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Luo D, Ottesen EW, Lee JH, Singh RN. Transcriptome- and proteome-wide effects of a circular RNA encompassing four early exons of the spinal muscular atrophy genes. Sci Rep 2024; 14:10442. [PMID: 38714739 PMCID: PMC11076517 DOI: 10.1038/s41598-024-60593-7] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/28/2023] [Accepted: 04/25/2024] [Indexed: 05/10/2024] Open
Abstract
Spinal muscular atrophy (SMA) genes, SMN1 and SMN2 (hereinafter referred to as SMN1/2), produce multiple circular RNAs (circRNAs), including C2A-2B-3-4 that encompasses early exons 2A, 2B, 3 and 4. C2A-2B-3-4 is a universally and abundantly expressed circRNA of SMN1/2. Here we report the transcriptome- and proteome-wide effects of overexpression of C2A-2B-3-4 in inducible HEK293 cells. Our RNA-Seq analysis revealed altered expression of ~ 15% genes (4172 genes) by C2A-2B-3-4. About half of the affected genes by C2A-2B-3-4 remained unaffected by L2A-2B-3-4, a linear transcript encompassing exons 2A, 2B, 3 and 4 of SMN1/2. These findings underscore the unique role of the structural context of C2A-2B-3-4 in gene regulation. A surprisingly high number of upregulated genes by C2A-2B-3-4 were located on chromosomes 4 and 7, whereas many of the downregulated genes were located on chromosomes 10 and X. Supporting a cross-regulation of SMN1/2 transcripts, C2A-2B-3-4 and L2A-2B-3-4 upregulated and downregulated SMN1/2 mRNAs, respectively. Proteome analysis revealed 61 upregulated and 57 downregulated proteins by C2A-2B-3-4 with very limited overlap with those affected by L2A-2B-3-4. Independent validations confirmed the effect of C2A-2B-3-4 on expression of genes associated with chromatin remodeling, transcription, spliceosome function, ribosome biogenesis, lipid metabolism, cytoskeletal formation, cell proliferation and neuromuscular junction formation. Our findings reveal a broad role of C2A-2B-3-4, and expands our understanding of functions of SMN1/2 genes.
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Affiliation(s)
- Diou Luo
- Department of Biomedical Sciences, College of Veterinary Medicine, Iowa State University, Ames, IA, 50011, USA
| | - Eric W Ottesen
- Department of Biomedical Sciences, College of Veterinary Medicine, Iowa State University, Ames, IA, 50011, USA
| | - Ji Heon Lee
- Department of Biomedical Sciences, College of Veterinary Medicine, Iowa State University, Ames, IA, 50011, USA
| | - Ravindra N Singh
- Department of Biomedical Sciences, College of Veterinary Medicine, Iowa State University, Ames, IA, 50011, USA.
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Luo D, Ottesen E, Lee JH, Singh R. Transcriptome- and proteome-wide effects of a circular RNA encompassing four early exons of the spinal muscular atrophy genes. RESEARCH SQUARE 2024:rs.3.rs-3818622. [PMID: 38464174 PMCID: PMC10925445 DOI: 10.21203/rs.3.rs-3818622/v1] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 03/12/2024]
Abstract
Spinal muscular atrophy (SMA) genes, SMN1 and SMN2, produce multiple circular RNAs (circRNAs), including C2A-2B-3-4 that encompasses early exons 2A, 2B, 3 and 4. Here we report the transcriptome- and proteome-wide effects of overexpression of C2A-2B-3-4 in inducible HEK293 cells. Our RNA-Seq analysis revealed altered expression of ~ 15% genes (4,172 genes) by C2A-2B-3-4. About half of the affected genes by C2A-2B-3-4 remained unaffected by L2A-2B-3-4, a linear transcript encompassing exons 2A, 2B, 3 and 4 of SMN1/SMN2. These fifindings underscore the unique role of the structural context of C2A-2B-3-4 in gene regulation. A surprisingly high number of upregulated genes by C2A-2B-3-4 were located on chromosomes 4 and 7, whereas many of the downregulated genes were located on chromosomes 10 and X. Supporting a cross-regulation of SMN1/SMN2 transcripts, C2A-2B-3-4 and L2A-2B-3-4 upregulated and downregulated SMN1/SMN2 mRNAs, respectively. Proteome analysis revealed 61 upregulated and 57 downregulated proteins by C2A-2B-3-4 with very limited overlap with those affected by L2A-2B-3-4. Independent validations confirmed the effect of C2A-2B-3-4 on expression of genes associated with chromatin remodeling, transcription, spliceosome function, ribosome biogenesis, lipid metabolism, cytoskeletal formation, cell proliferation and neuromuscular junction formation. Our findings reveal a broad role of C2A-2B-3-4, a universally expressed circRNA produced by SMN1/SMN2.
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Chmielewska K, Vittorio S, Gervasoni S, Dzierzbicka K, Inkielewicz-Stepniak I, Vistoli G. Human carnosinases: A brief history, medicinal relevance, and in silico analyses. Drug Discov Today 2024; 29:103860. [PMID: 38128717 DOI: 10.1016/j.drudis.2023.103860] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/25/2023] [Revised: 12/03/2023] [Accepted: 12/14/2023] [Indexed: 12/23/2023]
Abstract
Carnosine, an endogenous dipeptide, has been found to have a plethora of medicinal properties, such as antioxidant, antiageing, and chelating effects, but with one downside: a short half-life. Carnosinases and two hydrolytic enzymes, which remain enigmatic, are responsible for these features. Hence, here we emphasize why research is valuable for better understanding crucial concepts like ageing, neurodegradation, and cancerogenesis, given that inhibition of carnosinases might significantly prolong carnosine bioavailability and allow its further use in medicine. Herein, we explore the literature regarding carnosinases and present a short in silico analysis aimed at elucidating the possible recognition pattern between CN1 and its ligands.
