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Yu Z, Bian C, Liu G, Zhang S, Wong KC, Li X. Elucidating transcriptomic profiles from single-cell RNA sequencing data using nature-inspired compressed sensing. Brief Bioinform 2021; 22:6225863. [PMID: 33855366 DOI: 10.1093/bib/bbab125] [Citation(s) in RCA: 4] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [Abstract] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/29/2020] [Revised: 03/07/2021] [Accepted: 03/16/2021] [Indexed: 11/12/2022] Open
Abstract
Gene-expression profiling can define the cell state and gene-expression pattern of cells at the genetic level in a high-throughput manner. With the development of transcriptome techniques, processing high-dimensional genetic data has become a major challenge in expression profiling. Thanks to the recent widespread use of matrix decomposition methods in bioinformatics, a computational framework based on compressed sensing was adopted to reduce dimensionality. However, compressed sensing requires an optimization strategy to learn the modular dictionaries and activity levels from the low-dimensional random composite measurements to reconstruct the high-dimensional gene-expression data. Considering this, here we introduce and compare four compressed sensing frameworks coming from nature-inspired optimization algorithms (CSCS, ABCCS, BACS and FACS) to improve the quality of the decompression process. Several experiments establish that the three proposed methods outperform benchmark methods on nine different datasets, especially the FACS method. We illustrate therefore, the robustness and convergence of FACS in various aspects; notably, time complexity and parameter analyses highlight properties of our proposed FACS. Furthermore, differential gene-expression analysis, cell-type clustering, gene ontology enrichment and pathology analysis are conducted, which bring novel insights into cell-type identification and characterization mechanisms from different perspectives. All algorithms are written in Python and available at https://github.com/Philyzh8/Nature-inspired-CS.
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Affiliation(s)
- Zhuohan Yu
- school of Artificial Intelligence, Jilin University, Jilin, China
| | - Chuang Bian
- school of Artificial Intelligence, Jilin University, Jilin, China
| | - Genggeng Liu
- Suzhou Institute of Biomedical Engineering and Technology Chinese Academy of Sciences, China
| | - Shixiong Zhang
- School of Computer Science and Technology, Xidian University, Xi'an, China 710000
| | | | - Xiangtao Li
- School of Artificial Intelligence, Jilin University, Jilin, China
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52
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DNA-targeted formation and catalytic reactions of DNAzymes for label-free ratiometric electrochemiluminescence biosensing. Talanta 2021; 225:121964. [PMID: 33592718 DOI: 10.1016/j.talanta.2020.121964] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.7] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/01/2020] [Revised: 11/26/2020] [Accepted: 11/30/2020] [Indexed: 01/18/2023]
Abstract
A label-free ratiometric electrochemiluminescence (ECL) sensing strategy for the sensitive detection of target DNA (T-DNA) was proposed on the basis of G-quadruplex/hemin-regulated ECL emissions of CdS quantum dots (QDs) and luminol with their common coreactant of H2O2. The ECL biosensor was constructed through stepwise assemblies of CdS QDs and hairpin DNA (H-DNA) on a glassy carbon electrode, and subsequent introduction of T-DNA resulted in the development of G-quadruplex/hemin DNAzymes via the specific recognition of T-DNA and H-DNA in the presence of hemin and K+ ions. The formed DNAzymes not only prompted the catalytic oxidation of hydroquinone followed by deposition of insoluble oxidation oligomers on the electrode surface to attenuate the cathodic ECL emission of CdS QDs but also triggered the catalytic oxidation of luminol to enhance the anodic ECL emission. The label-free ratiometric ECL biosensor for the detection of T-DNA showed a wide response range from 1 to 10,000 fM (10-15 M) with a low detection limit of 0.2 fM and exhibited excellent selectivity against mismatched base sequences. This work provides a reliable and sensitive sensing platform for the detection of targets in analytical community by means of rational design of DNA sequences.
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53
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He J, Jia Y. Application of omics technologies in dermatological research and skin management. J Cosmet Dermatol 2021; 21:451-460. [PMID: 33759323 DOI: 10.1111/jocd.14100] [Citation(s) in RCA: 5] [Impact Index Per Article: 1.7] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/11/2020] [Revised: 01/19/2021] [Accepted: 03/10/2021] [Indexed: 12/23/2022]
Abstract
BACKGROUND "Omics" are usually based on the use of high-throughput analysis methods for global analysis of biological samples and the discovery of biomarkers, and may provide new insights into biological phenomena. Over the last few years, the development of omics technologies has considerably accelerated the pace of dermatological research. AIMS The purpose of this article was to review the development of omics in recent decades and their application in dermatological research. METHODS An extensive literature search was conducted on omics technologies since the first research on omics. RESULTS This article summarizes the history and main research methods of the six omics technologies, including genomics, transcriptomics, proteomics, metabolomics, lipidomics, and microbiomics. Their application in certain skin diseases and cosmetics research and development are also summarized. CONCLUSIONS This information will help to understand the mechanism of some skin diseases and the discovery of potential biomarkers, and provide new insights for skin health management and cosmetics research and development.
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Affiliation(s)
- Jianbiao He
- Beijing Key Laboratory of Plant Resources Research and Development, College of Chemistry and Materials Engineering, Beijing Technology and Business University, Beijing, China.,Key Laboratory of Cosmetic of China National Light Industry, College of Chemistry and Materials Engineering, Beijing Technology and Business University, Beijing, China.,Institute of cosmetic regulatory science, Beijing Technology and Business University, Beijing, China
| | - Yan Jia
- Beijing Key Laboratory of Plant Resources Research and Development, College of Chemistry and Materials Engineering, Beijing Technology and Business University, Beijing, China.,Key Laboratory of Cosmetic of China National Light Industry, College of Chemistry and Materials Engineering, Beijing Technology and Business University, Beijing, China.,Institute of cosmetic regulatory science, Beijing Technology and Business University, Beijing, China
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54
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Chen J, Chen L, Hua J, Song W. Long-term dynamic compression enhancement TGF-β3-induced chondrogenesis in bovine stem cells: a gene expression analysis. BMC Genom Data 2021; 22:13. [PMID: 33743603 PMCID: PMC7981793 DOI: 10.1186/s12863-021-00967-2] [Citation(s) in RCA: 6] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/18/2021] [Accepted: 03/11/2021] [Indexed: 02/02/2023] Open
Abstract
Background Bioengineering has demonstrated the potential of utilising mesenchymal stem cells (MSCs), growth factors, and mechanical stimuli to treat cartilage defects. However, the underlying genes and pathways are largely unclear. This is the first study on screening and identifying the hub genes involved in mechanically enhanced chondrogenesis and their potential molecular mechanisms. Methods The datasets were downloaded from the Gene Expression Omnibus (GEO) database and contain six transforming growth factor-beta-3 (TGF-β3) induced bovine bone marrow-derived MSCs specimens and six TGF-β3/dynamic-compression-induced specimens at day 42. Screening differentially expressed genes (DEGs) was performed and then analysed via bioinformatics methods. The Database for Annotation, Visualisation, and Integrated Discovery (DAVID) online analysis was utilised to obtain the Gene Ontology (GO) and Kyoto Encyclopaedia of Genes and Genomes (KEGG) pathway enrichment. The protein-protein interaction (PPI) network of the DEGs was constructed based on data from the STRING database and visualised through the Cytoscape software. The functional modules were extracted from the PPI network for further analysis. Results The top 10 hub genes ranked by their connection degrees were IL6, UBE2C, TOP2A, MCM4, PLK2, SMC2, BMP2, LMO7, TRIM36, and MAPK8. Multiple signalling pathways (including the PI3K-Akt signalling pathway, the toll-like receptor signalling pathway, the TNF signalling pathway, and the MAPK pathway) may impact the sensation, transduction, and reaction of external mechanical stimuli. Conclusions This study provides a theoretical finding showing that gene UBE2C, IL6, and MAPK8, and multiple signalling pathways may play pivotal roles in dynamic compression-enhanced chondrogenesis.
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Affiliation(s)
- Jishizhan Chen
- UCL Centre for Biomaterials in Surgical Reconstruction and Regeneration, Division of Surgery & Interventional Science, University College London, London, NW3 2PF, UK
| | - Lidan Chen
- UCL Centre for Biomaterials in Surgical Reconstruction and Regeneration, Division of Surgery & Interventional Science, University College London, London, NW3 2PF, UK.,Centre of Maxillofacial Surgery and Digital Plastic Surgery, Plastic Surgery Hospital, Chinese Academy of Medical Sciences and Peking Union Medical College, Beijing, 100144, People's Republic of China
| | - Jia Hua
- UCL Institute of Orthopaedics and Musculoskeletal Science, Division of Surgery & Interventional Science, University College London, Stanmore, London, HA7 4AP, UK.,The Griffin Institute (Northwick Park Institute for Medical Research), Harrow, London, HA1 3UJ, UK.,Faculty of Science and Technology, Middlesex University, London, NW4 4BT, UK
| | - Wenhui Song
- UCL Centre for Biomaterials in Surgical Reconstruction and Regeneration, Division of Surgery & Interventional Science, University College London, London, NW3 2PF, UK.
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Di Fiore R, Suleiman S, Ellul B, O’Toole SA, Savona-Ventura C, Felix A, Napolioni V, Conlon NT, Kahramanoglu I, Azzopardi MJ, Dalmas M, Calleja N, Brincat MR, Muscat-Baron Y, Sabol M, Dimitrievska V, Yordanov A, Vasileva-Slaveva M, von Brockdorff K, Micallef RA, Kubelac P, Achimas-Cadariu P, Vlad C, Tzortzatou O, Poka R, Giordano A, Felice A, Reed N, Herrington CS, Faraggi D, Calleja-Agius J. GYNOCARE Update: Modern Strategies to Improve Diagnosis and Treatment of Rare Gynecologic Tumors—Current Challenges and Future Directions. Cancers (Basel) 2021; 13:cancers13030493. [PMID: 33514073 PMCID: PMC7865420 DOI: 10.3390/cancers13030493] [Citation(s) in RCA: 12] [Impact Index Per Article: 4.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/31/2020] [Revised: 01/19/2021] [Accepted: 01/22/2021] [Indexed: 12/11/2022] Open
Abstract
Simple Summary More than 50% of all the tumors affecting the female genital tract can be classified as rare and usually have a poor prognosis owing to delayed diagnosis and treatment. Currently, gynecologic cancer research, due to distinct scientific and technological challenges, is lagging behind. Moreover, the overall efforts for addressing these challenges are fragmented across different countries. The European Network for Gynecological Rare Cancer Research: GYNOCARE aims to address these challenges by creating a unique network between key stakeholders covering distinct domains from basic research to cure. GYNOCARE is part of a European Collaboration in Science and Technology (COST) with the aim to focus on the development of new approaches to improve the diagnosis and treatment of rare gynecological tumors. Here, we provide a brief overview describing the goals of this COST Action and its future challenges with the aim to continue fighting against this rare cancer. Abstract More than 50% of all gynecologic tumors can be classified as rare (defined as an incidence of ≤6 per 100,000 women) and usually have a poor prognosis owing to delayed diagnosis and treatment. In contrast to almost all other common solid tumors, the treatment of rare gynecologic tumors (RGT) is often based on expert opinion, retrospective studies, or extrapolation from other tumor sites with similar histology, leading to difficulty in developing guidelines for clinical practice. Currently, gynecologic cancer research, due to distinct scientific and technological challenges, is lagging behind. Moreover, the overall efforts for addressing these challenges are fragmented across different European countries and indeed, worldwide. The GYNOCARE, COST Action CA18117 (European Network for Gynecological Rare Cancer Research) programme aims to address these challenges through the creation of a unique network between key stakeholders covering distinct domains from concept to cure: basic research on RGT, biobanking, bridging with industry, and setting up the legal and regulatory requirements for international innovative clinical trials. On this basis, members of this COST Action, (Working Group 1, “Basic and Translational Research on Rare Gynecological Cancer”) have decided to focus their future efforts on the development of new approaches to improve the diagnosis and treatment of RGT. Here, we provide a brief overview of the current state-of-the-art and describe the goals of this COST Action and its future challenges with the aim to stimulate discussion and promote synergy across scientists engaged in the fight against this rare cancer worldwide.
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Affiliation(s)
- Riccardo Di Fiore
- Department of Anatomy, Faculty of Medicine and Surgery, University of Malta, MSD 2080 Msida, Malta; (R.D.F.); (S.S.)
- Center for Biotechnology, Sbarro Institute for Cancer Research and Molecular Medicine, College of Science and Technology, Temple University, Philadelphia, PA 19122, USA;
| | - Sherif Suleiman
- Department of Anatomy, Faculty of Medicine and Surgery, University of Malta, MSD 2080 Msida, Malta; (R.D.F.); (S.S.)
| | - Bridget Ellul
- Centre for Molecular Medicine & Biobanking, University of Malta, MSD 2080 Msida, Malta;
| | - Sharon A. O’Toole
- Departments of Obstetrics and Gynaecology and Histopathology, Trinity St James’s Cancer Institute, Trinity College Dublin, Dublin 8, Ireland;
| | - Charles Savona-Ventura
- Department of Obstetrics and Gynaecology, Faculty of Medicine and Surgery, University of Malta, MSD 2080 Msida, Malta;
| | - Ana Felix
- Department of Pathology, Campo dos Mártires da Pátria, Instituto Portugues de Oncologia de Lisboa, NOVA Medical School, UNL, 130, 1169-056 Lisboa, Portugal;
| | - Valerio Napolioni
- Genomic And Molecular Epidemiology (GAME) Lab., School of Biosciences and Veterinary Medicine, University of Camerino, 62032 Camerino, Italy;
| | - Neil T. Conlon
- National Institute for Cellular Biotechnology, Dublin City University, Glasnevin, 9 Dublin, Ireland;
| | - Ilker Kahramanoglu
- Department of Gynecologic Oncology, Emsey Hospital, Istanbul 3400, Turkey;
| | - Miriam J. Azzopardi
- Directorate for Health Information and Research, PTA 1313 G’Mangia, Malta; (M.J.A.); (N.C.)
| | - Miriam Dalmas
- Office of the Chief Medical Officer, Department of Policy in Health, Ministry for Health, 15 Merchants Street, VLT 1171 Valletta, Malta;
| | - Neville Calleja
- Directorate for Health Information and Research, PTA 1313 G’Mangia, Malta; (M.J.A.); (N.C.)
| | - Mark R. Brincat
- Department of Obstetrics and Gynaecology, Mater Dei Hospital, Triq Dun Karm, MSD 2090 Msida, Malta; (M.R.B.); (Y.M.-B.)
| | - Yves Muscat-Baron
- Department of Obstetrics and Gynaecology, Mater Dei Hospital, Triq Dun Karm, MSD 2090 Msida, Malta; (M.R.B.); (Y.M.-B.)
| | - Maja Sabol
- Laboratory for Hereditary Cancer, Division of Molecular Medicine, Ruđer Bošković Institute, 10000 Zagreb, Croatia;
| | | | - Angel Yordanov
- Department of Gynecologic Oncology, Medical University Pleven, 5800 Pleven, Bulgaria;
| | | | - Kristelle von Brockdorff
- Sir Anthony Mamo Oncology Centre, Department of Oncology and Radiotherapy, Mater Dei Hospital, MSD 2090 Msida, Malta; (K.v.B.); (R.A.M.)
| | - Rachel A. Micallef
- Sir Anthony Mamo Oncology Centre, Department of Oncology and Radiotherapy, Mater Dei Hospital, MSD 2090 Msida, Malta; (K.v.B.); (R.A.M.)
| | - Paul Kubelac
- Department of Medical Oncology, The Oncology Institute “Prof. Dr. Ion Chiricuţă”. 34–36 Republicii Street, 400015 Cluj-Napoca, Romania;
- Department of Oncology, “Iuliu Hatieganu” University of Medicine and Pharmacy, 400012 Cluj-Napoca, Romania; (P.A.-C.); (C.V.)
| | - Patriciu Achimas-Cadariu
- Department of Oncology, “Iuliu Hatieganu” University of Medicine and Pharmacy, 400012 Cluj-Napoca, Romania; (P.A.-C.); (C.V.)
- Department of Surgical Oncology, The Oncology Institute “Prof. Dr. Ion Chiricuta”, 400015 Cluj-Napoca, Romania
| | - Catalin Vlad
- Department of Oncology, “Iuliu Hatieganu” University of Medicine and Pharmacy, 400012 Cluj-Napoca, Romania; (P.A.-C.); (C.V.)
- Department of Surgery, The Oncology Institute “Prof. Dr. Ion Chiricuta”, 400015 Cluj Napoca, Romania
| | - Olga Tzortzatou
- Biomedical Research Foundation of the Academy of Athens, Soranou Efesiou 4 str., 11527 Athens, Greece;
| | - Robert Poka
- Institute of Obstetrics and Gynaecology, University of Debrecen, Nagyerdei krt. 98, 4032 Debrecen, Hungary;
| | - Antonio Giordano
- Center for Biotechnology, Sbarro Institute for Cancer Research and Molecular Medicine, College of Science and Technology, Temple University, Philadelphia, PA 19122, USA;
- Department of Medical Biotechnologies, University of Siena, 53100 Siena, Italy
| | - Alex Felice
- Centre of Molecular Medicine and BioBanking, Department of Physiology & Biochemistry, Faculty of Medicine & Surgery, University of Malta, MSD 2080 Msida, Malta;
| | - Nicholas Reed
- Beatson Oncology Centre, Gartnavel General Hospital, 1053 Great Western Road, Glasgow G12 0YN, UK;
| | - C. Simon Herrington
- Cancer Research UK Edinburgh Centre, Western General Hospital, University of Edinburgh, Crewe Road South, Edinburgh EH4 2XR, UK;
| | - David Faraggi
- Department of Statistics, University of Haifa, Haifa 31905, Israel;
| | - Jean Calleja-Agius
- Department of Anatomy, Faculty of Medicine and Surgery, University of Malta, MSD 2080 Msida, Malta; (R.D.F.); (S.S.)
- Correspondence: ; Tel.: +356-2340-1892
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O'Sullivan MP, Casey S, Finder M, Ahearne C, Clarke G, Hallberg B, Boylan GB, Murray DM. Up-Regulation of Nfat5 mRNA and Fzd4 mRNA as a Marker of Poor Outcome in Neonatal Hypoxic-Ischemic Encephalopathy. J Pediatr 2021; 228:74-81.e2. [PMID: 32828883 DOI: 10.1016/j.jpeds.2020.08.051] [Citation(s) in RCA: 4] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Received: 03/16/2020] [Revised: 08/17/2020] [Accepted: 08/18/2020] [Indexed: 12/11/2022]
Abstract
OBJECTIVE To evaluate umbilical cord messenger RNA (mRNA) expression as biomarkers for the grade of hypoxic-ischemic encephalopathy (HIE) and long-term neurodevelopment outcome. STUDY DESIGN Infants were recruited from the BiHiVE1 study, Ireland (2009-2011), and the BiHiVE2 study, Ireland, and Sweden (2013-2015). Infants with HIE were assigned modified Sarnat scores at 24 hours and followed at 18-36 months. mRNA expression from cord blood was measured using quantitative real-time polymerase chain reaction. RESULTS We studied 124 infants (controls, n = 37; perinatal asphyxia, n = 43; and HIE, n = 44). Fzd4 mRNA increased in severe HIE (median relative quantification, 2.98; IQR, 2.23-3.68) vs mild HIE (0.88; IQR, 0.46-1.37; P = .004), and in severe HIE vs moderate HIE (1.06; IQR, 0.81-1.20; P = .003). Fzd4 mRNA also increased in infants eligible for therapeutic hypothermia (1.20; IQR, 0.92-2.37) vs those who were ineligible for therapeutic hypothermia group (0.81; IQR, 0.46-1.53; P = .017). Neurodevelopmental outcome was analyzed for 56 infants. Nfat5 mRNA increased in infants with severely abnormal (1.26; IQR, 1.17-1.39) vs normal outcomes (0.97; IQR, 0.83-1.24; P = .036), and also in infants with severely abnormal vs mildly abnormal outcomes (0.96; IQR, 0.80-1.06; P = .013). Fzd4 mRNA increased in infants with severely abnormal (2.51; IQR, 1.60-3.56) vs normal outcomes (0.74; IQR, 0.48-1.49; P = .004) and in infants with severely abnormal vs mildly abnormal outcomes (0.97; IQR, 0.75-1.34; P = .026). CONCLUSIONS Increased Fzd4 mRNA expression was observed in cord blood of infants with severe HIE; Nfat5 mRNA and Fzd4 mRNA expression were increased in infants with severely abnormal long-term outcomes. These mRNA may augment current measures as early objective markers of HIE severity at delivery.
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Affiliation(s)
- Marc Paul O'Sullivan
- INFANT Research Centre, Ireland; Department of Paediatrics and Child Health, University College Cork, Cork, Ireland; National Children's Research Centre, Crumlin, Dublin, Ireland.
| | - Sophie Casey
- INFANT Research Centre, Ireland; Department of Paediatrics and Child Health, University College Cork, Cork, Ireland
| | - Mikael Finder
- Department of Clinical Science, Intervention, and Technology, Karolinska Institutet, Stockholm, Sweden; Neonatal Department, Karolinska University Hospital, Stockholm, Sweden
| | - Caroline Ahearne
- INFANT Research Centre, Ireland; Department of Paediatrics and Child Health, University College Cork, Cork, Ireland
| | - Gerard Clarke
- INFANT Research Centre, Ireland; Department of Psychiatry and Neurobehavioural Science, University College Cork, Cork, Ireland; APC Microbiome, Ireland, University College Cork, Cork, Ireland
| | - Boubou Hallberg
- Department of Clinical Science, Intervention, and Technology, Karolinska Institutet, Stockholm, Sweden; Neonatal Department, Karolinska University Hospital, Stockholm, Sweden
| | - Geraldine B Boylan
- INFANT Research Centre, Ireland; Department of Paediatrics and Child Health, University College Cork, Cork, Ireland
| | - Deirdre M Murray
- INFANT Research Centre, Ireland; Department of Paediatrics and Child Health, University College Cork, Cork, Ireland; National Children's Research Centre, Crumlin, Dublin, Ireland
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Qin X, Chen J, Zhou T. 22q11.2 deletion syndrome and schizophrenia. Acta Biochim Biophys Sin (Shanghai) 2020; 52:1181-1190. [PMID: 33098288 DOI: 10.1093/abbs/gmaa113] [Citation(s) in RCA: 8] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/20/2020] [Revised: 08/16/2020] [Accepted: 08/17/2020] [Indexed: 12/22/2022] Open
Abstract
22q11.2 deletion is a common microdeletion that causes an array of developmental defects including 22q11.2 deletion syndrome (22q11DS) or DiGeorge syndrome and velocardiofacial syndrome. About 30% of patients with 22q11.2 deletion develop schizophrenia. Mice with deletion of the ortholog region in mouse chromosome 16qA13 exhibit schizophrenia-like abnormal behaviors. It is suggested that the genes deleted in 22q11DS are involved in the pathogenesis of schizophrenia. Among these genes, COMT, ZDHHC8, DGCR8, and PRODH have been identified as schizophrenia susceptibility genes. And DGCR2 is also found to be associated with schizophrenia. In this review, we focused on these five genes and reviewed their functions in the brain and the potential pathophysiological mechanisms in schizophrenia, which will give us a deeper understanding of the pathology of schizophrenia.
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Affiliation(s)
- Xianzheng Qin
- Queen Mary School of Nanchang University, Nanchang University, Nanchang 330031, China
| | - Jiang Chen
- Laboratory of Synaptic Development and Plasticity, Institute of Life Science, Nanchang University, Nanchang 330031, China
| | - Tian Zhou
- School of Basic Medical Sciences, Nanchang University, Nanchang 330031, China
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Lambrou GI, Hatziagapiou K, Zaravinos A. The Non-Coding RNA GAS5 and Its Role in Tumor Therapy-Induced Resistance. Int J Mol Sci 2020; 21:ijms21207633. [PMID: 33076450 PMCID: PMC7588928 DOI: 10.3390/ijms21207633] [Citation(s) in RCA: 16] [Impact Index Per Article: 4.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/28/2020] [Revised: 10/13/2020] [Accepted: 10/13/2020] [Indexed: 02/07/2023] Open
Abstract
The growth arrest-specific transcript 5 (GAS5) is a >200-nt lncRNA molecule that regulates several cellular functions, including proliferation, apoptosis, invasion and metastasis, across different types of human cancers. Here, we reviewed the current literature on the expression of GAS5 in leukemia, cervical, breast, ovarian, prostate, urinary bladder, lung, gastric, colorectal, liver, osteosarcoma and brain cancers, as well as its interaction with various miRNAs and its effect on therapy-related resistance in these malignancies. The general consensus is that GAS5 acts as a tumor suppressor across different tumor types and that its up-regulation results in tumor sensitization to chemotherapy or radiotherapy. GAS5 seems to play a previously unappreciated, but significant role in tumor therapy-induced resistance.
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Affiliation(s)
- George I. Lambrou
- Choremeio Research Laboratory, First Department of Pediatrics, National and Kapodistrian University of Athens, Thivon & Levadeias 8, 11527 Goudi, Athens, Greece;
- Correspondence: (G.I.L.); (A.Z.); Tel.: +30-210-7467427 (G.I.L.); +974-4403-7819 (A.Z.)
| | - Kyriaki Hatziagapiou
- Choremeio Research Laboratory, First Department of Pediatrics, National and Kapodistrian University of Athens, Thivon & Levadeias 8, 11527 Goudi, Athens, Greece;
| | - Apostolos Zaravinos
- Department of Basic Medical Sciences, College of Medicine, Member of QU Health, Qatar University, 2713 Doha, Qatar
- Correspondence: (G.I.L.); (A.Z.); Tel.: +30-210-7467427 (G.I.L.); +974-4403-7819 (A.Z.)
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Ganger MT, Dietz GD, Headley P, Ewing SJ. Application of the common base method to regression and analysis of covariance (ANCOVA) in qPCR experiments and subsequent relative expression calculation. BMC Bioinformatics 2020; 21:423. [PMID: 32993490 PMCID: PMC7523404 DOI: 10.1186/s12859-020-03696-y] [Citation(s) in RCA: 5] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/22/2020] [Accepted: 07/23/2020] [Indexed: 11/11/2022] Open
Abstract
Background Quantitative polymerase chain reaction (qPCR) is the technique of choice for quantifying gene expression. While the technique itself is well established, approaches for the analysis of qPCR data continue to improve. Results Here we expand on the common base method to develop procedures for testing linear relationships between gene expression and either a measured dependent variable, independent variable, or expression of another gene. We further develop functions relating variables to a relative expression value and develop calculations for determination of associated confidence intervals. Conclusions Traditional qPCR analysis methods typically rely on paired designs. The common base method does not require such pairing of samples. It is therefore applicable to other designs within the general linear model such as linear regression and analysis of covariance. The methodology presented here is also simple enough to be performed using basic spreadsheet software.
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Affiliation(s)
- Michael T Ganger
- Department of Biology, Gannon University, Erie, PA, 16541-0001, USA.
| | - Geoffrey D Dietz
- Department of Mathematics, Gannon University, Erie, PA, 16541-0001, USA
| | - Patrick Headley
- Department of Mathematics, Gannon University, Erie, PA, 16541-0001, USA
| | - Sarah J Ewing
- Department of Biology, Gannon University, Erie, PA, 16541-0001, USA
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Rubanova N, Pinna G, Kropp J, Campalans A, Radicella JP, Polesskaya A, Harel-Bellan A, Morozova N. MasterPATH: network analysis of functional genomics screening data. BMC Genomics 2020; 21:632. [PMID: 32928103 PMCID: PMC7491077 DOI: 10.1186/s12864-020-07047-2] [Citation(s) in RCA: 3] [Impact Index Per Article: 0.8] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/02/2019] [Accepted: 09/01/2020] [Indexed: 12/18/2022] Open
Abstract
Background Functional genomics employs several experimental approaches to investigate gene functions. High-throughput techniques, such as loss-of-function screening and transcriptome profiling, allow to identify lists of genes potentially involved in biological processes of interest (so called hit list). Several computational methods exist to analyze and interpret such lists, the most widespread of which aim either at investigating of significantly enriched biological processes, or at extracting significantly represented subnetworks. Results Here we propose a novel network analysis method and corresponding computational software that employs the shortest path approach and centrality measure to discover members of molecular pathways leading to the studied phenotype, based on functional genomics screening data. The method works on integrated interactomes that consist of both directed and undirected networks – HIPPIE, SIGNOR, SignaLink, TFactS, KEGG, TransmiR, miRTarBase. The method finds nodes and short simple paths with significant high centrality in subnetworks induced by the hit genes and by so-called final implementers – the genes that are involved in molecular events responsible for final phenotypic realization of the biological processes of interest. We present the application of the method to the data from miRNA loss-of-function screen and transcriptome profiling of terminal human muscle differentiation process and to the gene loss-of-function screen exploring the genes that regulates human oxidative DNA damage recognition. The analysis highlighted the possible role of several known myogenesis regulatory miRNAs (miR-1, miR-125b, miR-216a) and their targets (AR, NR3C1, ARRB1, ITSN1, VAV3, TDGF1), as well as linked two major regulatory molecules of skeletal myogenesis, MYOD and SMAD3, to their previously known muscle-related targets (TGFB1, CDC42, CTCF) and also to a number of proteins such as C-KIT that have not been previously studied in the context of muscle differentiation. The analysis also showed the role of the interaction between H3 and SETDB1 proteins for oxidative DNA damage recognition. Conclusion The current work provides a systematic methodology to discover members of molecular pathways in integrated networks using functional genomics screening data. It also offers a valuable instrument to explain the appearance of a set of genes, previously not associated with the process of interest, in the hit list of each particular functional genomics screening.
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Affiliation(s)
- Natalia Rubanova
- Institut des Hautes Etudes Scientifiques, Le Bois-Marie 35 rte de Chartres, 91440, Bures-sur-Yvette, France. .,Université Paris Diderot, Paris, France. .,Skolkovo Institute of Science and Technology, Skolkovo, Russia.
| | - Guillaume Pinna
- Institute for Integrative Biology of the Cell (I2BC), CEA, CNRS, Univ. Paris-Sud, Université Paris-Saclay, 91198, Gif-sur-Yvette cedex, France
| | - Jeremie Kropp
- Institut des Hautes Etudes Scientifiques, Le Bois-Marie 35 rte de Chartres, 91440, Bures-sur-Yvette, France
| | - Anna Campalans
- Institute of Molecular and Cellular Radiobiology, Institut François Jacob, CEA, F-92265, Fontenay-aux-Roses, France.,INSERM, U967, bâtiment 56 PC 103 18 route du Panorama, BP6 92265, Fontenay-aux-Roses Cedex, France.,Université Paris Sud, U967, bâtiment 56 PC 103 18 route du Panorama, BP6 92265, Fontenay-aux-Roses Cedex, France
| | - Juan Pablo Radicella
- Institute of Molecular and Cellular Radiobiology, Institut François Jacob, CEA, F-92265, Fontenay-aux-Roses, France.,INSERM, U967, bâtiment 56 PC 103 18 route du Panorama, BP6 92265, Fontenay-aux-Roses Cedex, France.,Université Paris Sud, U967, bâtiment 56 PC 103 18 route du Panorama, BP6 92265, Fontenay-aux-Roses Cedex, France
| | - Anna Polesskaya
- Ecole Polytechnique, Université Paris-Saclay, CNRS UMR 7654, Laboratoire de Biochimie, Ecole Polytechnique, 91128, Palaiseau, France
| | - Annick Harel-Bellan
- Institut des Hautes Etudes Scientifiques, Le Bois-Marie 35 rte de Chartres, 91440, Bures-sur-Yvette, France
| | - Nadya Morozova
- Institut des Hautes Etudes Scientifiques, Le Bois-Marie 35 rte de Chartres, 91440, Bures-sur-Yvette, France.,Institute for Integrative Biology of the Cell (I2BC), CEA, CNRS, Univ. Paris-Sud, Université Paris-Saclay, 91198, Gif-sur-Yvette cedex, France
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Khwatenge CN, Kimathi BM, Nahashon SN. Transcriptome Analysis and Expression of Selected Cationic Amino Acid Transporters in the Liver of Broiler Chicken Fed Diets with Varying Concentrations of Lysine. Int J Mol Sci 2020; 21:E5594. [PMID: 32764289 PMCID: PMC7460557 DOI: 10.3390/ijms21165594] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/27/2020] [Revised: 07/24/2020] [Accepted: 08/03/2020] [Indexed: 11/28/2022] Open
Abstract
Amino acids are known to play a key role in gene expression regulation. Amino acid signaling is mediated via two pathways: the mammalian target of rapamycin complex 1 (mTORC1) and the amino acid responsive (AAR) pathways. Cationic amino acid transporters (CATs) are crucial in these pathways due to their sensing, signaling and transport functions. The availability of certain amino acids plays a key role in the intake of other amino acids, hence affecting growth in young birds. However, the specific mechanism for regulating lysine transport for growth is not clear. In this study, we analyze the transcriptome profiles and mRNA expression of selected cationic amino acid transporters in the livers of broilers fed low and high lysine diets. Birds consumed high-lysine (1.42% lysine) or low-lysine (0.85% lysine) diets while the control group consumed 1.14% lysine diet. These concentrations of lysine represent 125% (high lysine), 75% (low lysine) and 100% (control), respectively, of the National Research Council's (NRC) recommendation for broiler chickens. After comparing the two groups, 210 differentially expressed genes (DEGs) were identified (fold change >1 and false discovery rate (FDR) <0.05). When comparing the high lysine and the low lysine treatments, there were 67 upregulated genes and 143 downregulated genes among these DEGs. Analysis of Kyoto Encyclopedia of Genes and Genomes (KEGG) and the Gene Ontology (GO) enrichment analysis show that cellular growth, lipid metabolism and lysine metabolism pathways were among the significantly enriched pathways. This study contributes to a better understanding of the potential molecular mechanisms underlying the correlation between lysine intake, body weight gain (BWG) and feed intake (FI) in broiler chickens. Moreover, the DEGs obtained in this study may be used as potential candidate genes for further investigation of broiler growth customized responses to individualized nutrients such as amino acids.
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Affiliation(s)
- Collins N. Khwatenge
- Department of Biological Sciences, Tennessee State University, Nashville, TN 37209, USA; (C.N.K.); (B.M.K.)
- Department of Agricultural and Environmental Sciences, Tennessee State University, Nashville, TN 37209, USA
| | - Boniface M. Kimathi
- Department of Biological Sciences, Tennessee State University, Nashville, TN 37209, USA; (C.N.K.); (B.M.K.)
- Department of Agricultural and Environmental Sciences, Tennessee State University, Nashville, TN 37209, USA
| | - Samuel N. Nahashon
- Department of Agricultural and Environmental Sciences, Tennessee State University, Nashville, TN 37209, USA
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Njoku K, Sutton CJ, Whetton AD, Crosbie EJ. Metabolomic Biomarkers for Detection, Prognosis and Identifying Recurrence in Endometrial Cancer. Metabolites 2020; 10:E314. [PMID: 32751940 PMCID: PMC7463916 DOI: 10.3390/metabo10080314] [Citation(s) in RCA: 34] [Impact Index Per Article: 8.5] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/02/2020] [Revised: 07/24/2020] [Accepted: 07/27/2020] [Indexed: 12/24/2022] Open
Abstract
Metabolic reprogramming is increasingly recognised as one of the defining hallmarks of tumorigenesis. There is compelling evidence to suggest that endometrial cancer develops and progresses in the context of profound metabolic dysfunction. Whilst the incidence of endometrial cancer continues to rise in parallel with the global epidemic of obesity, there are, as yet, no validated biomarkers that can aid risk prediction, early detection, prognostic evaluation or surveillance. Advances in high-throughput technologies have, in recent times, shown promise for biomarker discovery based on genomic, transcriptomic, proteomic and metabolomic platforms. Metabolomics, the large-scale study of metabolites, deals with the downstream products of the other omics technologies and thus best reflects the human phenotype. This review aims to provide a summary and critical synthesis of the existing literature with the ultimate goal of identifying the most promising metabolite biomarkers that can augment current endometrial cancer diagnostic, prognostic and recurrence surveillance strategies. Identified metabolites and their biochemical pathways are discussed in the context of what we know about endometrial carcinogenesis and their potential clinical utility is evaluated. Finally, we underscore the challenges inherent in metabolomic biomarker discovery and validation and provide fresh perspectives and directions for future endometrial cancer biomarker research.
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Affiliation(s)
- Kelechi Njoku
- Division of Cancer Sciences, School of Medical Sciences, Faculty of Biology, Medicine and Health, University of Manchester, 5th Floor Research, St Mary’s Hospital, Oxford Road, Manchester M13 9WL, UK;
- Stoller Biomarker Discovery Centre, Institute of Cancer Sciences, Faculty of Biology, Medicine and Health, University of Manchester, Manchester M13 9PL, UK;
| | - Caroline J.J Sutton
- School of Biological Sciences, Faculty of Biology, Medicine and Health, University of Manchester, Oxford Road, Manchester M13 9WL, UK;
| | - Anthony D. Whetton
- Stoller Biomarker Discovery Centre, Institute of Cancer Sciences, Faculty of Biology, Medicine and Health, University of Manchester, Manchester M13 9PL, UK;
| | - Emma J. Crosbie
- Division of Cancer Sciences, School of Medical Sciences, Faculty of Biology, Medicine and Health, University of Manchester, 5th Floor Research, St Mary’s Hospital, Oxford Road, Manchester M13 9WL, UK;
- Department of Obstetrics and Gynaecology, Manchester University NHS Foundation Trust, Manchester Academic Health Science Centre, Manchester M13 9WL, UK
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63
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Transcriptome Analysis of Testes and Uterus: Reproductive Dysfunction Induced by Toxoplasma gondii in Mice. Microorganisms 2020; 8:microorganisms8081136. [PMID: 32731337 PMCID: PMC7464677 DOI: 10.3390/microorganisms8081136] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/23/2020] [Revised: 07/03/2020] [Accepted: 07/20/2020] [Indexed: 11/17/2022] Open
Abstract
Toxoplasma gondii (T. gondii) infection in female mammals during pregnancy can result in poor pregnancy. Similarly, it can result in male reproductive disorders in male mammals. Although the testes and uterus have very different biological makeup, they are still both attacked by T. gondii resulting in reproductive dysfunctions. We hypothesized that there are significant common genes in the testes and uterus that interact with T. gondii. Finding out and studying these genes is vital to understand the infection mechanism of T. gondii and the induced disease pathogenesis. To achieve this goal, we built a mice model of acute infection with T. gondii and the testes and uterus of the mice were sequenced by RNA-Seq. A total of 291 and 679 significantly differently expressed genes (DEGs) were obtained from the testes and the uterus, respectively. In the Gene Ontology (GO) analysis, part of the DEGs in the testes and uterus were related to 35 GO functions. When compared with the KEGG database, seven pathways affecting both the testes and uterus during the course of T. gondii infection were identified. In addition, Toxoplasmosis can significantly affect the expression of Nlrp5 and Insc leading to negative outcomes in the host. On the other hand, the host regulates Gbp7, Gbp2b, and Ifit3 to defend against T. gondii infection.
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64
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Zhou Z, Sohn YS, Nechushtai R, Willner I. DNA Tetrahedra Modules as Versatile Optical Sensing Platforms for Multiplexed Analysis of miRNAs, Endonucleases, and Aptamer-Ligand Complexes. ACS NANO 2020; 14:9021-9031. [PMID: 32539340 PMCID: PMC7467810 DOI: 10.1021/acsnano.0c04031] [Citation(s) in RCA: 78] [Impact Index Per Article: 19.5] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 05/14/2020] [Accepted: 06/15/2020] [Indexed: 05/21/2023]
Abstract
The sensing modules for analyzing miRNAs or the endonucleases consist of tetrahedra functionalized with three different fluorophore-quencher pairs in spatially quenched configurations and hairpin units acting as recognition elements for the analytes. Three different miRNAs (miRNA-21, miRNA-221, and miRNA-155) or three different endonucleases (Nt.BbvCI, EcoRI, and HindIII) uncage the respective hairpins, leading to the switched-on fluorescence of the respective fluorophores and to the multiplex detection of the respective analytes. In addition, a tetrahedron module for the multiplexed analysis of aptamer ligand complexes (ligands = ATP, thrombin, VEGF) is introduced. The module includes edges modified with three spatially separated fluorophore-quencher pairs that were stretched by the respective aptamer strands to yield a switched-on fluorescent state. Formation of the respective aptamer ligands reconfigures the edges into fluorophore-quenched caged-hairpin structures that enable the multiplexed analysis of the aptamer-ligand complexes. The facile permeation of the tetrahedra structures into cells is used for the imaging of MCF-7 and HepG2 cancer cells and their discrimination from normal epithelial MCF-10A breast cells.
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Affiliation(s)
- Zhixin Zhou
- Institute
of Chemistry, The Minerva Center for Biohybrid Complex Systems, The Hebrew University of Jerusalem, Jerusalem 91904, Israel
| | - Yang Sung Sohn
- Institute
of Life Sciences, The Hebrew University
of Jerusalem, Jerusalem 91904, Israel
| | - Rachel Nechushtai
- Institute
of Life Sciences, The Hebrew University
of Jerusalem, Jerusalem 91904, Israel
| | - Itamar Willner
- Institute
of Chemistry, The Minerva Center for Biohybrid Complex Systems, The Hebrew University of Jerusalem, Jerusalem 91904, Israel
- E-mail:
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65
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Wu LR, Fang JZ, Khodakov D, Zhang DY. Nucleic Acid Quantitation with Log-Linear Response Hybridization Probe Sets. ACS Sens 2020; 5:1604-1614. [PMID: 32475109 DOI: 10.1021/acssensors.0c00052] [Citation(s) in RCA: 3] [Impact Index Per Article: 0.8] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/15/2023]
Abstract
Concentrations of different nucleic acid species in biological samples span many orders of magnitude. A real-time polymerase chain reaction maps the concentration of a target nucleic acid sequence log-linearly into cycle threshold to enable quantitation with a wide dynamic range but suffers from enzymatic biases. Here, we present a general design for constructing hybridization probe sets with highly log-linear response curves to enable accurate enzyme-free quantitation across large ranges (more than 6 logs) of target DNA concentrations. The sensitivity of each component probe is accurately adjusted via formulation stoichiometry to reduce the standard error of target quantitation down to 7%. As a proof of concept, we show multiplexed quantitation of three microRNA species in total RNA of the human brain and liver.
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Affiliation(s)
- Lucia R. Wu
- Department of Bioengineering, Rice University, Houston, Texas 77005, United States
| | - John Z. Fang
- Department of Bioengineering, Rice University, Houston, Texas 77005, United States
| | - Dmitriy Khodakov
- Department of Bioengineering, Rice University, Houston, Texas 77005, United States
| | - David Yu Zhang
- Department of Bioengineering, Rice University, Houston, Texas 77005, United States
- Systems, Synthetic, and Physical Biology, Rice University, Houston, Texas 77005, United States
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66
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Yan F, Gao F. A systematic strategy for the investigation of vaccines and drugs targeting bacteria. Comput Struct Biotechnol J 2020; 18:1525-1538. [PMID: 32637049 PMCID: PMC7327267 DOI: 10.1016/j.csbj.2020.06.008] [Citation(s) in RCA: 8] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/28/2020] [Revised: 06/02/2020] [Accepted: 06/03/2020] [Indexed: 02/07/2023] Open
Abstract
Infectious and epidemic diseases induced by bacteria have historically caused great distress to people, and have even resulted in a large number of deaths worldwide. At present, many researchers are working on the discovery of viable drug and vaccine targets for bacteria through multiple methods, including the analyses of comparative subtractive genome, core genome, replication-related proteins, transcriptomics and riboswitches, which plays a significant part in the treatment of infectious and pandemic diseases. The 3D structures of the desired target proteins, drugs and epitopes can be predicted and modeled through target analysis. Meanwhile, molecular dynamics (MD) analysis of the constructed drug/epitope-protein complexes is an important standard for testing the suitability of these screened drugs and vaccines. Currently, target discovery, target analysis and MD analysis are integrated into a systematic set of drug and vaccine analysis strategy for bacteria. We hope that this comprehensive strategy will help in the design of high-performance vaccines and drugs.
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Affiliation(s)
- Fangfang Yan
- Department of Physics, School of Science, Tianjin University, Tianjin 300072, China
| | - Feng Gao
- Department of Physics, School of Science, Tianjin University, Tianjin 300072, China
- Frontiers Science Center for Synthetic Biology and Key Laboratory of Systems Bioengineering (Ministry of Education), Tianjin University, Tianjin 300072, China
- SynBio Research Platform, Collaborative Innovation Center of Chemical Science and Engineering (Tianjin), Tianjin 300072, China
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67
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Gal J, Bailleux C, Chardin D, Pourcher T, Gilhodes J, Jing L, Guigonis JM, Ferrero JM, Milano G, Mograbi B, Brest P, Chateau Y, Humbert O, Chamorey E. Comparison of unsupervised machine-learning methods to identify metabolomic signatures in patients with localized breast cancer. Comput Struct Biotechnol J 2020; 18:1509-1524. [PMID: 32637048 PMCID: PMC7327012 DOI: 10.1016/j.csbj.2020.05.021] [Citation(s) in RCA: 10] [Impact Index Per Article: 2.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/11/2020] [Revised: 05/15/2020] [Accepted: 05/16/2020] [Indexed: 02/08/2023] Open
Abstract
Genomics and transcriptomics have led to the widely-used molecular classification of breast cancer (BC). However, heterogeneous biological behaviors persist within breast cancer subtypes. Metabolomics is a rapidly-expanding field of study dedicated to cellular metabolisms affected by the environment. The aim of this study was to compare metabolomic signatures of BC obtained by 5 different unsupervised machine learning (ML) methods. Fifty-two consecutive patients with BC with an indication for adjuvant chemotherapy between 2013 and 2016 were retrospectively included. We performed metabolomic profiling of tumor resection samples using liquid chromatography-mass spectrometry. Here, four hundred and forty-nine identified metabolites were selected for further analysis. Clusters obtained using 5 unsupervised ML methods (PCA k-means, sparse k-means, spectral clustering, SIMLR and k-sparse) were compared in terms of clinical and biological characteristics. With an optimal partitioning parameter k = 3, the five methods identified three prognosis groups of patients (favorable, intermediate, unfavorable) with different clinical and biological profiles. SIMLR and K-sparse methods were the most effective techniques in terms of clustering. In-silico survival analysis revealed a significant difference for 5-year predicted OS between the 3 clusters. Further pathway analysis using the 449 selected metabolites showed significant differences in amino acid and glucose metabolism between BC histologic subtypes. Our results provide proof-of-concept for the use of unsupervised ML metabolomics enabling stratification and personalized management of BC patients. The design of novel computational methods incorporating ML and bioinformatics techniques should make available tools particularly suited to improving the outcome of cancer treatment and reducing cancer-related mortalities.
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Affiliation(s)
- Jocelyn Gal
- University Côte d’Azur, Epidemiology and Biostatistics Department, Centre Antoine Lacassagne, Nice F-06189, France
| | - Caroline Bailleux
- University Côte d’Azur, Medical Oncology Department Centre Antoine Lacassagne, Nice F-06189, France
| | - David Chardin
- University Côte d’Azur, Nuclear Medicine Department, Centre Antoine Lacassagne, Nice F-06189, France
- University Côte d’Azur, Commissariat à l’Energie Atomique, Institut de Biosciences et Biotechnologies d'Aix-Marseille, Laboratory Transporters in Imaging and Radiotherapy in Oncology, Faculty of Medicine, Nice F-06100, France
| | - Thierry Pourcher
- University Côte d’Azur, Commissariat à l’Energie Atomique, Institut de Biosciences et Biotechnologies d'Aix-Marseille, Laboratory Transporters in Imaging and Radiotherapy in Oncology, Faculty of Medicine, Nice F-06100, France
| | - Julia Gilhodes
- Department of Biostatistics, Institut Claudius Regaud, IUCT-O Toulouse, France
| | - Lun Jing
- University Côte d’Azur, Commissariat à l’Energie Atomique, Institut de Biosciences et Biotechnologies d'Aix-Marseille, Laboratory Transporters in Imaging and Radiotherapy in Oncology, Faculty of Medicine, Nice F-06100, France
| | - Jean-Marie Guigonis
- University Côte d’Azur, Commissariat à l’Energie Atomique, Institut de Biosciences et Biotechnologies d'Aix-Marseille, Laboratory Transporters in Imaging and Radiotherapy in Oncology, Faculty of Medicine, Nice F-06100, France
| | - Jean-Marc Ferrero
- University Côte d’Azur, Medical Oncology Department Centre Antoine Lacassagne, Nice F-06189, France
| | - Gerard Milano
- University Côte d’Azur, Centre Antoine Lacassagne, Oncopharmacology Unit, Nice F-06189, France
| | - Baharia Mograbi
- University Côte d’Azur, CNRS UMR7284, INSERM U1081, IRCAN TEAM4 Centre Antoine Lacassagne FHU-Oncoage, Nice F-06189, France
| | - Patrick Brest
- University Côte d’Azur, CNRS UMR7284, INSERM U1081, IRCAN TEAM4 Centre Antoine Lacassagne FHU-Oncoage, Nice F-06189, France
| | - Yann Chateau
- University Côte d’Azur, Epidemiology and Biostatistics Department, Centre Antoine Lacassagne, Nice F-06189, France
| | - Olivier Humbert
- University Côte d’Azur, Nuclear Medicine Department, Centre Antoine Lacassagne, Nice F-06189, France
- University Côte d’Azur, Commissariat à l’Energie Atomique, Institut de Biosciences et Biotechnologies d'Aix-Marseille, Laboratory Transporters in Imaging and Radiotherapy in Oncology, Faculty of Medicine, Nice F-06100, France
| | - Emmanuel Chamorey
- University Côte d’Azur, Epidemiology and Biostatistics Department, Centre Antoine Lacassagne, Nice F-06189, France
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Masterson AN, Liyanage T, Berman C, Kaimakliotis H, Johnson M, Sardar R. A novel liquid biopsy-based approach for highly specific cancer diagnostics: mitigating false responses in assaying patient plasma-derived circulating microRNAs through combined SERS and plasmon-enhanced fluorescence analyses. Analyst 2020; 145:4173-4180. [PMID: 32490854 DOI: 10.1039/d0an00538j] [Citation(s) in RCA: 20] [Impact Index Per Article: 5.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/16/2022]
Abstract
Studies have shown that microRNAs, which are small noncoding RNAs, hold tremendous promise as next-generation circulating biomarkers for early cancer detection via liquid biopsies. A novel, solid-state nanoplasmonic sensor capable of assaying circulating microRNAs through a combined surface-enhanced Raman scattering (SERS) and plasmon-enhanced fluorescence (PEF) approach has been developed. Here, the unique localized surface plasmon resonance properties of chemically-synthesized gold triangular nanoprisms (Au TNPs) are utilized to create large SERS and PEF enhancements. With careful modification to the surface of Au TNPs, this sensing approach is capable of quantifying circulating microRNAs at femtogram/microliter concentrations. Uniquely, the multimodal analytical methods mitigate both false positive and false negative responses and demonstrate the high stability of our sensors within bodily fluids. As a proof of concept, microRNA-10b and microRNA-96 were directly assayed from the plasma of six bladder cancer patients. Results show potential for a highly specific liquid biopsy method that could be used in point-of-care clinical diagnostics to increase early cancer detection or any other diseases including SARS-CoV-2 in which RNAs can be used as biomarkers.
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Affiliation(s)
- Adrianna N Masterson
- Department of Chemistry & Chemical Biology, Indiana University-Purdue University Indianapolis, 402 N. Blackford Street, Indianapolis, Indiana 46202, USA.
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69
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Chen C, Li R, Shu L, He Z, Wang J, Zhang C, Ma H, Aihara K, Chen L. Predicting future dynamics from short-term time series using an Anticipated Learning Machine. Natl Sci Rev 2020; 7:1079-1091. [PMID: 34692127 PMCID: PMC8288952 DOI: 10.1093/nsr/nwaa025] [Citation(s) in RCA: 15] [Impact Index Per Article: 3.8] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/01/2019] [Revised: 01/07/2020] [Accepted: 02/06/2020] [Indexed: 12/29/2022] Open
Abstract
Predicting time series has significant practical applications over different disciplines. Here, we propose an Anticipated Learning Machine (ALM) to achieve precise future-state predictions based on short-term but high-dimensional data. From non-linear dynamical systems theory, we show that ALM can transform recent correlation/spatial information of high-dimensional variables into future dynamical/temporal information of any target variable, thereby overcoming the small-sample problem and achieving multistep-ahead predictions. Since the training samples generated from high-dimensional data also include information of the unknown future values of the target variable, it is called anticipated learning. Extensive experiments on real-world data demonstrate significantly superior performances of ALM over all of the existing 12 methods. In contrast to traditional statistics-based machine learning, ALM is based on non-linear dynamics, thus opening a new way for dynamics-based machine learning.
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Affiliation(s)
- Chuan Chen
- School of Data and Computer Science, Sun Yat-sen University, Guangzhou 510275, China
| | - Rui Li
- School of Data and Computer Science, Sun Yat-sen University, Guangzhou 510275, China
| | - Lin Shu
- School of Data and Computer Science, Sun Yat-sen University, Guangzhou 510275, China
| | - Zhiyu He
- School of Data and Computer Science, Sun Yat-sen University, Guangzhou 510275, China
| | - Jining Wang
- School of Data and Computer Science, Sun Yat-sen University, Guangzhou 510275, China
| | - Chengming Zhang
- Center for Excellence in Molecular Cell Science, Shanghai Institute of Biochemistry and Cell Biology, Chinese Academy of Sciences, Shanghai 200031, China
| | - Huanfei Ma
- School of Mathematical Sciences, Soochow University, Suzhou 215006, China
| | - Kazuyuki Aihara
- Institute of Industrial Science, The University of Tokyo, Tokyo 153–8505, Japan
- International Research Center for Neurointelligence, The University of Tokyo, Tokyo 113-0033, Japan
| | - Luonan Chen
- Center for Excellence in Molecular Cell Science, Shanghai Institute of Biochemistry and Cell Biology, Chinese Academy of Sciences, Shanghai 200031, China
- Center for Excellence in Animal Evolution and Genetics, Chinese Academy of Sciences, Kunming 650223, China
- Key Laboratory of Systems Biology, Hangzhou Institute for Advanced Study, University of Chinese Academy of Sciences, Hangzhou 310024, China
- Shanghai Research Center for Brain Science and Brain-Inspired Intelligence, Shanghai 201210, China
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Fan L, Cao Q, Ding X, Gao D, Yang Q, Li B. Radiotranscriptomics signature-based predictive nomograms for radiotherapy response in patients with nonsmall cell lung cancer: Combination and association of CT features and serum miRNAs levels. Cancer Med 2020; 9:5065-5074. [PMID: 32458566 PMCID: PMC7367624 DOI: 10.1002/cam4.3115] [Citation(s) in RCA: 13] [Impact Index Per Article: 3.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/17/2019] [Revised: 02/10/2020] [Accepted: 04/16/2020] [Indexed: 12/24/2022] Open
Abstract
Purpose We aimed to establish radiotranscriptomics signatures based on serum miRNA levels and computed tomography (CT) texture features and develop nomogram models for predicting radiotherapy response in patients with nonsmall cell lung cancer (NSCLC). Methods We first used established radioresistant NSCLC cell lines for miRNA selection. At the same time, patients (103 for training set and 71 for validation set) with NSCLC were enrolled. Their pretreatment contrast‐enhanced CT texture features were extracted and their serum miRNA levels were obtained. Then, radiotranscriptomics feature selection was implemented with the least absolute shrinkage and selection operator (LASSO), and signatures were generated by logistic or Cox regression for objective response rate (ORR), overall survival (OS), and progression‐free survival (PFS). Afterward, radiotranscriptomics signature‐based nomograms were constructed and assessed for clinical use. Results Four miRNAs and 22 reproducible contrast‐enhanced CT features were used for radiotranscriptomics feature selection and we generated ORR‐, OS‐, and PFS‐ related radiotranscriptomics signatures. In patients with NSCLC who received radiotherapy, the radiotranscriptomics signatures were independently associated with ORR, OS, and PFS in both the training (OR: 2.94, P < .001; HR: 2.90, P < .001; HR: 3.58, P = .001) and validation set (OR: 2.94, P = .026; HR: 2.14, P = .004; HR: 2.64, P = .016). We also obtained a satisfactory nomogram for ORR. The C‐index values for the ORR nomogram were 0.86 [95% confidence interval (CI), 0.75 to 0.92] in the training set and 0.81 (95% CI, 0.69 to 0.89) in the validation set. The calibration‐in‐the‐large and calibration slope performed well. Decision curve analysis indicated a satisfactory net benefit. Conclusions The radiotranscriptomics signature could be an independent biomarker for evaluating radiotherapeutic responses in patients with NSCLC. The radiotranscriptomics signature‐based nomogram could be used to predict patients’ ORR, which would represent progress in individualized medicine.
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Affiliation(s)
- Liyuan Fan
- Cheeloo College of Medicine, Shandong University, Jinan, Shandong, China.,Department of Radiation Oncology, Shandong First Medical University and Shandong Academy of Medical Sciences, Shandong Cancer Hospital and Institute, Huaiyin Region, Jinan, Shandong, China
| | - Qiang Cao
- School of Computer Science and Engineering, Southeast University, Nanjing, Jiangsu, China
| | - Xiuping Ding
- Department of Radiation Oncology, Shandong First Medical University and Shandong Academy of Medical Sciences, Shandong Cancer Hospital and Institute, Huaiyin Region, Jinan, Shandong, China
| | - Dongni Gao
- Cheeloo College of Medicine, Shandong University, Jinan, Shandong, China
| | - Qiwei Yang
- Cheeloo College of Medicine, Shandong University, Jinan, Shandong, China
| | - Baosheng Li
- Department of Radiation Oncology, Shandong First Medical University and Shandong Academy of Medical Sciences, Shandong Cancer Hospital and Institute, Huaiyin Region, Jinan, Shandong, China
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71
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Gysi DM, Nowick K. Construction, comparison and evolution of networks in life sciences and other disciplines. J R Soc Interface 2020; 17:20190610. [PMID: 32370689 PMCID: PMC7276545 DOI: 10.1098/rsif.2019.0610] [Citation(s) in RCA: 9] [Impact Index Per Article: 2.3] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/03/2019] [Accepted: 04/09/2020] [Indexed: 12/12/2022] Open
Abstract
Network approaches have become pervasive in many research fields. They allow for a more comprehensive understanding of complex relationships between entities as well as their group-level properties and dynamics. Many networks change over time, be it within seconds or millions of years, depending on the nature of the network. Our focus will be on comparative network analyses in life sciences, where deciphering temporal network changes is a core interest of molecular, ecological, neuropsychological and evolutionary biologists. Further, we will take a journey through different disciplines, such as social sciences, finance and computational gastronomy, to present commonalities and differences in how networks change and can be analysed. Finally, we envision how borrowing ideas from these disciplines could enrich the future of life science research.
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Affiliation(s)
- Deisy Morselli Gysi
- Department of Computer Science, Interdisciplinary Center of Bioinformatics, University of Leipzig, 04109 Leipzig, Germany
- Swarm Intelligence and Complex Systems Group, Faculty of Mathematics and Computer Science, University of Leipzig, 04109 Leipzig, Germany
- Center for Complex Networks Research, Northeastern University, 177 Huntington Avenue, Boston, MA 02115, USA
| | - Katja Nowick
- Human Biology Group, Institute for Biology, Faculty of Biology, Chemistry, Pharmacy, Freie Universität Berlin, Königin-Luise-Straβe 1-3, 14195 Berlin, Germany
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72
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Hackett MJ, Hollings A, Caine S, Bewer BE, Alaverdashvili M, Takechi R, Mamo JCL, Jones MWM, de Jonge MD, Paterson PG, Pickering IJ, George GN. Elemental characterisation of the pyramidal neuron layer within the rat and mouse hippocampus. Metallomics 2020; 11:151-165. [PMID: 30398510 DOI: 10.1039/c8mt00230d] [Citation(s) in RCA: 14] [Impact Index Per Article: 3.5] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/23/2023]
Abstract
A unique combination of sensitivity, resolution, and penetration make X-ray fluorescence imaging (XFI) ideally suited to investigate trace elemental distributions in the biological context. XFI has gained widespread use as an analytical technique in the biological sciences, and in particular enables exciting new avenues of research in the field of neuroscience. In this study, elemental mapping by XFI was applied to characterise the elemental content within neuronal cell layers of hippocampal sub-regions of mice and rats. Although classical histochemical methods for metal detection exist, such approaches are typically limited to qualitative analysis. Specifically, histochemical methods are not uniformly sensitive to all chemical forms of a metal, often displaying variable sensitivity to specific "pools" or chemical forms of a metal. In addition, histochemical methods require fixation and extensive chemical treatment of samples, creating the strong likelihood for metal redistribution, leaching, or contamination. Direct quantitative elemental mapping of total elemental pools, in situ within ex vivo tissue sections, without the need for chemical fixation or addition of staining reagents is not possible with traditional histochemical methods; however, such a capability, which is provided by XFI, can offer an enormous analytical advantage. The results we report herein demonstrate the analytical advantage of XFI elemental mapping for direct, label-free metal quantification, in situ within ex vivo brain tissue sections. Specifically, we definitively characterise for the first time, the abundance of Fe within the pyramidal cell layers of the hippocampus. Localisation of Fe to this cell layer is not reproducibly achieved with classical Perls histochemical Fe stains. The ability of XFI to directly quantify neuronal elemental (P, S, Cl, K, Ca, Fe, Cu, Zn) distributions, revealed unique profiles of Fe and Zn within anatomical sub-regions of the hippocampus i.e., cornu ammonis 1, 2 or 3 (CA1, CA2 or CA3) sub-regions. Interestingly, our study reveals a unique Fe gradient across neuron populations within the non-degenerating and pathology free rat hippocampus, which curiously mirrors the pattern of region-specific vulnerability of the hippocampus that has previously been established to occur in various neurodegenerative diseases.
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Affiliation(s)
- M J Hackett
- Curtin Institute for Functional Molecules and Interfaces, School of Molecular and Life Sciences, Curtin University, GPOBox U1987, Bentley, WA 6845, Australia.
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73
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Scoffone VC, Barbieri G, Buroni S, Scarselli M, Pizza M, Rappuoli R, Riccardi G. Vaccines to Overcome Antibiotic Resistance: The Challenge of Burkholderia cenocepacia. Trends Microbiol 2020; 28:315-326. [DOI: 10.1016/j.tim.2019.12.005] [Citation(s) in RCA: 11] [Impact Index Per Article: 2.8] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/02/2019] [Revised: 12/03/2019] [Accepted: 12/09/2019] [Indexed: 12/26/2022]
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74
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Nguyen VT, Pandith A, Seo YJ. Propargylamine-selective dual fluorescence turn-on method for post-synthetic labeling of DNA. Chem Commun (Camb) 2020; 56:3199-3202. [PMID: 32068200 DOI: 10.1039/d0cc00255k] [Citation(s) in RCA: 5] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/12/2022]
Abstract
We have developed a propargylamine-selective dual fluorescence turn-on system, using ylidenemalononitrile enamines, for post-synthetic DNA labeling, allowing the direct monitoring of DNA using dual emission in living cells.
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Affiliation(s)
- Van Thang Nguyen
- Department of Bioactive Material Sciences, Jeonbuk National University, South Korea
| | - Anup Pandith
- Department of Chemistry, Jeonbuk National University, South Korea.
| | - Young Jun Seo
- Department of Bioactive Material Sciences, Jeonbuk National University, South Korea and Department of Chemistry, Jeonbuk National University, South Korea.
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75
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Yang CG, Cheng L, Ye WQ, Zheng DH, Xu ZR. Preparation of encoded bar-like core-shell microparticles on a microfluidic chip. Colloids Surf A Physicochem Eng Asp 2020. [DOI: 10.1016/j.colsurfa.2019.124373] [Citation(s) in RCA: 3] [Impact Index Per Article: 0.8] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/29/2022]
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76
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Feng Q, Wang M, Han X, Chen Q, Dou B, Wang P. Construction of an Electrochemical Biosensing Platform Based on Hierarchical Mesoporous NiO@N-Doped C Microspheres Coupled with Catalytic Hairpin Assembly. ACS APPLIED BIO MATERIALS 2020; 3:1276-1282. [DOI: 10.1021/acsabm.9b01145] [Citation(s) in RCA: 12] [Impact Index Per Article: 3.0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/01/2023]
Affiliation(s)
- Qiumei Feng
- School of Chemistry and Materials Science, Jiangsu Normal University, Xuzhou 221116, China
| | - Mengying Wang
- School of Chemistry and Materials Science, Jiangsu Normal University, Xuzhou 221116, China
| | - Xiguang Han
- School of Chemistry and Materials Science, Jiangsu Normal University, Xuzhou 221116, China
| | - Qian Chen
- School of Chemistry and Materials Science, Jiangsu Normal University, Xuzhou 221116, China
| | - Baoting Dou
- School of Chemistry and Materials Science, Jiangsu Normal University, Xuzhou 221116, China
| | - Po Wang
- School of Chemistry and Materials Science, Jiangsu Normal University, Xuzhou 221116, China
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77
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Armstrong JPK, Stevens MM. Emerging Technologies for Tissue Engineering: From Gene Editing to Personalized Medicine. Tissue Eng Part A 2019; 25:688-692. [PMID: 30794069 DOI: 10.1089/ten.tea.2019.0026] [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] [Indexed: 01/29/2023] Open
Abstract
IMPACT STATEMENT History has shown us how tissue engineering can be advanced by embracing technological innovation. In this perspective, we highlight some of the most promising emerging technologies and discuss how they can be integrated into existing tissue engineering protocols. The proposed technologies offer the opportunity to reshape how we currently design, engineer, and characterize tissue grafts for improved in vivo regeneration.
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Affiliation(s)
- James P K Armstrong
- Department of Materials, Department of Bioengineering, and Institute of Biomedical Engineering, Imperial College London, London, United Kingdom
| | - Molly M Stevens
- Department of Materials, Department of Bioengineering, and Institute of Biomedical Engineering, Imperial College London, London, United Kingdom
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78
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Chen LD, Chen Q, Lin XJ, Chen QS, Huang YZ, Wu RH, Lin GF, Huang XY, Lin QC. Effect of chronic intermittent hypoxia on gene expression profiles of rat liver: a better understanding of OSA-related liver disease. Sleep Breath 2019; 24:761-770. [PMID: 31845084 DOI: 10.1007/s11325-019-01987-0] [Citation(s) in RCA: 5] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/16/2019] [Revised: 11/24/2019] [Accepted: 11/29/2019] [Indexed: 10/25/2022]
Abstract
PURPOSE Obstructive sleep apnea (OSA) and OSA-associated chronic intermittent hypoxia (CIH) have been suggested to be associated with increased risk of liver disease. Little is known about the biological pathophysiology and underlying molecular mechanisms. Here we use whole-genome expression profiling to explore the transcriptomic changes induced by CIH in rat liver. METHODS Rats (n = 3) were exposed to CIH for 8 weeks and were compared with rats exposed to normoxia (n = 3). Illumina HiSeq 4000 platform was used to examine differentially expressed genes (DEGs) in the liver between control group and CIH rat model. Quantitative reverse transcription polymerase chain reaction (qRT-PCR) was used to validate DEGs. Biological functions of DEGs were determined by Gene Ontology and Kyoto Encyclopedia of Genes and Genomes. RESULTS Compared with control group, 318 genes were identified to be dysregulated in the liver of CIH rat model, with 211genes upregulated and 107 genes downregulated. Bioinformatics analysis showed that these genes were extensively related to various physiologic processes such as hepatic metabolism, apoptotic process, and oxidative stress. 10 genes with 5 upregulated and 5 downregulated were selected and further verified by qRT-PCR. CONCLUSIONS CIH resulted in altered gene expression patterns in the liver of rat. The DEGs were related to various physiological and pathological processes in CIH rat liver. These data provide a better understanding of the mechanisms and underlying molecular changes of OSA-related liver disease.
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Affiliation(s)
- Li-Da Chen
- Department of Respiratory and Critical Care Medicine, The First Affiliated Hospital of Fujian Medical University, Fuzhou, Fujian Province, People's Republic of China.,Department of Respiratory and Critical Care Medicine, Zhangzhou Affiliated Hospital of Fujian Medical University, Zhangzhou, Fujian Province, People's Republic of China
| | - Qin Chen
- College of Integrative Medicine, Fujian University of Traditional Chinese Medicine, Fuzhou, Fujian Province, People's Republic of China
| | - Xue-Jun Lin
- Department of Laboratory Medicine, Zhangzhou Affiliated Hospital of Fujian Medical University, Zhangzhou,, Fujian Province, People's Republic of China
| | - Qing-Shi Chen
- Department of Respiratory and Critical Care Medicine, The First Affiliated Hospital of Fujian Medical University, Fuzhou, Fujian Province, People's Republic of China.,The Second Affiliated Hospital of Fujian Medical University, Quanzhou, Fujian Province, People's Republic of China
| | - Yu-Zhen Huang
- Department of Pathology, Zhangzhou Affiliated Hospital of Fujian Medical University, Zhangzhou, Fujian Province, People's Republic of China
| | - Run-Hua Wu
- College of Integrative Medicine, Fujian University of Traditional Chinese Medicine, Fuzhou, Fujian Province, People's Republic of China
| | - Guo-Fu Lin
- Department of Respiratory and Critical Care Medicine, The First Affiliated Hospital of Fujian Medical University, Fuzhou, Fujian Province, People's Republic of China.,Fujian Provincial Sleep-Disordered Breathing Clinic Center, Fuzhou, Fujian Province, People's Republic of China.,Laboratory of Respiratory Disease of the Fujian Medical University, Fuzhou, Fujian Province, People's Republic of China
| | - Xiao-Yun Huang
- Department of Respiratory and Critical Care Medicine, The First Affiliated Hospital of Fujian Medical University, Fuzhou, Fujian Province, People's Republic of China.,Fujian Provincial Sleep-Disordered Breathing Clinic Center, Fuzhou, Fujian Province, People's Republic of China.,Laboratory of Respiratory Disease of the Fujian Medical University, Fuzhou, Fujian Province, People's Republic of China
| | - Qi-Chang Lin
- Department of Respiratory and Critical Care Medicine, The First Affiliated Hospital of Fujian Medical University, Fuzhou, Fujian Province, People's Republic of China. .,Fujian Provincial Sleep-Disordered Breathing Clinic Center, Fuzhou, Fujian Province, People's Republic of China. .,Laboratory of Respiratory Disease of the Fujian Medical University, Fuzhou, Fujian Province, People's Republic of China.
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79
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Ma X, Jia C, Chu M, Fu D, Lei Q, Ding X, Wu X, Guo X, Pei J, Bao P, Yan P, Liang C. Transcriptome and DNA Methylation Analyses of the Molecular Mechanisms Underlying with Longissimus dorsi Muscles at Different Stages of Development in the Polled Yak. Genes (Basel) 2019; 10:genes10120970. [PMID: 31779203 PMCID: PMC6947547 DOI: 10.3390/genes10120970] [Citation(s) in RCA: 12] [Impact Index Per Article: 2.4] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/29/2019] [Revised: 11/21/2019] [Accepted: 11/21/2019] [Indexed: 02/04/2023] Open
Abstract
DNA methylation modifications are implicated in many biological processes. As the most common epigenetic mechanism DNA methylation also affects muscle growth and development. The majority of previous studies have focused on different varieties of yak, but little is known about the epigenetic regulation mechanisms in different age groups of animals. The development of muscles in the different stages of yak growth remains unclear. In this study, we selected the longissimus dorsi muscle tissue at three different growth stages of the yak, namely, 90-day-old fetuses (group E), six months old (group M), and three years old (group A). Using RNA-Seq transcriptome sequencing and methyl-RAD whole-genome methylation sequencing technology, changes in gene expression levels and DNA methylation status throughout the genome were investigated during the stages of yak development. Each group was represented by three biological replicates. The intersections of expression patterns of 7694 differentially expressed genes (DEGs) were identified (padj < 0.01, |log2FC| > 1.2) at each of the three developmental periods. Time-series expression profile clustering analysis indicated that the DEGs were significantly arranged into eight clusters which could be divided into two classes (padj < 0.05), class I profiles that were downregulated and class II profiles that were upregulated. Based on this cluster analysis, Kyoto Encyclopedia of Genes and Genomes (KEGG) pathway analysis revealed that DEGs from class I profiles were significantly (padj < 0.05) enriched in 21 pathways, the most enriched pathway being the Axon guidance signaling pathway. DEGs from the class II profile were significantly enriched in 58 pathways, the pathway most strongly enriched being Metabolic pathway. After establishing the methylation profiles of the whole genomes, and using two groups of comparisons, the three combinations of groups (M-vs.-E, M-vs.-A, A-vs.-E) were found to have 1344, 822, and 420 genes, respectively, that were differentially methylated at CCGG sites and 2282, 3056, and 537 genes, respectively, at CCWGG sites. The two sets of data were integrated and the negative correlations between DEGs and differentially methylated promoters (DMPs) analyzed, which confirmed that TMEM8C, IGF2, CACNA1S and MUSTN1 were methylated in the promoter region and that expression of the modified genes was negatively correlated. Interestingly, these four genes, from what was mentioned above, perform vital roles in yak muscle growth and represent a reference for future genomic and epigenomic studies in muscle development, in addition to enabling marker-assisted selection of growth traits.
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Affiliation(s)
- Xiaoming Ma
- Animal Science Department, Lanzhou Institute of Husbandry and Pharmaceutical Sciences, Chinese Academy of Agricultural Sciences, Lanzhou 730050, China; (X.M.); (C.J.); (M.C.); (D.F.); (Q.L.); (X.D.); (X.W.); (X.G.); (J.P.); (P.B.)
- Key Laboratory for Yak Genetics, Breeding, and Reproduction Engineering of Gansu Province, Chinese Academy of Agricultural Sciences, Lanzhou 730050, China
| | - Congjun Jia
- Animal Science Department, Lanzhou Institute of Husbandry and Pharmaceutical Sciences, Chinese Academy of Agricultural Sciences, Lanzhou 730050, China; (X.M.); (C.J.); (M.C.); (D.F.); (Q.L.); (X.D.); (X.W.); (X.G.); (J.P.); (P.B.)
- Key Laboratory for Yak Genetics, Breeding, and Reproduction Engineering of Gansu Province, Chinese Academy of Agricultural Sciences, Lanzhou 730050, China
| | - Min Chu
- Animal Science Department, Lanzhou Institute of Husbandry and Pharmaceutical Sciences, Chinese Academy of Agricultural Sciences, Lanzhou 730050, China; (X.M.); (C.J.); (M.C.); (D.F.); (Q.L.); (X.D.); (X.W.); (X.G.); (J.P.); (P.B.)
- Key Laboratory for Yak Genetics, Breeding, and Reproduction Engineering of Gansu Province, Chinese Academy of Agricultural Sciences, Lanzhou 730050, China
| | - Donghai Fu
- Animal Science Department, Lanzhou Institute of Husbandry and Pharmaceutical Sciences, Chinese Academy of Agricultural Sciences, Lanzhou 730050, China; (X.M.); (C.J.); (M.C.); (D.F.); (Q.L.); (X.D.); (X.W.); (X.G.); (J.P.); (P.B.)
- Key Laboratory for Yak Genetics, Breeding, and Reproduction Engineering of Gansu Province, Chinese Academy of Agricultural Sciences, Lanzhou 730050, China
| | - Qinhui Lei
- Animal Science Department, Lanzhou Institute of Husbandry and Pharmaceutical Sciences, Chinese Academy of Agricultural Sciences, Lanzhou 730050, China; (X.M.); (C.J.); (M.C.); (D.F.); (Q.L.); (X.D.); (X.W.); (X.G.); (J.P.); (P.B.)
- Key Laboratory for Yak Genetics, Breeding, and Reproduction Engineering of Gansu Province, Chinese Academy of Agricultural Sciences, Lanzhou 730050, China
| | - Xuezhi Ding
- Animal Science Department, Lanzhou Institute of Husbandry and Pharmaceutical Sciences, Chinese Academy of Agricultural Sciences, Lanzhou 730050, China; (X.M.); (C.J.); (M.C.); (D.F.); (Q.L.); (X.D.); (X.W.); (X.G.); (J.P.); (P.B.)
- Key Laboratory for Yak Genetics, Breeding, and Reproduction Engineering of Gansu Province, Chinese Academy of Agricultural Sciences, Lanzhou 730050, China
| | - Xiaoyun Wu
- Animal Science Department, Lanzhou Institute of Husbandry and Pharmaceutical Sciences, Chinese Academy of Agricultural Sciences, Lanzhou 730050, China; (X.M.); (C.J.); (M.C.); (D.F.); (Q.L.); (X.D.); (X.W.); (X.G.); (J.P.); (P.B.)
- Key Laboratory for Yak Genetics, Breeding, and Reproduction Engineering of Gansu Province, Chinese Academy of Agricultural Sciences, Lanzhou 730050, China
| | - Xian Guo
- Animal Science Department, Lanzhou Institute of Husbandry and Pharmaceutical Sciences, Chinese Academy of Agricultural Sciences, Lanzhou 730050, China; (X.M.); (C.J.); (M.C.); (D.F.); (Q.L.); (X.D.); (X.W.); (X.G.); (J.P.); (P.B.)
- Key Laboratory for Yak Genetics, Breeding, and Reproduction Engineering of Gansu Province, Chinese Academy of Agricultural Sciences, Lanzhou 730050, China
| | - Jie Pei
- Animal Science Department, Lanzhou Institute of Husbandry and Pharmaceutical Sciences, Chinese Academy of Agricultural Sciences, Lanzhou 730050, China; (X.M.); (C.J.); (M.C.); (D.F.); (Q.L.); (X.D.); (X.W.); (X.G.); (J.P.); (P.B.)
- Key Laboratory for Yak Genetics, Breeding, and Reproduction Engineering of Gansu Province, Chinese Academy of Agricultural Sciences, Lanzhou 730050, China
| | - Pengjia Bao
- Animal Science Department, Lanzhou Institute of Husbandry and Pharmaceutical Sciences, Chinese Academy of Agricultural Sciences, Lanzhou 730050, China; (X.M.); (C.J.); (M.C.); (D.F.); (Q.L.); (X.D.); (X.W.); (X.G.); (J.P.); (P.B.)
- Key Laboratory for Yak Genetics, Breeding, and Reproduction Engineering of Gansu Province, Chinese Academy of Agricultural Sciences, Lanzhou 730050, China
| | - Ping Yan
- Animal Science Department, Lanzhou Institute of Husbandry and Pharmaceutical Sciences, Chinese Academy of Agricultural Sciences, Lanzhou 730050, China; (X.M.); (C.J.); (M.C.); (D.F.); (Q.L.); (X.D.); (X.W.); (X.G.); (J.P.); (P.B.)
- Correspondence: (P.Y.); (C.L.); Tel.: +86-0931-2115288 (P.Y.); +86-0931-2115271 (C.L.)
| | - Chunnian Liang
- Key Laboratory for Yak Genetics, Breeding, and Reproduction Engineering of Gansu Province, Chinese Academy of Agricultural Sciences, Lanzhou 730050, China
- Correspondence: (P.Y.); (C.L.); Tel.: +86-0931-2115288 (P.Y.); +86-0931-2115271 (C.L.)
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80
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Mok L, Kim Y, Lee S, Choi S, Lee S, Jang JY, Park T. HisCoM-PAGE: Hierarchical Structural Component Models for Pathway Analysis of Gene Expression Data. Genes (Basel) 2019; 10:E931. [PMID: 31739607 PMCID: PMC6896173 DOI: 10.3390/genes10110931] [Citation(s) in RCA: 5] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/23/2019] [Revised: 11/06/2019] [Accepted: 11/07/2019] [Indexed: 01/10/2023] Open
Abstract
Although there have been several analyses for identifying cancer-associated pathways, based on gene expression data, most of these are based on single pathway analyses, and thus do not consider correlations between pathways. In this paper, we propose a hierarchical structural component model for pathway analysis of gene expression data (HisCoM-PAGE), which accounts for the hierarchical structure of genes and pathways, as well as the correlations among pathways. Specifically, HisCoM-PAGE focuses on the survival phenotype and identifies its associated pathways. Moreover, its application to real biological data analysis of pancreatic cancer data demonstrated that HisCoM-PAGE could successfully identify pathways associated with pancreatic cancer prognosis. Simulation studies comparing the performance of HisCoM-PAGE with other competing methods such as Gene Set Enrichment Analysis (GSEA), Global Test, and Wald-type Test showed HisCoM-PAGE to have the highest power to detect causal pathways in most simulation scenarios.
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Affiliation(s)
- Lydia Mok
- Interdisciplinary Program in Bioinformatics, Seoul National University, Seoul 08826, Korea
| | - Yongkang Kim
- Department of Statistics, Seoul National University, Seoul 08826, Korea
| | - Sungyoung Lee
- Center for Precision Medicine, Seoul National University Hospital, Seoul 03080, Korea
| | - Sungkyoung Choi
- Department of Applied Mathematics, Hanyang University (ERICA), Ansan 15588, Korea
| | - Seungyeoun Lee
- Department of Mathematics and Statistics, Sejong University, Seoul 05006, Korea
| | - Jin-Young Jang
- Department of Surgery, Seoul National University College of Medicine, Seoul 03080, Korea
| | - Taesung Park
- Interdisciplinary Program in Bioinformatics, Seoul National University, Seoul 08826, Korea
- Department of Statistics, Seoul National University, Seoul 08826, Korea
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81
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Zheng YX, Zhang XX, Hernandez JA, Mahmmod YS, Huang WY, Li GF, Wang YP, Zhou X, Li XM, Yuan ZG. Transcriptomic analysis of reproductive damage in the epididymis of male Kunming mice induced by chronic infection of Toxoplasma gondii PRU strain. Parasit Vectors 2019; 12:529. [PMID: 31703718 PMCID: PMC6839085 DOI: 10.1186/s13071-019-3783-2] [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: 03/21/2019] [Accepted: 10/30/2019] [Indexed: 11/10/2022] Open
Abstract
BACKGROUND Some researchers have reported that Toxoplasma gondii can cause serious reproductive impairment in male animals. Specifically, T. gondii destroy the quality of sperm in the epididymis, which affects their sexual ability. However, among such studies, none have investigated the male reproductive transcriptome. Therefore, to investigate the relationship between T. gondii and sperm maturation, we infected mice with T. gondii prugniaud (PRU) strain and performed transcriptome sequencing of the epididymis. RESULTS Compared with the control group, 431 upregulated and 229 downregulated differentially expressed genes (DEGs) were found (P-value < 0.05, false discovery rate (FDR) < 0.05 and |log2 (fold change)| ≥ 1). According to results of a bioinformatics analysis, Gene Ontology (GO) function is divided into three categories: cellular component, molecular function and biological process. Upon performing GO analysis, we found that some DEGs correlated with an integral part of membrane, protein complex, cell surface, ATP binding, immune system process, signal transduction and metabolic process which are responsible for the epididymal injury. DEGs were mapped to 101 unique KEGG pathways. Pathways such as cytokine-cytokine receptor interaction, glycolysis/gluconeogenesis and apoptosis are closely related to sperm quality. Moreover, Tnfsf10 and spata18 can damage the mitochondria in sperm, which decreases sperm motility and morphology. CONCLUSIONS We sequenced the reproductive system of male mice chronically infected with T. gondii, which provides a new direction for research into male sterility caused by Toxoplasma infection. This work provides valuable information and a comprehensive database for future studies of the interaction between T. gondii infection and the male reproductive system.
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Affiliation(s)
- Yu-Xiang Zheng
- College of Veterinary Medicine, South China Agricultural University, Guangzhou, 510642, Guangdong, People's Republic of China.,Key Laboratory of Zoonosis Prevention and Control of Guangdong Province, Guangzhou, 510642, People's Republic of China
| | - Xiu-Xiang Zhang
- College of plant, South China Agricultural University, Guangzhou, 510642, Guangdong, People's Republic of China
| | - Jorge A Hernandez
- College of Veterinary Medicine, University of Florida, 2015 SW 16th Avenue, Gainesville, FL, 32610-0136, USA
| | - Yasser S Mahmmod
- Infectious Diseases, Department of Animal Medicine, Faculty of Veterinary Medicine, Zagazig University, Zagazig, Sharkia Province, 44511, Egypt.,IRTA, Centre for Research into Animal Health (CReSA-IRTA), Campus of Autonomous University of Barcelona, Bellaterra, 08193, Barcelona, Spain
| | - Wan-Yi Huang
- College of Veterinary Medicine, South China Agricultural University, Guangzhou, 510642, Guangdong, People's Republic of China.,Key Laboratory of Zoonosis Prevention and Control of Guangdong Province, Guangzhou, 510642, People's Republic of China
| | - Gui-Feng Li
- College of Veterinary Medicine, South China Agricultural University, Guangzhou, 510642, Guangdong, People's Republic of China.,Key Laboratory of Zoonosis Prevention and Control of Guangdong Province, Guangzhou, 510642, People's Republic of China
| | - Ya-Pei Wang
- College of Veterinary Medicine, South China Agricultural University, Guangzhou, 510642, Guangdong, People's Republic of China.,Key Laboratory of Zoonosis Prevention and Control of Guangdong Province, Guangzhou, 510642, People's Republic of China
| | - Xue Zhou
- College of Veterinary Medicine, South China Agricultural University, Guangzhou, 510642, Guangdong, People's Republic of China.,Key Laboratory of Zoonosis Prevention and Control of Guangdong Province, Guangzhou, 510642, People's Republic of China
| | - Xiu-Ming Li
- College of Animal Science and Technology, Heilongjiang BaYi Agricultural University, Daqing, 163319, People's Republic of China.
| | - Zi-Guo Yuan
- College of Veterinary Medicine, South China Agricultural University, Guangzhou, 510642, Guangdong, People's Republic of China. .,Key Laboratory of Zoonosis Prevention and Control of Guangdong Province, Guangzhou, 510642, People's Republic of China.
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82
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Lin WR, Tan SI, Hsiang CC, Sung PK, Ng IS. Challenges and opportunity of recent genome editing and multi-omics in cyanobacteria and microalgae for biorefinery. BIORESOURCE TECHNOLOGY 2019; 291:121932. [PMID: 31387837 DOI: 10.1016/j.biortech.2019.121932] [Citation(s) in RCA: 44] [Impact Index Per Article: 8.8] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 06/06/2019] [Revised: 07/26/2019] [Accepted: 07/27/2019] [Indexed: 06/10/2023]
Abstract
Microalgae and cyanobacteria are easy to culture, with higher growth rates and photosynthetic efficiencies compared to terrestrial plants, and thus generating higher productivity. The concept of microalgal biorefinery is to assimilate carbon dioxide and convert it to chemical energy/value-added products, such as vitamins, carotenoids, fatty acids, proteins and nucleic acids, to be applied in bioenergy, health foods, aquaculture feed, pharmaceutical and medical fields. Therefore, microalgae are annotated as the third generation feedstock in bioenergy and biorefinery. In past decades, many studies thrived to improve the carbon sequestration efficiency as well as enhance value-added compounds from different algae, especially via genetic engineering, synthetic biology, metabolic design and regulation. From the traditional Agrobacterium-mediated transformation DNA to novel CRISPR (clustered regularly interspaced short palindromic repeats) technology applied in microalgae and cyanobacteria, this review has highlighted the genome editing technology for biorefinery that is a highly environmental friendly trend to sustainable and renewable development.
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Affiliation(s)
- Way-Rong Lin
- Department of Chemical Engineering, National Cheng Kung University, Tainan 701, Taiwan, ROC
| | - Shih-I Tan
- Department of Chemical Engineering, National Cheng Kung University, Tainan 701, Taiwan, ROC
| | - Chuan-Chieh Hsiang
- Department of Chemical Engineering, National Cheng Kung University, Tainan 701, Taiwan, ROC
| | - Po-Kuei Sung
- Department of Chemical Engineering, National Cheng Kung University, Tainan 701, Taiwan, ROC
| | - I-Son Ng
- Department of Chemical Engineering, National Cheng Kung University, Tainan 701, Taiwan, ROC.
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83
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Njoku K, Chiasserini D, Whetton AD, Crosbie EJ. Proteomic Biomarkers for the Detection of Endometrial Cancer. Cancers (Basel) 2019; 11:cancers11101572. [PMID: 31623106 PMCID: PMC6826703 DOI: 10.3390/cancers11101572] [Citation(s) in RCA: 54] [Impact Index Per Article: 10.8] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/10/2019] [Revised: 10/07/2019] [Accepted: 10/11/2019] [Indexed: 01/01/2023] Open
Abstract
Endometrial cancer is the leading gynaecological malignancy in the western world and its incidence is rising in tandem with the global epidemic of obesity. Early diagnosis is key to improving survival, which at 5 years is less than 20% in advanced disease and over 90% in early-stage disease. As yet, there are no validated biological markers for its early detection. Advances in high-throughput technologies and machine learning techniques now offer unique and promising perspectives for biomarker discovery, especially through the integration of genomic, transcriptomic, proteomic, metabolomic and imaging data. Because the proteome closely mirrors the dynamic state of cells, tissues and organisms, proteomics has great potential to deliver clinically relevant biomarkers for cancer diagnosis. In this review, we present the current progress in endometrial cancer diagnostic biomarker discovery using proteomics. We describe the various mass spectrometry-based approaches and highlight the challenges inherent in biomarker discovery studies. We suggest novel strategies for endometrial cancer detection exploiting biologically important protein biomarkers and set the scene for future directions in endometrial cancer biomarker research.
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Affiliation(s)
- Kelechi Njoku
- Division of Cancer Sciences, School of Medical Sciences, Faculty of Biology, Medicine and Health, University of Manchester, 5th Floor Research, St Mary's Hospital, Oxford Road, Manchester M13 9WL, UK.
- Department of Obstetrics and Gynaecology, Manchester Academic Health Science Centre, Manchester University NHS Foundation Trust, Manchester M13 9WL, UK.
- Stoller Biomarker Discovery Centre, Institute of Cancer Sciences, Faculty of Medical and Human Sciences, University of Manchester, Manchester M13 9PL, UK.
| | - Davide Chiasserini
- Stoller Biomarker Discovery Centre, Institute of Cancer Sciences, Faculty of Medical and Human Sciences, University of Manchester, Manchester M13 9PL, UK.
| | - Anthony D Whetton
- Stoller Biomarker Discovery Centre, Institute of Cancer Sciences, Faculty of Medical and Human Sciences, University of Manchester, Manchester M13 9PL, UK.
| | - Emma J Crosbie
- Division of Cancer Sciences, School of Medical Sciences, Faculty of Biology, Medicine and Health, University of Manchester, 5th Floor Research, St Mary's Hospital, Oxford Road, Manchester M13 9WL, UK.
- Department of Obstetrics and Gynaecology, Manchester Academic Health Science Centre, Manchester University NHS Foundation Trust, Manchester M13 9WL, UK.
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84
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Shanmugasundaram M, Senthilvelan A, Kore AR. C-5 Substituted Pyrimidine Nucleotides/Nucleosides: Recent Progress in Synthesis, Functionalization, and Applications. CURR ORG CHEM 2019. [DOI: 10.2174/1385272823666190809124310] [Citation(s) in RCA: 5] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/11/2022]
Abstract
The chemistry of C5 substituted pyrimidine nucleotide serves as a versatile molecular
biology probe for the incorporation of DNA/RNA that has been involved in various
molecular biology applications such as gene expression, chromosome, and mRNA
fluorescence in situ hybridization (FISH) experiment, mutation detection on arrays and
microarrays, in situ RT-PCR, and PCR. In addition to C5 substituted pyrimidine nucleotide,
C5 substituted pyrimidine nucleoside displays a broad spectrum of biological applications
such as antibacterial, antiviral and anticancer activities. This review focusses on
the recent development in the synthesis of aminoallyl pyrimidine nucleotide, aminopropargyl
pyrimidine nucleotide, fluorescent probes containing C5 substituted pyrimidine nucleotide,
2′-deoxycytidine nucleoside containing vinylsulfonamide and acrylamide modification,
C5 alkenyl, C5 alkynyl, and C5 aryl pyrimidine nucleosides through palladium-catalyzed reaction,
pyrimidine nucleoside containing triazole moiety through Click reaction, 5-isoxazol-3-yl-pyrimidine nucleoside,
C5 azide modified pyrimidine nucleoside, 2′-deoxycytidine nucleotide containing photocleavable moiety,
and uridine nucleoside containing germane and their biological applications are outlined.
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Affiliation(s)
- Muthian Shanmugasundaram
- Life Sciences Solutions Group, Thermo Fisher Scientific, 2130 Woodward Street, Austin, TX 78744-1832, United States
| | - Annamalai Senthilvelan
- Life Sciences Solutions Group, Thermo Fisher Scientific, 2130 Woodward Street, Austin, TX 78744-1832, United States
| | - Anilkumar R. Kore
- Life Sciences Solutions Group, Thermo Fisher Scientific, 2130 Woodward Street, Austin, TX 78744-1832, United States
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85
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The influence of geometry and other fundamental challenges for bio-sensing with field effect transistors. Biophys Rev 2019; 11:757-763. [PMID: 31588960 DOI: 10.1007/s12551-019-00592-5] [Citation(s) in RCA: 6] [Impact Index Per Article: 1.2] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/25/2019] [Accepted: 09/03/2019] [Indexed: 12/24/2022] Open
Abstract
We present a review of field effect transistors (FET) from the point of view of their applications to label-free sensing in the era of genomics and proteomics. Here, rather than a collection of Bio-FET achievements, we propose an analysis of the different issues hampering the use of these devices into clinical applications. We make a particular emphasis on the influence of the sensor geometry in the phenomena of mass transport of analytes, which is a topic that has been traditionally overlooked in the analysis and design of biosensors, but that plays a central role in the achievement of low limits of detection. Other issues like the screening of charges by the ions in liquids with physiological ionic strength and the non-specific binding are also reviewed. In conclusion, we give an overview of different solutions that have been proposed to address all these challenges, demonstrating the potential of field effect transistors owing to their ease of integration with other semiconductor components for developing cost-effective, highly multiplexed sensors for next-generation medicines.
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86
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Park YS, Kim S, Park DG, Kim DH, Yoon KW, Shin W, Han K. Comparison of library construction kits for mRNA sequencing in the Illumina platform. Genes Genomics 2019; 41:1233-1240. [PMID: 31350733 DOI: 10.1007/s13258-019-00853-3] [Citation(s) in RCA: 10] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/07/2019] [Accepted: 07/15/2019] [Indexed: 12/28/2022]
Abstract
BACKGROUND The emergence of next-generation sequencing (NGS) technologies has made a tremendous contribution to the deciphering and significance of transcriptome analysis in biological fields. Since the advent of NGS technology in 2007, Illumina, Inc. has provided one of the most widely used sequencing platforms for NGS analysis. OBJECTIVE Although reagents and protocols provided by Illumina are adequately performed in transcriptome sequencing, recently, alternative reagents and protocols which are relatively cost effective are accessible. However, the kits derived from various manufacturers have advantages and disadvantages when researchers carry out the transcriptome library construction. METHODS We compared them using a variety of protocols to produce Illumina-compatible libraries based on transcriptome. Three different mRNA sequencing kits were selected for this study: TruSeq® RNA Sample Preparation V2 (Illumina, Inc., USA), Universal Plus mRNA-Seq (NuGEN, Ltd., UK), and NEBNext® Ultra™ Directional RNA Library Prep Kit for Illumina® (New England BioLabs, Ltd., USA). We compared them focusing on cost, experimental time, and data output. RESULTS The quality and quantity of sequencing data obtained through the NGS technique were strongly influenced by the type of the sequencing library kits. It suggests that for transcriptome studies, researchers should select a suitable library construction kit according to the goal and resources of experiments. CONCLUSION The present work will help researchers to choose the right sequencing library construction kit for transcriptome analyses.
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Affiliation(s)
- Yong-Soo Park
- Department of Equine Industry, Korea National College of Agriculture and Fisheries, Jeonju, 54874, Republic of Korea
| | - Songmi Kim
- Department of Nanobiomedical Science and BK21 PLUS NBM Global Research Center for Regenerative Medicine, Dankook University, Cheonan, 31116, Republic of Korea
- Center for Bio-Medical Engineering Core Facility, Dankook University, Cheonan, 31116, Republic of Korea
| | - Dong-Guk Park
- Department of Surgery, Dankook University College of Medicine, Cheonan, 31116, Republic of Korea
| | - Dong Hee Kim
- Department of Anesthesiology and Pain Management, Dankook University College of Medicine, Cheonan, 31116, Republic of Korea
| | - Kyeong-Wook Yoon
- Department of Neurosurgery, Dankook University College of Medicine, Cheonan, 31116, Republic of Korea
| | - Wonseok Shin
- Department of Nanobiomedical Science and BK21 PLUS NBM Global Research Center for Regenerative Medicine, Dankook University, Cheonan, 31116, Republic of Korea.
- Center for Bio-Medical Engineering Core Facility, Dankook University, Cheonan, 31116, Republic of Korea.
| | - Kyudong Han
- Department of Nanobiomedical Science and BK21 PLUS NBM Global Research Center for Regenerative Medicine, Dankook University, Cheonan, 31116, Republic of Korea.
- Center for Bio-Medical Engineering Core Facility, Dankook University, Cheonan, 31116, Republic of Korea.
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87
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Jiang CK, Ma JQ, Apostolides Z, Chen L. Metabolomics for a Millenniums-Old Crop: Tea Plant ( Camellia sinensis). JOURNAL OF AGRICULTURAL AND FOOD CHEMISTRY 2019; 67:6445-6457. [PMID: 31117495 DOI: 10.1021/acs.jafc.9b01356] [Citation(s) in RCA: 16] [Impact Index Per Article: 3.2] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 05/21/2023]
Abstract
Tea cultivation and utilization dates back to antiquity. Today it is the most widely consumed beverage on earth due to its pleasant taste and several beneficial health properties attributed to specific metabolites. Metabolomics has a tremendous potential to correlate tea metabolites with taste and health properties in humans. Our review on the current application of metabolomics in the science of tea suggests that metabolomics is a promising frontier in the evaluation of tea quality, identification of functional genes responsible for key metabolites, investigation of their metabolic regulation, and pathway analysis in the tea plant. Furthermore, the challenges, possible solutions, and the prospects of metabolomics in tea science are reviewed.
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Affiliation(s)
- Chen-Kai Jiang
- Key Laboratory of Tea Biology and Resources Utilization, Ministry of Agriculture and Rural Affairs , Tea Research Institute of the Chinese Academy of Agricultural Sciences , Hangzhou 310008 , China
| | - Jian-Qiang Ma
- Key Laboratory of Tea Biology and Resources Utilization, Ministry of Agriculture and Rural Affairs , Tea Research Institute of the Chinese Academy of Agricultural Sciences , Hangzhou 310008 , China
| | - Zeno Apostolides
- Department of Biochemistry, Genetics and Microbiology , University of Pretoria , Pretoria 0002 , South Africa
| | - Liang Chen
- Key Laboratory of Tea Biology and Resources Utilization, Ministry of Agriculture and Rural Affairs , Tea Research Institute of the Chinese Academy of Agricultural Sciences , Hangzhou 310008 , China
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88
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Bhattacharjee A, Vishwakarma GK. Time-course data prediction for repeatedly measured gene expression. INT J BIOMATH 2019. [DOI: 10.1142/s1793524519500335] [Citation(s) in RCA: 4] [Impact Index Per Article: 0.8] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/15/2022]
Abstract
Variability in time course gene expression data is a natural phenomenon. The intention of this work is to predict the future time point data through observed sample data point. The Bayesian inference is carried to serve the objective. A total of 6 replicates 3 time point’s data of 218 genes expression is adopted to illustrate the method. The estimates are found consistent with HPD interval to predict the future time point gene expression value. This proposed method can be adopted in other gene expression data setup to predict the future time course data.
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Affiliation(s)
- Atanu Bhattacharjee
- Section of Biostatistics, Centre for Cancer Epidemiology, Tata Memorial Centre, Navi Mumbai 410210, India
| | - Gajendra K. Vishwakarma
- Department of Applied Mathematics, Indian Institute of Technology (ISM), Dhanbad-826004, India
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89
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Mattes DS, Jung N, Weber LK, Bräse S, Breitling F. Miniaturized and Automated Synthesis of Biomolecules-Overview and Perspectives. ADVANCED MATERIALS (DEERFIELD BEACH, FLA.) 2019; 31:e1806656. [PMID: 31033052 DOI: 10.1002/adma.201806656] [Citation(s) in RCA: 8] [Impact Index Per Article: 1.6] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 10/14/2018] [Revised: 02/02/2019] [Indexed: 06/09/2023]
Abstract
Chemical synthesis is performed by reacting different chemical building blocks with defined stoichiometry, while meeting additional conditions, such as temperature and reaction time. Such a procedure is especially suited for automation and miniaturization. Life sciences lead the way to synthesizing millions of different oligonucleotides in extremely miniaturized reaction sites, e.g., pinpointing active genes in whole genomes, while chemistry advances different types of automation. Recent progress in matrix-assisted laser desorption/ionization mass spectrometry (MALDI-MS) imaging could match miniaturized chemical synthesis with a powerful analytical tool to validate the outcome of many different synthesis pathways beyond applications in the life sciences. Thereby, due to the radical miniaturization of chemical synthesis, thousands of molecules can be synthesized. This in turn should allow ambitious research, e.g., finding novel synthesis routes or directly screening for photocatalysts. Herein, different technologies are discussed that might be involved in this endeavor. A special emphasis is given to the obstacles that need to be tackled when depositing tiny amounts of materials to many different extremely miniaturized reaction sites.
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Affiliation(s)
- Daniela S Mattes
- Institute of Microstructure Technology (IMT), Karlsruhe Institute of Technology (KIT), Hermann-von-Helmholtz-Platz 1, 76344, Eggenstein-Leopoldshafen, Germany
| | - Nicole Jung
- Institute of Organic Chemistry (IOC), Karlsruhe Institute of Technology (KIT), Fritz-Haber-Weg 6, 76131, Karlsruhe, Germany
| | - Laura K Weber
- Institute of Microstructure Technology (IMT), Karlsruhe Institute of Technology (KIT), Hermann-von-Helmholtz-Platz 1, 76344, Eggenstein-Leopoldshafen, Germany
| | - Stefan Bräse
- Institute of Organic Chemistry (IOC), Karlsruhe Institute of Technology (KIT), Fritz-Haber-Weg 6, 76131, Karlsruhe, Germany
| | - Frank Breitling
- Institute of Microstructure Technology (IMT), Karlsruhe Institute of Technology (KIT), Hermann-von-Helmholtz-Platz 1, 76344, Eggenstein-Leopoldshafen, Germany
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90
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Pereira FL, Tavares GC, de Carvalho AF, Rosa JCC, Rezende CP, Leal CAG, Figueiredo HCP. Effects of temperature changes in the transcriptional profile of the emerging fish pathogen Francisella noatunensis subsp. orientalis. Microb Pathog 2019; 133:103548. [PMID: 31112771 DOI: 10.1016/j.micpath.2019.103548] [Citation(s) in RCA: 3] [Impact Index Per Article: 0.6] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/24/2019] [Revised: 05/16/2019] [Accepted: 05/17/2019] [Indexed: 01/05/2023]
Abstract
One of the major challenges in Nile tilapia (Oreochromis niloticus L.) farming is the occurrence of bacterial infections, and the Francisella noatunensis subsp. orientalis (FNO) is an important pathogen that has emerged in last decades. Francisellosis outbreaks have been reported in the literature as occurring seasonally when water temperature is below 24 °C. The aim of this study was to quantify the median lethal doses (LD50) of FNO in experimental challenges at 28 °C and 22 °C, and to investigate the impact of temperature changes in whole genome expression using microarray technology. The LD50 for Nile tilapia at 28 °C was ∼105.7, whereas at 22 °C, the LD50 was ∼102.2, showing that the decrease in temperature enhanced disease outcome. Out of 1917 genes screened, a total of 31 and 19 genes were down- and up-regulated at 22 °C, respectively. These genes were grouped by orthology into functional categories of: amino acid, inorganic ion, and carbohydrate transport and metabolism; transcription; and posttranslational modification, protein turnover, and chaperones. Expression of genes related to metabolism, oxidative stress, and thermal shock were regulated by temperature changes, reflecting an ability of FNO to adapt to the environment. Expression of virulence genes usually required for the Francisella genus was not changed between tested temperatures, including that of genes located on the Francisella Pathogenicity Island.
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Affiliation(s)
- Felipe Luiz Pereira
- AQUACEN, National Reference Laboratory for Aquatic Animal Diseases, Ministry of Agriculture, Livestock and Food Supply, Federal University of Minas Gerais, Brazil.
| | - Guilherme Campos Tavares
- AQUACEN, National Reference Laboratory for Aquatic Animal Diseases, Ministry of Agriculture, Livestock and Food Supply, Federal University of Minas Gerais, Brazil.
| | - Alex Fiorini de Carvalho
- AQUACEN, National Reference Laboratory for Aquatic Animal Diseases, Ministry of Agriculture, Livestock and Food Supply, Federal University of Minas Gerais, Brazil.
| | - Júlio César Camara Rosa
- AQUACEN, National Reference Laboratory for Aquatic Animal Diseases, Ministry of Agriculture, Livestock and Food Supply, Federal University of Minas Gerais, Brazil.
| | - Cristiana Perdigão Rezende
- AQUACEN, National Reference Laboratory for Aquatic Animal Diseases, Ministry of Agriculture, Livestock and Food Supply, Federal University of Minas Gerais, Brazil.
| | - Carlos Augusto Gomes Leal
- AQUACEN, National Reference Laboratory for Aquatic Animal Diseases, Ministry of Agriculture, Livestock and Food Supply, Federal University of Minas Gerais, Brazil.
| | - Henrique César Pereira Figueiredo
- AQUACEN, National Reference Laboratory for Aquatic Animal Diseases, Ministry of Agriculture, Livestock and Food Supply, Federal University of Minas Gerais, Brazil. http://www.vet.ufmg.br/
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91
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Pushie MJ, Kelly ME, Hackett MJ. Direct label-free imaging of brain tissue using synchrotron light: a review of new spectroscopic tools for the modern neuroscientist. Analyst 2019; 143:3761-3774. [PMID: 29961790 DOI: 10.1039/c7an01904a] [Citation(s) in RCA: 11] [Impact Index Per Article: 2.2] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/05/2023]
Abstract
The incidence of brain disease and brain disorders is increasing on a global scale. Unfortunately, development of new therapeutic strategies has not increased at the same rate, and brain diseases and brain disorders now inflict substantial health and economic impacts. A greater understanding of the fundamental neurochemistry that underlies healthy brain function, and the chemical pathways that manifest in brain damage or malfunction, are required to enable and accelerate therapeutic development. A previous limitation to the study of brain function and malfunction has been the limited number of techniques that provide both a wealth of biochemical information, and spatially resolved information (i.e., there was a previous lack of techniques that provided direct biochemical or elemental imaging at the cellular level). In recent times, a suite of direct spectroscopic imaging techniques, such as Fourier transform infrared spectroscopy (FTIR), X-ray fluorescence microscopy (XFM), and X-ray absorption spectroscopy (XAS) have been adapted, optimized and integrated into the field of neuroscience, to fill the above mentioned capability-gap. Advancements at synchrotron light sources, such as improved light intensity/flux, increased detector sensitivities and new capabilities of imaging/optics, has pushed the above suite of techniques beyond "proof-of-concept" studies, to routine application to study complex research problems in the field of neuroscience (and other scientific disciplines). This review examines several of the major advancements that have occurred over the last several years, with respect to FTIR, XFM and XAS capabilities at synchrotron facilities, and how the increases in technical capabilities have being integrated and used in the field of neuroscience.
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Affiliation(s)
- M J Pushie
- Department of Surgery, Division of Neurosurgery, College of Medicine, University of Saskatchewan, 107 Wiggins Road, Saskatoon, Saskatchewan S7N 5E5, Canada
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Zhang J, Liu Q, Wu W, Peng J, Zhang H, Song F, He B, Wang X, Sung HHY, Chen M, Li BS, Liu SH, Lam JWY, Tang BZ. Real-Time Monitoring of Hierarchical Self-Assembly and Induction of Circularly Polarized Luminescence from Achiral Luminogens. ACS NANO 2019; 13:3618-3628. [PMID: 30835442 DOI: 10.1021/acsnano.9b00218] [Citation(s) in RCA: 75] [Impact Index Per Article: 15.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 06/09/2023]
Abstract
Constructing artificial helical structures through hierarchical self-assembly and exploring the underlying mechanism are important, and they help gain insight from the structures, processes, and functions from the biological helices and facilitate the development of material science and nanotechnology. Herein, the two enantiomers of chiral Au(I) complexes ( S)-1 and ( R)-1 were synthesized, and they exhibited impressive spontaneous hierarchical self-assembly transitions from vesicles to helical fibers. An impressive chirality inversion and amplification was accompanied by the assembly transition, as elucidated by the results of in situ and time-dependent circular dichroism spectroscopy and scanning electron microscope imaging. The two enantiomers could serve as ideal chiral templates to co-assemble with other achiral luminogens to efficiently induce the resulting co-assembly systems to show circularly polarized luminescence (CPL). Our work has provided a simple but efficient way to explore the sophisticated self-assembly process and presented a facile and effective strategy to fabricate architectures with CPL properties.
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Affiliation(s)
- Jing Zhang
- Department of Chemistry, Hong Kong Branch of Chinese National Engineering Research Center for Tissue Restoration and Reconstruction, Institute for Advanced Study, and Department of Chemical and Biological Engineering , The Hong Kong University of Science and Technology , Clear Water Bay , Kowloon , 999077 , Hong Kong, China
| | - Qiuming Liu
- College of Chemistry and Environmental Engineering , Shenzhen University , Shenzhen 518060 , China
- Center for Aggregation-Induced Emission, SCUT-HKUST Joint Research Institute, State Key Laboratory of Luminescent Materials and Devices , South China University of Technology , Guangzhou 510640 , China
| | - Wenjie Wu
- Department of Chemistry, Hong Kong Branch of Chinese National Engineering Research Center for Tissue Restoration and Reconstruction, Institute for Advanced Study, and Department of Chemical and Biological Engineering , The Hong Kong University of Science and Technology , Clear Water Bay , Kowloon , 999077 , Hong Kong, China
| | - Junhui Peng
- Department of Chemistry, Hong Kong Branch of Chinese National Engineering Research Center for Tissue Restoration and Reconstruction, Institute for Advanced Study, and Department of Chemical and Biological Engineering , The Hong Kong University of Science and Technology , Clear Water Bay , Kowloon , 999077 , Hong Kong, China
| | - Haoke Zhang
- Department of Chemistry, Hong Kong Branch of Chinese National Engineering Research Center for Tissue Restoration and Reconstruction, Institute for Advanced Study, and Department of Chemical and Biological Engineering , The Hong Kong University of Science and Technology , Clear Water Bay , Kowloon , 999077 , Hong Kong, China
| | - Fengyan Song
- Department of Chemistry, Hong Kong Branch of Chinese National Engineering Research Center for Tissue Restoration and Reconstruction, Institute for Advanced Study, and Department of Chemical and Biological Engineering , The Hong Kong University of Science and Technology , Clear Water Bay , Kowloon , 999077 , Hong Kong, China
| | - Benzhao He
- Department of Chemistry, Hong Kong Branch of Chinese National Engineering Research Center for Tissue Restoration and Reconstruction, Institute for Advanced Study, and Department of Chemical and Biological Engineering , The Hong Kong University of Science and Technology , Clear Water Bay , Kowloon , 999077 , Hong Kong, China
| | - Xiaoyan Wang
- Key Laboratory of Pesticide and Chemical Biology, Ministry of Education, College of Chemistry , Central China Normal University , Wuhan 430079 , China
| | - Herman H-Y Sung
- Department of Chemistry, Hong Kong Branch of Chinese National Engineering Research Center for Tissue Restoration and Reconstruction, Institute for Advanced Study, and Department of Chemical and Biological Engineering , The Hong Kong University of Science and Technology , Clear Water Bay , Kowloon , 999077 , Hong Kong, China
| | - Ming Chen
- Department of Chemistry, Hong Kong Branch of Chinese National Engineering Research Center for Tissue Restoration and Reconstruction, Institute for Advanced Study, and Department of Chemical and Biological Engineering , The Hong Kong University of Science and Technology , Clear Water Bay , Kowloon , 999077 , Hong Kong, China
| | - Bing Shi Li
- College of Chemistry and Environmental Engineering , Shenzhen University , Shenzhen 518060 , China
| | - Sheng Hua Liu
- Key Laboratory of Pesticide and Chemical Biology, Ministry of Education, College of Chemistry , Central China Normal University , Wuhan 430079 , China
| | - Jacky W Y Lam
- Department of Chemistry, Hong Kong Branch of Chinese National Engineering Research Center for Tissue Restoration and Reconstruction, Institute for Advanced Study, and Department of Chemical and Biological Engineering , The Hong Kong University of Science and Technology , Clear Water Bay , Kowloon , 999077 , Hong Kong, China
| | - Ben Zhong Tang
- Department of Chemistry, Hong Kong Branch of Chinese National Engineering Research Center for Tissue Restoration and Reconstruction, Institute for Advanced Study, and Department of Chemical and Biological Engineering , The Hong Kong University of Science and Technology , Clear Water Bay , Kowloon , 999077 , Hong Kong, China
- Center for Aggregation-Induced Emission, SCUT-HKUST Joint Research Institute, State Key Laboratory of Luminescent Materials and Devices , South China University of Technology , Guangzhou 510640 , China
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Cho J, Ahn S, Son DS, Kim NK, Lee KW, Kim S, Lee J, Park SH, Park JO, Kang WK, An JY, Choi MG, Lee JH, Sohn TS, Bae JM, Kim S, Kim KM. Bridging genomics and phenomics of gastric carcinoma. Int J Cancer 2019; 145:2407-2417. [PMID: 30801717 DOI: 10.1002/ijc.32228] [Citation(s) in RCA: 31] [Impact Index Per Article: 6.2] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/15/2018] [Revised: 12/26/2018] [Accepted: 01/28/2019] [Indexed: 12/25/2022]
Abstract
Genetic alterations are the starting point leading to numerous changes in clinical and pathologic features (phenotypes) of individual cancers; however, their inter-relationships in gastric cancers (GC) are unclear. We performed massive parallel sequencing of 381 cancer-related genes and compared the results with clinical and pathologic findings in 330 GC. High tumor mutation burden (TMB) accounted for 11% of GC (n = 37) and all 19 MSI-H GCs were high TMB. High TMB was significantly more frequent in intestinal-type by Lauren, tumor with higher host cellular immune response, earlier AJCC stage and favorable prognosis. The most significantly mutated genes were TP53 (54%), ARID1A (23%), CDH1 (22%), PIK3CA (12%), RNF43 (10%) and KRAS (9%). For receptor tyrosine kinases, amplifications detected by immunohistochemistry were higher than sequencing (HER2, 9.1% vs. 5.8%; EGFR, 11.2% vs. 6.1%; FGFR2, 4.6% vs. 3.9%, c-MET, 3.4% vs. 0.9%). PTEN protein loss (22%) correlated well with underlying PTEN alterations while ATM loss (27%) was not significantly correlated with genetic alterations of ATM. p53 protein expression predicted alterations of TP53 with high sensitivity (97.8%) and low (15.9%) specificity. The poorly cohesive histology/CDH1-mutant GC subgroup showed the worst survival (p < 0.001). PD-L1 expression was significantly associated with MSI-H, MLH1 loss, ATM loss, MET positivity, higher host immune response, and genetic alterations of ARID1A, BRD3, PIK3CA, KRAS, MAP3K13, CDH2, PTEN and ESR1. The merged clinical, pathology and genomics of GC provide a better understanding of GC and new insights into the treatment of GC.
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Affiliation(s)
- Junhun Cho
- Department of Pathology and Translational Genomics, Samsung Medical Center, Sungkyunkwan University School of Medicine, Seoul, Korea
| | - Soomin Ahn
- Department of Pathology and Translational Genomics, Samsung Medical Center, Sungkyunkwan University School of Medicine, Seoul, Korea.,Department of Pathology, Seoul National University Bundang Hospital, Seongnam City, Korea
| | - Dae-Soon Son
- Samsung Genome Institute, Samsung Medical Center, Seoul, Korea
| | - Nayoung Kd Kim
- Samsung Genome Institute, Samsung Medical Center, Seoul, Korea
| | - Ki-Wook Lee
- Samsung Genome Institute, Samsung Medical Center, Seoul, Korea
| | - Seungtae Kim
- Department of Medicine, Division of Hematology-Oncology, Samsung Medical Center, Sungkyunkwan University School of Medicine, Seoul, Korea
| | - Jeeyun Lee
- Department of Medicine, Division of Hematology-Oncology, Samsung Medical Center, Sungkyunkwan University School of Medicine, Seoul, Korea
| | - Se Hoon Park
- Department of Medicine, Division of Hematology-Oncology, Samsung Medical Center, Sungkyunkwan University School of Medicine, Seoul, Korea
| | - Joon Oh Park
- Department of Medicine, Division of Hematology-Oncology, Samsung Medical Center, Sungkyunkwan University School of Medicine, Seoul, Korea
| | - Won Ki Kang
- Department of Medicine, Division of Hematology-Oncology, Samsung Medical Center, Sungkyunkwan University School of Medicine, Seoul, Korea
| | - Ji Yeong An
- Department of Surgery, Samsung Medical Center, Sungkyunkwan University School of Medicine, Seoul, Korea
| | - Min Gew Choi
- Department of Surgery, Samsung Medical Center, Sungkyunkwan University School of Medicine, Seoul, Korea
| | - Jun-Ho Lee
- Department of Surgery, Samsung Medical Center, Sungkyunkwan University School of Medicine, Seoul, Korea
| | - Tae Sung Sohn
- Department of Surgery, Samsung Medical Center, Sungkyunkwan University School of Medicine, Seoul, Korea
| | - Jae Moon Bae
- Department of Surgery, Samsung Medical Center, Sungkyunkwan University School of Medicine, Seoul, Korea
| | - Sung Kim
- Department of Surgery, Samsung Medical Center, Sungkyunkwan University School of Medicine, Seoul, Korea
| | - Kyoung-Mee Kim
- Department of Pathology and Translational Genomics, Samsung Medical Center, Sungkyunkwan University School of Medicine, Seoul, Korea.,Samsung Advanced Institute for Health Sciences & Technology (SAIHST), Samsung Medical Center, Sungkyunkwan University School of Medicine, Seoul, