochemistry (IHC) and proteogenomic technologies. METHODS IHC of EZH2 was performed using a tissue microarray of 79 HGSOC scored (+/-) for lymphovascular invasion (LVI), tumor-infiltrating lymphocytic aggregates ≥1 mm (TIL) and architectural growth patterns. The association of EZH2 H-score with response to therapy and overall survival was evaluated by tumor features. We also evaluated EZH2 transcriptional (RNA sequencing) and protein (mass spectrometry) expression from bulk tumor samples from 336 HGSOC from The Cancer Genome Atlas (TCGA). EZH2 expression and co-expression networks were compared by clinical outcomes. RESULTS For HGSOC without TIL (58%), EZH2 expression was almost 2-fold higher in platinum resistant tumors (P = 0.01). Conversely, EZH2 was not associated with platinum resistance among TIL+ HGSOC (P = 0.41). EZH2 expression was associated with reduced survival for tumors with LVI (P = 0.04). Analysis of TCGA found higher EZH2 expression in immunoreactive and proliferative tumors (P = 6.7 × 10- 5) although protein levels were similar across molecular subtypes (P = 0.52). Both mRNA and protein levels of EZH2 were lower in platinum resistant tumors although they were not associated with survival. Co-expression analysis revealed EZH2 networks totaling 1049 mRNA and 448 proteins that were exclusive to platinum sensitive or resistant tumors. The EZH2 network in resistant HGSOC included CARM1 which was positively correlated with EZH2 at both mRNA (r = 0.33, p = 0.003) and protein (r = 0.14, P = 0.01) levels. Further, EZH2 co-expression with CARM1 corresponded to a decreased prognostic significance of EZH2 expression in resistant tumors. CONCLUSIONS Our findings demonstrate that EZH2 expression varies based on its interactions with immunologic pathways and tumor microenvironment, impacting the prognostic interpretation. The association between high EZH2 expression and platinum resistance in TIL- HGSOC warrants further study of the implications for therapeutic strategies.
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Affiliation(s)
- Brett M Reid
- Cancer Epidemiology, Moffitt Cancer Center, Tampa, FL, USA.
| | - Shraddha Vyas
- Cancer Epidemiology, Moffitt Cancer Center, Tampa, FL, USA
| | - Zhihua Chen
- Biostatistics and Bioinformatics, Moffitt Cancer Center, Tampa, FL, USA
| | - Ann Chen
- Biostatistics and Bioinformatics, Moffitt Cancer Center, Tampa, FL, USA
| | | | | | | | - Ozlen Saglam
- Department of Pathology, Moffitt Cancer Center, 12902 USF Magnolia Dr, Tampa, FL, 33612, USA
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99912
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Kohchi T, Yamato KT, Ishizaki K, Yamaoka S, Nishihama R. Development and Molecular Genetics of Marchantia polymorpha. ANNUAL REVIEW OF PLANT BIOLOGY 2021; 72:677-702. [PMID: 33684298 DOI: 10.1146/annurev-arplant-082520-094256] [Citation(s) in RCA: 48] [Impact Index Per Article: 16.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 05/05/2023]
Abstract
Bryophytes occupy a basal position in the monophyletic evolution of land plants and have a life cycle in which the gametophyte generation dominates over the sporophyte generation, offering a significant advantage in conducting genetics. Owing to its low genetic redundancy and the availability of an array of versatile molecular tools, including efficient genome editing, the liverwort Marchantia polymorpha has become a model organism of choice that provides clues to the mechanisms underlying eco-evo-devo biology in plants. Recent analyses of developmental mutants have revealed that key genes in developmental processes are functionally well conserved in plants, despite their morphological differences, and that lineage-specific evolution occurred by neo/subfunctionalization of common ancestral genes. We suggest that M. polymorpha is an excellent platform to uncover the conserved and diversified mechanisms underlying land plant development.
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Affiliation(s)
- Takayuki Kohchi
- Graduate School of Biostudies, Kyoto University, Kyoto 606-8502, Japan; , ,
| | - Katsuyuki T Yamato
- Faculty of Biology-Oriented Science and Technology, Kindai University, Kinokawa 649-6493, Japan;
| | | | - Shohei Yamaoka
- Graduate School of Biostudies, Kyoto University, Kyoto 606-8502, Japan; , ,
| | - Ryuichi Nishihama
- Graduate School of Biostudies, Kyoto University, Kyoto 606-8502, Japan; , ,
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99913
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Riwaldt S, Corydon TJ, Pantalone D, Sahana J, Wise P, Wehland M, Krüger M, Melnik D, Kopp S, Infanger M, Grimm D. Role of Apoptosis in Wound Healing and Apoptosis Alterations in Microgravity. Front Bioeng Biotechnol 2021; 9:679650. [PMID: 34222218 PMCID: PMC8248797 DOI: 10.3389/fbioe.2021.679650] [Citation(s) in RCA: 42] [Impact Index Per Article: 14.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/12/2021] [Accepted: 05/19/2021] [Indexed: 12/15/2022] Open
Abstract
Functioning as the outermost self-renewing protective layer of the human organism, skin protects against a multitude of harmful biological and physical stimuli. Consisting of ectodermal, mesenchymal, and neural crest-derived cell lineages, tissue homeostasis, and signal transduction are finely tuned through the interplay of various pathways. A health problem of astronauts in space is skin deterioration. Until today, wound healing has not been considered as a severe health concern for crew members. This can change with deep space exploration missions and commercial spaceflights together with space tourism. Albeit the molecular process of wound healing is not fully elucidated yet, there have been established significant conceptual gains and new scientific methods. Apoptosis, e.g., programmed cell death, enables orchestrated development and cell removal in wounded or infected tissue. Experimental designs utilizing microgravity allow new insights into the role of apoptosis in wound healing. Furthermore, impaired wound healing in unloading conditions would depict a significant challenge in human-crewed exploration space missions. In this review, we provide an overview of alterations in the behavior of cutaneous cell lineages under microgravity in regard to the impact of apoptosis in wound healing. We discuss the current knowledge about wound healing in space and simulated microgravity with respect to apoptosis and available therapeutic strategies.
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Affiliation(s)
- Stefan Riwaldt
- Department of Microgravity and Translational Regenerative Medicine, University Clinic for Plastic, Aesthetic and Hand Surgery, Otto-von-Guericke University, Magdeburg, Germany
| | - Thomas J. Corydon
- Department of Biomedicine, Aarhus University, Aarhus, Denmark
- Department of Ophthalmology, Aarhus University Hospital, Aarhus, Denmark
| | - Desiré Pantalone
- Department of Experimental and Clinical Medicine, University of Florence, Florence, Italy
| | | | - Petra Wise
- The Saban Research Institute, Children's Hospital Los Angeles, University of Southern California, Los Angeles, CA, United States
| | - Markus Wehland
- Department of Microgravity and Translational Regenerative Medicine, University Clinic for Plastic, Aesthetic and Hand Surgery, Otto-von-Guericke University, Magdeburg, Germany
- Research Group “Magdeburger Arbeitsgemeinschaft für Forschung unter Raumfahrt-und Schwerelosigkeitsbedingungen” (MARS), Otto-von-Guericke University, Magdeburg, Germany
| | - Marcus Krüger
- Department of Microgravity and Translational Regenerative Medicine, University Clinic for Plastic, Aesthetic and Hand Surgery, Otto-von-Guericke University, Magdeburg, Germany
- Research Group “Magdeburger Arbeitsgemeinschaft für Forschung unter Raumfahrt-und Schwerelosigkeitsbedingungen” (MARS), Otto-von-Guericke University, Magdeburg, Germany
| | - Daniela Melnik
- Department of Microgravity and Translational Regenerative Medicine, University Clinic for Plastic, Aesthetic and Hand Surgery, Otto-von-Guericke University, Magdeburg, Germany
| | - Sascha Kopp
- Department of Microgravity and Translational Regenerative Medicine, University Clinic for Plastic, Aesthetic and Hand Surgery, Otto-von-Guericke University, Magdeburg, Germany
- Research Group “Magdeburger Arbeitsgemeinschaft für Forschung unter Raumfahrt-und Schwerelosigkeitsbedingungen” (MARS), Otto-von-Guericke University, Magdeburg, Germany
| | - Manfred Infanger
- Department of Microgravity and Translational Regenerative Medicine, University Clinic for Plastic, Aesthetic and Hand Surgery, Otto-von-Guericke University, Magdeburg, Germany
- Research Group “Magdeburger Arbeitsgemeinschaft für Forschung unter Raumfahrt-und Schwerelosigkeitsbedingungen” (MARS), Otto-von-Guericke University, Magdeburg, Germany
| | - Daniela Grimm
- Department of Microgravity and Translational Regenerative Medicine, University Clinic for Plastic, Aesthetic and Hand Surgery, Otto-von-Guericke University, Magdeburg, Germany
- Department of Biomedicine, Aarhus University, Aarhus, Denmark
- Research Group “Magdeburger Arbeitsgemeinschaft für Forschung unter Raumfahrt-und Schwerelosigkeitsbedingungen” (MARS), Otto-von-Guericke University, Magdeburg, Germany
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99914
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Abstract
The gametophyte represents the sexual phase in the alternation of generations in plants; the other, nonsexual phase is the sporophyte. Here, we review the evolutionary origins of the male gametophyte among land plants and, in particular, its ontogenesis in flowering plants. The highly reduced male gametophyte of angiosperm plants is a two- or three-celled pollen grain. Its task is the production of two male gametes and their transport to the female gametophyte, the embryo sac, where double fertilization takes place. We describe two phases of pollen ontogenesis-a developmental phase leading to the differentiation of the male germline and the formation of a mature pollen grain and a functional phase representing the pollen tube growth, beginning with the landing of the pollen grain on the stigma and ending with double fertilization. We highlight recent advances in the complex regulatory mechanisms involved, including posttranscriptional regulation and transcript storage, intracellular metabolic signaling, pollen cell wall structure and synthesis, protein secretion, and phased cell-cell communication within the reproductive tissues.
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Affiliation(s)
- Said Hafidh
- Laboratory of Pollen Biology, Institute of Experimental Botany of the Czech Academy of Sciences, 165 02 Prague 6, Czech Republic; ,
| | - David Honys
- Laboratory of Pollen Biology, Institute of Experimental Botany of the Czech Academy of Sciences, 165 02 Prague 6, Czech Republic; ,
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99915
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Cavanaugh KE, Oakes PW, Gardel ML. Optogenetic Control of RhoA to Probe Subcellular Mechanochemical Circuitry. ACTA ACUST UNITED AC 2021; 86:e102. [PMID: 32031760 DOI: 10.1002/cpcb.102] [Citation(s) in RCA: 7] [Impact Index Per Article: 2.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/01/2023]
Abstract
Spatiotemporal localization of protein function is essential for physiological processes from subcellular to tissue scales. Genetic and pharmacological approaches have played instrumental roles in isolating molecular components necessary for subcellular machinery. However, these approaches have limited capabilities to reveal the nature of the spatiotemporal regulation of subcellular machineries like those of cytoskeletal organelles. With the recent advancement of optogenetic probes, the field now has a powerful tool to localize cytoskeletal stimuli in both space and time. Here, we detail the use of tunable light-controlled interacting protein tags (TULIPs) to manipulate RhoA signaling in vivo. This is an optogenetic dimerization system that rapidly, reversibly, and efficiently directs a cytoplasmic RhoGEF to the plasma membrane for activation of RhoA using light. We first compare this probe to other available optogenetic systems and outline the engineering logic for the chosen recruitable RhoGEFs. We also describe how to generate the cell line, spatially control illumination, confirm optogenetic control of RhoA, and mechanically induce cell-cell junction deformation in cultured tissues. Together, these protocols detail how to probe the mechanochemical circuitry downstream of RhoA signaling. © 2020 by John Wiley & Sons, Inc. Basic Protocol 1: Generation of a stable cell line expressing TULIP constructs Basic Protocol 2: Preparation of collagen substrate for imaging Basic Protocol 3: Transient transfection for visualization of downstream effectors Basic Protocol 4: Calibration of spatial illumination Basic Protocol 5: Optogenetic activation of a region of interest.
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Affiliation(s)
- Kate E Cavanaugh
- Department of Molecular Genetics and Cell Biology, University of Chicago, Chicago, Illinois
| | - Patrick W Oakes
- Department of Cell & Molecular Physiology, Stritch School of Medicine, Loyola University Chicago, Maywood, Illinois
| | - Margaret L Gardel
- Department of Molecular Genetics and Cell Biology, University of Chicago, Chicago, Illinois
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99916
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A comprehensive prognostic signature for glioblastoma patients based on transcriptomics and single cell sequencing. Cell Oncol (Dordr) 2021; 44:917-935. [PMID: 34142341 DOI: 10.1007/s13402-021-00612-1] [Citation(s) in RCA: 6] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/09/2020] [Accepted: 05/17/2021] [Indexed: 10/21/2022] Open
Abstract
PURPOSE Glioblastoma (GBM) is the most common and deadly brain tumor. We aimed to reveal potential prognostic GBM marker genes, elaborate their functions, and build an effective a prognostic model for GBM patients. METHODS Through data mining of The Cancer Genome Atlas (TCGA) and the Chinese Glioma Genome Atlas (CGGA), we screened for significantly differentially expressed genes (DEGs) to calculate risk scores for individual patients. Published data of somatic mutation and copy number variation profiles were analyzed for distinct genomic alterations associated with risk scores. In addition, single-cell sequencing was used to explore the biological functions of the identified prognostic marker genes. By combining risk scores and other clinical features, we built a comprehensive prognostic GBM model. RESULTS Seven DEGs (CLEC5A, HOXC6, HOXA5, CCL2, GPRASP1, BSCL2 and PTX3) were identified as being prognostic for GBM. Expression of these genes was confirmed in different GBM cell lines using real-time PCR. Risk scores calculated from the seven DEGs revealed prognostic value irrespective of other clinical factors, including IDH mutation status, and were negatively correlated with TP53 expression. The prognostic genes were found to be associated with tumor proliferation and progression based on pseudo-time analysis in neoplastic cells. A final prognostic model was developed and validated with a good performance, especially in geriatric GBM patients. CONCLUSIONS Using genetic profiles, age, IDH mutation status, and chemotherapy and radiotherapy, we constructed a comprehensive prognostic model for GBM patients. The model has a good performance, especially in geriatric GBM patients.
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99917
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Schneider KL, Wollman AJM, Nyström T, Shashkova S. Comparison of endogenously expressed fluorescent protein fusions behaviour for protein quality control and cellular ageing research. Sci Rep 2021; 11:12819. [PMID: 34140587 PMCID: PMC8211707 DOI: 10.1038/s41598-021-92249-1] [Citation(s) in RCA: 4] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [Abstract] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/22/2021] [Accepted: 06/07/2021] [Indexed: 12/16/2022] Open
Abstract
The yeast Hsp104 protein disaggregase is often used as a reporter for misfolded or damaged protein aggregates and protein quality control and ageing research. Observing Hsp104 fusions with fluorescent proteins is a popular approach to follow post stress protein aggregation, inclusion formation and disaggregation. While concerns that bigger protein tags, such as genetically encoded fluorescent tags, may affect protein behaviour and function have been around for quite some time, experimental evidence of how exactly the physiology of the protein of interest is altered within fluorescent protein fusions remains limited. To address this issue, we performed a comparative assessment of endogenously expressed Hsp104 fluorescent fusions function and behaviour. We provide experimental evidence that molecular behaviour may not only be altered by introducing a fluorescent protein tag but also varies depending on such a tag within the fusion. Although our findings are especially applicable to protein quality control and ageing research in yeast, similar effects may play a role in other eukaryotic systems.
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Affiliation(s)
- Kara L Schneider
- Department of Microbiology and Immunology, Institute of Biomedicine, Sahlgrenska Academy, University of Gothenburg, 405 30, Gothenburg, Sweden
| | - Adam J M Wollman
- Newcastle University Biosciences Institute, Newcastle, NE2 4HH, UK
| | - Thomas Nyström
- Department of Microbiology and Immunology, Institute of Biomedicine, Sahlgrenska Academy, University of Gothenburg, 405 30, Gothenburg, Sweden
| | - Sviatlana Shashkova
- Department of Microbiology and Immunology, Institute of Biomedicine, Sahlgrenska Academy, University of Gothenburg, 405 30, Gothenburg, Sweden.
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99918
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Rosińska S, Gavard J. Tumor Vessels Fuel the Fire in Glioblastoma. Int J Mol Sci 2021; 22:6514. [PMID: 34204510 PMCID: PMC8235363 DOI: 10.3390/ijms22126514] [Citation(s) in RCA: 32] [Impact Index Per Article: 10.7] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/31/2021] [Revised: 06/14/2021] [Accepted: 06/15/2021] [Indexed: 02/07/2023] Open
Abstract
Glioblastoma, a subset of aggressive brain tumors, deploy several means to increase blood vessel supply dedicated to the tumor mass. This includes typical program borrowed from embryonic development, such as vasculogenesis and sprouting angiogenesis, as well as unconventional processes, including co-option, vascular mimicry, and transdifferentiation, in which tumor cells are pro-actively engaged. However, these neo-generated vascular networks are morphologically and functionally abnormal, suggesting that the vascularization processes are rather inefficient in the tumor ecosystem. In this review, we reiterate the specificities of each neovascularization modality in glioblastoma, and, how they can be hampered mechanistically in the perspective of anti-cancer therapies.
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Affiliation(s)
- Sara Rosińska
- CRCINA, Inserm, CNRS, Université de Nantes, 44000 Nantes, France;
| | - Julie Gavard
- CRCINA, Inserm, CNRS, Université de Nantes, 44000 Nantes, France;
- Integrated Center for Oncology, ICO, 44800 St. Herblain, France
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99919
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Emenecker RJ, Holehouse AS, Strader LC. Biological Phase Separation and Biomolecular Condensates in Plants. ANNUAL REVIEW OF PLANT BIOLOGY 2021; 72:17-46. [PMID: 33684296 PMCID: PMC8221409 DOI: 10.1146/annurev-arplant-081720-015238] [Citation(s) in RCA: 46] [Impact Index Per Article: 15.3] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 05/04/2023]
Abstract
A surge in research focused on understanding the physical principles governing the formation, properties, and function of membraneless compartments has occurred over the past decade. Compartments such as the nucleolus, stress granules, and nuclear speckles have been designated as biomolecular condensates to describe their shared property of spatially concentrating biomolecules. Although this research has historically been carried out in animal and fungal systems, recent work has begun to explore whether these same principles are relevant in plants. Effectively understanding and studying biomolecular condensates require interdisciplinary expertise that spans cell biology, biochemistry, and condensed matter physics and biophysics. As such, some involved concepts may be unfamiliar to any given individual. This review focuses on introducing concepts essential to the study of biomolecular condensates and phase separation for biologists seeking to carry out research in this area and further examines aspects of biomolecular condensates that are relevant to plant systems.
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Affiliation(s)
- Ryan J Emenecker
- Department of Biology, Washington University, St. Louis, Missouri 63130, USA
- Department of Biochemistry and Molecular Biophysics, Washington University School of Medicine, St. Louis, Missouri 63110, USA;
- Center for Science and Engineering of Living Systems, Washington University, St. Louis, Missouri 63130, USA
- Center for Engineering MechanoBiology, Washington University, St. Louis, Missouri 63130, USA
| | - Alex S Holehouse
- Department of Biochemistry and Molecular Biophysics, Washington University School of Medicine, St. Louis, Missouri 63110, USA;
- Center for Science and Engineering of Living Systems, Washington University, St. Louis, Missouri 63130, USA
| | - Lucia C Strader
- Center for Science and Engineering of Living Systems, Washington University, St. Louis, Missouri 63130, USA
- Center for Engineering MechanoBiology, Washington University, St. Louis, Missouri 63130, USA
- Department of Biology, Duke University, Durham, North Carolina 27708, USA;
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99920
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Maraldi T, Angeloni C, Prata C, Hrelia S. NADPH Oxidases: Redox Regulators of Stem Cell Fate and Function. Antioxidants (Basel) 2021; 10:973. [PMID: 34204425 PMCID: PMC8234808 DOI: 10.3390/antiox10060973] [Citation(s) in RCA: 20] [Impact Index Per Article: 6.7] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/29/2021] [Revised: 06/15/2021] [Accepted: 06/15/2021] [Indexed: 12/12/2022] Open
Abstract
One of the major sources of reactive oxygen species (ROS) generated within stem cells is the nicotinamide adenine dinucleotide phosphate (NADPH) oxidase family of enzymes (NOXs), which are critical determinants of the redox state beside antioxidant defense mechanisms. This balance is involved in another one that regulates stem cell fate: indeed, self-renewal, proliferation, and differentiation are decisive steps for stem cells during embryo development, adult tissue renovation, and cell therapy application. Ex vivo culture-expanded stem cells are being investigated for tissue repair and immune modulation, but events such as aging, senescence, and oxidative stress reduce their ex vivo proliferation, which is crucial for their clinical applications. Here, we review the role of NOX-derived ROS in stem cell biology and functions, focusing on positive and negative effects triggered by the activity of different NOX isoforms. We report recent findings on downstream molecular targets of NOX-ROS signaling that can modulate stem cell homeostasis and lineage commitment and discuss the implications in ex vivo expansion and in vivo engraftment, function, and longevity. This review highlights the role of NOX as a pivotal regulator of several stem cell populations, and we conclude that these aspects have important implications in the clinical utility of stem cells, but further studies on the effects of pharmacological modulation of NOX in human stem cells are imperative.
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Affiliation(s)
- Tullia Maraldi
- Department of Biomedical, Metabolic and Neural Sciences, University of Modena and Reggio Emilia, Via del Pozzo 71, 41124 Modena, Italy;
| | - Cristina Angeloni
- School of Pharmacy, University of Camerino, Via Gentile III da Varano, 62032 Camerino, Italy;
| | - Cecilia Prata
- Department of Pharmacy and Biotechnology, Alma Mater Studiorum—University of Bologna, Via Irnerio 48, 40126 Bologna, Italy
| | - Silvana Hrelia
- Department for Life Quality Studies, Alma Mater Studiorum—University of Bologna, Corso d’Augusto 237, 47921 Rimini, Italy;
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99921
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Khan MIK, Charles RCM, Ramachandran R, Gupta S, Govindaraju G, Mishra R, Rajavelu A, Coumar MS, Chavali S, Dhayalan A. The ribosomal protein eL21 interacts with the protein lysine methyltransferase SMYD2 and regulates its steady state levels. BIOCHIMICA ET BIOPHYSICA ACTA-MOLECULAR CELL RESEARCH 2021; 1868:119079. [PMID: 34147559 DOI: 10.1016/j.bbamcr.2021.119079] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Abstract] [Key Words] [Subscribe] [Scholar Register] [Received: 02/10/2021] [Revised: 05/24/2021] [Accepted: 06/13/2021] [Indexed: 01/23/2023]
Abstract
The protein lysine methyltransferase, SMYD2 is involved in diverse cellular events by regulating protein functions through lysine methylation. Though several substrate proteins of SMYD2 are well-studied, only a limited number of its interaction partners have been identified and characterized. Here, we performed a yeast two-hybrid screening of SMYD2 and found that the ribosomal protein, eL21 could interact with SMYD2. SMYD2-eL21 interaction in the human cells was confirmed by immunoprecipitation methods. In vitro pull-down assays revealed that SMYD2 interacts with eL21 directly through its SET and MYND domain. Computational mapping, followed by experimental studies identified that Lys81 and Lys83 residues of eL21 are important for the SMYD2-eL21 interaction. Evolutionary analysis showed that these residues might have co-evolved with the emergence of SMYD2. We found that eL21 regulates the steady state levels of SMYD2 by promoting its transcription and inhibiting its proteasomal degradation. Importantly, SMYD2-eL21 interaction plays an important role in regulating cell proliferation and its dysregulation might lead to tumorigenesis. Our findings highlight a novel extra-ribosomal function of eL21 on regulating SMYD2 levels and imply that ribosomal proteins might regulate wide range of cellular functions through protein-protein interactions in addition to their core function in translation.
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Affiliation(s)
- Mohd Imran K Khan
- Department of Biotechnology, Pondicherry University, Puducherry 605 014, India
| | | | - Reshma Ramachandran
- Department of Biology, Indian Institute of Science Education and Research (IISER) Tirupati, Tirupati 517 507, India
| | - Somlee Gupta
- Department of Biotechnology, Pondicherry University, Puducherry 605 014, India
| | - Gayathri Govindaraju
- Interdisciplinary Biology, Rajiv Gandhi Centre for Biotechnology, Trivandrum 695 014, India
| | - Rashmi Mishra
- Department of Biotechnology, Pondicherry University, Puducherry 605 014, India
| | - Arumugam Rajavelu
- Interdisciplinary Biology, Rajiv Gandhi Centre for Biotechnology, Trivandrum 695 014, India
| | | | - Sreenivas Chavali
- Department of Biology, Indian Institute of Science Education and Research (IISER) Tirupati, Tirupati 517 507, India.
| | - Arunkumar Dhayalan
- Department of Biotechnology, Pondicherry University, Puducherry 605 014, India.
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99922
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Faranda AP, Shihan MH, Wang Y, Duncan MK. The effect of sex on the mouse lens transcriptome. Exp Eye Res 2021; 209:108676. [PMID: 34146586 DOI: 10.1016/j.exer.2021.108676] [Citation(s) in RCA: 4] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/21/2021] [Revised: 05/31/2021] [Accepted: 06/09/2021] [Indexed: 02/08/2023]
Abstract
The transcriptome of mammalian tissues differs between males and females, and these differences can change across the lifespan, likely regulating known sexual dimorphisms in disease prevalence and severity. Cataract, the most prevalent disease of the ocular lens, occurs at similar rates in young individuals, but its incidence is elevated in older women compared to men of the same age. However, the influence of sex on the lens transcriptome was unknown. RNAseq based transcriptomic profiling of young adult C57BL/6J mouse lens epithelial and fiber cells revealed that few genes are differentially expressed between the sexes. In contrast, lens cells from aged (24 month old) male and female C57BL/6J mice differentially expressed many genes, including several whose expression is lens preferred. Like cataracts, posterior capsular opacification (PCO), a major sequela of cataract surgery, may also be more prevalent in women. Lens epithelial cells isolated from mouse eyes 24 h after lens fiber cell removal exhibited numerous transcriptomic differences between the sexes, including genes implicated in complement cascades and extracellular matrix regulation, and these differences are much more pronounced in aged mice than in young mice. These results provide an unbiased basis for future studies on how sex affects the lens response to aging, cataract development, and cataract surgery.
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Affiliation(s)
- Adam P Faranda
- Department of Biological Sciences University of Delaware, Newark, DE, 19716, USA
| | - Mahbubul H Shihan
- Department of Biological Sciences University of Delaware, Newark, DE, 19716, USA
| | - Yan Wang
- Department of Biological Sciences University of Delaware, Newark, DE, 19716, USA
| | - Melinda K Duncan
- Department of Biological Sciences University of Delaware, Newark, DE, 19716, USA.
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99923
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Sachana M, Willett C, Pistollato F, Bal-Price A. The potential of mechanistic information organised within the AOP framework to increase regulatory uptake of the developmental neurotoxicity (DNT) in vitro battery of assays. Reprod Toxicol 2021; 103:159-170. [PMID: 34147625 PMCID: PMC8279093 DOI: 10.1016/j.reprotox.2021.06.006] [Citation(s) in RCA: 9] [Impact Index Per Article: 3.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/12/2021] [Revised: 05/19/2021] [Accepted: 06/04/2021] [Indexed: 12/24/2022]
Abstract
Current in vivo DNT testing for regulatory purposes is not effective. In vitro assays anchored to key neurodevelopmental processes are available. Development of Adverse Outcome Pathways is required to increase mechanistic understanding of DNT effects. DNT Integrated Approaches to Testing and Assessment for various regulatory purposes should be developed. The OECD Guidance Document on use of in vitro DNT battery of assays is currently under development.
A major challenge in regulatory developmental neurotoxicity (DNT) assessment is lack of toxicological information for many compounds. Therefore, the Test Guidelines programme of the Organisation for Economic Cooperation and Development (OECD) took the initiative to coordinate an international collaboration between diverse stakeholders to consider integration of alternative approaches towards improving the current chemical DNT testing. During the past few years, a series of workshops was organized during which a consensus was reached that incorporation of a DNT testing battery that relies on in vitro assays anchored to key neurodevelopmental processes should be developed. These key developmental processes include neural progenitor cell proliferation, neuronal and oligodendrocyte differentiation, neural cell migration, neurite outgrowth, synaptogenesis and neuronal network formation, as well key events identified in the existing Adverse Outcome Pathways (AOPs). AOPs deliver mechanistic information on the causal links between molecular initiating event, intermediate key events and an adverse outcome of regulatory concern, providing the biological context to facilitate development of Integrated Approaches to Testing and Assessment (IATA) for various regulatory purposes. Developing IATA case studies, using mechanistic information derived from AOPs, is expected to increase scientific confidence for the use of in vitro methods within an IATA, thereby facilitating regulatory uptake. This manuscript summarizes the current state of international efforts to enhance DNT testing by using an in vitro battery of assays focusing on the role of AOPs in informing the development of IATA for different regulatory purposes, aiming to deliver an OECD guidance document on use of in vitro DNT battery of assays that include in vitro data interpretation.