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Affiliation(s)
- Klaudia Chmielewska
- Department of Organic Chemistry, Faculty of Chemistry, Gdansk University of Technology, Gdansk, Poland
| | - Serena Vittorio
- Dipartimento di Scienze Farmaceutiche, Università degli Studi di Milano, Via Mangiagalli 25, 20133, Milan, Italy
| | - Silvia Gervasoni
- Dipartimento di Scienze Farmaceutiche, Università degli Studi di Milano, Via Mangiagalli 25, 20133, Milan, Italy; Physics Department, University of Cagliari, Cittadella Universitaria, SP 8 km 0.700, 09042, Monserrato (CA), Italy
| | - Krystyna Dzierzbicka
- Department of Organic Chemistry, Faculty of Chemistry, Gdansk University of Technology, Gdansk, Poland
| | | | - Giulio Vistoli
- Dipartimento di Scienze Farmaceutiche, Università degli Studi di Milano, Via Mangiagalli 25, 20133, Milan, Italy.
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Ikeda Y, Fujii J. The Emerging Roles of γ-Glutamyl Peptides Produced by γ-Glutamyltransferase and the Glutathione Synthesis System. Cells 2023; 12:2831. [PMID: 38132151 PMCID: PMC10741565 DOI: 10.3390/cells12242831] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/24/2023] [Revised: 12/03/2023] [Accepted: 12/06/2023] [Indexed: 12/23/2023] Open
Abstract
L-γ-Glutamyl-L-cysteinyl-glycine is commonly referred to as glutathione (GSH); this ubiquitous thiol plays essential roles in animal life. Conjugation and electron donation to enzymes such as glutathione peroxidase (GPX) are prominent functions of GSH. Cellular glutathione balance is robustly maintained via regulated synthesis, which is catalyzed via the coordination of γ-glutamyl-cysteine synthetase (γ-GCS) and glutathione synthetase, as well as by reductive recycling by glutathione reductase. A prevailing short supply of L-cysteine (Cys) tends to limit glutathione synthesis, which leads to the production of various other γ-glutamyl peptides due to the unique enzymatic properties of γ-GCS. Extracellular degradation of glutathione by γ-glutamyltransferase (GGT) is a dominant source of Cys for some cells. GGT catalyzes the hydrolytic removal of the γ-glutamyl group of glutathione or transfers it to amino acids or to dipeptides outside cells. Such processes depend on an abundance of acceptor substrates. However, the physiological roles of extracellularly preserved γ-glutamyl peptides have long been unclear. The identification of γ-glutamyl peptides, such as glutathione, as allosteric modulators of calcium-sensing receptors (CaSRs) could provide insights into the significance of the preservation of γ-glutamyl peptides. It is conceivable that GGT could generate a new class of intercellular messaging molecules in response to extracellular microenvironments.
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Affiliation(s)
- Yoshitaka Ikeda
- Division of Molecular Cell Biology, Department of Biomolecular Sciences, Faculty of Medicine, Saga University, 5-1-1 Nabeshima, Saga 849-8501, Japan
| | - Junichi Fujii
- Department of Biochemistry and Molecular Biology, Graduate School of Medical Science, Yamagata University, 2-2-2 Iidanishi, Yamagata City 990-9585, Japan
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Fujii J, Osaki T, Soma Y, Matsuda Y. Critical Roles of the Cysteine-Glutathione Axis in the Production of γ-Glutamyl Peptides in the Nervous System. Int J Mol Sci 2023; 24:ijms24098044. [PMID: 37175751 PMCID: PMC10179188 DOI: 10.3390/ijms24098044] [Citation(s) in RCA: 8] [Impact Index Per Article: 8.0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/04/2023] [Revised: 04/24/2023] [Accepted: 04/26/2023] [Indexed: 05/15/2023] Open
Abstract
γ-Glutamyl moiety that is attached to the cysteine (Cys) residue in glutathione (GSH) protects it from peptidase-mediated degradation. The sulfhydryl group of the Cys residue represents most of the functions of GSH, which include electron donation to peroxidases, protection of reactive sulfhydryl in proteins via glutaredoxin, and glutathione conjugation of xenobiotics, whereas Cys-derived sulfur is also a pivotal component of some redox-responsive molecules. The amount of Cys that is available tends to restrict the capacity of GSH synthesis. In in vitro systems, cystine is the major form in the extracellular milieu, and a specific cystine transporter, xCT, is essential for survival in most lines of cells and in many primary cultivated cells as well. A reduction in the supply of Cys causes GPX4 to be inhibited due to insufficient GSH synthesis, which leads to iron-dependent necrotic cell death, ferroptosis. Cells generally cannot take up GSH without the removal of γ-glutamyl moiety by γ-glutamyl transferase (GGT) on the cell surface. Meanwhile, the Cys-GSH axis is essentially common to certain types of cells; primarily, neuronal cells that contain a unique metabolic system for intercellular communication concerning γ-glutamyl peptides. After a general description of metabolic processes concerning the Cys-GSH axis, we provide an overview and discuss the significance of GSH-related compounds in the nervous system.
