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Souza A, Kevin M, Rodriguez BJ, Reynaud EG. The use of fluid-phase 3D printing to pattern alginate-gelatin hydrogel properties to guide cell growth and behaviour in vitro. Biomed Mater 2024; 19:045024. [PMID: 38810635 DOI: 10.1088/1748-605x/ad51bf] [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: 11/01/2023] [Accepted: 05/29/2024] [Indexed: 05/31/2024]
Abstract
Three-dimensional (3D) (bio)printing technology has boosted the advancement of the biomedical field. However, tissue engineering is an evolving field and (bio)printing biomimetic constructions for tissue formation is still a challenge. As a new methodology to facilitate the construction of more complex structures, we suggest the use of the fluid-phase 3D printing to pattern the scaffold's properties. The methodology consists of an exchangeable fluid-phase printing medium in which the constructions are fabricated and patterned during the printing process. Using the fluid-phase methodology, the biological and mechanical properties can be tailored promoting cell behaviour guidance and compartmentalization. In this study, we first assessed different formulations of alginate/gelatin to create a stable substrate capable to promote massive cell colonizationin vitroover time. Overall, formulations with lower gelatin content and 2-(N-morpholino)ethanesulfonic acid (MES) buffer as a solvent showed better stability under cell culture conditions and enhanced U2OS cell growth. Next, the fluid-phase showed better printing fidelity and resolution in comparison to air printing as it diminished the collapsing and the spread of the hydrogel strand. In sequence, the fluid-phase methodology was used to create functionalized alginate-gelatin-arginylglycylaspartic acid peptide (RGD) hydrogels via carbodiimides chemistry. The alginate-gelatin-RGD hydrogels showed an increase of 2.97-fold in cell growth and more spread substrate colonization in comparison to alginate-gelatin hydrogel. Moreover, the fluid-phase methodology was used to add RGD molecules to pre-determined parts of the alginate-gelatin substrate during the printing process promoting U2OS cell compartmentalization. In addition, different substrate stiffnesses were also created via fluid-phase by crosslinking the hydrogel with different concentrations of CaCl2during the printing process. As a result, the U2OS cells were also compartmentalized on the stiffer parts of the printings. Finally, our results showed that by combining stiffer hydrogel with RGD increasing concentrations we can create a synergetic effect and boost cell metabolism by up to 3.17-fold. This work presents an idea of a new printing process for tailoring multiple parameters in hydrogel substrates by using fluid-phase to generate more faithful replication of thein vivoenvironment.
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Affiliation(s)
- Andrea Souza
- School of Biomolecular and Biomedical Science, University College Dublin, Belfield Dublin 4, Ireland
| | - McCarthy Kevin
- School of Biomolecular and Biomedical Science, University College Dublin, Belfield Dublin 4, Ireland
| | - Brian J Rodriguez
- School of Physics, University College Dublin, Belfield Dublin 4, Ireland
| | - Emmanuel G Reynaud
- School of Biomolecular and Biomedical Science, University College Dublin, Belfield Dublin 4, Ireland
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2
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Lian F, Yang H, Hong R, Xu H, Yu T, Sun G, Zheng G, Xie B. Evaluation of the antitumor effect of neoantigen peptide vaccines derived from the translatome of lung cancer. Cancer Immunol Immunother 2024; 73:129. [PMID: 38744688 PMCID: PMC11093939 DOI: 10.1007/s00262-024-03670-0] [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: 11/27/2023] [Accepted: 03/08/2024] [Indexed: 05/16/2024]
Abstract
Emerging evidence suggests that tumor-specific neoantigens are ideal targets for cancer immunotherapy. However, how to predict tumor neoantigens based on translatome data remains obscure. Through the extraction of ribosome-nascent chain complexes (RNCs) from LLC cells, followed by RNC-mRNA extraction, RNC-mRNA sequencing, and comprehensive bioinformatic analysis, we successfully identified proteins undergoing translatome and exhibiting mutations in the cells. Subsequently, novel antigens identification was analyzed by the interaction between their high affinity and the Major Histocompatibility Complex (MHC). Neoantigens immunogenicity was analyzed by enzyme-linked immunospot assay (ELISpot). Finally, in vivo experiments in mice were conducted to evaluate the antitumor effects of translatome-derived neoantigen peptides on lung cancer. The results showed that ten neoantigen peptides were identified and synthesized by translatome data from LLC cells; 8 out of the 10 neoantigens had strong immunogenicity. The neoantigen peptide vaccine group exhibited significant tumor growth inhibition effect. In conclusion, neoantigen peptide vaccine derived from the translatome of lung cancer exhibited significant tumor growth inhibition effect.
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Affiliation(s)
- Fenbao Lian
- Shengli Clinical Medical College, Fujian Medical University, No. 134 East Street, Fuzhou City, 350001, Fujian Province, China
- Department of Respiratory Medicine and Critical Care Medicine, Fujian Provincial Hospital, No. 134 East Street, Fuzhou, 350001, China
| | - Haitao Yang
- Shengli Clinical Medical College, Fujian Medical University, No. 134 East Street, Fuzhou City, 350001, Fujian Province, China
- Department of Respiratory Medicine and Critical Care Medicine, Fujian Provincial Hospital, No. 134 East Street, Fuzhou, 350001, China
| | - Rujun Hong
- Shengli Clinical Medical College, Fujian Medical University, No. 134 East Street, Fuzhou City, 350001, Fujian Province, China
- Department of Respiratory Medicine and Critical Care Medicine, Fujian Provincial Hospital, No. 134 East Street, Fuzhou, 350001, China
| | - Hang Xu
- Shengli Clinical Medical College, Fujian Medical University, No. 134 East Street, Fuzhou City, 350001, Fujian Province, China
- Department of Respiratory Medicine and Critical Care Medicine, Fujian Provincial Hospital, No. 134 East Street, Fuzhou, 350001, China
| | - Tingting Yu
- Department of Thoracic Oncology, The Affiliated Tumor Hospital of Xinjiang Medical University, Urumqi, 830011, Xinjiang, China
| | - Gang Sun
- Department of Breast and Thyroid Surgery, The Affiliated Tumor Hospital of Xinjiang Medical University, 789 East Suzhou Street, Xinshi District, Urumqi, 830011, Xinjiang, China.
- Xinjiang Cancer Center/Key Laboratory of Oncology of Xinjiang Uyghur Autonomous Region, Urumqi, 830011, Xinjiang, China.
| | - Guanying Zheng
- Shengli Clinical Medical College, Fujian Medical University, No. 134 East Street, Fuzhou City, 350001, Fujian Province, China.
- Department of Respiratory Medicine and Critical Care Medicine, Fujian Provincial Hospital, No. 134 East Street, Fuzhou, 350001, China.
| | - Baosong Xie
- Shengli Clinical Medical College, Fujian Medical University, No. 134 East Street, Fuzhou City, 350001, Fujian Province, China.
- Department of Respiratory Medicine and Critical Care Medicine, Fujian Provincial Hospital, No. 134 East Street, Fuzhou, 350001, China.
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Luz IS, Takaya R, Ribeiro DG, Castro MS, Fontes W. Proteomics: Unraveling the Cross Talk Between Innate Immunity and Disease Pathophysiology, Diagnostics, and Treatment Options. ADVANCES IN EXPERIMENTAL MEDICINE AND BIOLOGY 2024; 1443:221-242. [PMID: 38409424 DOI: 10.1007/978-3-031-50624-6_12] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 02/28/2024]
Abstract
Inflammation is crucial in diseases, and proteins play a key role in the interplay between innate immunity and pathology. This review explores how proteomics helps understanding this relationship, focusing on diagnosis and treatment. We explore the dynamic innate response and the significance of proteomic techniques in deciphering the complex network of proteins involved in prevalent diseases, including infections, cancer, autoimmune and neurodegenerative disorders. Proteomics identifies key proteins in host-pathogen interactions, shedding light on infection mechanisms and inflammation. These discoveries hold promise for diagnostic tools, therapies, and vaccines. In cancer research, proteomics reveals innate signatures associated with tumor development, immune evasion, and therapeutic response. Additionally, proteomic analysis has unveiled autoantigens and dysregulation of the innate immune system in autoimmunity, offering opportunities for early diagnosis, disease monitoring, and new therapeutic targets. Moreover, proteomic analysis has identified altered protein expression patterns in neurodegenerative diseases like Alzheimer's and Parkinson's, providing insights into potential therapeutic strategies. Proteomics of the innate immune system provides a comprehensive understanding of disease mechanisms, identifies biomarkers, and enables effective interventions in various diseases. Despite still in its early stages, this approach holds great promise to revolutionize innate immunity research and significantly improve patient outcomes across a wide range of diseases.
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Affiliation(s)
- Isabelle Souza Luz
- Laboratory of Protein Chemistry and Biochemistry, Department of Cell Biology, University of Brasilia, Brasília, Federal District, Brazil
| | - Raquel Takaya
- Laboratory of Protein Chemistry and Biochemistry, Department of Cell Biology, University of Brasilia, Brasília, Federal District, Brazil
| | - Daiane Gonzaga Ribeiro
- Laboratory of Protein Chemistry and Biochemistry, Department of Cell Biology, University of Brasilia, Brasília, Federal District, Brazil
| | - Mariana S Castro
- Laboratory of Protein Chemistry and Biochemistry, Department of Cell Biology, University of Brasilia, Brasília, Federal District, Brazil
| | - Wagner Fontes
- Laboratory of Protein Chemistry and Biochemistry, Department of Cell Biology, University of Brasilia, Brasília, Federal District, Brazil.
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Payne K, Brooks J, Batis N, Khan N, El-Asrag M, Nankivell P, Mehanna H, Taylor G. Feasibility of mass cytometry proteomic characterisation of circulating tumour cells in head and neck squamous cell carcinoma for deep phenotyping. Br J Cancer 2023; 129:1590-1598. [PMID: 37735243 PMCID: PMC10645808 DOI: 10.1038/s41416-023-02428-2] [Citation(s) in RCA: 1] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/08/2023] [Revised: 09/01/2023] [Accepted: 09/05/2023] [Indexed: 09/23/2023] Open
Abstract
BACKGROUND Circulating tumour cells (CTCs) are a potential cancer biomarker, but current methods of CTC analysis at single-cell resolution are limited. Here, we describe high-dimensional single-cell mass cytometry proteomic analysis of CTCs in HNSCC. METHODS Parsortix microfluidic-enriched CTCs from 14 treatment-naïve HNSCC patients were analysed by mass cytometry analysis using 41 antibodies. Immune cell lineage, epithelial-mesenchymal transition (EMT), stemness, proliferation and immune checkpoint expression was assessed alongside phosphorylation status of multiple signalling proteins. Patient-matched tumour gene expression and CTC EMT profiles were compared. Standard bulk CTC RNAseq was performed as a baseline comparator to assess mass cytometry data. RESULTS CTCs were detected in 13/14 patients with CTC counts of 2-24 CTCs/ml blood. Unsupervised clustering separated CTCs into epithelial, early EMT and advanced EMT groups that differed in signalling pathway activation state. Patient-specific CTC cluster patterns separated into immune checkpoint low and high groups. Patient tumour and CTC EMT profiles differed. Mass cytometry outperformed bulk RNAseq to detect CTCs and characterise cell phenotype. DISCUSSION We demonstrate mass cytometry allows high-plex proteomic characterisation of CTCs at single-cell resolution and identify common CTC sub-groups with potential for novel biomarker development and immune checkpoint inhibitor treatment stratification.