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Affiliation(s)
- Magdalini Sachana
- Environment Health and Safety Division, Environment Directorate, Organisation for Economic Co-Operation and Development (OECD), 75775, Paris Cedex 16, France
| | - Catherine Willett
- Humane Society International, 1255 23rd Street NW, Washington, DC, 20037, USA
| | | | - Anna Bal-Price
- European Commission Joint Research Centre (JRC), Ispra, Italy.
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99924
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Taylor HB, Klaeger S, Clauser KR, Sarkizova S, Weingarten-Gabbay S, Graham DB, Carr SA, Abelin JG. MS-Based HLA-II Peptidomics Combined With Multiomics Will Aid the Development of Future Immunotherapies. Mol Cell Proteomics 2021; 20:100116. [PMID: 34146720 PMCID: PMC8327157 DOI: 10.1016/j.mcpro.2021.100116] [Citation(s) in RCA: 11] [Impact Index Per Article: 3.7] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/19/2021] [Revised: 06/02/2021] [Accepted: 06/03/2021] [Indexed: 12/25/2022] Open
Abstract
Immunotherapies have emerged to treat diseases by selectively modulating a patient's immune response. Although the roles of T and B cells in adaptive immunity have been well studied, it remains difficult to select targets for immunotherapeutic strategies. Because human leukocyte antigen class II (HLA-II) peptides activate CD4+ T cells and regulate B cell activation, proliferation, and differentiation, these peptide antigens represent a class of potential immunotherapy targets and biomarkers. To better understand the molecular basis of how HLA-II antigen presentation is involved in disease progression and treatment, systematic HLA-II peptidomics combined with multiomic analyses of diverse cell types in healthy and diseased states is required. For this reason, MS-based innovations that facilitate investigations into the interplay between disease pathologies and the presentation of HLA-II peptides to CD4+ T cells will aid in the development of patient-focused immunotherapies.
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Affiliation(s)
- Hannah B Taylor
- Broad Institute of MIT and Harvard, Cambridge, Massachusetts, USA
| | - Susan Klaeger
- Broad Institute of MIT and Harvard, Cambridge, Massachusetts, USA
| | - Karl R Clauser
- Broad Institute of MIT and Harvard, Cambridge, Massachusetts, USA
| | | | - Shira Weingarten-Gabbay
- Broad Institute of MIT and Harvard, Cambridge, Massachusetts, USA; Department of Organismic and Evolutionary Biology, Harvard University, Cambridge, Massachusetts, USA
| | - Daniel B Graham
- Broad Institute of MIT and Harvard, Cambridge, Massachusetts, USA; Center for Computational and Integrative Biology, Massachusetts General Hospital and Harvard Medical School, Boston, Massachusetts, USA; Department of Molecular Biology, Massachusetts General Hospital and Harvard Medical School, Boston, Massachusetts, USA
| | - Steven A Carr
- Broad Institute of MIT and Harvard, Cambridge, Massachusetts, USA
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99925
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Murray-Nerger LA, Cristea IM. Lamin post-translational modifications: emerging toggles of nuclear organization and function. Trends Biochem Sci 2021; 46:832-847. [PMID: 34148760 DOI: 10.1016/j.tibs.2021.05.007] [Citation(s) in RCA: 16] [Impact Index Per Article: 5.3] [Reference Citation Analysis] [Abstract] [Key Words] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/09/2021] [Revised: 05/03/2021] [Accepted: 05/18/2021] [Indexed: 01/03/2023]
Abstract
Nuclear lamins are ancient type V intermediate filaments with diverse functions that include maintaining nuclear shape, mechanosignaling, tethering and stabilizing chromatin, regulating gene expression, and contributing to cell cycle progression. Despite these numerous roles, an outstanding question has been how lamins are regulated. Accumulating work indicates that a range of lamin post-translational modifications (PTMs) control their functions both in homeostatic cells and in disease states such as progeria, muscular dystrophy, and viral infection. Here, we review the current knowledge of the diverse types of PTMs that regulate lamins in a site-specific manner. We highlight methods that can be used to characterize lamin PTMs whose functions are currently unknown and provide a perspective on the future of the lamin PTM field.
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Affiliation(s)
- Laura A Murray-Nerger
- Department of Molecular Biology, Princeton University, Lewis Thomas Laboratory, Washington Road, Princeton, NJ 08544, USA
| | - Ileana M Cristea
- Department of Molecular Biology, Princeton University, Lewis Thomas Laboratory, Washington Road, Princeton, NJ 08544, USA.
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99926
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Furman CM, Elbashir R, Pannafino G, Clark NL, Alani E. Experimental exchange of paralogous domains in the MLH family provides evidence of sub-functionalization after gene duplication. G3 (BETHESDA, MD.) 2021; 11:jkab111. [PMID: 33871573 PMCID: PMC8495741 DOI: 10.1093/g3journal/jkab111] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Subscribe] [Scholar Register] [Received: 03/08/2021] [Accepted: 03/31/2021] [Indexed: 01/24/2023]
Abstract
Baker's yeast contains a large number of duplicated genes; some function redundantly, whereas others have more specialized roles. We used the MLH family of DNA mismatch repair (MMR) proteins as a model to better understand the steps that lead to gene specialization following a gene duplication event. We focused on two highly conserved yeast MLH proteins, Pms1 and Mlh3, with Pms1 having a major role in the repair of misincorporation events during DNA replication and Mlh3 acting to resolve recombination intermediates in meiosis to form crossovers. The baker's yeast Mlh3 and Pms1 proteins are significantly diverged (19% overall identity), suggesting that an extensive number of evolutionary steps, some major, others involving subtle refinements, took place to diversify the MLH proteins. Using phylogenetic and molecular approaches, we provide evidence that all three domains (N-terminal ATP binding, linker, C-terminal endonuclease/MLH interaction) in the MLH protein family are critical for conferring pathway specificity. Importantly, mlh3 alleles in the ATP binding and endonuclease domains improved MMR functions in strains lacking the Pms1 protein and did not disrupt Mlh3 meiotic functions. This ability for mlh3 alleles to complement the loss of Pms1 suggests that an ancestral Pms1/Mlh3 protein was capable of performing both MMR and crossover functions. Our strategy for analyzing MLH pathway specificity provides an approach to understand how paralogs have evolved to support distinct cellular processes.
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Affiliation(s)
- Christopher M Furman
- Department of Molecular Biology and Genetics, Cornell University, Ithaca, NY 14853-2703, USA
| | - Ryan Elbashir
- Department of Molecular Biology and Genetics, Cornell University, Ithaca, NY 14853-2703, USA
| | - Gianno Pannafino
- Department of Molecular Biology and Genetics, Cornell University, Ithaca, NY 14853-2703, USA
| | - Nathan L Clark
- Department of Human Genetics, University of Utah, Salt Lake City, UT 84132, USA
| | - Eric Alani
- Department of Molecular Biology and Genetics, Cornell University, Ithaca, NY 14853-2703, USA
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99927
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Flausino CS, Daniel FI, Modolo F. DNA methylation in oral squamous cell carcinoma: from its role in carcinogenesis to potential inhibitor drugs. Crit Rev Oncol Hematol 2021; 164:103399. [PMID: 34147646 DOI: 10.1016/j.critrevonc.2021.103399] [Citation(s) in RCA: 18] [Impact Index Per Article: 6.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/02/2020] [Revised: 06/02/2021] [Accepted: 06/04/2021] [Indexed: 02/06/2023] Open
Abstract
DNA methylation is one of epigenetic changes most frequently studied nowadays, together with its relationship with oral carcinogenesis. A group of enzymes is responsible for methylation process, known as DNA methyltransferases (DNMT). Although essential during embryogenesis, DNA methylation pattern alterations, including global hypomethylation or gene promoter hypermethylation, can be respectively associated with chromosomal instability and tumor suppressor gene silencing. Higher expression of DNA methyltransferases is a common finding in oral cancer and may contribute to inactivation of important tumor suppressor genes, influencing development, progression, metastasis, and prognosis of the tumor. To control these alterations, inhibitor drugs have been developed as a way to regulate DNMT overexpression, and they are intended to be associated with ongoing chemo- and radiotherapy in oral cancer treatments. In this article, we aimed to highlight the current knowledge about DNA methylation in oral cancer, including main hyper/hypomethylated genes, DNMT expression and its inhibitor treatments.
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Affiliation(s)
| | - Filipe Ivan Daniel
- Federal University of Santa Catarina, Florianópolis, Santa Catarina, Brazil.
| | - Filipe Modolo
- Federal University of Santa Catarina, Florianópolis, Santa Catarina, Brazil
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99928
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Eibl G, Rozengurt E. Metformin: review of epidemiology and mechanisms of action in pancreatic cancer. Cancer Metastasis Rev 2021; 40:865-878. [PMID: 34142285 DOI: 10.1007/s10555-021-09977-z] [Citation(s) in RCA: 20] [Impact Index Per Article: 6.7] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Received: 04/26/2021] [Accepted: 05/27/2021] [Indexed: 12/15/2022]
Abstract
Pancreatic ductal adenocarcinoma continues to be a lethal disease, for which efficient treatment options are very limited. Increasing efforts have been taken to understand how to prevent or intercept this disease at an early stage. There is convincing evidence from epidemiologic and preclinical studies that the antidiabetic drug metformin possesses beneficial effects in pancreatic cancer, including reducing the risk of developing the disease and improving survival in patients with early-stage disease. This review will summarize the current literature about the epidemiological data on metformin and pancreatic cancer as well as describe the preclinical evidence illustrating the anticancer effects of metformin in pancreatic cancer. Underlying mechanisms and targets of metformin will also be discussed. These include direct effects on transformed pancreatic epithelial cells and indirect, systemic effects on extra-pancreatic tissues.
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Affiliation(s)
- Guido Eibl
- Department of Surgery, David Geffen School of Medicine At UCLA, Los Angeles, CA, USA.
| | - Enrique Rozengurt
- Department of Medicine, David Geffen School of Medicine At UCLA, Los Angeles, CA, USA
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99929
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Abstract
Salicylic acid (SA) is an essential plant defense hormone that promotes immunity against biotrophic and semibiotrophic pathogens. It plays crucial roles in basal defense and the amplification of local immune responses, as well as the establishment of systemic acquired resistance. During the past three decades, immense progress has been made in understanding the biosynthesis, homeostasis, perception, and functions of SA. This review summarizes the current knowledge regarding SA in plant immunity and other biological processes. We highlight recent breakthroughs that substantially advanced our understanding of how SA is biosynthesized from isochorismate, how it is perceived, and how SA receptors regulate different aspects of plant immunity. Some key questions in SA biosynthesis and signaling, such as how SA is produced via another intermediate, benzoic acid, and how SA affects the activities of its receptors in the transcriptional regulation of defense genes, remain to be addressed.
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Affiliation(s)
- Yujun Peng
- Department of Botany, University of British Columbia, Vancouver, British Columbia V6T 1Z4, Canada; , , ,
| | - Jianfei Yang
- Department of Botany, University of British Columbia, Vancouver, British Columbia V6T 1Z4, Canada; , , ,
- College of Life Science, Northeast Forestry University, Harbin 150040, China
| | - Xin Li
- Department of Botany, University of British Columbia, Vancouver, British Columbia V6T 1Z4, Canada; , , ,
- Michael Smith Laboratories, University of British Columbia, Vancouver, British Columbia V6T 1Z4, Canada
| | - Yuelin Zhang
- Department of Botany, University of British Columbia, Vancouver, British Columbia V6T 1Z4, Canada; , , ,
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99930
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Villa R, Jagtap PKA, Thomae AW, Campos Sparr A, Forné I, Hennig J, Straub T, Becker PB. Divergent evolution toward sex chromosome-specific gene regulation in Drosophila. Genes Dev 2021; 35:1055-1070. [PMID: 34140353 PMCID: PMC8247607 DOI: 10.1101/gad.348411.121] [Citation(s) in RCA: 9] [Impact Index Per Article: 3.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/26/2021] [Accepted: 05/04/2021] [Indexed: 02/07/2023]
Abstract
The dosage compensation complex (DCC) of Drosophila identifies its X-chromosomal binding sites with exquisite selectivity. The principles that assure this vital targeting are known from the D. melanogaster model: DCC-intrinsic specificity of DNA binding, cooperativity with the CLAMP protein, and noncoding roX2 RNA transcribed from the X chromosome. We found that in D. virilis, a species separated from melanogaster by 40 million years of evolution, all principles are active but contribute differently to X specificity. In melanogaster, the DCC subunit MSL2 evolved intrinsic DNA-binding selectivity for rare PionX sites, which mark the X chromosome. In virilis, PionX motifs are abundant and not X-enriched. Accordingly, MSL2 lacks specific recognition. Here, roX2 RNA plays a more instructive role, counteracting a nonproductive interaction of CLAMP and modulating DCC binding selectivity. Remarkably, roX2 triggers a stable chromatin binding mode characteristic of DCC. Evidently, X-specific regulation is achieved by divergent evolution of protein, DNA, and RNA components.