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Affiliation(s)
- Junichi Fujii
- Department of Biochemistry and Molecular Biology, Graduate School of Medical Science, Yamagata University, Yamagata 990-9585, Japan
| | - Tsukasa Osaki
- Department of Biochemistry and Molecular Biology, Graduate School of Medical Science, Yamagata University, Yamagata 990-9585, Japan
| | - Yuya Soma
- Graduate School of Nursing, Yamagata University Faculty of Medicine, Yamagata 990-9585, Japan
| | - Yumi Matsuda
- Graduate School of Nursing, Yamagata University Faculty of Medicine, Yamagata 990-9585, Japan
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Belal R, Gad A. Zinc oxide nanoparticles induce oxidative stress, genotoxicity, and apoptosis in the hemocytes of Bombyx mori larvae. Sci Rep 2023; 13:3520. [PMID: 36864109 PMCID: PMC9981692 DOI: 10.1038/s41598-023-30444-y] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/21/2022] [Accepted: 02/23/2023] [Indexed: 03/04/2023] Open
Abstract
The expanded uses of zinc oxide nanoparticles (ZnO-NPs) have grown rapidly in the field of nanotechnology. Thus, the increased production of nanoparticles (NPs) increases the potential risks to the environment and occupationally exposed humans. Hence, safety and toxicity assessment including genotoxicity of these NPs is indispensable. In the present study, we have evaluated the genotoxic effect of ZnO-NPs on 5th larval instar of Bombyx mori after feeding on mulberry leaves treated with ZnO-NPs at concentrations 50 and 100 μg/ml. Moreover, we evaluated its effects on total and different hemocyte count, antioxidant potential and catalase activity on the hemolymph of treated larvae. Results showed that ZnO-NPs at concentrations of 50 and 100 µg/ml have significantly decreased the total hemocyte count (THC) and different hemocyte count (DHC) except the number of oenocytes as they were significantly increased. Gene expression profile also showed up-regulation of GST, CNDP2 and CE genes suggesting increase in antioxidant activity and alteration in cell viability as well as cell signaling.
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Affiliation(s)
- Rania Belal
- Department of Genetics, Faculty of Agriculture, University of Alexandria, Alexandria, 21545, Egypt
| | - Abir Gad
- Department of Applied Entomology and Zoology, Faculty of Agriculture, University of Alexandria, Alexandria, 21545, Egypt.
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Ma T, Li H, Zhang X. Discovering single-cell eQTLs from scRNA-seq data only. Gene 2022; 829:146520. [PMID: 35452708 DOI: 10.1016/j.gene.2022.146520] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/21/2021] [Revised: 01/12/2022] [Accepted: 04/15/2022] [Indexed: 12/14/2022]
Abstract
eQTL studies are essential for understanding genomic regulation. The effects of genetic variations on gene regulation are cell-type-specific and cellular-context-related, so studying eQTLs at a single-cell level is crucial. The ideal solution is to use both mutation and expression data from the same cells. However, the current technology of such paired data in single cells is still immature. We present a new method, eQTLsingle, to discover eQTLs only with single-cell RNA-seq (scRNA-seq) data, without genomic data. It detects mutations from scRNA-seq data and models gene expression of different genotypes with the zero-inflated negative binomial (ZINB) model to find associations between genotypes and phenotypes at the single-cell level. On a glioblastoma and gliomasphere scRNA-seq dataset, eQTLsingle discovered hundreds of cell-type-specific tumor-related eQTLs, most of which cannot be found in bulk eQTL studies. Detailed analyses on examples of the discovered eQTLs revealed important underlying regulatory mechanisms. eQTLsingle is a uniquely powerful tool for utilizing the vast scRNA-seq resources for single-cell eQTL studies, and it is available for free academic use at https://github.com/horsedayday/eQTLsingle.
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Affiliation(s)
- Tianxing Ma
- MOE Key Laboratory of Bioinformatics, Bioinformatics Division, BNRIST and Department of Automation, Tsinghua University, Beijing 100084, China
| | - Haochen Li
- School of Medicine, Center for Synthetic and Systems Biology, Tsinghua University, Beijing 100084, China
| | - Xuegong Zhang
- MOE Key Laboratory of Bioinformatics, Bioinformatics Division, BNRIST and Department of Automation, Tsinghua University, Beijing 100084, China; School of Medicine, Center for Synthetic and Systems Biology, Tsinghua University, Beijing 100084, China.
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Kobayashi S, Homma T, Okumura N, Han J, Nagaoka K, Sato H, Konno H, Yamada S, Takao T, Fujii J. Carnosine dipeptidase II (CNDP2) protects cells under cysteine insufficiency by hydrolyzing glutathione-related peptides. Free Radic Biol Med 2021; 174:12-27. [PMID: 34324979 DOI: 10.1016/j.freeradbiomed.2021.07.036] [Citation(s) in RCA: 12] [Impact Index Per Article: 4.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Received: 04/19/2021] [Revised: 07/06/2021] [Accepted: 07/25/2021] [Indexed: 01/18/2023]
Abstract
The knockout (KO) of the cystine transporter xCT causes ferroptosis, a type of iron-dependent necrotic cell death, in mouse embryonic fibroblasts, but this does not occur in macrophages. In this study, we explored the gene that supports cell survival under a xCT deficiency using a proteomics approach. Analysis of macrophage-derived peptides that were tagged with iTRAQ by liquid chromatography-mass spectrometry revealed a robust elevation in the levels of carnosine dipeptidase II (CNDP2) in xCT KO macrophages. The elevation in the CNDP2 protein levels was confirmed by immunoblot analyses and this elevation was accompanied by an increase in hydrolytic activity towards cysteinylglycine, the intermediate degradation product of glutathione after the removal of the γ-glutamyl group, in xCT KO macrophages. Supplementation of the cystine-free media of Hepa1-6 cells with glutathione or cysteinylglycine extended their survival, whereas the inclusion of bestatin, an inhibitor of CNDP2, counteracted the effects of these compounds. We established CNDP2 KO mice by means of the CRISPR/Cas9 system and found a decrease in dipeptidase activity in the liver, kidney, and brain. An acetaminophen overdose (350 mg/kg) showed not only aggravated hepatic damage but also renal injury in the CNDP2 KO mice, which was not evident in the wild-type mice that were receiving the same dose. The aggravated renal damage in the CNDP2 KO mice was consistent with the presence of abundant levels of CNDP2 in the kidney, the organ prone to developing ferroptosis. These collective data imply that cytosolic CNDP2, in conjugation with the removal of the γ-glutamyl group, recruits Cys from extracellular GSH and supports redox homeostasis of cells, particularly in epithelial cells of proximal tubules that are continuously exposed to oxidative insult from metabolic wastes that are produced in the body.