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Affiliation(s)
- Karl Payne
- Institute of Head and Neck Studies and Education, Institute of Cancer and Genomic Sciences, University of Birmingham, Birmingham, UK
| | - Jill Brooks
- Institute of Head and Neck Studies and Education, Institute of Cancer and Genomic Sciences, University of Birmingham, Birmingham, UK
| | - Nikolaos Batis
- School of Biomedical Sciences, Institute of Clinical Sciences, College of Medical and Dental Sciences, University of Birmingham, Birmingham, UK
| | - Naeem Khan
- Clinical Immunology Service, Institute of Immunology and Immunotherapy, University of Birmingham, Birmingham, UK
| | - Mohammed El-Asrag
- Institute of Cancer and Genomic Sciences, University of Birmingham, Birmingham, UK
| | - Paul Nankivell
- Institute of Head and Neck Studies and Education, Institute of Cancer and Genomic Sciences, University of Birmingham, Birmingham, UK
| | - Hisham Mehanna
- Institute of Head and Neck Studies and Education, Institute of Cancer and Genomic Sciences, University of Birmingham, Birmingham, UK
| | - Graham Taylor
- Institute of Immunology and Immunotherapy, University of Birmingham, Birmingham, UK.
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5
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van Gerven MR, Bozsaky E, Matser YAH, Vosseberg J, Taschner-Mandl S, Koster J, Tytgat GAM, Molenaar JJ, van den Boogaard M. The mutational spectrum of ATRX aberrations in neuroblastoma and the associated patient and tumor characteristics. Cancer Sci 2022; 113:2167-2178. [PMID: 35384159 PMCID: PMC9207354 DOI: 10.1111/cas.15363] [Citation(s) in RCA: 6] [Impact Index Per Article: 3.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/01/2021] [Revised: 03/18/2022] [Accepted: 04/02/2022] [Indexed: 11/30/2022] Open
Abstract
Neuroblastoma is the most common extracranial solid tumor in children. The chromatin remodeler ATRX is frequently mutated in high‐risk patients with a poor prognosis. Although many studies have reported ATRX aberrations and the associated clinical characteristics in neuroblastoma, a comprehensive overview is currently lacking. In this study, we extensively characterize the mutational spectrum of ATRX aberrations in neuroblastoma tumors reported in previous studies and present an overview of patient and tumor characteristics. We collected the data of a total of 127 neuroblastoma patients and three cell lines with ATRX aberrations originating from 20 papers. We subdivide the ATRX aberrations into nonsense, missense, and multiexon deletions (MEDs) and show that 68% of them are MEDs. Of these MEDs, 75% are predicted to be in‐frame. Furthermore, we identify a missense mutational hotspot region in the helicase domain. We also confirm that all three ATRX mutation types are more often identified in patients diagnosed at an older age, but still approximately 40% of the patients are aged 5 years or younger at diagnosis. Surprisingly, we found that 11q deletions are enriched in neuroblastomas with ATRX deletions compared to a reference cohort, but not in neuroblastomas with ATRX point mutations. Taken together, our data emphasizes a distinct ATRX mutation spectrum in neuroblastoma, which should be considered when studying molecular phenotypes and therapeutic strategies.
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Affiliation(s)
| | - Eva Bozsaky
- Tumor biology group, St Anna Children's Cancer Research Institute, Vienna, Austria
| | - Yvette A H Matser
- Princess Máxima Center for Pediatric Oncology, Utrecht, the Netherlands
| | - Julian Vosseberg
- Theoretical Biology and Bioinformatics, Department of Biology, Faculty of Science, Utrecht University, Utrecht, the Netherlands
| | | | - Jan Koster
- Department of Oncogenomics, Amsterdam UMC, location AMC, Amsterdam, the Netherlands
| | | | - Jan J Molenaar
- Princess Máxima Center for Pediatric Oncology, Utrecht, the Netherlands.,Department of Pharmaceutical Sciences, Faculty of Science, Utrecht University, Utrecht, the Netherlands
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Experimental investigation of a combinational iron chelating protoporphyrin IX prodrug for fluorescence detection and photodynamic therapy. Lasers Med Sci 2021; 37:1155-1166. [PMID: 34218351 PMCID: PMC8918167 DOI: 10.1007/s10103-021-03367-1] [Citation(s) in RCA: 4] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/15/2020] [Accepted: 06/21/2021] [Indexed: 10/31/2022]
Abstract
Photodynamic therapy (PDT) is an oxygen-dependent, light-activated, and locally destructive drug treatment of cancer. Protoporphyrin IX (PpIX)-induced PDT exploits cancer cells' own innate heme biosynthesis to hyper-accumulate the naturally fluorescent and photoactive precursor to heme, PpIX. This occurs as a result of administering heme precursors (e.g., aminolevulinic acid; ALA) because the final step of the pathway (the insertion of ferrous iron into PpIX by ferrochelatase to form heme) is relatively slow. Separate administration of an iron chelating agent has previously been demonstrated to significantly improve dermatological PpIX-PDT by further limiting heme production. A newly synthesized combinational iron chelating PpIX prodrug (AP2-18) has been assessed experimentally in cultured primary human cells of bladder and dermatological origin, as an alternative photosensitizing agent to ALA or its methyl or hexyl esters (MAL and HAL respectively) for photodetection/PDT. Findings indicated that the technique of iron chelation (either through the separate administration of the established hydroxypyridinone iron chelator CP94 or the just as effective combined AP2-18) did not enhance either PpIX fluorescence or PDT-induced (neutral red assessed) cell death in human primary normal and malignant bladder cells. However, 500 µM AP2-18 significantly increased PpIX accumulation and produced a trend of increased cell death within epithelial squamous carcinoma cells. PpIX accumulation destabilized the actin cytoskeleton in bladder cancer cells prior to PDT and resulted in caspase-3 cleavage/early apoptosis afterwards. AP2-18 iron chelation should continue to be investigated for the enhancement of dermatological PpIX-PDT applications but not bladder photodetection/PDT.
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Garribba L, Vogel I, Lerdrup M, Gonçalves Dinis MM, Ren L, Liu Y. Folate Deficiency Triggers the Abnormal Segregation of a Region With Large Cluster of CG-Rich Trinucleotide Repeats on Human Chromosome 2. Front Genet 2021; 12:695124. [PMID: 34276797 PMCID: PMC8281231 DOI: 10.3389/fgene.2021.695124] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/14/2021] [Accepted: 06/08/2021] [Indexed: 11/13/2022] Open
Abstract
Folate deficiency is associated with a broad range of human disorders, including anemia, fetal neural tube defects, age-associated dementia and several types of cancer. It is well established that a subgroup of rare fragile sites (RFSs) containing expanded CGG trinucleotide repeat (TNR) sequences display instability when cells are deprived of folate. However, given that folate sensitive RFSs exist in a very small percentage of the population, they are unlikely to be the cause of the widespread health problems associated with folate deficiency. We hypothesized that folate deficiency could specifically affect DNA replication at regions containing CG-rich repeat sequences. For this, we identified a region on human chromosome 2 (Chr2) comprising more than 300 CG-rich TNRs (termed “FOLD1”) by examining the human genome database. Via the analysis of chromosome shape and segregation in mitosis, we demonstrate that, when human cells are cultured under folate stress conditions, Chr2 is prone to display a “kink” or “bending” at FOLD1 in metaphase and nondisjunction in anaphase. Furthermore, long-term folate deprivation causes Chr2 aneuploidy. Our results provide new evidence on the abnormalities folate deficiency could cause in human cells. This could facilitate future studies on the deleterious health conditions associated with folate deficiency.
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Affiliation(s)
- Lorenza Garribba
- Center for Chromosome Stability and Center for Healthy Aging, Department of Cellular and Molecular Medicine, University of Copenhagen, Copenhagen, Denmark
| | - Ivan Vogel
- Center for Chromosome Stability and Center for Healthy Aging, Department of Cellular and Molecular Medicine, University of Copenhagen, Copenhagen, Denmark
| | - Mads Lerdrup
- Center for Chromosome Stability and Center for Healthy Aging, Department of Cellular and Molecular Medicine, University of Copenhagen, Copenhagen, Denmark
| | - Marisa M Gonçalves Dinis
- Center for Chromosome Stability and Center for Healthy Aging, Department of Cellular and Molecular Medicine, University of Copenhagen, Copenhagen, Denmark
| | - Liqun Ren
- Center for Chromosome Stability and Center for Healthy Aging, Department of Cellular and Molecular Medicine, University of Copenhagen, Copenhagen, Denmark
| | - Ying Liu
- Center for Chromosome Stability and Center for Healthy Aging, Department of Cellular and Molecular Medicine, University of Copenhagen, Copenhagen, Denmark
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8
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Chung CH, Allen AG, Sullivan NT, Atkins A, Nonnemacher MR, Wigdahl B, Dampier W. Computational Analysis Concerning the Impact of DNA Accessibility on CRISPR-Cas9 Cleavage Efficiency. Mol Ther 2020; 28:19-28. [PMID: 31672284 PMCID: PMC6953893 DOI: 10.1016/j.ymthe.2019.10.008] [Citation(s) in RCA: 20] [Impact Index Per Article: 5.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/23/2019] [Revised: 09/26/2019] [Accepted: 10/10/2019] [Indexed: 12/15/2022] Open
Abstract
Defining the variables that impact the specificity of CRISPR/Cas9 has been a major research focus. Whereas sequence complementarity between guide RNA and target DNA substantially dictates cleavage efficiency, DNA accessibility of the targeted loci has also been hypothesized to be an important factor. In this study, functional data from two genome-wide assays, genome-wide, unbiased identification of DSBs enabled by sequencing (GUIDE-seq) and circularization for in vitro reporting of cleavage effects by sequencing (CIRCLE-seq), have been computationally analyzed in conjunction with DNA accessibility determined via DNase I-hypersensitive sequencing from the Encyclopedia of DNA Elements (ENCODE) Database and transcriptome from the Sequence Read Archive to determine whether cellular factors influence CRISPR-induced cleavage efficiency. CIRCLE-seq and GUIDE-seq datasets were selected to represent the absence and presence of cellular factors, respectively. Data analysis revealed that correlations between sequence similarity and CRISPR-induced cleavage frequency were altered by the presence of cellular factors that modulated the level of DNA accessibility. The above-mentioned correlation was abolished when cleavage sites were located in less accessible regions. Furthermore, CRISPR-mediated edits were permissive even at regions that were insufficient for most endogenous genes to be expressed. These results provide a strong basis to dissect the contribution of local chromatin modulation markers on CRISPR-induced cleavage efficiency.
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Affiliation(s)
- Cheng-Han Chung
- Department of Microbiology and Immunology, Drexel University College of Medicine, Philadelphia, PA 19129, USA; Center for Molecular Virology and Translational Neuroscience, Institute for Molecular Medicine and Infectious Disease, Drexel University College of Medicine, Philadelphia, PA 19129, USA
| | - Alexander G Allen
- Department of Microbiology and Immunology, Drexel University College of Medicine, Philadelphia, PA 19129, USA; Center for Molecular Virology and Translational Neuroscience, Institute for Molecular Medicine and Infectious Disease, Drexel University College of Medicine, Philadelphia, PA 19129, USA
| | - Neil T Sullivan
- Department of Microbiology and Immunology, Drexel University College of Medicine, Philadelphia, PA 19129, USA; Center for Molecular Virology and Translational Neuroscience, Institute for Molecular Medicine and Infectious Disease, Drexel University College of Medicine, Philadelphia, PA 19129, USA
| | - Andrew Atkins
- Department of Microbiology and Immunology, Drexel University College of Medicine, Philadelphia, PA 19129, USA; Center for Molecular Virology and Translational Neuroscience, Institute for Molecular Medicine and Infectious Disease, Drexel University College of Medicine, Philadelphia, PA 19129, USA
| | - Michael R Nonnemacher
- Department of Microbiology and Immunology, Drexel University College of Medicine, Philadelphia, PA 19129, USA; Center for Molecular Virology and Translational Neuroscience, Institute for Molecular Medicine and Infectious Disease, Drexel University College of Medicine, Philadelphia, PA 19129, USA; Sidney Kimmel Cancer Center, Thomas Jefferson University, Philadelphia, PA 19107, USA
| | - Brian Wigdahl
- Department of Microbiology and Immunology, Drexel University College of Medicine, Philadelphia, PA 19129, USA; Center for Molecular Virology and Translational Neuroscience, Institute for Molecular Medicine and Infectious Disease, Drexel University College of Medicine, Philadelphia, PA 19129, USA; Sidney Kimmel Cancer Center, Thomas Jefferson University, Philadelphia, PA 19107, USA.
| | - Will Dampier
- Department of Microbiology and Immunology, Drexel University College of Medicine, Philadelphia, PA 19129, USA; Center for Molecular Virology and Translational Neuroscience, Institute for Molecular Medicine and Infectious Disease, Drexel University College of Medicine, Philadelphia, PA 19129, USA; School of Biomedical Engineering, Science, and Health Systems, Drexel University, Philadelphia, PA 19104, USA.
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9
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Berens ME, Sood A, Barnholtz-Sloan JS, Graf JF, Cho S, Kim S, Kiefer J, Byron SA, Halperin RF, Nasser S, Adkins J, Cuyugan L, Devine K, Ostrom Q, Couce M, Wolansky L, McDonough E, Schyberg S, Dinn S, Sloan AE, Prados M, Phillips JJ, Nelson SJ, Liang WS, Al-Kofahi Y, Rusu M, Zavodszky MI, Ginty F. Multiscale, multimodal analysis of tumor heterogeneity in IDH1 mutant vs wild-type diffuse gliomas. PLoS One 2019; 14:e0219724. [PMID: 31881020 PMCID: PMC6934292 DOI: 10.1371/journal.pone.0219724] [Citation(s) in RCA: 25] [Impact Index Per Article: 5.0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/27/2019] [Accepted: 11/12/2019] [Indexed: 12/31/2022] Open
Abstract
Glioma is recognized to be a highly heterogeneous CNS malignancy, whose diverse cellular composition and cellular interactions have not been well characterized. To gain new clinical- and biological-insights into the genetically-bifurcated IDH1 mutant (mt) vs wildtype (wt) forms of glioma, we integrated data from protein, genomic and MR imaging from 20 treatment-naïve glioma cases and 16 recurrent GBM cases. Multiplexed immunofluorescence (MxIF) was used to generate single cell data for 43 protein markers representing all cancer hallmarks, Genomic sequencing (exome and RNA (normal and tumor) and magnetic resonance imaging (MRI) quantitative features (protocols were T1-post, FLAIR and ADC) from whole tumor, peritumoral edema and enhancing core vs equivalent normal region were also collected from patients. Based on MxIF analysis, 85,767 cells (glioma cases) and 56,304 cells (GBM cases) were used to generate cell-level data for 24 biomarkers. K-means clustering was used to generate 7 distinct groups of cells with divergent biomarker profiles and deconvolution was used to assign RNA data into three classes. Spatial and molecular heterogeneity metrics were generated for the cell data. All features were compared between IDH mt and IDHwt patients and were finally combined to provide a holistic/integrated comparison. Protein expression by hallmark was generally lower in the IDHmt vs wt patients. Molecular and spatial heterogeneity scores for angiogenesis and cell invasion also differed between IDHmt and wt gliomas irrespective of prior treatment and tumor grade; these differences also persisted in the MR imaging features of peritumoral edema and contrast enhancement volumes. A coherent picture of enhanced angiogenesis in IDHwt tumors was derived from multiple platforms (genomic, proteomic and imaging) and scales from individual proteins to cell clusters and heterogeneity, as well as bulk tumor RNA and imaging features. Longer overall survival for IDH1mt glioma patients may reflect mutation-driven alterations in cellular, molecular, and spatial heterogeneity which manifest in discernable radiological manifestations.
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Affiliation(s)
- Michael E. Berens
- Translational Genomics Research Institute, Phoenix, AZ, United States of America
- * E-mail: (MEB); (AS); (FG)
| | - Anup Sood
- GE Research Center, Niskayuna, NY, United States of America
- * E-mail: (MEB); (AS); (FG)
| | - Jill S. Barnholtz-Sloan
- Department of Population and Quantitative Health Sciences and Case Comprehensive Cancer Center, Case Western Reserve University School of Medicine, Cleveland, OH, United States of America
| | - John F. Graf
- GE Research Center, Niskayuna, NY, United States of America
| | - Sanghee Cho
- GE Research Center, Niskayuna, NY, United States of America
| | - Seungchan Kim
- Department of Electrical and Computer Engineering, Roy G. Perry College of Engineering, Prairie View A&M University, Prairie View, TX, United States of America
| | - Jeffrey Kiefer
- Translational Genomics Research Institute, Phoenix, AZ, United States of America
| | - Sara A. Byron
- Translational Genomics Research Institute, Phoenix, AZ, United States of America
| | - Rebecca F. Halperin
- Translational Genomics Research Institute, Phoenix, AZ, United States of America
| | - Sara Nasser
- Translational Genomics Research Institute, Phoenix, AZ, United States of America
| | - Jonathan Adkins
- Translational Genomics Research Institute, Phoenix, AZ, United States of America
| | - Lori Cuyugan
- Translational Genomics Research Institute, Phoenix, AZ, United States of America
| | - Karen Devine
- Department of Population and Quantitative Health Sciences and Case Comprehensive Cancer Center, Case Western Reserve University School of Medicine, Cleveland, OH, United States of America
| | - Quinn Ostrom
- Department of Population and Quantitative Health Sciences and Case Comprehensive Cancer Center, Case Western Reserve University School of Medicine, Cleveland, OH, United States of America
| | - Marta Couce
- Department of Population and Quantitative Health Sciences and Case Comprehensive Cancer Center, Case Western Reserve University School of Medicine, Cleveland, OH, United States of America
| | - Leo Wolansky
- Department of Population and Quantitative Health Sciences and Case Comprehensive Cancer Center, Case Western Reserve University School of Medicine, Cleveland, OH, United States of America
| | | | | | - Sean Dinn
- GE Research Center, Niskayuna, NY, United States of America
| | - Andrew E. Sloan
- Department of Neurosurgery, University Hospitals-Seidman Cancer Center, Cleveland, OH, United States of America
| | - Michael Prados
- Department of Neurological Surgery, Helen Diller Cancer Center, University of California San Francisco, San Francisco, CA, United States of America
| | - Joanna J. Phillips
- Department of Neurological Surgery, Helen Diller Cancer Center, University of California San Francisco, San Francisco, CA, United States of America
| | - Sarah J. Nelson
- Department of Radiology and Biomedical Imaging, University of California, San Francisco, CA, United States of America
| | - Winnie S. Liang
- Translational Genomics Research Institute, Phoenix, AZ, United States of America
| | | | - Mirabela Rusu
- GE Research Center, Niskayuna, NY, United States of America
| | | | - Fiona Ginty
- GE Research Center, Niskayuna, NY, United States of America
- * E-mail: (MEB); (AS); (FG)
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10
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Rana S, Sieck GC, Mantilla CB. Heterogeneous glutamatergic receptor mRNA expression across phrenic motor neurons in rats. J Neurochem 2019; 153:586-598. [PMID: 31563147 DOI: 10.1111/jnc.14881] [Citation(s) in RCA: 19] [Impact Index Per Article: 3.8] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/13/2019] [Revised: 09/16/2019] [Accepted: 09/23/2019] [Indexed: 12/12/2022]
Abstract
The diaphragm muscle comprises various types of motor units that are recruited in an orderly fashion governed by the intrinsic electrophysiological properties (membrane capacitance as a function of somal surface area) of phrenic motor neurons (PhMNs). Glutamate is the main excitatory neurotransmitter at PhMNs and acts primarily via fast acting AMPA and N-methyl-D-aspartic acid (NMDA) receptors. Differences in receptor expression may also contribute to motor unit recruitment order. We used single cell, multiplex fluorescence in situ hybridization to determine glutamatergic receptor mRNA expression across PhMNs based on their somal surface area. In adult male and female rats (n = 9) PhMNs were retrogradely labeled for analyses (n = 453 neurons). Differences in the total number and density of mRNA transcripts were evident across PhMNs grouped into tertiles according to somal surface area. A ~ 25% higher density of AMPA (Gria2) and NMDA (Grin1) mRNA expression was evident in PhMNs in the lower tertile compared to the upper tertile. These smaller PhMNs likely comprise type S motor units that are recruited first to accomplish lower force, ventilatory behaviors. In contrast, larger PhMNs with lower volume densities of AMPA and NMDA mRNA expression presumably comprise type FInt and FF motor units that are recruited during higher force, expulsive behaviors. Furthermore, there was a significantly higher cytosolic NMDA mRNA expression in small PhMNs suggesting a more important role for NMDA-mediated glutamatergic neurotransmission at smaller PhMNs. These results are consistent with the observed order of motor unit recruitment and suggest a role for glutamatergic receptors in support of this orderly recruitment. Cover Image for this issue: doi: 10.1111/jnc.14747.
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Affiliation(s)
- Sabhya Rana
- Departments of Physiology & Biomedical Engineering, Mayo Clinic, Rochester, Minnesota, USA
| | - Gary C Sieck
- Departments of Physiology & Biomedical Engineering, Mayo Clinic, Rochester, Minnesota, USA.,Departments of Anesthesiology and Perioperative Medicine, Mayo Clinic, Rochester, Minnesota, USA
| | - Carlos B Mantilla
- Departments of Physiology & Biomedical Engineering, Mayo Clinic, Rochester, Minnesota, USA.,Departments of Anesthesiology and Perioperative Medicine, Mayo Clinic, Rochester, Minnesota, USA
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11
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Udroiu I, Marinaccio J, Sgura A. Epigallocatechin-3-gallate induces telomere shortening and clastogenic damage in glioblastoma cells. ENVIRONMENTAL AND MOLECULAR MUTAGENESIS 2019; 60:683-692. [PMID: 31026358 DOI: 10.1002/em.22295] [Citation(s) in RCA: 17] [Impact Index Per Article: 3.4] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 11/05/2018] [Revised: 03/11/2019] [Accepted: 04/24/2019] [Indexed: 06/09/2023]
Abstract
Epigallocatechingallate (EGCG) is the major polyphenol in green tea, to which many anticancer features, such as antioxidative, antigenotoxic, and antiangiogenetic properties, are attributed. Moreover, it is also well known as a telomerase inhibitor. In this work, we have chronically treated U251 glioblastoma cells with low, physiologically realistic concentrations, of EGCG, in order to investigate its effects both on telomeres and on genome integrity. Inhibition of telomerase activity caused telomere shortening, ultimately leading to senescence and telomere dysfunction at 98 days. Remarkably, we have observed DNA damage through an increase of phosphorylation of γ-H2AX histone and micronuclei also with doses and at timepoints when telomere shortening was not present. Therefore, we concluded that this DNA damage was not correlated with telomere shortening and that EGCG treatment induced not only an increase of telomere-shortening-induced senescence but also telomere-independent genotoxicity. This study questions the common knowledge about EGCG properties, but confirms the few works that indicated the clastogenic properties of this molecule, probably due to DNA reductive damage and topoisomerase II poisoning. Environ. Mol. Mutagen., 60:683-692, 2019. © 2019 Wiley Periodicals, Inc.