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Affiliation(s)
- Raffaella Villa
- Molecular Biology Division, Biomedical Center, Ludwig-Maximilians-University Munich, 82152 Planegg-Martinsried, Germany
| | - Pravin Kumar Ankush Jagtap
- Structural and Computational Biology Unit, European Molecular Biology Laboratory (EMBL), 69117 Heidelberg, Germany
| | - Andreas W Thomae
- Molecular Biology Division, Biomedical Center, Ludwig-Maximilians-University Munich, 82152 Planegg-Martinsried, Germany.,Core Facility Bioimaging, Biomedical Center, Ludwig-Maximilians-University Munich, 82152 Planegg-Martinsried, Germany
| | - Aline Campos Sparr
- Molecular Biology Division, Biomedical Center, Ludwig-Maximilians-University Munich, 82152 Planegg-Martinsried, Germany
| | - Ignasi Forné
- Protein Analysis Unit, Biomedical Center, Ludwig-Maximilians-University Munich, 82152 Planegg-Martinsried, Germany
| | - Janosch Hennig
- Structural and Computational Biology Unit, European Molecular Biology Laboratory (EMBL), 69117 Heidelberg, Germany
| | - Tobias Straub
- Bioinformatics Unit, Biomedical Center, Ludwig-Maximilians-University Munich, 82152 Planegg-Martinsried, Germany
| | - Peter B Becker
- Molecular Biology Division, Biomedical Center, Ludwig-Maximilians-University Munich, 82152 Planegg-Martinsried, Germany
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99931
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González-González R, Ortiz-Sarabia G, Molina-Frechero N, Salas-Pacheco JM, Salas-Pacheco SM, Lavalle-Carrasco J, López-Verdín S, Tremillo-Maldonado O, Bologna-Molina R. Epithelial-Mesenchymal Transition Associated with Head and Neck Squamous Cell Carcinomas: A Review. Cancers (Basel) 2021; 13:cancers13123027. [PMID: 34204259 PMCID: PMC8234594 DOI: 10.3390/cancers13123027] [Citation(s) in RCA: 13] [Impact Index Per Article: 4.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/22/2021] [Revised: 06/09/2021] [Accepted: 06/15/2021] [Indexed: 02/07/2023] Open
Abstract
Head and neck squamous cell carcinomas (HNSCCs) are aggressive, recurrent, and metastatic neoplasms with a high occurrence around the world and can lead to death when not treated appropriately. Several molecules and signaling pathways are involved in the malignant conversion process. Epithelial-mesenchymal transition (EMT) has been described in HNSCCs, a major type of aggressive carcinoma. EMT describes the development of epithelial cells into mesenchymal cells, which depends on several molecular interactions and signaling pathways that facilitate mesenchymal conversion. This is related to interactions with the microenvironment of the tumor, hypoxia, growth factors, matrix metalloproteinases, and the presence of viral infections. In this review, we focus on the main molecules related to EMT, their interactions with the tumor microenvironment, plasticity phenomena, epigenetic regulation, hypoxia, inflammation, their relationship with immune cells, and the inhibition of EMT in the context of HNSCCs.
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Affiliation(s)
- Rogelio González-González
- Department of Research, School of Dentistry, Universidad Juárez del Estado de Durango, Durango 34000, Mexico; (R.G.-G.); (G.O.-S.); (O.T.-M.)
| | - Gamaliel Ortiz-Sarabia
- Department of Research, School of Dentistry, Universidad Juárez del Estado de Durango, Durango 34000, Mexico; (R.G.-G.); (G.O.-S.); (O.T.-M.)
| | - Nelly Molina-Frechero
- Xochimilco Unit, Department of Health Care, Universidad Autónoma Metropolitana (UAM) Xochimilco, Mexico City 04960, Mexico; (N.M.-F.); (J.L.-C.)
| | - José Manuel Salas-Pacheco
- Scientific Research Institute, Universidad Juárez del Estado de Durango, Avenida Universidad S/N, Durango 34000, Mexico; (J.M.S.-P.); (S.M.S.-P.)
| | - Sergio Manuel Salas-Pacheco
- Scientific Research Institute, Universidad Juárez del Estado de Durango, Avenida Universidad S/N, Durango 34000, Mexico; (J.M.S.-P.); (S.M.S.-P.)
| | - Jesús Lavalle-Carrasco
- Xochimilco Unit, Department of Health Care, Universidad Autónoma Metropolitana (UAM) Xochimilco, Mexico City 04960, Mexico; (N.M.-F.); (J.L.-C.)
| | - Sandra López-Verdín
- Health Science Center, Dentistry Research Institute, Universidad de Guadalajara, Guadalajara 4430, Mexico;
| | - Omar Tremillo-Maldonado
- Department of Research, School of Dentistry, Universidad Juárez del Estado de Durango, Durango 34000, Mexico; (R.G.-G.); (G.O.-S.); (O.T.-M.)
| | - Ronell Bologna-Molina
- Department of Research, School of Dentistry, Universidad Juárez del Estado de Durango, Durango 34000, Mexico; (R.G.-G.); (G.O.-S.); (O.T.-M.)
- Molecular Pathology Area, School of Dentistry, Universidad de la República, Montevideo 11600, Uruguay
- Correspondence:
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99932
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Yesharim L, Mojbafan M, Abiri M. Hints From the Cellular Functions to the Practical Outlook of Circular RNAs. Front Genet 2021; 12:679446. [PMID: 34220952 PMCID: PMC8247595 DOI: 10.3389/fgene.2021.679446] [Citation(s) in RCA: 3] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/11/2021] [Accepted: 05/25/2021] [Indexed: 12/29/2022] Open
Abstract
Although it has been about 30 years since the discovery of circular RNAs (circRNAs) in mammalian cells, these subtypes of RNAs' capabilities have come into focus in recent years. The unique structure and various functional roles of circRNAs in many cellular processes have aroused researchers' interest and raised many questions about whether circRNAs can facilitate the diagnosis and treatment of diseases. To answer these questions, we will illustrate the main known functions and regulatory roles of circRNAs in the cell after presenting a brief history of the discovery of circRNAs and the main proposed theories of the biogenesis of circRNAs. Afterward, the practical application of circRNAs as biomarkers of different pathophysiological conditions will be discussed, mentioning some examples and challenges in this area. We also consider one of the main questions that human beings have always been faced, "the origin of life," and its possible connection to circRNAs. Finally, focusing on the various capabilities of circRNAs, we discuss their potential therapeutic applications considering the immunity response toward exogenous circRNAs. However, there are still disputes about the exact immune system reaction, which we will discuss in detail.
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Affiliation(s)
- Liora Yesharim
- Department of Medical Genetics and Molecular Biology, School of Medicine, Iran University of Medical Sciences, Tehran, Iran
| | - Marzieh Mojbafan
- Department of Medical Genetics and Molecular Biology, School of Medicine, Iran University of Medical Sciences, Tehran, Iran
- Department of Medical Genetics, Ali-Asghar Children’s Hospital, Tehran, Iran
| | - Maryam Abiri
- Department of Medical Genetics and Molecular Biology, School of Medicine, Iran University of Medical Sciences, Tehran, Iran
- Shahid Akbarabadi Clinical Research Development Unit (ShACRDU), Iran University of Medical Sciences, Tehran, Iran
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99933
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Tran S, Fairlie WD, Lee EF. BECLIN1: Protein Structure, Function and Regulation. Cells 2021; 10:cells10061522. [PMID: 34204202 PMCID: PMC8235419 DOI: 10.3390/cells10061522] [Citation(s) in RCA: 63] [Impact Index Per Article: 21.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/31/2021] [Revised: 06/15/2021] [Accepted: 06/16/2021] [Indexed: 02/06/2023] Open
Abstract
BECLIN1 is a well-established regulator of autophagy, a process essential for mammalian survival. It functions in conjunction with other proteins to form Class III Phosphoinositide 3-Kinase (PI3K) complexes to generate phosphorylated phosphatidylinositol (PtdIns), lipids essential for not only autophagy but other membrane trafficking processes. Over the years, studies have elucidated the structural, biophysical, and biochemical properties of BECLIN1, which have shed light on how this protein functions to allosterically regulate these critical processes of autophagy and membrane trafficking. Here, we review these findings and how BECLIN1’s diverse protein interactome regulates it, as well as its impact on organismal physiology.
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Affiliation(s)
- Sharon Tran
- Olivia Newton-John Cancer Research Institute, Heidelberg, VIC 3084, Australia;
- School of Cancer Medicine, La Trobe University, Bundoora, VIC 3086, Australia
| | - W. Douglas Fairlie
- Olivia Newton-John Cancer Research Institute, Heidelberg, VIC 3084, Australia;
- School of Cancer Medicine, La Trobe University, Bundoora, VIC 3086, Australia
- La Trobe Institute for Molecular Science, La Trobe University, Melbourne, VIC 3086, Australia
- Correspondence: (W.D.F.); (E.F.L.)
| | - Erinna F. Lee
- Olivia Newton-John Cancer Research Institute, Heidelberg, VIC 3084, Australia;
- School of Cancer Medicine, La Trobe University, Bundoora, VIC 3086, Australia
- La Trobe Institute for Molecular Science, La Trobe University, Melbourne, VIC 3086, Australia
- Correspondence: (W.D.F.); (E.F.L.)
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99934
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Functional Redundancy of Cyclase-Associated Proteins CAP1 and CAP2 in Differentiating Neurons. Cells 2021; 10:cells10061525. [PMID: 34204261 PMCID: PMC8234816 DOI: 10.3390/cells10061525] [Citation(s) in RCA: 5] [Impact Index Per Article: 1.7] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/14/2021] [Revised: 06/11/2021] [Accepted: 06/14/2021] [Indexed: 01/03/2023] Open
Abstract
Cyclase-associated proteins (CAPs) are evolutionary-conserved actin-binding proteins with crucial functions in regulating actin dynamics, the spatiotemporally controlled assembly and disassembly of actin filaments (F-actin). Mammals possess two family members (CAP1 and CAP2) with different expression patterns. Unlike most other tissues, both CAPs are expressed in the brain and present in hippocampal neurons. We recently reported crucial roles for CAP1 in growth cone function, neuron differentiation, and neuron connectivity in the mouse brain. Instead, CAP2 controls dendritic spine morphology and synaptic plasticity, and its dysregulation contributes to Alzheimer's disease pathology. These findings are in line with a model in which CAP1 controls important aspects during neuron differentiation, while CAP2 is relevant in differentiated neurons. We here report CAP2 expression during neuron differentiation and its enrichment in growth cones. We therefore hypothesized that CAP2 is relevant not only in excitatory synapses, but also in differentiating neurons. However, CAP2 inactivation neither impaired growth cone morphology and motility nor neuron differentiation. Moreover, CAP2 mutant mice did not display any obvious changes in brain anatomy. Hence, differently from CAP1, CAP2 was dispensable for neuron differentiation and brain development. Interestingly, overexpression of CAP2 rescued not only growth cone size in CAP1-deficient neurons, but also their morphology and differentiation. Our data provide evidence for functional redundancy of CAP1 and CAP2 in differentiating neurons, and they suggest compensatory mechanisms in single mutant neurons.
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99935
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Balberova OV, Bykov EV, Shnayder NA, Petrova MM, Gavrilyuk OA, Kaskaeva DS, Soloveva IA, Petrov KV, Mozheyko EY, Medvedev GV, Nasyrova RF. The "Angiogenic Switch" and Functional Resources in Cyclic Sports Athletes. Int J Mol Sci 2021; 22:ijms22126496. [PMID: 34204341 PMCID: PMC8234968 DOI: 10.3390/ijms22126496] [Citation(s) in RCA: 6] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/26/2021] [Revised: 06/08/2021] [Accepted: 06/10/2021] [Indexed: 12/22/2022] Open
Abstract
Regular physical activity in cyclic sports can influence the so-called “angiogenic switch”, which is considered as an imbalance between proangiogenic and anti-angiogenic molecules. Disruption of the synthesis of angiogenic molecules can be caused by local changes in tissues under the influence of excessive physical exertion and its consequences, such as chronic oxidative stress and associated hypoxia, metabolic acidosis, sports injuries, etc. A review of publications on signaling pathways that activate and inhibit angiogenesis in skeletal muscles, myocardium, lung, and nervous tissue under the influence of intense physical activity in cyclic sports. Materials: We searched PubMed, SCOPUS, Web of Science, Google Scholar, Clinical keys, and e-LIBRARY databases for full-text articles published from 2000 to 2020, using keywords and their combinations. Results: An important aspect of adaptation to training loads in cyclic sports is an increase in the number of capillaries in muscle fibers, which improves the metabolism of skeletal muscles and myocardium, as well as nervous and lung tissue. Recent studies have shown that myocardial endothelial cells not only respond to hemodynamic forces and paracrine signals from neighboring cells, but also take an active part in heart remodeling processes, stimulating the growth and contractility of cardiomyocytes or the production of extracellular matrix proteins in myofibroblasts. As myocardial vascularization plays a central role in the transition from adaptive heart hypertrophy to heart failure, further study of the signaling mechanisms involved in the regulation of angiogenesis in the myocardium is important in sports practice. The study of the “angiogenic switch” problem in the cerebrovascular and cardiovascular systems allows us to claim that the formation of new vessels is mediated by a complex interaction of all growth factors. Although the lungs are one of the limiting systems of the body in cyclic sports, their response to high-intensity loads and other environmental stresses is often overlooked. Airway epithelial cells are the predominant source of several growth factors throughout lung organogenesis and appear to be critical for normal alveolarization, rapid alveolar proliferation, and normal vascular development. There are many controversial questions about the role of growth factors in the physiology and pathology of the lungs. The presented review has demonstrated that when doing sports, it is necessary to give a careful consideration to the possible positive and negative effects of growth factors on muscles, myocardium, lung tissue, and brain. Primarily, the “angiogenic switch” is important in aerobic sports (long distance running). Conclusions: Angiogenesis is a physiological process of the formation of new blood capillaries, which play an important role in the functioning of skeletal muscles, myocardium, lung, and nervous tissue in athletes. Violation of the “angiogenic switch” as a balance between proangiogenic and anti-angiogenic molecules can lead to a decrease in the functional resources of the nervous, musculoskeletal, cardiovascular, and respiratory systems in athletes and, as a consequence, to a decrease in sports performance.
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Affiliation(s)
- Olga V. Balberova
- Research Institute of Olympic Sports, Ural State University of Physical Culture, 454091 Chelyabinsk, Russia;
- Correspondence: (O.V.B.); (N.A.S.); (R.F.N.)
| | - Evgeny V. Bykov
- Research Institute of Olympic Sports, Ural State University of Physical Culture, 454091 Chelyabinsk, Russia;
| | - Natalia A. Shnayder
- V.M. Bekhterev National Medical Research Center for Neurology and Psychiatry, Department of Personalized Psychiatry and Neurology, 192019 Saint Petersburg, Russia
- Department of Outpatient Therapy and Family Medicine with a Postgraduate Course, Shared Core Facilities Molecular and Cell Technologies, Professor V.F. Voino-Yasenetsky Krasnoyarsk State Medical University, 660022 Krasnoyarsk, Russia; (M.M.P.); (D.S.K.)
- Correspondence: (O.V.B.); (N.A.S.); (R.F.N.)
| | - Marina M. Petrova
- Department of Outpatient Therapy and Family Medicine with a Postgraduate Course, Shared Core Facilities Molecular and Cell Technologies, Professor V.F. Voino-Yasenetsky Krasnoyarsk State Medical University, 660022 Krasnoyarsk, Russia; (M.M.P.); (D.S.K.)
| | - Oksana A. Gavrilyuk
- The Department of Polyclinic Therapy and Family Medicine and Healthy Lifesttyle with a Course of PE, V. F. Voino-Yasenetsky Krasnoyarsk State Medical University, 660022 Krasnoyarsk, Russia;
| | - Daria S. Kaskaeva
- Department of Outpatient Therapy and Family Medicine with a Postgraduate Course, Shared Core Facilities Molecular and Cell Technologies, Professor V.F. Voino-Yasenetsky Krasnoyarsk State Medical University, 660022 Krasnoyarsk, Russia; (M.M.P.); (D.S.K.)
| | - Irina A. Soloveva
- Department of Hospital Therapy and Immunology with a Postgraduate Course, Shared Core Facilities Molecular and Cell Technologies, Professor V.F. Voino-Yasenetsky Krasnoyarsk State Medical University, 660022 Krasnoyarsk, Russia;
| | - Kirill V. Petrov
- Department of Physical and Rehabilitation Medicine with a Postgraduate Course, Shared Core Facilities Molecular and Cell Technologies, Professor V.F. Voino-Yasenetsky Krasnoyarsk State Medical University, 660022 Krasnoyarsk, Russia; (K.V.P.); (E.Y.M.)
| | - Elena Y. Mozheyko
- Department of Physical and Rehabilitation Medicine with a Postgraduate Course, Shared Core Facilities Molecular and Cell Technologies, Professor V.F. Voino-Yasenetsky Krasnoyarsk State Medical University, 660022 Krasnoyarsk, Russia; (K.V.P.); (E.Y.M.)
| | - German V. Medvedev
- R. R. Vreden National Medical Research Center for Traumatology and Orthopedics, Department of Hand Surgery with Microsurgical Equipment, 195427 Saint-Petersburg, Russia;
| | - Regina F. Nasyrova
- V.M. Bekhterev National Medical Research Center for Neurology and Psychiatry, Department of Personalized Psychiatry and Neurology, 192019 Saint Petersburg, Russia
- Correspondence: (O.V.B.); (N.A.S.); (R.F.N.)
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99936
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Huo M, Wang Z, Fu W, Tian L, Li W, Zhou Z, Chen Y, Wei J, Abliz Z. Spatially Resolved Metabolomics Based on Air-Flow-Assisted Desorption Electrospray Ionization-Mass Spectrometry Imaging Reveals Region-Specific Metabolic Alterations in Diabetic Encephalopathy. J Proteome Res 2021; 20:3567-3579. [PMID: 34137614 DOI: 10.1021/acs.jproteome.1c00179] [Citation(s) in RCA: 12] [Impact Index Per Article: 4.0] [Reference Citation Analysis] [Abstract] [Key Words] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/17/2022]
Abstract
Spatially resolved metabolic profiling of brain is vital for elucidating tissue-specific molecular histology and pathology underlying diabetic encephalopathy (DE). In this study, a spatially resolved metabolomic method based on air-flow-assisted desorption electrospray ionization-mass spectrometry imaging (AFADESI-MSI) was developed for investigating the region-specific metabolic disturbances in the brain of DE model rats induced by a high-fat diet in combination with streptozotocin administration. A total of 19 discriminating metabolites associated with glycolysis and the pentose phosphate pathway (PPP); the glutamate/gamma aminobutyric acid-glutamine cycle and tricarboxylic acid cycle; nucleotide metabolism; lipid metabolism; carnitine homeostasis; and taurine, ascorbic acid, histidine, and choline metabolism were identified and located in the brains of the diabetic rats simultaneously for the first time. The results indicated that increased glycolytic and PPP activity; dysfunction of mitochondrial metabolism; dysregulation of adenosinergic, glutamatergic, dopaminergic, cholinergic, and histaminergic systems; disorder of osmotic regulation and antioxidant system; and disorder of lipid metabolism occur in a region-specific fashion in the brains of DE rats. Thus, this study provides valuable information regarding the molecular pathological signature of DE. These findings also underline the high potential of AFADESI-MSI for applications in various central nervous system diseases.
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Affiliation(s)
- Meiling Huo
- Key Laboratory of Mass Spectrometry Imaging and Metabolomics (Minzu University of China), National Ethnic Affairs Commission, Beijing 100081, China.,Center for Imaging and Systems Biology, College of Life and Environmental Sciences, Minzu University of China, 27 Zhongguancun South Avenue, Beijing 100081, China
| | - Zhonghua Wang
- Key Laboratory of Mass Spectrometry Imaging and Metabolomics (Minzu University of China), National Ethnic Affairs Commission, Beijing 100081, China.,Center for Imaging and Systems Biology, College of Life and Environmental Sciences, Minzu University of China, 27 Zhongguancun South Avenue, Beijing 100081, China
| | - Wenqing Fu
- Key Laboratory of Mass Spectrometry Imaging and Metabolomics (Minzu University of China), National Ethnic Affairs Commission, Beijing 100081, China.,Center for Imaging and Systems Biology, College of Life and Environmental Sciences, Minzu University of China, 27 Zhongguancun South Avenue, Beijing 100081, China
| | - Lu Tian
- New Drug Safety Evaluation Center, Chinese Academy of Medical Sciences, Beijing 100050, China
| | - Wanfang Li
- New Drug Safety Evaluation Center, Chinese Academy of Medical Sciences, Beijing 100050, China
| | - Zhi Zhou
- Key Laboratory of Mass Spectrometry Imaging and Metabolomics (Minzu University of China), National Ethnic Affairs Commission, Beijing 100081, China.,Center for Imaging and Systems Biology, College of Life and Environmental Sciences, Minzu University of China, 27 Zhongguancun South Avenue, Beijing 100081, China
| | - Yanhua Chen
- Key Laboratory of Mass Spectrometry Imaging and Metabolomics (Minzu University of China), National Ethnic Affairs Commission, Beijing 100081, China.,Center for Imaging and Systems Biology, College of Life and Environmental Sciences, Minzu University of China, 27 Zhongguancun South Avenue, Beijing 100081, China
| | - Jinfeng Wei
- New Drug Safety Evaluation Center, Chinese Academy of Medical Sciences, Beijing 100050, China
| | - Zeper Abliz
- Key Laboratory of Mass Spectrometry Imaging and Metabolomics (Minzu University of China), National Ethnic Affairs Commission, Beijing 100081, China.,Center for Imaging and Systems Biology, College of Life and Environmental Sciences, Minzu University of China, 27 Zhongguancun South Avenue, Beijing 100081, China.,Key Laboratory of Ethnomedicine of Ministry of Education, School of Pharmacy, Minzu University of China, Beijing 100081, P. R. China
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99937
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Jin L, Tang Q, Hu S, Chen Z, Zhou X, Zeng B, Wang Y, He M, Li Y, Gui L, Shen L, Long K, Ma J, Wang X, Chen Z, Jiang Y, Tang G, Zhu L, Liu F, Zhang B, Huang Z, Li G, Li D, Gladyshev VN, Yin J, Gu Y, Li X, Li M. A pig BodyMap transcriptome reveals diverse tissue physiologies and evolutionary dynamics of transcription. Nat Commun 2021; 12:3715. [PMID: 34140474 PMCID: PMC8211698 DOI: 10.1038/s41467-021-23560-8] [Citation(s) in RCA: 51] [Impact Index Per Article: 17.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/03/2020] [Accepted: 05/04/2021] [Indexed: 12/13/2022] Open
Abstract
A comprehensive transcriptomic survey of pigs can provide a mechanistic understanding of tissue specialization processes underlying economically valuable traits and accelerate their use as a biomedical model. Here we characterize four transcript types (lncRNAs, TUCPs, miRNAs, and circRNAs) and protein-coding genes in 31 adult pig tissues and two cell lines. We uncover the transcriptomic variability among 47 skeletal muscles, and six adipose depots linked to their different origins, metabolism, cell composition, physical activity, and mitochondrial pathways. We perform comparative analysis of the transcriptomes of seven tissues from pigs and nine other vertebrates to reveal that evolutionary divergence in transcription potentially contributes to lineage-specific biology. Long-range promoter–enhancer interaction analysis in subcutaneous adipose tissues across species suggests evolutionarily stable transcription patterns likely attributable to redundant enhancers buffering gene expression patterns against perturbations, thereby conferring robustness during speciation. This study can facilitate adoption of the pig as a biomedical model for human biology and disease and uncovers the molecular bases of valuable traits. A comprehensive transcriptomic survey of the pig could enable mechanistic understanding of tissue specialization and accelerate its use as a biomedical model. Here the authors characterize four distinct transcript types in 31 adult pig tissues to dissect their distinct structural and transcriptional features and uncover transcriptomic variability related to tissue physiology.
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Affiliation(s)
- Long Jin
- Institute of Animal Genetics and Breeding, College of Animal Science and Technology, Sichuan Agricultural University, Chengdu, Sichuan, China
| | - Qianzi Tang
- Institute of Animal Genetics and Breeding, College of Animal Science and Technology, Sichuan Agricultural University, Chengdu, Sichuan, China.
| | - Silu Hu
- Institute of Animal Genetics and Breeding, College of Animal Science and Technology, Sichuan Agricultural University, Chengdu, Sichuan, China
| | - Zhongxu Chen
- Department of Life Science, Tcuni Inc., Chengdu, Sichuan, China
| | - Xuming Zhou
- Institute of Zoology, Chinese Academy of Sciences, Beijing, China
| | - Bo Zeng
- Institute of Animal Genetics and Breeding, College of Animal Science and Technology, Sichuan Agricultural University, Chengdu, Sichuan, China
| | - Yuhao Wang
- Institute of Animal Genetics and Breeding, College of Animal Science and Technology, Sichuan Agricultural University, Chengdu, Sichuan, China
| | - Mengnan He
- Institute of Animal Genetics and Breeding, College of Animal Science and Technology, Sichuan Agricultural University, Chengdu, Sichuan, China
| | - Yan Li
- Institute of Animal Genetics and Breeding, College of Animal Science and Technology, Sichuan Agricultural University, Chengdu, Sichuan, China
| | - Lixuan Gui
- Department of Life Science, Tcuni Inc., Chengdu, Sichuan, China
| | - Linyuan Shen
- Institute of Animal Genetics and Breeding, College of Animal Science and Technology, Sichuan Agricultural University, Chengdu, Sichuan, China
| | - Keren Long
- Institute of Animal Genetics and Breeding, College of Animal Science and Technology, Sichuan Agricultural University, Chengdu, Sichuan, China
| | - Jideng Ma
- Institute of Animal Genetics and Breeding, College of Animal Science and Technology, Sichuan Agricultural University, Chengdu, Sichuan, China
| | - Xun Wang
- Institute of Animal Genetics and Breeding, College of Animal Science and Technology, Sichuan Agricultural University, Chengdu, Sichuan, China
| | - Zhengli Chen
- Key Laboratory of Animal Disease and Human Health of Sichuan Province, College of Veterinary Medicine, Sichuan Agricultural University, Chengdu, Sichuan, China
| | - Yanzhi Jiang
- College of Life Science, Sichuan Agricultural University, Ya'an, Sichuan, China
| | - Guoqing Tang
- Institute of Animal Genetics and Breeding, College of Animal Science and Technology, Sichuan Agricultural University, Chengdu, Sichuan, China
| | - Li Zhu
- Institute of Animal Genetics and Breeding, College of Animal Science and Technology, Sichuan Agricultural University, Chengdu, Sichuan, China
| | - Fei Liu
- Information and Educational Technology Center, Sichuan Agricultural University, Chengdu, Sichuan, China
| | - Bo Zhang
- Ya'an Digital Economy Operation Company, Ya'an, Sichuan, China
| | - Zhiqing Huang
- Institute of Animal Nutrition, Sichuan Agricultural University, Chengdu, Sichuan, China
| | - Guisen Li
- Renal Department and Nephrology Institute, Sichuan Provincial People's Hospital, Chengdu, Sichuan, China
| | - Diyan Li
- Institute of Animal Genetics and Breeding, College of Animal Science and Technology, Sichuan Agricultural University, Chengdu, Sichuan, China
| | - Vadim N Gladyshev
- Division of Genetics, Department of Medicine, Brigham and Women's Hospital, Boston, MA, USA
| | - Jingdong Yin
- State Key Laboratory of Animal Nutrition, College of Animal Science and Technology, China Agricultural University, Beijing, China
| | - Yiren Gu
- Animal Breeding and Genetics Key Laboratory of Sichuan Province, Sichuan Animal Science Academy, Chengdu, Sichuan, China
| | - Xuewei Li
- Institute of Animal Genetics and Breeding, College of Animal Science and Technology, Sichuan Agricultural University, Chengdu, Sichuan, China
| | - Mingzhou Li
- Institute of Animal Genetics and Breeding, College of Animal Science and Technology, Sichuan Agricultural University, Chengdu, Sichuan, China.
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99938
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Ni P, Su Z. Accurate prediction of cis-regulatory modules reveals a prevalent regulatory genome of humans. NAR Genom Bioinform 2021; 3:lqab052. [PMID: 34159315 PMCID: PMC8210889 DOI: 10.1093/nargab/lqab052] [Citation(s) in RCA: 12] [Impact Index Per Article: 4.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/26/2021] [Revised: 05/01/2021] [Accepted: 06/14/2021] [Indexed: 02/07/2023] Open
Abstract
cis-regulatory modules(CRMs) formed by clusters of transcription factor (TF) binding sites (TFBSs) are as important as coding sequences in specifying phenotypes of humans. It is essential to categorize all CRMs and constituent TFBSs in the genome. In contrast to most existing methods that predict CRMs in specific cell types using epigenetic marks, we predict a largely cell type agonistic but more comprehensive map of CRMs and constituent TFBSs in the gnome by integrating all available TF ChIP-seq datasets. Our method is able to partition 77.47% of genome regions covered by available 6092 datasets into a CRM candidate (CRMC) set (56.84%) and a non-CRMC set (43.16%). Intriguingly, the predicted CRMCs are under strong evolutionary constraints, while the non-CRMCs are largely selectively neutral, strongly suggesting that the CRMCs are likely cis-regulatory, while the non-CRMCs are not. Our predicted CRMs are under stronger evolutionary constraints than three state-of-the-art predictions (GeneHancer, EnhancerAtlas and ENCODE phase 3) and substantially outperform them for recalling VISTA enhancers and non-coding ClinVar variants. We estimated that the human genome might encode about 1.47M CRMs and 68M TFBSs, comprising about 55% and 22% of the genome, respectively; for both of which, we predicted 80%. Therefore, the cis-regulatory genome appears to be more prevalent than originally thought.
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Affiliation(s)
- Pengyu Ni
- Department of Bioinformatics and Genomics, the University of North Carolina at Charlotte, 9201 University City Boulevard, Charlotte, NC 28223, USA
| | - Zhengchang Su
- Department of Bioinformatics and Genomics, the University of North Carolina at Charlotte, 9201 University City Boulevard, Charlotte, NC 28223, USA
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99939
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Zatreanu D, Robinson HMR, Alkhatib O, Boursier M, Finch H, Geo L, Grande D, Grinkevich V, Heald RA, Langdon S, Majithiya J, McWhirter C, Martin NMB, Moore S, Neves J, Rajendra E, Ranzani M, Schaedler T, Stockley M, Wiggins K, Brough R, Sridhar S, Gulati A, Shao N, Badder LM, Novo D, Knight EG, Marlow R, Haider S, Callen E, Hewitt G, Schimmel J, Prevo R, Alli C, Ferdinand A, Bell C, Blencowe P, Bot C, Calder M, Charles M, Curry J, Ekwuru T, Ewings K, Krajewski W, MacDonald E, McCarron H, Pang L, Pedder C, Rigoreau L, Swarbrick M, Wheatley E, Willis S, Wong AC, Nussenzweig A, Tijsterman M, Tutt A, Boulton SJ, Higgins GS, Pettitt SJ, Smith GCM, Lord CJ. Polθ inhibitors elicit BRCA-gene synthetic lethality and target PARP inhibitor resistance. Nat Commun 2021; 12:3636. [PMID: 34140467 PMCID: PMC8211653 DOI: 10.1038/s41467-021-23463-8] [Citation(s) in RCA: 169] [Impact Index Per Article: 56.3] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/17/2021] [Accepted: 04/30/2021] [Indexed: 02/05/2023] Open
Abstract
To identify approaches to target DNA repair vulnerabilities in cancer, we discovered nanomolar potent, selective, low molecular weight (MW), allosteric inhibitors of the polymerase function of DNA polymerase Polθ, including ART558. ART558 inhibits the major Polθ-mediated DNA repair process, Theta-Mediated End Joining, without targeting Non-Homologous End Joining. In addition, ART558 elicits DNA damage and synthetic lethality in BRCA1- or BRCA2-mutant tumour cells and enhances the effects of a PARP inhibitor. Genetic perturbation screening revealed that defects in the 53BP1/Shieldin complex, which cause PARP inhibitor resistance, result in in vitro and in vivo sensitivity to small molecule Polθ polymerase inhibitors. Mechanistically, ART558 increases biomarkers of single-stranded DNA and synthetic lethality in 53BP1-defective cells whilst the inhibition of DNA nucleases that promote end-resection reversed these effects, implicating these in the synthetic lethal mechanism-of-action. Taken together, these observations describe a drug class that elicits BRCA-gene synthetic lethality and PARP inhibitor synergy, as well as targeting a biomarker-defined mechanism of PARPi-resistance.
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Affiliation(s)
- Diana Zatreanu
- CRUK Gene Function Laboratory, The Institute of Cancer Research, London, UK
- The Breast Cancer Now Toby Robins Research Centre, The Institute of Cancer Research, London, UK
| | - Helen M R Robinson
- Artios Pharma, The Glenn Berge Building, Babraham Research Campus, Cambridge, UK
| | - Omar Alkhatib
- Artios Pharma, The Glenn Berge Building, Babraham Research Campus, Cambridge, UK
| | - Marie Boursier
- Artios Pharma, The Glenn Berge Building, Babraham Research Campus, Cambridge, UK
| | - Harry Finch
- Artios Pharma, The Glenn Berge Building, Babraham Research Campus, Cambridge, UK
| | - Lerin Geo
- Artios Pharma, The Glenn Berge Building, Babraham Research Campus, Cambridge, UK
| | - Diego Grande
- Artios Pharma, The Glenn Berge Building, Babraham Research Campus, Cambridge, UK
| | - Vera Grinkevich
- Artios Pharma, The Glenn Berge Building, Babraham Research Campus, Cambridge, UK
| | - Robert A Heald
- Artios Pharma, The Glenn Berge Building, Babraham Research Campus, Cambridge, UK
| | - Sophie Langdon
- Artios Pharma, The Glenn Berge Building, Babraham Research Campus, Cambridge, UK
| | - Jayesh Majithiya
- Artios Pharma, The Glenn Berge Building, Babraham Research Campus, Cambridge, UK
| | - Claire McWhirter
- Artios Pharma, The Glenn Berge Building, Babraham Research Campus, Cambridge, UK
| | - Niall M B Martin
- Artios Pharma, The Glenn Berge Building, Babraham Research Campus, Cambridge, UK
| | - Shaun Moore
- Artios Pharma, The Glenn Berge Building, Babraham Research Campus, Cambridge, UK
| | - Joana Neves
- Artios Pharma, The Glenn Berge Building, Babraham Research Campus, Cambridge, UK
| | - Eeson Rajendra
- Artios Pharma, The Glenn Berge Building, Babraham Research Campus, Cambridge, UK
| | - Marco Ranzani
- Artios Pharma, The Glenn Berge Building, Babraham Research Campus, Cambridge, UK
| | - Theresia Schaedler
- Artios Pharma, The Glenn Berge Building, Babraham Research Campus, Cambridge, UK
| | - Martin Stockley
- Artios Pharma, The Glenn Berge Building, Babraham Research Campus, Cambridge, UK
| | - Kimberley Wiggins
- Artios Pharma, The Glenn Berge Building, Babraham Research Campus, Cambridge, UK
| | - Rachel Brough
- CRUK Gene Function Laboratory, The Institute of Cancer Research, London, UK
- The Breast Cancer Now Toby Robins Research Centre, The Institute of Cancer Research, London, UK
| | - Sandhya Sridhar
- CRUK Gene Function Laboratory, The Institute of Cancer Research, London, UK
- The Breast Cancer Now Toby Robins Research Centre, The Institute of Cancer Research, London, UK
| | - Aditi Gulati
- CRUK Gene Function Laboratory, The Institute of Cancer Research, London, UK
- The Breast Cancer Now Toby Robins Research Centre, The Institute of Cancer Research, London, UK
| | - Nan Shao
- CRUK Gene Function Laboratory, The Institute of Cancer Research, London, UK
- The Breast Cancer Now Toby Robins Research Centre, The Institute of Cancer Research, London, UK
| | - Luned M Badder
- The Breast Cancer Now Research Unit, King's College London, London, UK
| | - Daniela Novo
- The Breast Cancer Now Toby Robins Research Centre, The Institute of Cancer Research, London, UK
| | - Eleanor G Knight
- The Breast Cancer Now Toby Robins Research Centre, The Institute of Cancer Research, London, UK
| | - Rebecca Marlow
- The Breast Cancer Now Toby Robins Research Centre, The Institute of Cancer Research, London, UK
- The Breast Cancer Now Research Unit, King's College London, London, UK
| | - Syed Haider
- The Breast Cancer Now Toby Robins Research Centre, The Institute of Cancer Research, London, UK
| | - Elsa Callen
- Laboratory of Genome Integrity, National Cancer Institute, NIH, Bethesda, MD, USA
| | | | - Joost Schimmel
- Department of Human Genetics, Leiden University Medical Center, Leiden, The Netherlands
| | - Remko Prevo
- Medical Research Council Oxford Institute for Radiation Oncology, University of Oxford, Old Road Campus Research Building, Roosevelt Drive, Oxford, UK
| | - Christina Alli
- Cancer Research UK, Therapeutic Discovery Laboratories, Jonas Webb Building, Babraham Research Campus, Cambridge, UK
| | - Amanda Ferdinand
- Cancer Research UK, Therapeutic Discovery Laboratories, Jonas Webb Building, Babraham Research Campus, Cambridge, UK
| | - Cameron Bell
- Cancer Research UK, Therapeutic Discovery Laboratories, Jonas Webb Building, Babraham Research Campus, Cambridge, UK
| | - Peter Blencowe
- Cancer Research UK, Therapeutic Discovery Laboratories, Jonas Webb Building, Babraham Research Campus, Cambridge, UK
| | - Chris Bot
- Cancer Research UK, Therapeutic Discovery Laboratories, Jonas Webb Building, Babraham Research Campus, Cambridge, UK
| | - Mathew Calder
- Cancer Research UK, Therapeutic Discovery Laboratories, Jonas Webb Building, Babraham Research Campus, Cambridge, UK
| | - Mark Charles
- Cancer Research UK, Therapeutic Discovery Laboratories, Jonas Webb Building, Babraham Research Campus, Cambridge, UK
| | - Jayne Curry
- Cancer Research UK, Therapeutic Discovery Laboratories, Jonas Webb Building, Babraham Research Campus, Cambridge, UK
| | - Tennyson Ekwuru
- Cancer Research UK, Therapeutic Discovery Laboratories, Jonas Webb Building, Babraham Research Campus, Cambridge, UK
| | - Katherine Ewings
- Cancer Research UK, Therapeutic Discovery Laboratories, Jonas Webb Building, Babraham Research Campus, Cambridge, UK
| | - Wojciech Krajewski
- Cancer Research UK, Therapeutic Discovery Laboratories, Jonas Webb Building, Babraham Research Campus, Cambridge, UK
| | - Ellen MacDonald
- Cancer Research UK, Therapeutic Discovery Laboratories, Jonas Webb Building, Babraham Research Campus, Cambridge, UK
| | - Hollie McCarron
- Cancer Research UK, Therapeutic Discovery Laboratories, Jonas Webb Building, Babraham Research Campus, Cambridge, UK
| | - Leon Pang
- Cancer Research UK, Therapeutic Discovery Laboratories, Jonas Webb Building, Babraham Research Campus, Cambridge, UK
| | - Chris Pedder
- Cancer Research UK, Therapeutic Discovery Laboratories, Jonas Webb Building, Babraham Research Campus, Cambridge, UK
| | - Laurent Rigoreau
- Cancer Research UK, Therapeutic Discovery Laboratories, Jonas Webb Building, Babraham Research Campus, Cambridge, UK
| | - Martin Swarbrick
- Cancer Research UK, Therapeutic Discovery Laboratories, Jonas Webb Building, Babraham Research Campus, Cambridge, UK
| | - Ed Wheatley
- Cancer Research UK, Therapeutic Discovery Laboratories, Jonas Webb Building, Babraham Research Campus, Cambridge, UK
| | - Simon Willis
- Cancer Research UK, Therapeutic Discovery Laboratories, Jonas Webb Building, Babraham Research Campus, Cambridge, UK
| | - Ai Ching Wong
- Cancer Research UK, Therapeutic Discovery Laboratories, Jonas Webb Building, Babraham Research Campus, Cambridge, UK
| | - Andre Nussenzweig
- Laboratory of Genome Integrity, National Cancer Institute, NIH, Bethesda, MD, USA
| | - Marcel Tijsterman
- Department of Human Genetics, Leiden University Medical Center, Leiden, The Netherlands
| | - Andrew Tutt
- The Breast Cancer Now Toby Robins Research Centre, The Institute of Cancer Research, London, UK
- The Breast Cancer Now Research Unit, King's College London, London, UK
| | - Simon J Boulton
- Artios Pharma, The Glenn Berge Building, Babraham Research Campus, Cambridge, UK
- The Francis Crick Institute, London, UK
| | - Geoff S Higgins
- Medical Research Council Oxford Institute for Radiation Oncology, University of Oxford, Old Road Campus Research Building, Roosevelt Drive, Oxford, UK
| | - Stephen J Pettitt
- CRUK Gene Function Laboratory, The Institute of Cancer Research, London, UK.
- The Breast Cancer Now Toby Robins Research Centre, The Institute of Cancer Research, London, UK.
| | - Graeme C M Smith
- Artios Pharma, The Glenn Berge Building, Babraham Research Campus, Cambridge, UK.
| | - Christopher J Lord
- CRUK Gene Function Laboratory, The Institute of Cancer Research, London, UK.
- The Breast Cancer Now Toby Robins Research Centre, The Institute of Cancer Research, London, UK.
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99940
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Lorenzi L, Chiu HS, Avila Cobos F, Gross S, Volders PJ, Cannoodt R, Nuytens J, Vanderheyden K, Anckaert J, Lefever S, Tay AP, de Bony EJ, Trypsteen W, Gysens F, Vromman M, Goovaerts T, Hansen TB, Kuersten S, Nijs N, Taghon T, Vermaelen K, Bracke KR, Saeys Y, De Meyer T, Deshpande NP, Anande G, Chen TW, Wilkins MR, Unnikrishnan A, De Preter K, Kjems J, Koster J, Schroth GP, Vandesompele J, Sumazin P, Mestdagh P. The RNA Atlas expands the catalog of human non-coding RNAs. Nat Biotechnol 2021; 39:1453-1465. [PMID: 34140680 DOI: 10.1038/s41587-021-00936-1] [Citation(s) in RCA: 65] [Impact Index Per Article: 21.7] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/10/2019] [Accepted: 04/26/2021] [Indexed: 12/24/2022]
Abstract
Existing compendia of non-coding RNA (ncRNA) are incomplete, in part because they are derived almost exclusively from small and polyadenylated RNAs. Here we present a more comprehensive atlas of the human transcriptome, which includes small and polyA RNA as well as total RNA from 300 human tissues and cell lines. We report thousands of previously uncharacterized RNAs, increasing the number of documented ncRNAs by approximately 8%. To infer functional regulation by known and newly characterized ncRNAs, we exploited pre-mRNA abundance estimates from total RNA sequencing, revealing 316 microRNAs and 3,310 long non-coding RNAs with multiple lines of evidence for roles in regulating protein-coding genes and pathways. Our study both refines and expands the current catalog of human ncRNAs and their regulatory interactions. All data, analyses and results are available for download and interrogation in the R2 web portal, serving as a basis for future exploration of RNA biology and function.
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Affiliation(s)
- Lucia Lorenzi
- Center for Medical Genetics, Ghent University, Ghent, Belgium.,Cancer Research Institute Ghent (CRIG), Ghent, Belgium
| | - Hua-Sheng Chiu
- Texas Children's Cancer Center, Baylor College of Medicine, Houston, TX, USA
| | - Francisco Avila Cobos
- Center for Medical Genetics, Ghent University, Ghent, Belgium.,Cancer Research Institute Ghent (CRIG), Ghent, Belgium
| | | | - Pieter-Jan Volders
- Center for Medical Genetics, Ghent University, Ghent, Belgium.,Cancer Research Institute Ghent (CRIG), Ghent, Belgium.,VIB-UGent Center for Medical Biotechnology, VIB, Ghent, Belgium
| | - Robrecht Cannoodt
- Center for Medical Genetics, Ghent University, Ghent, Belgium.,Cancer Research Institute Ghent (CRIG), Ghent, Belgium.,Data Mining and Modelling for Biomedicine Group, VIB Center for Inflammation Research, Ghent, Belgium.,Department of Applied Mathematics, Computer Science, and Statistics, Ghent University, Ghent, Belgium.,Data Intuitive, Lebbeke, Belgium
| | - Justine Nuytens
- Center for Medical Genetics, Ghent University, Ghent, Belgium.,Cancer Research Institute Ghent (CRIG), Ghent, Belgium
| | - Katrien Vanderheyden
- Center for Medical Genetics, Ghent University, Ghent, Belgium.,Cancer Research Institute Ghent (CRIG), Ghent, Belgium
| | - Jasper Anckaert
- Center for Medical Genetics, Ghent University, Ghent, Belgium.,Cancer Research Institute Ghent (CRIG), Ghent, Belgium
| | - Steve Lefever
- Center for Medical Genetics, Ghent University, Ghent, Belgium.,Cancer Research Institute Ghent (CRIG), Ghent, Belgium
| | - Aidan P Tay
- Australian e-Health Research Centre, Commonwealth Scientific and Industrial Research Organisation, New South Wales, Sydney NSW, Australia.,Department of Biomedical Sciences, Macquarie University, New South Wales, Sydney NSW, Australia
| | - Eric J de Bony
- Center for Medical Genetics, Ghent University, Ghent, Belgium.,Cancer Research Institute Ghent (CRIG), Ghent, Belgium
| | - Wim Trypsteen
- Center for Medical Genetics, Ghent University, Ghent, Belgium.,Cancer Research Institute Ghent (CRIG), Ghent, Belgium
| | - Fien Gysens
- Center for Medical Genetics, Ghent University, Ghent, Belgium.,Cancer Research Institute Ghent (CRIG), Ghent, Belgium
| | - Marieke Vromman
- Center for Medical Genetics, Ghent University, Ghent, Belgium.,Cancer Research Institute Ghent (CRIG), Ghent, Belgium
| | - Tine Goovaerts
- Department of Data Analysis and Mathematical Modelling, Ghent University, Ghent, Belgium
| | - Thomas Birkballe Hansen
- Interdisciplinary Nanoscience Centre (iNANO), Department of Molecular Biology and Genetics, Aarhus University, Aarhus, Denmark
| | | | | | - Tom Taghon
- Department of Diagnostic Sciences, Ghent University, Ghent, Belgium
| | - Karim Vermaelen
- Department of Respiratory Medicine, Ghent University, Ghent, Belgium
| | - Ken R Bracke
- Department of Respiratory Medicine, Ghent University, Ghent, Belgium
| | - Yvan Saeys
- VIB-UGent Center for Medical Biotechnology, VIB, Ghent, Belgium.,Data Mining and Modelling for Biomedicine Group, VIB Center for Inflammation Research, Ghent, Belgium
| | - Tim De Meyer
- Cancer Research Institute Ghent (CRIG), Ghent, Belgium.,Department of Data Analysis and Mathematical Modelling, Ghent University, Ghent, Belgium
| | - Nandan P Deshpande
- Systems Biology Initiative, School of Biotechnology and Biomolecular Sciences, UNSW Sydney, Sydney NSW, Australia
| | - Govardhan Anande
- Adult Cancer Program, Lowy Cancer Research Centre, UNSW Sydney, Sydney NSW, Australia.,Prince of Wales Clinical School, UNSW Sydney, Sydney NSW, Australia
| | - Ting-Wen Chen
- Institute of Bioinformatics and Systems Biology, National Yang Ming Chiao Tung University, Hsinchu, Taiwan
| | - Marc R Wilkins
- Systems Biology Initiative, School of Biotechnology and Biomolecular Sciences, UNSW Sydney, Sydney NSW, Australia
| | - Ashwin Unnikrishnan
- Adult Cancer Program, Lowy Cancer Research Centre, UNSW Sydney, Sydney NSW, Australia.,Prince of Wales Clinical School, UNSW Sydney, Sydney NSW, Australia
| | - Katleen De Preter
- Center for Medical Genetics, Ghent University, Ghent, Belgium.,Cancer Research Institute Ghent (CRIG), Ghent, Belgium
| | - Jørgen Kjems
- Interdisciplinary Nanoscience Centre (iNANO), Department of Molecular Biology and Genetics, Aarhus University, Aarhus, Denmark
| | - Jan Koster
- Department of Oncogenomics, Amsterdam UMC, University of Amsterdam, Amsterdam, The Netherlands
| | | | - Jo Vandesompele
- Center for Medical Genetics, Ghent University, Ghent, Belgium.,Cancer Research Institute Ghent (CRIG), Ghent, Belgium
| | - Pavel Sumazin
- Texas Children's Cancer Center, Baylor College of Medicine, Houston, TX, USA.
| | - Pieter Mestdagh
- Center for Medical Genetics, Ghent University, Ghent, Belgium. .,Cancer Research Institute Ghent (CRIG), Ghent, Belgium.
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99941
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Ras Variant Biology and Contributions to Human Disease. METHODS IN MOLECULAR BIOLOGY (CLIFTON, N.J.) 2021; 2262:3-18. [PMID: 33977468 DOI: 10.1007/978-1-0716-1190-6_1] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Abstract] [Key Words] [Subscribe] [Scholar Register] [Indexed: 12/26/2022]
Abstract
Analysis of cancer and RASopathy genetic databases reveals that ~19% of all cancer cases and ~4% of developmental disorders contain Ras mutations. Ras isoform and mutation variants differentially contribute to these diseases and provide an opportunity for deeper understanding of Ras function. The putative mechanisms underpinning these differences, new approaches that are being applied, and some of the key questions and challenges that remain are discussed.
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99942
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Sawant M, Hinz B, Schönborn K, Zeinert I, Eckes B, Krieg T, Schuster R. A story of fibers and stress: Matrix-embedded signals for fibroblast activation in the skin. Wound Repair Regen 2021; 29:515-530. [PMID: 34081361 DOI: 10.1111/wrr.12950] [Citation(s) in RCA: 14] [Impact Index Per Article: 4.7] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/25/2021] [Revised: 05/13/2021] [Accepted: 05/28/2021] [Indexed: 12/12/2022]
Abstract
Our skin is continuously exposed to mechanical challenge, including shear, stretch, and compression. The extracellular matrix of the dermis is perfectly suited to resist these challenges and maintain integrity of normal skin even upon large strains. Fibroblasts are the key cells that interpret mechanical and chemical cues in their environment to turnover matrix and maintain homeostasis in the skin of healthy adults. Upon tissue injury, fibroblasts and an exclusive selection of other cells become activated into myofibroblasts with the task to restore skin integrity by forming structurally imperfect but mechanically stable scar tissue. Failure of myofibroblasts to terminate their actions after successful repair or upon chronic inflammation results in dysregulated myofibroblast activities which can lead to hypertrophic scarring and/or skin fibrosis. After providing an overview on the major fibrillar matrix components in normal skin, we will interrogate the various origins of fibroblasts and myofibroblasts in the skin. We then examine the role of the matrix as signaling hub and how fibroblasts respond to mechanical matrix cues to restore order in the confusing environment of a healing wound.
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Affiliation(s)
- Mugdha Sawant
- Translational Matrix Biology, University of Cologne, Medical Faculty, Cologne, Germany
| | - Boris Hinz
- Laboratory of Tissue Repair and Regeneration, Faculty of Dentistry, University of Toronto, Toronto, Canada
| | - Katrin Schönborn
- Translational Matrix Biology, University of Cologne, Medical Faculty, Cologne, Germany
| | - Isabel Zeinert
- Translational Matrix Biology, University of Cologne, Medical Faculty, Cologne, Germany
| | - Beate Eckes
- Translational Matrix Biology, University of Cologne, Medical Faculty, Cologne, Germany
| | - Thomas Krieg
- Translational Matrix Biology, University of Cologne, Medical Faculty, Cologne, Germany.,Cologne Excellence Cluster on Cellular Stress Responses in Aging-Associated Diseases (CECAD), University of Cologne, Cologne, Germany.,Center for Molecular Medicine (CMMC), University of Cologne, Cologne, Germany
| | - Ronen Schuster
- Laboratory of Tissue Repair and Regeneration, Faculty of Dentistry, University of Toronto, Toronto, Canada.,PhenomicAI, MaRS Centre, 661 University Avenue, Toronto, Canada
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99943
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Characterizing Autophagy in the Cold Ischemic Injury of Small Bowel Grafts: Evidence from Rat Jejunum. Metabolites 2021; 11:metabo11060396. [PMID: 34204418 PMCID: PMC8234201 DOI: 10.3390/metabo11060396] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.7] [Reference Citation Analysis] [Abstract] [Key Words] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/01/2021] [Revised: 06/14/2021] [Accepted: 06/14/2021] [Indexed: 01/07/2023] Open
Abstract
Cold ischemic injury to the intestine during preservation remains an unresolved issue in transplantation medicine. Autophagy, a cytoplasmic protein degradation pathway, is essential for metabolic adaptation to starvation, hypoxia, and ischemia. It has been implicated in the cold ischemia (CI) of other transplantable organs. This study determines the changes in intestinal autophagy evoked by cold storage and explores the effects of autophagy on ischemic grafts. Cold preservation was simulated by placing the small intestines of Wistar rats in an IGL-1 (Institute George Lopez) solution at 4 °C for varying periods (3, 6, 9, and 12 h). The extent of graft preservation injury (mucosal and cellular injury) and changes in autophagy were measured after each CI time. Subsequently, we determined the differences in apoptosis and preservation injury after activating autophagy with rapamycin or inhibiting it with 3-methyladenine. The results revealed that ischemic injury and autophagy were induced by cold storage. Autophagy peaked at 3 h and subsequently declined. After 12 h of storage, autophagic expression was reduced significantly. Additionally, enhanced intestinal autophagy by rapamycin was associated with less tissue, cellular, and apoptotic damage during and after the 12-h long preservation. After reperfusion, grafts with enhanced autophagy still presented with less injury. Inhibiting autophagy exhibited the opposite trend. These findings demonstrate intestinal autophagy changes in cold preservation. Furthermore, enhanced autophagy was protective against cold ischemia-reperfusion damage of the small bowels.
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99944
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Fernández-Medarde A, Santos E. Ras GEF Mouse Models for the Analysis of Ras Biology and Signaling. METHODS IN MOLECULAR BIOLOGY (CLIFTON, N.J.) 2021; 2262:361-395. [PMID: 33977490 DOI: 10.1007/978-1-0716-1190-6_23] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Subscribe] [Scholar Register] [Indexed: 11/30/2022]
Abstract
Animal models have become in recent years a crucial tool to understand the physiological and pathological roles of many cellular proteins. They allow analysis of the functional consequences of [1] complete or partial (time- or organ-limited) removal of specific proteins (knockout animals), [2] the exchange of a wild-type allele for a mutant or truncated version found in human illnesses (knock-in), or [3] the effect of overexpression of a given protein in the whole body or in specific organs (transgenic mice). In this regard, the study of phenotypes in Ras GEF animal models has allowed researchers to find specific functions for otherwise very similar proteins, uncovering their role in physiological contexts such as memory formation, lymphopoiesis, photoreception, or body homeostasis. In addition, mouse models have been used to unveil the functional role of Ras GEFs under pathological conditions, including Noonan syndrome, skin tumorigenesis, inflammatory diseases, diabetes, or ischemia among others. In the following sections, we will describe the methodological approaches employed for Ras GEF animal model analyses, as well as the main discoveries made.
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Affiliation(s)
- Alberto Fernández-Medarde
- Centro de Investigación del Cáncer-Instituto de Biología Molecular y Celular del Cáncer (CSIC-Universidad de Salamanca) and CIBERONC, Salamanca, Spain.
| | - Eugenio Santos
- Centro de Investigación del Cáncer-Instituto de Biología Molecular y Celular del Cáncer (CSIC-Universidad de Salamanca) and CIBERONC, Salamanca, Spain
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99945
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Giagnorio E, Malacarne C, Mantegazza R, Bonanno S, Marcuzzo S. MyomiRs and their multifaceted regulatory roles in muscle homeostasis and amyotrophic lateral sclerosis. J Cell Sci 2021; 134:269129. [PMID: 34137441 DOI: 10.1242/jcs.258349] [Citation(s) in RCA: 11] [Impact Index Per Article: 3.7] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/11/2022] Open
Abstract
Amyotrophic lateral sclerosis (ALS) is a fatal neurodegenerative disease characterized by loss of both upper and lower motor neurons (MNs). The main clinical features of ALS are motor function impairment, progressive muscle weakness, muscle atrophy and, ultimately, paralysis. Intrinsic skeletal muscle deterioration plays a crucial role in the disease and contributes to ALS progression. Currently, there are no effective treatments for ALS, highlighting the need to obtain a deeper understanding of the molecular events underlying degeneration of both MNs and muscle tissue, with the aim of developing successful therapies. Muscle tissue is enriched in a group of microRNAs called myomiRs, which are effective regulators of muscle homeostasis, plasticity and myogenesis in both physiological and pathological conditions. After providing an overview of ALS pathophysiology, with a focus on the role of skeletal muscle, we review the current literature on myomiR network dysregulation as a contributing factor to myogenic perturbations and muscle atrophy in ALS. We argue that, in view of their critical regulatory function at the interface between MNs and skeletal muscle fiber, myomiRs are worthy of further investigation as potential molecular targets of therapeutic strategies to improve ALS symptoms and counteract disease progression.
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Affiliation(s)
- Eleonora Giagnorio
- Neurology IV - Neuroimmunology and Neuromuscular Diseases Unit, Fondazione IRCCS Istituto Neurologico Carlo Besta, Milan 20133, Italy.,PhD program in Neuroscience, University of Milano-Bicocca, via Cadore 48, 20900 Monza, Italy
| | - Claudia Malacarne
- Neurology IV - Neuroimmunology and Neuromuscular Diseases Unit, Fondazione IRCCS Istituto Neurologico Carlo Besta, Milan 20133, Italy.,PhD program in Neuroscience, University of Milano-Bicocca, via Cadore 48, 20900 Monza, Italy
| | - Renato Mantegazza
- Neurology IV - Neuroimmunology and Neuromuscular Diseases Unit, Fondazione IRCCS Istituto Neurologico Carlo Besta, Milan 20133, Italy
| | - Silvia Bonanno
- Neurology IV - Neuroimmunology and Neuromuscular Diseases Unit, Fondazione IRCCS Istituto Neurologico Carlo Besta, Milan 20133, Italy
| | - Stefania Marcuzzo
- Neurology IV - Neuroimmunology and Neuromuscular Diseases Unit, Fondazione IRCCS Istituto Neurologico Carlo Besta, Milan 20133, Italy
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99946
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Li Z, McKibben MTW, Finch GS, Blischak PD, Sutherland BL, Barker MS. Patterns and Processes of Diploidization in Land Plants. ANNUAL REVIEW OF PLANT BIOLOGY 2021; 72:387-410. [PMID: 33684297 DOI: 10.1146/annurev-arplant-050718-100344] [Citation(s) in RCA: 50] [Impact Index Per Article: 16.7] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 05/23/2023]
Abstract
Most land plants are now known to be ancient polyploids that have rediploidized. Diploidization involves many changes in genome organization that ultimately restore bivalent chromosome pairing and disomic inheritance, and resolve dosage and other issues caused by genome duplication. In this review, we discuss the nature of polyploidy and its impact on chromosome pairing behavior. We also provide an overview of two major and largely independent processes of diploidization: cytological diploidization and genic diploidization/fractionation. Finally, we compare variation in gene fractionation across land plants and highlight the differences in diploidization between plants and animals. Altogether, we demonstrate recent advancements in our understanding of variation in the patterns and processes of diploidization in land plants and provide a road map for future research to unlock the mysteries of diploidization and eukaryotic genome evolution.
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Affiliation(s)
- Zheng Li
- Department of Ecology and Evolutionary Biology, University of Arizona, Tucson, Arizona 85721, USA; , , , , ,
| | - Michael T W McKibben
- Department of Ecology and Evolutionary Biology, University of Arizona, Tucson, Arizona 85721, USA; , , , , ,
| | - Geoffrey S Finch
- Department of Ecology and Evolutionary Biology, University of Arizona, Tucson, Arizona 85721, USA; , , , , ,
| | - Paul D Blischak
- Department of Ecology and Evolutionary Biology, University of Arizona, Tucson, Arizona 85721, USA; , , , , ,
| | - Brittany L Sutherland
- Department of Ecology and Evolutionary Biology, University of Arizona, Tucson, Arizona 85721, USA; , , , , ,
| | - Michael S Barker
- Department of Ecology and Evolutionary Biology, University of Arizona, Tucson, Arizona 85721, USA; , , , , ,
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99947
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Barrado-Gil L, del Puerto A, Galindo I, Cuesta-Geijo MÁ, García-Dorival I, de Motes CM, Alonso C. African Swine Fever Virus Ubiquitin-Conjugating Enzyme Is an Immunomodulator Targeting NF-κB Activation. Viruses 2021; 13:v13061160. [PMID: 34204411 PMCID: PMC8233900 DOI: 10.3390/v13061160] [Citation(s) in RCA: 21] [Impact Index Per Article: 7.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/14/2021] [Revised: 06/11/2021] [Accepted: 06/14/2021] [Indexed: 12/17/2022] Open
Abstract
African swine fever virus (ASFV) is an acute and persistent swine virus with a high economic burden that encodes multiple genes to evade host immune response. In this work, we have revealed that early viral protein UBCv1, the only known conjugating enzyme encoded by a virus, modulates innate immune and inflammatory signaling. Transient overexpression of UBCv1 impaired activation of NF-κB and AP-1 transcription factors induced by several agonists of these pathways. In contrast, activation of IRF3 and ISRE signaling upon stimulation with TRIFΔRIP, cGAS/STING or RIG-I-CARD remained unaltered. Experiments aimed at mapping UBCv1 inhibitory activity indicated that this viral protein acts upstream or at the level step of IKKβ. In agreement with this, UBCv1 was able to block p65 nuclear translocation upon cytokine stimulation, a key event in NF-ĸB signaling. Additionally, A549 stably transduced for UBCv1 showed a significant decrease in the levels of NF-ĸB dependent genes. Interestingly, despite the well-defined capacity of UBCv1 to conjugate ubiquitin chains, a mutant disabled for ubiquitylation activity retained similar immunomodulatory activity as the wild-type enzyme, suggesting that the two functions are segregated. Altogether these data suggest that ASFV UBCv1 manipulates the innate immune response targeting the NF-κB and AP-1 pathways and opens new questions about the multifunctionality of this enzyme.
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Affiliation(s)
- Lucía Barrado-Gil
- Department of Biotechnology, Instituto Nacional de Investigación y Tecnología Agraria y Alimentaria (INIA-CSIC), Ctra. de la Coruña km 7.5, 28040 Madrid, Spain; (L.B.-G.); (A.d.P.); (I.G.); (M.Á.C.-G.); (I.G.-D.)
| | - Ana del Puerto
- Department of Biotechnology, Instituto Nacional de Investigación y Tecnología Agraria y Alimentaria (INIA-CSIC), Ctra. de la Coruña km 7.5, 28040 Madrid, Spain; (L.B.-G.); (A.d.P.); (I.G.); (M.Á.C.-G.); (I.G.-D.)
| | - Inmaculada Galindo
- Department of Biotechnology, Instituto Nacional de Investigación y Tecnología Agraria y Alimentaria (INIA-CSIC), Ctra. de la Coruña km 7.5, 28040 Madrid, Spain; (L.B.-G.); (A.d.P.); (I.G.); (M.Á.C.-G.); (I.G.-D.)
| | - Miguel Ángel Cuesta-Geijo
- Department of Biotechnology, Instituto Nacional de Investigación y Tecnología Agraria y Alimentaria (INIA-CSIC), Ctra. de la Coruña km 7.5, 28040 Madrid, Spain; (L.B.-G.); (A.d.P.); (I.G.); (M.Á.C.-G.); (I.G.-D.)
| | - Isabel García-Dorival
- Department of Biotechnology, Instituto Nacional de Investigación y Tecnología Agraria y Alimentaria (INIA-CSIC), Ctra. de la Coruña km 7.5, 28040 Madrid, Spain; (L.B.-G.); (A.d.P.); (I.G.); (M.Á.C.-G.); (I.G.-D.)
| | - Carlos Maluquer de Motes
- Department of Microbial Sciences, School of Biosciences and Medicine, University of Surrey, Stag Hill, Guildford GU2 7XH, UK
- Correspondence: (C.M.d.M.); (C.A.)
| | - Covadonga Alonso
- Department of Biotechnology, Instituto Nacional de Investigación y Tecnología Agraria y Alimentaria (INIA-CSIC), Ctra. de la Coruña km 7.5, 28040 Madrid, Spain; (L.B.-G.); (A.d.P.); (I.G.); (M.Á.C.-G.); (I.G.-D.)
- Correspondence: (C.M.d.M.); (C.A.)
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99948
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Soto RA, Najia MAT, Hachimi M, Frame JM, Yette GA, Lummertz da Rocha E, Stankunas K, Daley GQ, North TE. Sequential regulation of hemogenic fate and hematopoietic stem and progenitor cell formation from arterial endothelium by Ezh1/2. Stem Cell Reports 2021; 16:1718-1734. [PMID: 34143974 PMCID: PMC8282472 DOI: 10.1016/j.stemcr.2021.05.014] [Citation(s) in RCA: 9] [Impact Index Per Article: 3.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/17/2020] [Revised: 05/18/2021] [Accepted: 05/19/2021] [Indexed: 12/13/2022] Open
Abstract
Across species, hematopoietic stem and progenitor cells (HSPCs) arise during embryogenesis from a specialized arterial population, termed hemogenic endothelium. Here, we describe a mechanistic role for the epigenetic regulator, Enhancer of zeste homolog-1 (Ezh1), in vertebrate HSPC production via regulation of hemogenic commitment. Loss of ezh1 in zebrafish embryos favored acquisition of hemogenic (gata2b) and HSPC (runx1) fate at the expense of the arterial program (ephrinb2a, dll4). In contrast, ezh1 overexpression blocked hematopoietic progression via maintenance of arterial gene expression. The related Polycomb group subunit, Ezh2, functioned in a non-redundant, sequential manner, whereby inhibition had no impact on arterial identity, but was capable of blocking ezh1-knockdown-associated HSPC expansion. Single-cell RNA sequencing across ezh1 genotypes revealed a dropout of ezh1+/− cells among arterial endothelium associated with positive regulation of gene transcription. Exploitation of Ezh1/2 modulation has potential functional relevance for improving in vitro HSPC differentiation from induced pluripotent stem cell sources. ezh1 loss increases HSPC and lymphoid progenitor formation during embryogenesis ezh1 loss promotes a developmental shift from arterial to hemogenic fate in the DA Ezh2 functions downstream of Ezh1-regulated arterial identity in HSPC commitment scRNA-seq confirms ezh1 loss modifies distinct arterial associated gene programs
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Affiliation(s)
- Rebecca A Soto
- Stem Cell Program, Department of Hematology/Oncology, Boston Children's Hospital, Boston, MA 02115, USA; Developmental and Regenerative Biology Program, Harvard Medical School, Boston, MA 02115, USA
| | - Mohamad Ali T Najia
- Stem Cell Program, Department of Hematology/Oncology, Boston Children's Hospital, Boston, MA 02115, USA; Division of Health Sciences & Technology, Massachusetts Institute of Technology, Cambridge, MA 02139, USA; Broad Institute of MIT and Harvard, Cambridge, MA 02142, USA
| | - Mariam Hachimi
- Stem Cell Program, Department of Hematology/Oncology, Boston Children's Hospital, Boston, MA 02115, USA
| | - Jenna M Frame
- Stem Cell Program, Department of Hematology/Oncology, Boston Children's Hospital, Boston, MA 02115, USA
| | - Gabriel A Yette
- Institute of Molecular Biology, Department of Biology, University of Oregon, Eugene, OR 97403, USA
| | - Edroaldo Lummertz da Rocha
- Department of Microbiology, Immunology and Parasitology, Federal University of Santa Catarina, Florianópolis, Brazil
| | - Kryn Stankunas
- Institute of Molecular Biology, Department of Biology, University of Oregon, Eugene, OR 97403, USA
| | - George Q Daley
- Stem Cell Program, Department of Hematology/Oncology, Boston Children's Hospital, Boston, MA 02115, USA; Developmental and Regenerative Biology Program, Harvard Medical School, Boston, MA 02115, USA
| | - Trista E North
- Stem Cell Program, Department of Hematology/Oncology, Boston Children's Hospital, Boston, MA 02115, USA; Developmental and Regenerative Biology Program, Harvard Medical School, Boston, MA 02115, USA.
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99949
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Suppression of mitochondrial ROS by prohibitin drives glioblastoma progression and therapeutic resistance. Nat Commun 2021; 12:3720. [PMID: 34140524 PMCID: PMC8211793 DOI: 10.1038/s41467-021-24108-6] [Citation(s) in RCA: 56] [Impact Index Per Article: 18.7] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/09/2020] [Accepted: 06/02/2021] [Indexed: 01/01/2023] Open
Abstract
Low levels of reactive oxygen species (ROS) are crucial for maintaining cancer stem cells (CSCs) and their ability to resist therapy, but the ROS regulatory mechanisms in CSCs remains to be explored. Here, we discover that prohibitin (PHB) specifically regulates mitochondrial ROS production in glioma stem-like cells (GSCs) and facilitates GSC radiotherapeutic resistance. We find that PHB is upregulated in GSCs and is associated with malignant gliomas progression and poor prognosis. PHB binds to peroxiredoxin3 (PRDX3), a mitochondrion-specific peroxidase, and stabilizes PRDX3 protein through the ubiquitin-proteasome pathway. Knockout of PHB dramatically elevates ROS levels, thereby inhibiting GSC self-renewal. Importantly, deletion or pharmacological inhibition of PHB potently slows tumor growth and sensitizes tumors to radiotherapy, thus providing significant survival benefits in GSC-derived orthotopic tumors and glioblastoma patient-derived xenografts. These results reveal a selective role of PHB in mitochondrial ROS regulation in GSCs and suggest that targeting PHB improves radiotherapeutic efficacy in glioblastoma. How ROS levels are regulated in cancer stem cells and their contribution to cancer resistance is currently not clear. Here, the authors show that prohibitin regulates mitochondrial ROS production stabilizing the peroxidase PRDX3 and this accounts for radiotherapy resistance in glioma stem-like cells.
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99950
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Guerreiro A, De Sousa F, Liaudet N, Ivanova D, Eskat A, Meraldi P. WDR62 localizes katanin at spindle poles to ensure synchronous chromosome segregation. J Cell Biol 2021; 220:212394. [PMID: 34137788 PMCID: PMC8240857 DOI: 10.1083/jcb.202007171] [Citation(s) in RCA: 3] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/27/2020] [Revised: 04/12/2021] [Accepted: 05/18/2021] [Indexed: 12/13/2022] Open
Abstract
Mutations in the WDR62 gene cause primary microcephaly, a pathological condition often associated with defective cell division that results in severe brain developmental defects. The precise function and localization of WDR62 within the mitotic spindle is, however, still under debate, as it has been proposed to act either at centrosomes or on the mitotic spindle. Here we explored the cellular functions of WDR62 in human epithelial cell lines using both short-term siRNA protein depletions and long-term CRISPR/Cas9 gene knockouts. We demonstrate that WDR62 localizes at spindle poles, promoting the recruitment of the microtubule-severing enzyme katanin. Depletion or loss of WDR62 stabilizes spindle microtubules due to insufficient microtubule minus-end depolymerization but does not affect plus-end microtubule dynamics. During chromosome segregation, WDR62 and katanin promote efficient poleward microtubule flux and favor the synchronicity of poleward movements in anaphase to prevent lagging chromosomes. We speculate that these lagging chromosomes might be linked to developmental defects in primary microcephaly.
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Affiliation(s)
- Amanda Guerreiro
- Department of Cell Physiology and Metabolism, Faculty of Medicine, University of Geneva, Geneva, Switzerland
| | - Filipe De Sousa
- Department of Cell Physiology and Metabolism, Faculty of Medicine, University of Geneva, Geneva, Switzerland.,Radiation Oncology Division, Geneva University Hospitals, Geneva, Switzerland
| | - Nicolas Liaudet
- Bioimaging Facility, Faculty of Medicine, University of Geneva, Geneva, Switzerland
| | - Daria Ivanova
- Department of Cell Physiology and Metabolism, Faculty of Medicine, University of Geneva, Geneva, Switzerland
| | - Anja Eskat
- Department of Cell Physiology and Metabolism, Faculty of Medicine, University of Geneva, Geneva, Switzerland
| | - Patrick Meraldi
- Department of Cell Physiology and Metabolism, Faculty of Medicine, University of Geneva, Geneva, Switzerland.,Translational Research Centre in Onco-hematology, Faculty of Medicine, University of Geneva, Geneva, Switzerland
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