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Affiliation(s)
- Sho Kobayashi
- Department of Biochemistry and Molecular Biology, Graduate School of Medical Science, Yamagata University, 2-2-2 Iidanishi, Yamagata, Yamagata, 990-9585, Japan
| | - Takujiro Homma
- Department of Biochemistry and Molecular Biology, Graduate School of Medical Science, Yamagata University, 2-2-2 Iidanishi, Yamagata, Yamagata, 990-9585, Japan
| | - Nobuaki Okumura
- Laboratory of Biomolecular Analysis, Institute for Protein Research, Osaka University, Suita, Osaka, 565-0871, Japan
| | - Jia Han
- Department of Pathology and Laboratory Medicine, Kanazawa Medical University, 1-1 Uchinada, Ishikawa, 920-0293, Japan
| | - Keita Nagaoka
- Department of Biological Engineering, Graduate School of Science and Engineering, Yamagata University, Yonezawa, Yamagata, 992-8510, Japan
| | - Hideyo Sato
- Laboratory of Biochemistry and Molecular Biology, Department of Medical Technology, Faculty of Medicine, Niigata University, 746-2 Asahimachi-dori, Chuo-ku, Niigata, 951-8518, Japan
| | - Hiroyuki Konno
- Department of Biological Engineering, Graduate School of Science and Engineering, Yamagata University, Yonezawa, Yamagata, 992-8510, Japan
| | - Sohsuke Yamada
- Department of Pathology and Laboratory Medicine, Kanazawa Medical University, 1-1 Uchinada, Ishikawa, 920-0293, Japan
| | - Toshifumi Takao
- Laboratory of Protein Profiling and Functional Proteomics, Institute for Protein Research, Osaka University, Suita, Osaka, 565-0871, Japan
| | - Junichi Fujii
- Department of Biochemistry and Molecular Biology, Graduate School of Medical Science, Yamagata University, 2-2-2 Iidanishi, Yamagata, Yamagata, 990-9585, Japan.
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Hishida S, Kawakami K, Fujita Y, Kato T, Takai M, Iinuma K, Nakane K, Tsuchiya T, Koie T, Miura Y, Ito M, Mizutani K. Proteomic analysis of extracellular vesicles identified PI3K pathway as a potential therapeutic target for cabazitaxel-resistant prostate cancer. Prostate 2021; 81:592-602. [PMID: 33905554 DOI: 10.1002/pros.24138] [Citation(s) in RCA: 5] [Impact Index Per Article: 1.7] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Received: 12/10/2020] [Revised: 03/07/2021] [Accepted: 04/11/2021] [Indexed: 11/07/2022]
Abstract
BACKGROUND Cabazitaxel (CBZ) is now widely used for prostate cancer (PC) patients resistant to docetaxel (DOC), however, most patients eventually acquire resistance. It will, therefore, be of great benefit to discover novel therapeutic target for the resistance. We aimed to identify candidate therapeutic targets for CBZ-resistance by proteomic analysis of extracellular vesicles (EVs) isolated from serum of DOC-resistant PC patients who later developed CBZ-resistance as well as those harvested from culture medium of DOC- and CBZ-resistant PC cell lines. METHODS Using T-cell immunoglobulin domain and mucin domain-containing protein 4 (Tim4) conjugated to magnetic beads, EVs were purified from serum of PC patients with DOC-resistance that was collected before and after acquiring CBZ-resistance and conditioned medium of DOC-resistant (22Rv1DR) and CBZ-resistant (22Rv1CR) PC cell lines. Protein analysis of EVs was performed by nanoLC-MS/MS, followed by a comparative analysis of protein expression and network analysis. The cytotoxic effect of a phosphatidylinositol-3-kinase (PI3K) inhibitor, ZSTK474, was evaluated by WST-1 assay. The expression and phosphorylation of PI3K and PTEN were examined by western blot analysis. RESULTS Among differentially regulated proteins, 77 and 61 proteins were significantly increased in EVs from CBZ-resistant PC cell line and patients, respectively. A comparison between the two datasets revealed that six proteins, fructose-bisphosphate aldolase, cytosolic nonspecific dipeptidase, CD63, CD151, myosin light chain 9, and peroxiredoxin-6 were elevated in EVs from both cell line and patients. Network analysis of the increased EV proteins identified pathways associated with CBZ-resistance including PI3K signaling pathway. ZSTK474 significantly inhibited growth of 22Rv1CR cells and improved their sensitivity to CBZ. In 22Rv1CR cells, PI3K was activated and PTEN that inhibits PI3K was deactivated. CONCLUSIONS Proteomic analysis of serum EVs was successfully accomplished by using Tim-4 as a tool to isolate highly purified EVs. Our results suggest that the combination use of CBZ and PI3K inhibitor could be a promising treatment option for CBZ-resistant PC patients.
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Affiliation(s)
- Seiji Hishida
- Department of Urology, Gifu University Graduate School of Medicine, Gifu, Japan
| | - Kyojiro Kawakami
- Research Team for Mechanism of Aging, Tokyo Metropolitan Institute of Gerontology, Tokyo, Japan
| | - Yasunori Fujita
- Research Team for Functional Biogerontology, Tokyo Metropolitan Institute of Gerontology, Tokyo, Japan
| | - Taku Kato
- Department of Urology, Asahi University Hospital, Gifu, Japan
| | - Manabu Takai
- Department of Urology, Gifu University Graduate School of Medicine, Gifu, Japan
| | - Koji Iinuma
- Department of Urology, Gifu University Graduate School of Medicine, Gifu, Japan
| | - Keita Nakane
- Department of Urology, Gifu University Graduate School of Medicine, Gifu, Japan
| | - Tomohiro Tsuchiya
- Department of Urology, Gifu University Graduate School of Medicine, Gifu, Japan
| | - Takuya Koie
- Department of Urology, Gifu University Graduate School of Medicine, Gifu, Japan
| | - Yuri Miura
- Research Team for Mechanism of Aging, Tokyo Metropolitan Institute of Gerontology, Tokyo, Japan
| | - Masafumi Ito
- Research Team for Functional Biogerontology, Tokyo Metropolitan Institute of Gerontology, Tokyo, Japan
| | - Kosuke Mizutani
- Department of Urology, Gifu University Graduate School of Medicine, Gifu, Japan
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Zhang LQ, Yang HQ, Yang SQ, Wang Y, Chen XJ, Lu HS, Zhao LP. CNDP2 Acts as an Activator for Human Ovarian Cancer Growth and Metastasis via the PI3K/AKT Pathway. Technol Cancer Res Treat 2020; 18:1533033819874773. [PMID: 31537175 PMCID: PMC6755628 DOI: 10.1177/1533033819874773] [Citation(s) in RCA: 7] [Impact Index Per Article: 1.8] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/19/2022] Open
Abstract
Introduction: The mechanism of tumorigenesis and metastasis of ovarian cancer has not yet been
elucidated. This study aimed to investigate the role and molecular mechanism of
cytosolic nonspecific dipeptidase 2 in tumorigenesis and metastasis. Methods: Cytosolic nonspecific dipeptidase 2 expression in human ovarian cancer tissues and cell
lines was assessed with methyl thiazolyl tetrazolium (MTT), clone formation, and
transwell assays performed to evaluate the ability of ovarian cancer cells to
proliferate and migrate. Nude mice tumor formation experiments were also performed by
subcutaneously injecting cells with stable cytosolic nonspecific dipeptidase 2 knockdown
and control SKOV3 cells into BALB/c female nude mice to detect changes in PI3K/AKT
pathway-related proteins by Western blotting. Results: Cytosolic nonspecific dipeptidase 2 was highly expressed in human ovarian cancer
tissues, with its expression associated with pathological data, including ovarian cancer
metastasis. A cytosolic nonspecific dipeptidase 2 stable knockdown or ectopic expression
ovarian cancer cell model was established and demonstrated that cytosolic nonspecific
dipeptidase 2 could promote the proliferation of ovarian cancer cells. Transwell cell
migration and invasion assays confirmed that cytosolic nonspecific dipeptidase 2
enhanced cell metastasis in ovarian cancer. Furthermore, in vivo
xenograft experiments demonstrated that cytosolic nonspecific dipeptidase 2 can promote
the development and progression of ovarian cancer, increasing the expression of
phosphorylated PI3K and AKT. Conclusions: Cytosolic nonspecific dipeptidase 2 promotes the occurrence and development of ovarian
cancer through the PI3K/AKT signaling pathway.
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Affiliation(s)
- Li Q Zhang
- Department of Gynecology, Taizhou Central Hospital, Taizhou, China
| | - Hua Q Yang
- Department of Gynecology, Taizhou Central Hospital, Taizhou, China
| | - Su Q Yang
- Department of Gynecology, Taizhou Central Hospital, Taizhou, China
| | - Ying Wang
- Department of Gynecology, Taizhou Central Hospital, Taizhou, China
| | - Xian J Chen
- Department of Clinical Laboratory, Taizhou Central Hospital, Taizhou, China
| | - Hong S Lu
- Department of Pathology, Taizhou Central Hospital, Taizhou, China
| | - Ling P Zhao
- Department of Gynecology, Taizhou Central Hospital, Taizhou, China
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11
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Andreyeva EN, Ogienko AA, Dubatolova TD, Oshchepkova AL, Kozhevnikova EN, Ivankin AV, Pavlova GA, Kopyl SA, Pindyurin AV. A toolset to study functions of Cytosolic non-specific dipeptidase 2 (CNDP2) using Drosophila as a model organism. BMC Genet 2019; 20:31. [PMID: 30885138 PMCID: PMC6421639 DOI: 10.1186/s12863-019-0726-z] [Citation(s) in RCA: 8] [Impact Index Per Article: 1.6] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/30/2022] Open
Abstract
Background Expression of the CNDP2 gene is frequently up- or down-regulated in different types of human cancers. However, how the product of this gene is involved in cell growth and proliferation is poorly understood. Moreover, our knowledge of the functions of the CNDP2 orthologs in well-established model organisms is scarce. In particular, the function of the D. melanogaster ortholog of CNDP2, encoded by the CG17337 gene (hereafter referred to as dCNDP2), is still unknown. Results This study was aimed at developing a set of genetic and molecular tools to study the roles of dCNDP2. We generated a dCNDP2 null mutation (hereafter ∆dCNDP2) using CRISPR/Cas9-mediated homologous recombination (HR) and found that the ∆dCNDP2 mutants are homozygous viable, morphologically normal and fertile. We also generated transgenic fly lines expressing eGFP-tagged and non-tagged dCNDP2 protein, all under the control of the UAS promoter, as well as polyclonal antibodies specific to dCNDP2. Using these tools, we demonstrate that only one of the two predicted dCNDP2 isoforms is expressed throughout the different tissues tested. dCNDP2 was detected in both the cytoplasm and the nucleus, and was found to be associated with multiple sites in the salivary gland polytene chromosomes. Conclusions The dCNDP2 gene is not essential for fly viability under standard laboratory conditions. The subcellular localization pattern of dCNDP2 suggests that this protein might have roles in both the cytoplasm and the nucleus. The genetic and molecular tools developed in this study will allow further functional characterization of the conserved CNDP2 protein using D. melanogaster as a model system. Electronic supplementary material The online version of this article (10.1186/s12863-019-0726-z) contains supplementary material, which is available to authorized users.