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Affiliation(s)
- Ion Udroiu
- Department of Science, University "Roma Tre", Rome, Italy
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12
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Shin J, Choi JH, Jung S, Jeong S, Oh J, Yoon DY, Rhee MH, Ahn J, Kim SH, Oh JW. MUDENG Expression Profiling in Cohorts and Brain Tumor Biospecimens to Evaluate Its Role in Cancer. Front Genet 2019; 10:884. [PMID: 31616474 PMCID: PMC6763691 DOI: 10.3389/fgene.2019.00884] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.4] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/29/2019] [Accepted: 08/21/2019] [Indexed: 01/22/2023] Open
Abstract
Mu-2-related death-inducing gene (MUDENG, MuD) has been reported to be involved in the tumor necrosis factor-related apoptosis-inducing ligand (TRAIL)-associated apoptotic pathway of glioblastoma multiforme (GBM) cells; however, its expression level, interactors, and role in tumors are yet to be discovered. To investigate whether MuD expression correlates with cancer progression, we analyzed The Cancer Genome Atlas (TCGA) database using UALCAN and Gene Expression Profiling Interactive Analysis (GEPIA). Differential expression of MuD was detected in 6 and 10 cancer types, respectively. Validation performed using data from the Gene Expression Omnibus database showed that MuD expression is downregulated in KIRC tumor and correlate with higher chance of survival. Upregulation of MuD expression in GBM tumors was detected through GEPIA and high MuD expression correlated with higher survival in proneural GBM, whereas the opposite was observed in classical GBM subtype. GBM biospecimens analysis shows that MuD protein level was upregulated in three of six specimens, whereas mRNA level remained relatively unaltered. Therefore, MuD may exert differential effects according to subtypes, and/or be subjected to post-translational regulation in GBM. Correlation analysis between GBM cohort database and experiments using GBM cell lines revealed its positive effect on regulation of protein phosphatase 2 regulatory subunit B’Epsilon (PPP2R5E) and son of sevenless homolog 2 (SOS2). STRING database analysis indicated that the components of adaptor protein complexes putatively interacted with MuD but showed no correlation in terms of survival of patients with different GBM subtypes. In summary, we analyzed the expression of MuD in publicly available cancer patient data sets, GBM cell lines, and biospecimens to demonstrate its potential role as a biomarker for cancer prognosis and identified its candidate interacting molecules.
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Affiliation(s)
- Juhyun Shin
- Animal Resources Research Center, Konkuk University, Seoul, South Korea.,Department of Stem Cell and Regenerative Biotechnology, Konkuk University, Seoul, South Korea
| | - Jun-Ha Choi
- Department of Stem Cell and Regenerative Biotechnology, Konkuk University, Seoul, South Korea
| | - Seunghwa Jung
- Department of Stem Cell and Regenerative Biotechnology, Konkuk University, Seoul, South Korea
| | - Somi Jeong
- Department of Stem Cell and Regenerative Biotechnology, Konkuk University, Seoul, South Korea
| | - Jeongheon Oh
- Department of Stem Cell and Regenerative Biotechnology, Konkuk University, Seoul, South Korea
| | - Do-Young Yoon
- Department of Bioscience and Biotechnology, Konkuk Institute of Technology, Konkuk University, Seoul, South Korea
| | - Man Hee Rhee
- Department of Veterinary Medicine, College of Veterinary Medicine, Kyungpook National University, Daegu, South Korea
| | - Jaehong Ahn
- Department of Ophthalmology, Ajou University School of Medicine, Suwon, South Korea
| | - Se-Hyuk Kim
- Department of Neurosurgery, Ajou University School of Medicine, Suwon, South Korea
| | - Jae-Wook Oh
- Animal Resources Research Center, Konkuk University, Seoul, South Korea.,Department of Stem Cell and Regenerative Biotechnology, Konkuk University, Seoul, South Korea
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13
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Jeggari A, Alekseenko Z, Petrov I, Dias JM, Ericson J, Alexeyenko A. EviNet: a web platform for network enrichment analysis with flexible definition of gene sets. Nucleic Acids Res 2019; 46:W163-W170. [PMID: 29893885 PMCID: PMC6030852 DOI: 10.1093/nar/gky485] [Citation(s) in RCA: 16] [Impact Index Per Article: 3.2] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/25/2018] [Accepted: 05/29/2018] [Indexed: 12/18/2022] Open
Abstract
The new web resource EviNet provides an easily run interface to network enrichment analysis for exploration of novel, experimentally defined gene sets. The major advantages of this analysis are (i) applicability to any genes found in the global network rather than only to those with pathway/ontology term annotations, (ii) ability to connect genes via different molecular mechanisms rather than within one high-throughput platform, and (iii) statistical power sufficient to detect enrichment of very small sets, down to individual genes. The users’ gene sets are either defined prior to upload or derived interactively from an uploaded file by differential expression criteria. The pathways and networks used in the analysis can be chosen from the collection menu. The calculation is typically done within seconds or minutes and the stable URL is provided immediately. The results are presented in both visual (network graphs) and tabular formats using jQuery libraries. Uploaded data and analysis results are kept in separated project directories not accessible by other users. EviNet is available at https://www.evinet.org/.
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Affiliation(s)
- Ashwini Jeggari
- Department of Cell and Molecular Biology, Karolinska Institutet, 171 77 Stockholm, Sweden
| | - Zhanna Alekseenko
- Department of Cell and Molecular Biology, Karolinska Institutet, 171 77 Stockholm, Sweden
| | - Iurii Petrov
- Department of Microbiology, Tumor and Cell Biology (MTC), Karolinska Institutet, Stockholm, Sweden
| | - José M Dias
- Department of Cell and Molecular Biology, Karolinska Institutet, 171 77 Stockholm, Sweden
| | - Johan Ericson
- Department of Cell and Molecular Biology, Karolinska Institutet, 171 77 Stockholm, Sweden
| | - Andrey Alexeyenko
- Department of Microbiology, Tumor and Cell Biology (MTC), Karolinska Institutet, Stockholm, Sweden.,National Bioinformatics Infrastructure Sweden, Science for Life Laboratory, Box 1031, 171 21 Solna, Sweden
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14
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Sharma G, Guardia CM, Roy A, Vassilev A, Saric A, Griner LN, Marugan J, Ferrer M, Bonifacino JS, DePamphilis ML. A family of PIKFYVE inhibitors with therapeutic potential against autophagy-dependent cancer cells disrupt multiple events in lysosome homeostasis. Autophagy 2019; 15:1694-1718. [PMID: 30806145 DOI: 10.1080/15548627.2019.1586257] [Citation(s) in RCA: 68] [Impact Index Per Article: 13.6] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/18/2022] Open
Abstract
High-throughput screening identified 5 chemical analogs (termed the WX8-family) that disrupted 3 events in lysosome homeostasis: (1) lysosome fission via tubulation without preventing homotypic lysosome fusion; (2) trafficking of molecules into lysosomes without altering lysosomal acidity, and (3) heterotypic fusion between lysosomes and autophagosomes. Remarkably, these compounds did not prevent homotypic fusion between lysosomes, despite the fact that homotypic fusion required some of the same machinery essential for heterotypic fusion. These effects varied 400-fold among WX8-family members, were time and concentration dependent, reversible, and resulted primarily from their ability to bind specifically to the PIKFYVE phosphoinositide kinase. The ability of the WX8-family to prevent lysosomes from participating in macroautophagy/autophagy suggested they have therapeutic potential in treating autophagy-dependent diseases. In fact, the most potent family member (WX8) was 100-times more lethal to 'autophagy-addicted' melanoma A375 cells than the lysosomal inhibitors hydroxychloroquine and chloroquine. In contrast, cells that were insensitive to hydroxychloroquine and chloroquine were also insensitive to WX8. Therefore, the WX8-family of PIKFYVE inhibitors provides a basis for developing drugs that could selectively kill autophagy-dependent cancer cells, as well as increasing the effectiveness of established anti-cancer therapies through combinatorial treatments. Abbreviations: ACTB: actin beta; Baf: bafilomycin A1; BECN1: beclin 1; BODIPY: boron-dipyrromethene; BORC: BLOC-1 related complex; BRAF: B-Raf proto-oncogene, serine/threonine kinase; BSA: bovine serum albumin; CTSD: cathepsin D; CQ: chloroquine; DNA: deoxyribonucleic acid; EC50: half maximal effective concentration; GAPDH: glyceraldehyde-3-phosphate dehydrogenase; GFP: green fluorescent protein; HCQ: hydroxychloroquine; HOPS complex: homotypic fusion and protein sorting complex; Kd: equilibrium binding constant; IC50: half maximal inhibitory concentration; KO: knockout; LAMP1: lysosomal associated membrane protein 1; MAP1LC3A: microtubule associated protein 1 light chain 3 alpha; MES: 2-(N-morpholino)ethanesulphonic acid; MTOR: mechanistic target of rapamycin kinase; μM: micromolar; NDF: 3-methylbenzaldehyde (2,6-dimorpholin-4-ylpyrimidin-4-yl)hydrazine;NEM: N-ethylmaleimide; NSF: N-ethylmaleimide sensitive factor; PBS: phosphate-buffered saline; PIKFYVE: phosphoinositide kinase, FYVE-type zinc finger containing; PIP4K2C: phosphatidylinositol-5-phosphate 4-kinase type 2 gamma; PtdIns3P: phosphatidylinositol 3-phosphate; PtdIns(3,5)P2: phosphatidylinositol 3,5-biphosphate; RFP: red fluorescent protein; RPS6: ribosomal protein S6; RPS6KB1: ribosomal protein S6 kinase B1; SQSTM1: sequestosome 1; TWEEN 20: polysorbate 20; V-ATPase: vacuolar-type H+-translocating ATPase; VPS39: VPS39 subunit of HOPS complex; VPS41: VPS41 subunit of HOPS complex; WWL: benzaldehyde [2,6-di(4-morpholinyl)-4-pyrimidinyl]hydrazone; WX8: 1H-indole-3-carbaldehyde [4-anilino-6-(4-morpholinyl)-1,3,5-triazin-2-yl]hydrazine; XBA: N-(3-chloro-4-fluorophenyl)-4,6-dimorpholino-1,3,5-triazin-2-amine hydrochloride; XB6: N-(4-ethylphenyl)-4,6-dimorpholino-1,3,5-triazin-2-amine hydrochloride.
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Affiliation(s)
- Gaurav Sharma
- Division of Developmental Biology, National Institute of Child Health & Human Development, National Institutes of Health , Bethesda , MD , USA
| | - Carlos M Guardia
- Cell Biology and Neurobiology Branch, National Institute of Child Health & Human Development, National Institutes of Health , Bethesda , MD , USA
| | - Ajit Roy
- Division of Developmental Biology, National Institute of Child Health & Human Development, National Institutes of Health , Bethesda , MD , USA
| | - Alex Vassilev
- Division of Developmental Biology, National Institute of Child Health & Human Development, National Institutes of Health , Bethesda , MD , USA
| | - Amra Saric
- Cell Biology and Neurobiology Branch, National Institute of Child Health & Human Development, National Institutes of Health , Bethesda , MD , USA
| | - Lori N Griner
- Division of Developmental Biology, National Institute of Child Health & Human Development, National Institutes of Health , Bethesda , MD , USA
| | - Juan Marugan
- Division of Pre-Clinical Innovation, NIH Chemical Genomics Center, National Center for Advancing Translational Sciences, National Institutes of Health , Rockville , MD , USA
| | - Marc Ferrer
- Division of Pre-Clinical Innovation, NIH Chemical Genomics Center, National Center for Advancing Translational Sciences, National Institutes of Health , Rockville , MD , USA
| | - Juan S Bonifacino
- Cell Biology and Neurobiology Branch, National Institute of Child Health & Human Development, National Institutes of Health , Bethesda , MD , USA
| | - Melvin L DePamphilis
- Division of Developmental Biology, National Institute of Child Health & Human Development, National Institutes of Health , Bethesda , MD , USA
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15
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Novel protein signatures suggest progression to muscular invasiveness in bladder cancer. PLoS One 2018; 13:e0206475. [PMID: 30419021 PMCID: PMC6231613 DOI: 10.1371/journal.pone.0206475] [Citation(s) in RCA: 3] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/23/2018] [Accepted: 10/12/2018] [Indexed: 11/21/2022] Open
Abstract
Patients with bladder cancer need frequent controls over long follow-up time due to high recurrence rate and risk of conversion to muscle invasive cancer with poor prognosis. We identified cancer-related molecular signatures in apparently healthy bladder in patients with subsequent muscular invasiveness during follow-up. Global proteomics of the normal tissue biopsies revealed specific proteome fingerprints in these patients prior to subsequent muscular invasiveness. In these presumed normal samples, we detected modulations of proteins previously associated with different cancer types. This study indicates that analyzing apparently healthy tissue of a cancer-invaded organ may suggest disease progression.
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16
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Ma H, Tu LC, Naseri A, Chung YC, Grunwald D, Zhang S, Pederson T. CRISPR-Sirius: RNA scaffolds for signal amplification in genome imaging. Nat Methods 2018; 15:928-931. [PMID: 30377374 PMCID: PMC6252086 DOI: 10.1038/s41592-018-0174-0] [Citation(s) in RCA: 101] [Impact Index Per Article: 16.8] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/15/2017] [Accepted: 08/09/2018] [Indexed: 11/09/2022]
Abstract
Clustered regularly interspaced short palindromic repeats (CRISPR) guide RNA scaffolds have been adapted to carry multiple binding sites for fluorescent proteins to enhance brightness for live cell imaging of genomic loci. However, many of these modifications result in guide RNA instability and thus produce lower genome-labeling efficiency than anticipated. Here we introduce CRISPR-Sirius, based on octet arrays of aptamers conferring both enhanced guide RNA stability and brightness, and provide initial biological applications of this platform.
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Affiliation(s)
- Hanhui Ma
- Department of Biochemistry and Molecular Pharmacology, University of Massachusetts Medical School, Worcester, MA, USA.
- School of Life Science and Technology, ShanghaiTech University, Shanghai, China.
| | - Li-Chun Tu
- RNA Therapeutics Institute, University of Massachusetts Medical School, Worcester, MA, USA
| | - Ardalan Naseri
- Department of Computer Science, University of Central Florida, Orlando, FL, USA
| | - Yu-Chieh Chung
- Kavli Institute for the Physics and Mathematics of the Universe, University of Tokyo, Kashiwa, Japan
| | - David Grunwald
- RNA Therapeutics Institute, University of Massachusetts Medical School, Worcester, MA, USA
| | - Shaojie Zhang
- Department of Computer Science, University of Central Florida, Orlando, FL, USA
| | - Thoru Pederson
- Department of Biochemistry and Molecular Pharmacology, University of Massachusetts Medical School, Worcester, MA, USA
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17
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Discovery of coding regions in the human genome by integrated proteogenomics analysis workflow. Nat Commun 2018; 9:903. [PMID: 29500430 PMCID: PMC5834625 DOI: 10.1038/s41467-018-03311-y] [Citation(s) in RCA: 86] [Impact Index Per Article: 14.3] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/08/2017] [Accepted: 02/02/2018] [Indexed: 01/23/2023] Open
Abstract
Proteogenomics enable the discovery of novel peptides (from unannotated genomic protein-coding loci) and single amino acid variant peptides (derived from single-nucleotide polymorphisms and mutations). Increasing the reliability of these identifications is crucial to ensure their usefulness for genome annotation and potential application as neoantigens in cancer immunotherapy. We here present integrated proteogenomics analysis workflow (IPAW), which combines peptide discovery, curation, and validation. IPAW includes the SpectrumAI tool for automated inspection of MS/MS spectra, eliminating false identifications of single-residue substitution peptides. We employ IPAW to analyze two proteomics data sets acquired from A431 cells and five normal human tissues using extended (pH range, 3–10) high-resolution isoelectric focusing (HiRIEF) pre-fractionation and TMT-based peptide quantitation. The IPAW results provide evidence for the translation of pseudogenes, lncRNAs, short ORFs, alternative ORFs, N-terminal extensions, and intronic sequences. Moreover, our quantitative analysis indicates that protein production from certain pseudogenes and lncRNAs is tissue specific. Proteogenomics enables the discovery of protein coding regions and disease-relevant mutations but their verification remains challenging. Here, the authors combine peptide discovery, curation and validation in an integrated proteogenomics workflow, robustly identifying unknown coding regions and mutations.
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18
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Sidorova J. A game of substrates: replication fork remodeling and its roles in genome stability and chemo-resistance. Cell Stress 2017; 1:115-133. [PMID: 29355244 PMCID: PMC5771654 DOI: 10.15698/cst2017.12.114] [Citation(s) in RCA: 16] [Impact Index Per Article: 2.3] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/18/2017] [Revised: 11/27/2017] [Accepted: 11/29/2017] [Indexed: 01/06/2023] Open
Abstract
During the hours that human cells spend in the DNA synthesis (S) phase of the cell cycle, they may encounter adversities such as DNA damage or shortage of nucleotides. Under these stresses, replication forks in DNA may experience slowing, stalling, and breakage. Fork remodeling mechanisms, which stabilize slow or stalled replication forks and ensure their ability to continue or resume replication, protect cells from genomic instability and carcinogenesis. Fork remodeling includes DNA strand exchanges that result in annealing of newly synthesized strands (fork reversal), controlled DNA resection, and cleavage of DNA strands. Defects in major tumor suppressor genes BRCA1 and BRCA2, and a subset of the Fanconi Anemia genes have been shown to result in deregulation in fork remodeling, and most prominently, loss of kilobases of nascent DNA from stalled replication forks. This phenomenon has recently gained spotlight as a potential marker and mediator of chemo-sensitivity in cancer cells and, conversely, its suppression - as a hallmark of acquired chemo-resistance. Moreover, nascent strand degradation at forks is now known to also trigger innate immune response to self-DNA. An increasingly sophisticated molecular description of these events now points at a combination of unbalanced fork reversal and end-resection as a root cause, yet also reveals the multi-layered complexity and heterogeneity of the underlying processes in normal and cancer cells.
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Affiliation(s)
- Julia Sidorova
- Department of Pathology, University of Washington, Seattle, Washington, USA
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19
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Chao HX, Poovey CE, Privette AA, Grant GD, Chao HY, Cook JG, Purvis JE. Orchestration of DNA Damage Checkpoint Dynamics across the Human Cell Cycle. Cell Syst 2017; 5:445-459.e5. [PMID: 29102360 PMCID: PMC5700845 DOI: 10.1016/j.cels.2017.09.015] [Citation(s) in RCA: 112] [Impact Index Per Article: 16.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/27/2017] [Revised: 06/26/2017] [Accepted: 09/22/2017] [Indexed: 10/18/2022]
Abstract
Although molecular mechanisms that prompt cell-cycle arrest in response to DNA damage have been elucidated, the systems-level properties of DNA damage checkpoints are not understood. Here, using time-lapse microscopy and simulations that model the cell cycle as a series of Poisson processes, we characterize DNA damage checkpoints in individual, asynchronously proliferating cells. We demonstrate that, within early G1 and G2, checkpoints are stringent: DNA damage triggers an abrupt, all-or-none cell-cycle arrest. The duration of this arrest correlates with the severity of DNA damage. After the cell passes commitment points within G1 and G2, checkpoint stringency is relaxed. By contrast, all of S phase is comparatively insensitive to DNA damage. This checkpoint is graded: instead of halting the cell cycle, increasing DNA damage leads to slower S phase progression. In sum, we show that a cell's response to DNA damage depends on its exact cell-cycle position and that checkpoints are phase-dependent, stringent or relaxed, and graded or all-or-none.
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Affiliation(s)
- Hui Xiao Chao
- Department of Genetics, University of North Carolina, Chapel Hill, Genetic Medicine Building 5061, CB#7264, 120 Mason Farm Road, Chapel Hill, NC 27599-7264, USA; Curriculum for Bioinformatics and Computational Biology, University of North Carolina, Chapel Hill, 120 Mason Farm Road, Chapel Hill, NC 27599-7264, USA
| | - Cere E Poovey
- Department of Genetics, University of North Carolina, Chapel Hill, Genetic Medicine Building 5061, CB#7264, 120 Mason Farm Road, Chapel Hill, NC 27599-7264, USA
| | - Ashley A Privette
- Department of Genetics, University of North Carolina, Chapel Hill, Genetic Medicine Building 5061, CB#7264, 120 Mason Farm Road, Chapel Hill, NC 27599-7264, USA
| | - Gavin D Grant
- Department of Biochemistry and Biophysics, University of North Carolina, Chapel Hill, 120 Mason Farm Road, Chapel Hill, NC 27599-7264, USA; Lineberger Comprehensive Cancer Center, University of North Carolina, Chapel Hill, 120 Mason Farm Road, Chapel Hill, NC 27599-7264, USA
| | - Hui Yan Chao
- Department of Genetics, University of North Carolina, Chapel Hill, Genetic Medicine Building 5061, CB#7264, 120 Mason Farm Road, Chapel Hill, NC 27599-7264, USA
| | - Jeanette G Cook
- Department of Biochemistry and Biophysics, University of North Carolina, Chapel Hill, 120 Mason Farm Road, Chapel Hill, NC 27599-7264, USA; Lineberger Comprehensive Cancer Center, University of North Carolina, Chapel Hill, 120 Mason Farm Road, Chapel Hill, NC 27599-7264, USA
| | - Jeremy E Purvis
- Department of Genetics, University of North Carolina, Chapel Hill, Genetic Medicine Building 5061, CB#7264, 120 Mason Farm Road, Chapel Hill, NC 27599-7264, USA; Curriculum for Bioinformatics and Computational Biology, University of North Carolina, Chapel Hill, 120 Mason Farm Road, Chapel Hill, NC 27599-7264, USA; Lineberger Comprehensive Cancer Center, University of North Carolina, Chapel Hill, 120 Mason Farm Road, Chapel Hill, NC 27599-7264, USA.
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20
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Abstract
Replication stress is a major source of DNA damage and an important driver of cancer development. Replication intermediates that occur upon mild forms of replication stress frequently escape cell cycle checkpoints and can be transmitted through mitosis into the next cell cycle. The consequences of such inherited DNA lesions for cell fate and survival are poorly understood. By using time-lapse microscopy and quantitative image-based cytometry to simultaneously monitor inherited DNA lesions marked by the genome caretaker protein 53BP1 and cell cycle progression, we show that inheritance of 53BP1-marked lesions from the previous S-phase is associated with a prolonged G1 duration in the next cell cycle. These results suggest that cell-to-cell variation in S-phase commitment is determined, at least partially, by the amount of replication-born inherited DNA damage in individual cells. We further show that loss of the tumor suppressor protein p53 overrides replication stress-induced G1 prolongation and allows S-phase entry with excessive amounts of inherited DNA lesions. Thus, replication stress and p53 loss may synergize during cancer development by promoting cell cycle re-entry with unrepaired mutagenic DNA lesions originating from the previous cell cycle.
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Affiliation(s)
- Aleksandra Lezaja
- a Department of Molecular Mechanisms of Disease , University of Zurich , Zurich , CH , Switzerland
| | - Matthias Altmeyer
- a Department of Molecular Mechanisms of Disease , University of Zurich , Zurich , CH , Switzerland
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21
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Soualmia LF, Lecroq T. Bioinformatics Methods and Tools to Advance Clinical Care. Findings from the Yearbook 2015 Section on Bioinformatics and Translational Informatics. Yearb Med Inform 2017; 10:170-3. [PMID: 26293864 DOI: 10.15265/iy-2015-026] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/14/2022] Open
Abstract
OBJECTIVES To summarize excellent current research in the field of Bioinformatics and Translational Informatics with application in the health domain and clinical care. METHOD We provide a synopsis of the articles selected for the IMIA Yearbook 2015, from which we attempt to derive a synthetic overview of current and future activities in the field. As last year, a first step of selection was performed by querying MEDLINE with a list of MeSH descriptors completed by a list of terms adapted to the section. Each section editor has evaluated separately the set of 1,594 articles and the evaluation results were merged for retaining 15 articles for peer-review. RESULTS The selection and evaluation process of this Yearbook's section on Bioinformatics and Translational Informatics yielded four excellent articles regarding data management and genome medicine that are mainly tool-based papers. In the first article, the authors present PPISURV a tool for uncovering the role of specific genes in cancer survival outcome. The second article describes the classifier PredictSNP which combines six performing tools for predicting disease-related mutations. In the third article, by presenting a high-coverage map of the human proteome using high resolution mass spectrometry, the authors highlight the need for using mass spectrometry to complement genome annotation. The fourth article is also related to patient survival and decision support. The authors present datamining methods of large-scale datasets of past transplants. The objective is to identify chances of survival. CONCLUSIONS The current research activities still attest the continuous convergence of Bioinformatics and Medical Informatics, with a focus this year on dedicated tools and methods to advance clinical care. Indeed, there is a need for powerful tools for managing and interpreting complex, large-scale genomic and biological datasets, but also a need for user-friendly tools developed for the clinicians in their daily practice. All the recent research and development efforts contribute to the challenge of impacting clinically the obtained results towards a personalized medicine.
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Affiliation(s)
- L F Soualmia
- Dr Lina F. Soualmia, Normandie Univ., Rouen University and Hospital, SIBM & LITIS EA 4108, Information Processing in Biology & Health, 1, rue de Germont, Cour Leschevin porte 21, 76031 Rouen Cedex, France, Tel : +33 232 885 869, E-mail:
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Impaired STING Pathway in Human Osteosarcoma U2OS Cells Contributes to the Growth of ICP0-Null Mutant Herpes Simplex Virus. J Virol 2017; 91:JVI.00006-17. [PMID: 28179534 DOI: 10.1128/jvi.00006-17] [Citation(s) in RCA: 29] [Impact Index Per Article: 4.1] [Reference Citation Analysis] [Abstract] [Key Words] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/02/2017] [Accepted: 02/06/2017] [Indexed: 01/30/2023] Open
Abstract
Human herpes simplex virus 1 (HSV-1) is a widespread pathogen, with 80% of the population being latently infected. To successfully evade the host, the virus has evolved strategies to counteract antiviral responses, including the gene-silencing and innate immunity machineries. The immediately early protein of the virus, infected cell protein 0 (ICP0), plays a central role in these processes. ICP0 blocks innate immunity, and one mechanism is by degrading hostile factors with its intrinsic E3 ligase activity. ICP0 also functions as a promiscuous transactivator, and it blocks repressor complexes to enable viral gene transcription. For these reasons, the growth of a ΔICP0 virus is impaired in most cells, except cells of the human osteosarcoma cell line U2OS, and it is only partially impaired in cells of the human osteosarcoma cell line Saos-2. We found that the two human osteosarcoma cell lines that supported the growth of the ΔICP0 virus failed to activate innate immune responses upon treatment with 2'3'-cyclic GAMP (2'3'-cGAMP), the natural agonist of STING (i.e., stimulator of interferon genes) or after infection with the ΔICP0 mutant virus. Innate immune responses were restored in these cells by transient expression of the STING protein but not after overexpression of interferon-inducible protein 16 (IFI16). Restoration of STING expression resulted in suppression of ΔICP0 virus gene expression and a decrease in viral yields. Overexpression of IFI16 also suppressed ΔICP0 virus gene expression, albeit to a lesser extent than STING. These data suggest that the susceptibility of U2OS and Saos-2 cells to the ΔICP0 HSV-1 is in part due to an impaired STING pathway.IMPORTANCE The DNA sensor STING plays pivotal role in controlling HSV-1 infection both in cell culture and in mice. The HSV-1 genome encodes numerous proteins that are dedicated to combat host antiviral responses. The immediate early protein of the virus ICP0 plays major role in this process as it targets hostile host proteins for degradation with its E3 ligase activity, and it disrupts repressor complexes via protein-protein interaction to enable viral gene transcription. Therefore, the ΔICP0 HSV-1 virus is defective for growth in most cells, except the human osteosarcoma cell lines U2OS and Saos-2. We found that both cell lines that support ΔICP0 virus infection have defects in the STING DNA-sensing pathway, which partially accounts for the rescue of the ΔICP0 virus growth. Restoration of STING expression in these cells rescued innate immunity and suppressed ΔICP0 virus infection. This study underscores the importance of STING in the control of HSV-1.
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Profiling DNA damage response following mitotic perturbations. Nat Commun 2016; 7:13887. [PMID: 27976684 PMCID: PMC5172227 DOI: 10.1038/ncomms13887] [Citation(s) in RCA: 35] [Impact Index Per Article: 4.4] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/02/2016] [Accepted: 11/09/2016] [Indexed: 01/01/2023] Open
Abstract
Genome integrity relies on precise coordination between DNA replication and chromosome segregation. Whereas replication stress attracted much attention, the consequences of mitotic perturbations for genome integrity are less understood. Here, we knockdown 47 validated mitotic regulators to show that a broad spectrum of mitotic errors correlates with increased DNA breakage in daughter cells. Unexpectedly, we find that only a subset of these correlations are functionally linked. We identify the genuine mitosis-born DNA damage events and sub-classify them according to penetrance of the observed phenotypes. To demonstrate the potential of this resource, we show that DNA breakage after cytokinesis failure is preceded by replication stress, which mounts during consecutive cell cycles and coincides with decreased proliferation. Together, our results provide a resource to gauge the magnitude and dynamics of DNA breakage associated with mitotic aberrations and suggest that replication stress might limit propagation of cells with abnormal karyotypes.
DNA damage arising from replication stress is well studied, but the effect of mitotic errors on genome integrity is less understood. Here the authors knock down 47 mitotic regulators and record how they impact on DNA breakage events, providing a resource for future studies on the relation between cell division and genome integrity.
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Tokarz SA, DeValk J, Luo W, Pattnaik BR, Schrodi SJ, Pillers DAM. Cell line donor genotype and its influence on experimental phenotype: Toll-like receptor SNPs and potential variability in innate immunity. Mol Genet Metab 2016; 118:147-152. [PMID: 27324283 DOI: 10.1016/j.ymgme.2016.04.011] [Citation(s) in RCA: 3] [Impact Index Per Article: 0.4] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Received: 02/25/2016] [Revised: 04/21/2016] [Accepted: 04/21/2016] [Indexed: 11/28/2022]
Abstract
Cell lines are used to model a disease and provide valuable information regarding phenotype, mechanism, and response to novel therapies. Derived from individuals of diverse genetic backgrounds, the cell's genetic complement predicts the phenotype, and although some lines have been sequenced, little emphasis has been placed on genotyping. Toll-like receptors (TLRs) are essential in initiating the inflammatory cascade in response to infection. TLR single nucleotide polymorphism (SNP) alleles may predict an altered innate immune response: a SNP can affect TLR-dependent pathways and may alter experimental results. Thus, genotype variation may have far-reaching implications when using cell lines to model phenotypes. We recommend that cell lines be genotyped and cataloged in a fashion similar to that used for bacteria, with cumulative information being archived in an accessible central database to facilitate the understanding of SNP cell phenotypes reported in the literature.
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Affiliation(s)
- Sara A Tokarz
- Division of Neonatology & Newborn Nursery, University of Wisconsin-Madison, Madison, WI 53706, USA; Department of Pediatrics, University of Wisconsin-Madison, Madison, WI 53706, USA
| | - Jessica DeValk
- Division of Neonatology & Newborn Nursery, University of Wisconsin-Madison, Madison, WI 53706, USA; Department of Pediatrics, University of Wisconsin-Madison, Madison, WI 53706, USA
| | - Wenxiang Luo
- Division of Neonatology & Newborn Nursery, University of Wisconsin-Madison, Madison, WI 53706, USA; Department of Pediatrics, University of Wisconsin-Madison, Madison, WI 53706, USA
| | - Bikash R Pattnaik
- Division of Neonatology & Newborn Nursery, University of Wisconsin-Madison, Madison, WI 53706, USA; Department of Pediatrics, University of Wisconsin-Madison, Madison, WI 53706, USA; Department of Ophthalmology and Visual Sciences, School of Medicine and Public Health, University of Wisconsin-Madison, Madison, WI 53706, USA; McPherson Eye Research Institute, University of Wisconsin-Madison, Madison, WI 53706, USA
| | - Steven J Schrodi
- Computation and Informatics in Biology and Medicine, University of Wisconsin-Madison, Madison, WI 53706, USA; Center for Human Genetics, Marshfield Clinic Research Foundation, Marshfield, WI 54449, USA
| | - De-Ann M Pillers
- Division of Neonatology & Newborn Nursery, University of Wisconsin-Madison, Madison, WI 53706, USA; Department of Pediatrics, University of Wisconsin-Madison, Madison, WI 53706, USA; Department of Medical Genetics, University of Wisconsin-Madison, Madison, WI 53706, USA; McPherson Eye Research Institute, University of Wisconsin-Madison, Madison, WI 53706, USA; J.F. Crow Institute for the Study of Evolution, University of Wisconsin-Madison, Madison, WI 53706, USA.