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Affiliation(s)
- Evgeniya N Andreyeva
- Institute of Molecular and Cellular Biology, Siberian Branch of the Russian Academy of Sciences, Novosibirsk, 630090, Russia.
| | - Anna A Ogienko
- Institute of Molecular and Cellular Biology, Siberian Branch of the Russian Academy of Sciences, Novosibirsk, 630090, Russia.,Novosibirsk State University, Novosibirsk, 630090, Russia
| | - Tatiana D Dubatolova
- Institute of Molecular and Cellular Biology, Siberian Branch of the Russian Academy of Sciences, Novosibirsk, 630090, Russia
| | - Anastasiya L Oshchepkova
- Institute of Molecular and Cellular Biology, Siberian Branch of the Russian Academy of Sciences, Novosibirsk, 630090, Russia.,Institute of Chemical Biology and Fundamental Medicine, Siberian Branch of the Russian Academy of Sciences, Novosibirsk, 630090, Russia
| | - Elena N Kozhevnikova
- Institute of Molecular and Cellular Biology, Siberian Branch of the Russian Academy of Sciences, Novosibirsk, 630090, Russia
| | - Anton V Ivankin
- Institute of Molecular and Cellular Biology, Siberian Branch of the Russian Academy of Sciences, Novosibirsk, 630090, Russia
| | - Gera A Pavlova
- Institute of Molecular and Cellular Biology, Siberian Branch of the Russian Academy of Sciences, Novosibirsk, 630090, Russia
| | - Sergei A Kopyl
- Institute of Molecular and Cellular Biology, Siberian Branch of the Russian Academy of Sciences, Novosibirsk, 630090, Russia
| | - Alexey V Pindyurin
- Institute of Molecular and Cellular Biology, Siberian Branch of the Russian Academy of Sciences, Novosibirsk, 630090, Russia. .,Novosibirsk State University, Novosibirsk, 630090, Russia.
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12
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Electroneutral polymersomes for combined cancer chemotherapy. Acta Biomater 2018; 80:327-340. [PMID: 30201433 DOI: 10.1016/j.actbio.2018.09.005] [Citation(s) in RCA: 15] [Impact Index Per Article: 2.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/15/2018] [Revised: 09/03/2018] [Accepted: 09/06/2018] [Indexed: 02/06/2023]
Abstract
Combination cancer chemotherapy provides an important treatment tool, both as an adjuvant and neoadjuvant treatment, this shift in focus from mono to combination therapies has led to increased interest in drug delivery systems (DDS). DDSs, such as polymersomes, are capable of encapsulating large amounts of multiple drugs with both hydrophilic and hydrophobic properties simultaneously, as well as offering a mechanism to combat multi drug resistant cancers and poor patient tolerance of the cytotoxic compounds utilised. In this article, we report the formulation and evaluation of a novel electroneutral polymersome capable of high encapsulation efficacies for multiple drugs (Doxorubicin, 5-Fluorouracil and leucovorin). The in-vivo biodistribution of the polymersome were established and they were found to accumulate largely in tumour tissue. Polymersome encapsulating the three chemotherapeutic drugs were assessed both in-vitro (BxPC-3 cell line) and in-vivo (following intratumoral and intravenous administration) and compared with the same concentration of the three drugs in solution. We report better efficacy and higher maximum tolerated dose for our combination drug loaded polymersomes in all experiments. Furthermore, intratumorally injected combination drug loaded polymersomes exhibited a 62% reduction in tumour volume after 13 days when compared with the free combination solutions. A smaller differential of 13% was observed for when treatment was administered intravenously however, importantly less cardiotoxicity was displayed from the polymersomal DDS. In this study, expression of a number of survival-relevant genes in tumours treated with the free chemotherapy combination was compared with expression of those genes in tumours treated with the polymersomes harbouring those drugs and the significance of findings is discussed. STATEMENT OF SIGNIFICANCE: The shift in focus from mono to combination chemotherapies has led to an increased interest in the role of drug delivery systems (DDS). Liposomes, although commercialized for mono therapy, have lower loading capacities and stability than their polymeric counterpart, polymersomes. Polymersomes are growing in prevalence as their advantageous properties are better understood and exploited. Here we present a novel polymersome for the encapsulation of three anticancer compounds. This is the first time this particular polymersome has been used to encapsulate these three compounds with both an in-vitro and in-vivo evaluation carried out. This work will be of interest to those in the field of combination therapy, drug delivery, drug toxicity, multidrug resistance, liposomes, DDS and polymersomes.
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Abstract
SIGNIFICANCE Glutathione degradation has for long been thought to occur only on noncytosolic pools. This is because there has been only one enzyme known to degrade glutathione (γ-glutamyl transpeptidase) and this localizes to either the plasma membrane (mammals, bacteria) or the vacuolar membrane (yeast, plants) and acts on extracellular or vacuolar pools. The last few years have seen the discovery of several new enzymes of glutathione degradation that function in the cytosol, throwing new light on glutathione degradation. Recent Advances: The new enzymes that have been identified in the last few years that can initiate glutathione degradation include the Dug enzyme found in yeast and fungi, the ChaC1 enzyme found among higher eukaryotes, the ChaC2 enzyme found from bacteria to man, and the RipAY enzyme found in some bacteria. These enzymes play roles ranging from housekeeping functions to stress responses and are involved in processes such as embryonic neural development and pathogenesis. CRITICAL ISSUES In addition to delineating the pathways of glutathione degradation in detail, a critical issue is to find how these new enzymes impact cellular physiology and homeostasis. FUTURE DIRECTIONS Glutathione degradation plays a far greater role in cellular physiology than previously envisaged. The differential regulation and differential specificities of various enzymes, each acting on distinct pools, can lead to different consequences to the cell. It is likely that the coming years will see these downstream effects being unraveled in greater detail and will lead to a better understanding and appreciation of glutathione degradation. Antioxid. Redox Signal. 27, 1200-1216.
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Affiliation(s)
- Anand Kumar Bachhawat
- Department of Biological Sciences, Indian Institute of Science Education and Research , Mohali, Mohali, India
| | - Amandeep Kaur
- Department of Biological Sciences, Indian Institute of Science Education and Research , Mohali, Mohali, India
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14
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Wang J, Mouradov D, Wang X, Jorissen RN, Chambers MC, Zimmerman LJ, Vasaikar S, Love CG, Li S, Lowes K, Leuchowius KJ, Jousset H, Weinstock J, Yau C, Mariadason J, Shi Z, Ban Y, Chen X, Coffey RJC, Slebos RJ, Burgess AW, Liebler DC, Zhang B, Sieber OM. Colorectal Cancer Cell Line Proteomes Are Representative of Primary Tumors and Predict Drug Sensitivity. Gastroenterology 2017; 153. [PMID: 28625833 PMCID: PMC5623120 DOI: 10.1053/j.gastro.2017.06.008] [Citation(s) in RCA: 47] [Impact Index Per Article: 6.7] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Indexed: 12/21/2022]
Abstract
BACKGROUND AND AIMS Proteomics holds promise for individualizing cancer treatment. We analyzed to what extent the proteomic landscape of human colorectal cancer (CRC) is maintained in established CRC cell lines and the utility of proteomics for predicting therapeutic responses. METHODS Proteomic and transcriptomic analyses were performed on 44 CRC cell lines, compared against primary CRCs (n=95) and normal tissues (n=60), and integrated with genomic and drug sensitivity data. RESULTS Cell lines mirrored the proteomic aberrations of primary tumors, in particular for intrinsic programs. Tumor relationships of protein expression with DNA copy number aberrations and signatures of post-transcriptional regulation were recapitulated in cell lines. The 5 proteomic subtypes previously identified in tumors were represented among cell lines. Nonetheless, systematic differences between cell line and tumor proteomes were apparent, attributable to stroma, extrinsic signaling, and growth conditions. Contribution of tumor stroma obscured signatures of DNA mismatch repair identified in cell lines with a hypermutation phenotype. Global proteomic data showed improved utility for predicting both known drug-target relationships and overall drug sensitivity as compared with genomic or transcriptomic measurements. Inhibition of targetable proteins associated with drug responses further identified corresponding synergistic or antagonistic drug combinations. Our data provide evidence for CRC proteomic subtype-specific drug responses. CONCLUSIONS Proteomes of established CRC cell line are representative of primary tumors. Proteomic data tend to exhibit improved prediction of drug sensitivity as compared with genomic and transcriptomic profiles. Our integrative proteogenomic analysis highlights the potential of proteome profiling to inform personalized cancer medicine.
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Affiliation(s)
- Jing Wang
- Lester and Sue Smith Breast Center, Baylor College of Medicine, Houston, TX 77030, USA,Department of Molecular and Human Genetics, Baylor College of Medicine, Houston, TX 77030, USA,CORRESPONDING AUTHORS: Oliver Sieber, Systems Biology and Personalised Medicine Division, The Walter and Eliza Hall Institute of Medial Research, 1G Royal Parade, Parkville, VIC 3052, Australia. . Bing Zhang, Lester and Sue Smith Breast Center, Baylor College of Medicine, Houston, TX 77030, USA.
| | - Dmitri Mouradov
- Systems Biology and Personalised Medicine Division, The Walter and Eliza Hall Institute of Medial Research, Parkville, VIC 3052, Australia,Department of Medical Biology, The University of Melbourne, Parkville, VIC 3052, Australia,CORRESPONDING AUTHORS: Oliver Sieber, Systems Biology and Personalised Medicine Division, The Walter and Eliza Hall Institute of Medial Research, 1G Royal Parade, Parkville, VIC 3052, Australia. . Bing Zhang, Lester and Sue Smith Breast Center, Baylor College of Medicine, Houston, TX 77030, USA.
| | - Xiaojing Wang
- Lester and Sue Smith Breast Center, Baylor College of Medicine, Houston, TX 77030, USA,Department of Molecular and Human Genetics, Baylor College of Medicine, Houston, TX 77030, USA,CORRESPONDING AUTHORS: Oliver Sieber, Systems Biology and Personalised Medicine Division, The Walter and Eliza Hall Institute of Medial Research, 1G Royal Parade, Parkville, VIC 3052, Australia. . Bing Zhang, Lester and Sue Smith Breast Center, Baylor College of Medicine, Houston, TX 77030, USA.
| | - Robert N. Jorissen
- Systems Biology and Personalised Medicine Division, The Walter and Eliza Hall Institute of Medial Research, Parkville, VIC 3052, Australia,Department of Medical Biology, The University of Melbourne, Parkville, VIC 3052, Australia
| | | | - Lisa J. Zimmerman
- Department of Biochemistry, Vanderbilt University, Nashville, TN 37232, USA
| | - Suhas Vasaikar
- Lester and Sue Smith Breast Center, Baylor College of Medicine, Houston, TX 77030, USA,Department of Molecular and Human Genetics, Baylor College of Medicine, Houston, TX 77030, USA
| | - Christopher G. Love
- Systems Biology and Personalised Medicine Division, The Walter and Eliza Hall Institute of Medial Research, Parkville, VIC 3052, Australia,Department of Medical Biology, The University of Melbourne, Parkville, VIC 3052, Australia
| | - Shan Li
- Systems Biology and Personalised Medicine Division, The Walter and Eliza Hall Institute of Medial Research, Parkville, VIC 3052, Australia
| | - Kym Lowes
- Systems Biology and Personalised Medicine Division, The Walter and Eliza Hall Institute of Medial Research, Parkville, VIC 3052, Australia
| | - Karl-Johan Leuchowius
- Systems Biology and Personalised Medicine Division, The Walter and Eliza Hall Institute of Medial Research, Parkville, VIC 3052, Australia
| | - Helene Jousset
- Systems Biology and Personalised Medicine Division, The Walter and Eliza Hall Institute of Medial Research, Parkville, VIC 3052, Australia
| | - Janet Weinstock
- Structural Biology Division, The Walter and Eliza Hall Institute of Medical Research, Parkville, VIC 3052, Australia
| | - Christopher Yau
- Wellcome Trust Centre for Human Genetics, University of Oxford, Oxford, OX3 7BN, United Kingdom,Department of Statistics, University of Oxford, Oxford, OX1 3LB, United Kingdom
| | - John Mariadason
- Olivia Newton-John Cancer Research Institute, Heidelberg, VIC 3084, Australia,La Trobe University School of Cancer Medicine, Melbourne, VIC 3086, Australia
| | - Zhiao Shi
- Lester and Sue Smith Breast Center, Baylor College of Medicine, Houston, TX 77030, USA
| | - Yuguang Ban
- Sylvester Comprehensive Cancer Center, University of Miami Miller School of Medicine, Miami, FL 33136, USA
| | - Xi Chen
- Sylvester Comprehensive Cancer Center, University of Miami Miller School of Medicine, Miami, FL 33136, USA,Department of Public Health Sciences, University of Miami Miller School of Medicine, Miami, FL 33136, USA
| | - Robert J. C. Coffey
- Department of Medicine, Vanderbilt University School of Medicine, Nashville, TN 37232, USA,Veterans Affairs Medical Center, Nashville, TN 37212, USA
| | | | - Antony W. Burgess
- Department of Medical Biology, The University of Melbourne, Parkville, VIC 3052, Australia,Structural Biology Division, The Walter and Eliza Hall Institute of Medical Research, Parkville, VIC 3052, Australia,Department of Surgery, The University of Melbourne, Parkville, VIC 3052, Australia
| | - Daniel C. Liebler
- Department of Biochemistry, Vanderbilt University, Nashville, TN 37232, USA
| | - Bing Zhang
- Lester and Sue Smith Breast Center, Baylor College of Medicine, Houston, Texas; Department of Molecular and Human Genetics, Baylor College of Medicine, Houston, Texas.
| | - Oliver M. Sieber
- Systems Biology and Personalised Medicine Division, The Walter and Eliza Hall Institute of Medial Research, Parkville, VIC 3052, Australia,Department of Medical Biology, The University of Melbourne, Parkville, VIC 3052, Australia,Department of Surgery, The University of Melbourne, Parkville, VIC 3052, Australia,School of Biomedical Sciences, Monash University, Clayton, VIC 3800, Australia,CORRESPONDING AUTHORS: Oliver Sieber, Systems Biology and Personalised Medicine Division, The Walter and Eliza Hall Institute of Medial Research, 1G Royal Parade, Parkville, VIC 3052, Australia. . Bing Zhang, Lester and Sue Smith Breast Center, Baylor College of Medicine, Houston, TX 77030, USA.
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15
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McCusker CD, Athippozhy A, Diaz-Castillo C, Fowlkes C, Gardiner DM, Voss SR. Positional plasticity in regenerating Amybstoma mexicanum limbs is associated with cell proliferation and pathways of cellular differentiation. BMC DEVELOPMENTAL BIOLOGY 2015; 15:45. [PMID: 26597593 PMCID: PMC4657325 DOI: 10.1186/s12861-015-0095-4] [Citation(s) in RCA: 26] [Impact Index Per Article: 2.9] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Subscribe] [Scholar Register] [Received: 08/21/2015] [Accepted: 11/16/2015] [Indexed: 01/07/2023]
Abstract
Background The endogenous ability to dedifferentiate, re-pattern, and re-differentiate adult cells to repair or replace damaged or missing structures is exclusive to only a few tetrapod species. The Mexican axolotl is one example of these species, having the capacity to regenerate multiple adult structures including their limbs by generating a group of progenitor cells, known as the blastema, which acquire pattern and differentiate into the missing tissues. The formation of a limb regenerate is dependent on cells in the connective tissues that retain memory of their original position in the limb, and use this information to generate the pattern of the missing structure. Observations from recent and historic studies suggest that blastema cells vary in their potential to pattern distal structures during the regeneration process; some cells are plastic and can be reprogrammed to obtain new positional information while others are stable. Our previous studies showed that positional information has temporal and spatial components of variation; early bud (EB) and apical late bud (LB) blastema cells are plastic while basal-LB cells are stable. To identify the potential cellular and molecular basis of this variation, we compared these three cell populations using histological and transcriptional approaches. Results Histologically, the basal-LB sample showed greater tissue organization than the EB and apical-LB samples. We also observed that cell proliferation was more abundant in EB and apical-LB tissue when compared to basal-LB and mature stump tissue. Lastly, we found that genes associated with cellular differentiation were expressed more highly in the basal-LB samples. Conclusions Our results characterize histological and transcriptional differences between EB and apical-LB tissue compared to basal-LB tissue. Combined with our results from a previous study, we hypothesize that the stability of positional information is associated with tissue organization, cell proliferation, and pathways of cellular differentiation. Electronic supplementary material The online version of this article (doi:10.1186/s12861-015-0095-4) contains supplementary material, which is available to authorized users.
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Affiliation(s)
| | - Antony Athippozhy
- Department of Biology, Spinal Cord and Brain Injury Research Center, University of Kentucky, Lexington, KY, 40506, USA.
| | - Carlos Diaz-Castillo
- Department of Developmental and Cellular Biology, University of California, Irvine, CA, 92602, USA.
| | - Charless Fowlkes
- Donald Bren School of Information and Computer Science, University of California, Irvine, CA, 92602, USA.
| | - David M Gardiner
- Department of Developmental and Cellular Biology, University of California, Irvine, CA, 92602, USA.
| | - S Randal Voss
- Department of Biology, Spinal Cord and Brain Injury Research Center, University of Kentucky, Lexington, KY, 40506, USA.
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