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Schwarzer C, Siatkowski M, Pfeiffer MJ, Baeumer N, Drexler HCA, Wang B, Fuellen G, Boiani M. Maternal age effect on mouse oocytes: new biological insight from proteomic analysis. Reproduction 2014; 148:55-72. [DOI: 10.1530/rep-14-0126] [Citation(s) in RCA: 42] [Impact Index Per Article: 4.2] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/12/2022]
Abstract
The long-standing view of ‘immortal germline vs mortal soma’ poses a fundamental question in biology concerning how oocytes age in molecular terms. A mainstream hypothesis is that maternal ageing of oocytes has its roots in gene transcription. Investigating the proteins resulting from mRNA translation would reveal how far the levels of functionally available proteins correlate with mRNAs and would offer novel insights into the changes oocytes undergo during maternal ageing. Gene ontology (GO) semantic analysis revealed a high similarity of the detected proteome (2324 proteins) to the transcriptome (22 334 mRNAs), although not all proteins had a cognate mRNA. Concerning their dynamics, fourfold changes of abundance were more frequent in the proteome (3%) than the transcriptome (0.05%), with no correlation. Whereas proteins associated with the nucleus (e.g. structural maintenance of chromosomes and spindle-assembly checkpoints) were largely represented among those that change in oocytes during maternal ageing; proteins associated with oxidative stress/damage (e.g. superoxide dismutase) were infrequent. These quantitative alterations are either impoverishing or enriching. Using GO analysis, these alterations do not relate in any simple way to the classic signature of ageing known from somatic tissues. Given the lack of correlation, we conclude that proteome analysis of mouse oocytes may not be surrogated with transcriptome analysis. Furthermore, we conclude that the classic features of ageing may not be transposed from somatic tissues to oocytes in a one-to-one fashion. Overall, there is more to the maternal ageing of oocytes than mere cellular deterioration exemplified by the notorious increase of meiotic aneuploidy.
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Mettler T, Mühlhaus T, Hemme D, Schöttler MA, Rupprecht J, Idoine A, Veyel D, Pal SK, Yaneva-Roder L, Winck FV, Sommer F, Vosloh D, Seiwert B, Erban A, Burgos A, Arvidsson S, Schönfelder S, Arnold A, Günther M, Krause U, Lohse M, Kopka J, Nikoloski Z, Mueller-Roeber B, Willmitzer L, Bock R, Schroda M, Stitt M. Systems Analysis of the Response of Photosynthesis, Metabolism, and Growth to an Increase in Irradiance in the Photosynthetic Model Organism Chlamydomonas reinhardtii. THE PLANT CELL 2014; 26:2310-2350. [PMID: 24894045 PMCID: PMC4114937 DOI: 10.1105/tpc.114.124537] [Citation(s) in RCA: 54] [Impact Index Per Article: 5.4] [Reference Citation Analysis] [Abstract] [Track Full Text] [Subscribe] [Scholar Register] [Received: 02/23/2014] [Revised: 04/17/2014] [Accepted: 05/06/2014] [Indexed: 05/18/2023]
Abstract
We investigated the systems response of metabolism and growth after an increase in irradiance in the nonsaturating range in the algal model Chlamydomonas reinhardtii. In a three-step process, photosynthesis and the levels of metabolites increased immediately, growth increased after 10 to 15 min, and transcript and protein abundance responded by 40 and 120 to 240 min, respectively. In the first phase, starch and metabolites provided a transient buffer for carbon until growth increased. This uncouples photosynthesis from growth in a fluctuating light environment. In the first and second phases, rising metabolite levels and increased polysome loading drove an increase in fluxes. Most Calvin-Benson cycle (CBC) enzymes were substrate-limited in vivo, and strikingly, many were present at higher concentrations than their substrates, explaining how rising metabolite levels stimulate CBC flux. Rubisco, fructose-1,6-biosphosphatase, and seduheptulose-1,7-bisphosphatase were close to substrate saturation in vivo, and flux was increased by posttranslational activation. In the third phase, changes in abundance of particular proteins, including increases in plastidial ATP synthase and some CBC enzymes, relieved potential bottlenecks and readjusted protein allocation between different processes. Despite reasonable overall agreement between changes in transcript and protein abundance (R2 = 0.24), many proteins, including those in photosynthesis, changed independently of transcript abundance.
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Affiliation(s)
- Tabea Mettler
- Max Planck Institute of Molecular Plant Physiology, 14476 Potsdam-Golm, Germany
| | - Timo Mühlhaus
- Max Planck Institute of Molecular Plant Physiology, 14476 Potsdam-Golm, Germany
| | - Dorothea Hemme
- Max Planck Institute of Molecular Plant Physiology, 14476 Potsdam-Golm, Germany
| | | | - Jens Rupprecht
- Max Planck Institute of Molecular Plant Physiology, 14476 Potsdam-Golm, Germany
| | - Adam Idoine
- Max Planck Institute of Molecular Plant Physiology, 14476 Potsdam-Golm, Germany
| | - Daniel Veyel
- Max Planck Institute of Molecular Plant Physiology, 14476 Potsdam-Golm, Germany
| | - Sunil Kumar Pal
- Max Planck Institute of Molecular Plant Physiology, 14476 Potsdam-Golm, Germany
| | - Liliya Yaneva-Roder
- Max Planck Institute of Molecular Plant Physiology, 14476 Potsdam-Golm, Germany
| | - Flavia Vischi Winck
- Max Planck Institute of Molecular Plant Physiology, 14476 Potsdam-Golm, Germany Institute of Biochemistry and Biology, University of Potsdam, 14476 Potsdam-Golm, Germany
| | - Frederik Sommer
- Max Planck Institute of Molecular Plant Physiology, 14476 Potsdam-Golm, Germany
| | - Daniel Vosloh
- Max Planck Institute of Molecular Plant Physiology, 14476 Potsdam-Golm, Germany
| | - Bettina Seiwert
- Max Planck Institute of Molecular Plant Physiology, 14476 Potsdam-Golm, Germany
| | - Alexander Erban
- Max Planck Institute of Molecular Plant Physiology, 14476 Potsdam-Golm, Germany
| | - Asdrubal Burgos
- Max Planck Institute of Molecular Plant Physiology, 14476 Potsdam-Golm, Germany
| | - Samuel Arvidsson
- Max Planck Institute of Molecular Plant Physiology, 14476 Potsdam-Golm, Germany Institute of Biochemistry and Biology, University of Potsdam, 14476 Potsdam-Golm, Germany
| | | | - Anne Arnold
- Max Planck Institute of Molecular Plant Physiology, 14476 Potsdam-Golm, Germany
| | - Manuela Günther
- Max Planck Institute of Molecular Plant Physiology, 14476 Potsdam-Golm, Germany
| | - Ursula Krause
- Max Planck Institute of Molecular Plant Physiology, 14476 Potsdam-Golm, Germany
| | - Marc Lohse
- Max Planck Institute of Molecular Plant Physiology, 14476 Potsdam-Golm, Germany
| | - Joachim Kopka
- Max Planck Institute of Molecular Plant Physiology, 14476 Potsdam-Golm, Germany
| | - Zoran Nikoloski
- Max Planck Institute of Molecular Plant Physiology, 14476 Potsdam-Golm, Germany
| | - Bernd Mueller-Roeber
- Max Planck Institute of Molecular Plant Physiology, 14476 Potsdam-Golm, Germany Institute of Biochemistry and Biology, University of Potsdam, 14476 Potsdam-Golm, Germany
| | - Lothar Willmitzer
- Max Planck Institute of Molecular Plant Physiology, 14476 Potsdam-Golm, Germany
| | - Ralph Bock
- Max Planck Institute of Molecular Plant Physiology, 14476 Potsdam-Golm, Germany
| | - Michael Schroda
- Max Planck Institute of Molecular Plant Physiology, 14476 Potsdam-Golm, Germany
| | - Mark Stitt
- Max Planck Institute of Molecular Plant Physiology, 14476 Potsdam-Golm, Germany
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Ionizing radiation-inducible miR-494 promotes glioma cell invasion through EGFR stabilization by targeting p190B rhoGAP. BIOCHIMICA ET BIOPHYSICA ACTA-MOLECULAR CELL RESEARCH 2014; 1843:508-16. [PMID: 24316134 DOI: 10.1016/j.bbamcr.2013.11.021] [Citation(s) in RCA: 37] [Impact Index Per Article: 3.7] [Reference Citation Analysis] [Abstract] [Track Full Text] [Subscribe] [Scholar Register] [Received: 07/12/2013] [Revised: 11/22/2013] [Accepted: 11/26/2013] [Indexed: 12/16/2022]
Abstract
MicroRNAs (miRNAs) play an important role in various stages of tumor progression. miR-494, which we had previously identified as a miRNA induced by ionizing radiation (IR) in the glioma cell line U-251, was observed to enhance invasion of U-251 cells by activating MMP-2. The miR-494-induced invasive potential was accompanied by, and dependent on, epidermal growth factor receptor (EGFR) upregulation and the activation of its downstream signaling constituents, Akt and ERK. The upregulation of EGFR by miR-494 involved the suppression of lysosomal protein turnover. Among the putative target proteins tested, p190B RhoGAP (p190B) was downregulated by miR-494, and its reduced expression was responsible for the increase in EGFR expression. A reporter assay using a luciferase construct containing p190B 3'-untranslated region (3'UTR) confirmed that p190B is a direct target of miR-494. Downregulation of p190B by small interfering RNA (siRNA) transfection closely mimicked the outcomes of miR-494 transfection, and showed increased EGFR expression, MMP-2 secretion, and invasion. Ectopic expression of p190B suppressed the miR-494-induced EGFR upregulation and invasion promotion, thereby suggesting that p190B depletion is critical for the invasion-promoting action of miR-494. Collectively, our results suggest a novel function for miR-494 and its potential application as a target to control invasiveness in cancer therapy.
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How to discover new proteins-translatome profiling. SCIENCE CHINA-LIFE SCIENCES 2014; 57:358-360. [PMID: 24532458 DOI: 10.1007/s11427-014-4618-1] [Citation(s) in RCA: 12] [Impact Index Per Article: 1.2] [Reference Citation Analysis] [Track Full Text] [Subscribe] [Scholar Register] [Received: 11/27/2013] [Accepted: 12/22/2013] [Indexed: 12/15/2022]
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Branca RMM, Orre LM, Johansson HJ, Granholm V, Huss M, Pérez-Bercoff Å, Forshed J, Käll L, Lehtiö J. HiRIEF LC-MS enables deep proteome coverage and unbiased proteogenomics. Nat Methods 2013; 11:59-62. [PMID: 24240322 DOI: 10.1038/nmeth.2732] [Citation(s) in RCA: 182] [Impact Index Per Article: 16.5] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/22/2013] [Accepted: 10/08/2013] [Indexed: 11/09/2022]
Abstract
We present a liquid chromatography-mass spectrometry (LC-MS)-based method permitting unbiased (gene prediction-independent) genome-wide discovery of protein-coding loci in higher eukaryotes. Using high-resolution isoelectric focusing (HiRIEF) at the peptide level in the 3.7-5.0 pH range and accurate peptide isoelectric point (pI) prediction, we probed the six-reading-frame translation of the human and mouse genomes and identified 98 and 52 previously undiscovered protein-coding loci, respectively. The method also enabled deep proteome coverage, identifying 13,078 human and 10,637 mouse proteins.
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Affiliation(s)
- Rui M M Branca
- 1] Department of Oncology-Pathology, Science for Life Laboratory, Karolinska Institutet, Stockholm, Sweden. [2]
| | - Lukas M Orre
- 1] Department of Oncology-Pathology, Science for Life Laboratory, Karolinska Institutet, Stockholm, Sweden. [2]
| | - Henrik J Johansson
- 1] Department of Oncology-Pathology, Science for Life Laboratory, Karolinska Institutet, Stockholm, Sweden. [2]
| | - Viktor Granholm
- Department of Biochemistry and Biophysics, Science for Life Laboratory, Stockholm University, Stockholm, Sweden
| | - Mikael Huss
- Department of Biochemistry and Biophysics, The Arrhenius Laboratories for Natural Sciences, Science for Life Laboratory, Stockholm University, Stockholm, Sweden
| | - Åsa Pérez-Bercoff
- Department of Oncology-Pathology, Science for Life Laboratory, Karolinska Institutet, Stockholm, Sweden
| | - Jenny Forshed
- Department of Oncology-Pathology, Science for Life Laboratory, Karolinska Institutet, Stockholm, Sweden
| | - Lukas Käll
- 1] School of Biotechnology, Science for Life Laboratory, KTH Royal Institute of Technology, Stockholm, Sweden. [2] Swedish e-Science Resource Center, KTH Royal Institute of Technology, Stockholm, Sweden
| | - Janne Lehtiö
- Department of Oncology-Pathology, Science for Life Laboratory, Karolinska Institutet, Stockholm, Sweden
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Zhong J, Cui Y, Guo J, Chen Z, Yang L, He QY, Zhang G, Wang T. Resolving chromosome-centric human proteome with translating mRNA analysis: a strategic demonstration. J Proteome Res 2013; 13:50-9. [PMID: 24200226 DOI: 10.1021/pr4007409] [Citation(s) in RCA: 35] [Impact Index Per Article: 3.2] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/13/2022]
Abstract
Chromosome-centric human proteome project (C-HPP) aims at differentiating chromosome-based and tissue-specific protein compositions in terms of protein expression, quantification, and modification. We previously found that the analysis of translating mRNA (mRNA attached to ribosome-nascent chain complex, RNC-mRNA) can explain over 94% of mRNA-protein abundance. Therefore, we propose here to use full-length RNC-mRNA information to illustrate protein expression both qualitatively and quantitatively. We performed RNA-seq on RNC-mRNA (RNC-seq) and detected 12,758 and 14,113 translating genes in human normal bronchial epithelial (HBE) cells and human colorectal adenocarcinoma Caco-2 cells, respectively. We found that most of these genes were mapped with >80% of coding sequence coverage. In Caco-2 cells, we provided translating evidence on 4180 significant single-nucleotide variations. While using RNC-mRNA data as a standard for proteomic data integration, both translating and protein evidence of 7876 genes can be acquired from four interlaboratory data sets with different MS platforms. In addition, we detected 1397 noncoding mRNAs that were attached to ribosomes, suggesting a potential source of new protein explorations. By comparing the two cell lines, a total of 677 differentially translated genes were found to be nonevenly distributed across chromosomes. In addition, 2105 genes in Caco-2 and 750 genes in HBE cells are expressed in a cell-specific manner. These genes are significantly and specifically clustered on multiple chromosomes, such as chromosome 19. We conclude that HPP/C-HPP investigations can be considerably improved by integrating RNC-mRNA analysis with MS, bioinformatics, and antibody-based verifications.
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Affiliation(s)
- Jiayong Zhong
- Key Laboratory of Functional Protein Research of Guangdong Higher Education Institutes, Institute of Life and Health Engineering, College of Life Science and Technology, Jinan University , 601 Huangpu Avenue West, Guangzhou 510632, China
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Proteome changes induced by c-myb silencing in human chronic myeloid leukemia cells suggest molecular mechanisms and putative biomarkers of hematopoietic malignancies. J Proteomics 2013; 96:200-22. [PMID: 24220303 DOI: 10.1016/j.jprot.2013.10.040] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.2] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/08/2013] [Revised: 10/18/2013] [Accepted: 10/30/2013] [Indexed: 11/23/2022]
Abstract
UNLABELLED To shed light on the molecular mechanisms associated with aberrant accumulation of c-Myb in chronic myeloid leukemia, comparative proteomic analysis was performed on c-myb RNAi-specifically silenced K562 cells, sampled on a time-course basis. 2D-DIGE technology highlighted 37 differentially-represented proteins that were further characterized by nLC-ESI-LIT-MS/MS and validated by western blotting and qRT-PCR analysis. Most of the deregulated proteins were related to protein folding, energy/primary metabolism, transcription/translation regulation and oxidative stress response. Protein network analysis suggested that glycolysis, gluconeogenesis and protein ubiquitination biosynthesis pathways were highly represented, confirming also the pivotal role of c-Myc. A specific reduced representation was observed for glyceraldehyde-3-phosphate-dehydrogenase and α-enolase, suggesting a possible role of c-Myb in the activation of aerobic glycolysis. A reduced amount was also observed for stress responsive heat shock 70kDa protein and 78kDa glucose-regulated protein, previously identified as direct targets of c-Myb. Among over-represented proteins, worth mentioning is the chromatin modifier chromobox protein homolog 3 that contributes to silencing of E2F- and Myc-responsive genes in quiescent G0 cells. Data here presented, while providing novel insights onto the molecular mechanisms underlying c-Myb activity, indicate potential protein biomarkers for monitoring the progression of chronic myeloid leukemia. BIOLOGICAL SIGNIFICANCE Myeloid leukemia is a malignant disease of the hematopoietic system in which cells of myeloid lineages accumulate to an undifferentiated state. In particular, it was shown that an aberrant accumulation of the c-Myb transcriptional factor is associated with the suppression of normal differentiation processes promoting the development of the hematopoietic malignancies. Many efforts have been recently made to identify novel genes directly targeted by c-Myb at a transcriptome level. In this work, we originally describe a differential proteomic approach to facilitate the comprehension of the regulation of the protein networks exerted by c-Myb. Our study reveals a complex network of proteins regulated by c-Myb. The functional heterogeneity of these proteins emphasizes the pleiotropic role of c-Myb as a regulator of genes that are crucial for energy production and stress response in leukemia. In fact, variations in glyceraldehyde-3-phosphate-dehydrogenase and α-enolase suggest a possible role of c-Myb in the activation of aerobic glycolysis. Moreover, significant differences were found for heat shock 70kDa protein and 78kDa glucose-regulated protein known as direct c-Myb targets. This work highlights potential protein biomarkers to look into disease progression and to develop translational medicine approaches in myeloid leukemia.
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Wang T, Cui Y, Jin J, Guo J, Wang G, Yin X, He QY, Zhang G. Translating mRNAs strongly correlate to proteins in a multivariate manner and their translation ratios are phenotype specific. Nucleic Acids Res 2013; 41:4743-54. [PMID: 23519614 PMCID: PMC3643591 DOI: 10.1093/nar/gkt178] [Citation(s) in RCA: 144] [Impact Index Per Article: 13.1] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/30/2022] Open
Abstract
As a well-known phenomenon, total mRNAs poorly correlate to proteins in their abundances as reported. Recent findings calculated with bivariate models suggested even poorer such correlation, whereas focusing on the translating mRNAs (ribosome nascent-chain complex-bound mRNAs, RNC-mRNAs) subset. In this study, we analysed the relative abundances of mRNAs, RNC-mRNAs and proteins on genome-wide scale, comparing human lung cancer A549 and H1299 cells with normal human bronchial epithelial (HBE) cells, respectively. As discovered, a strong correlation between RNC-mRNAs and proteins in their relative abundances could be established through a multivariate linear model by integrating the mRNA length as a key factor. The R2 reached 0.94 and 0.97 in A549 versus HBE and H1299 versus HBE comparisons, respectively. This correlation highlighted that the mRNA length significantly contributes to the translational modulation, especially to the translational initiation, favoured by its correlation with the mRNA translation ratio (TR) as observed. We found TR is highly phenotype specific, which was substantiated by both pathway analysis and biased TRs of the splice variants of BDP1 gene, which is a key transcription factor of transfer RNAs. These findings revealed, for the first time, the intrinsic and genome-wide translation modulations at translatomic level in human cells at steady-state, which are tightly correlated to the protein abundance and functionally relevant to cellular phenotypes.
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Affiliation(s)
- Tong Wang
- Key Laboratory of Functional Protein Research of Guangdong Higher Education Institutes, Institute of Life and Health Engineering, College of Life Science and Technology, Jinan University, Guangzhou 510632, China.
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Shirley BC, Mucaki EJ, Whitehead T, Costea PI, Akan P, Rogan PK. Interpretation, stratification and evidence for sequence variants affecting mRNA splicing in complete human genome sequences. GENOMICS PROTEOMICS & BIOINFORMATICS 2013; 11:77-85. [PMID: 23499923 PMCID: PMC4357664 DOI: 10.1016/j.gpb.2013.01.008] [Citation(s) in RCA: 19] [Impact Index Per Article: 1.7] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Subscribe] [Scholar Register] [Received: 12/06/2012] [Revised: 01/16/2013] [Accepted: 01/21/2013] [Indexed: 11/29/2022]
Abstract
Information theory-based methods have been shown to be sensitive and specific for predicting and quantifying the effects of non-coding mutations in Mendelian diseases. We present the Shannon pipeline software for genome-scale mutation analysis and provide evidence that the software predicts variants affecting mRNA splicing. Individual information contents (in bits) of reference and variant splice sites are compared and significant differences are annotated and prioritized. The software has been implemented for CLC-Bio Genomics platform. Annotation indicates the context of novel mutations as well as common and rare SNPs with splicing effects. Potential natural and cryptic mRNA splicing variants are identified, and null mutations are distinguished from leaky mutations. Mutations and rare SNPs were predicted in genomes of three cancer cell lines (U2OS, U251 and A431), which were supported by expression analyses. After filtering, tractable numbers of potentially deleterious variants are predicted by the software, suitable for further laboratory investigation. In these cell lines, novel functional variants comprised 6–17 inactivating mutations, 1–5 leaky mutations and 6–13 cryptic splicing mutations. Predicted effects were validated by RNA-seq analysis of the three aforementioned cancer cell lines, and expression microarray analysis of SNPs in HapMap cell lines.
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Affiliation(s)
- Ben C Shirley
- Department of Computer Science, Middlesex College, The University of Western Ontario, London, ON N6A 5B7, Canada
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Solnestam BW, Stranneheim H, Hällman J, Käller M, Lundberg E, Lundeberg J, Akan P. Comparison of total and cytoplasmic mRNA reveals global regulation by nuclear retention and miRNAs. BMC Genomics 2012; 13:574. [PMID: 23110385 PMCID: PMC3495644 DOI: 10.1186/1471-2164-13-574] [Citation(s) in RCA: 31] [Impact Index Per Article: 2.6] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/11/2012] [Accepted: 10/22/2012] [Indexed: 01/05/2023] Open
Abstract
BACKGROUND The majority of published gene-expression studies have used RNA isolated from whole cells, overlooking the potential impact of including nuclear transcriptome in the analyses. In this study, mRNA fractions from the cytoplasm and from whole cells (total RNA) were prepared from three human cell lines and sequenced using massive parallel sequencing. RESULTS For all three cell lines, of about 15000 detected genes approximately 400 to 1400 genes were detected in different amounts in the cytoplasmic and total RNA fractions. Transcripts detected at higher levels in the total RNA fraction had longer coding sequences and higher number of miRNA target sites. Transcripts detected at higher levels in the cytoplasmic fraction were shorter or contained shorter untranslated regions. Nuclear retention of transcripts and mRNA degradation via miRNA pathway might contribute to this differential detection of genes. The consequence of the differential detection was further investigated by comparison to proteomics data. Interestingly, the expression profiles of cytoplasmic and total RNA correlated equally well with protein abundance levels indicating regulation at a higher level. CONCLUSIONS We conclude that expression levels derived from the total RNA fraction be regarded as an appropriate estimate of the amount of mRNAs present in a given cell population, independent of the coding sequence length or UTRs.
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Affiliation(s)
- Beata Werne Solnestam
- KTH Royal Institute of Technology, Science for Life Laboratory (SciLifeLab Stockholm), School of Biotechnology, Division of Gene Technology, SE-171 65, Solna, Sweden
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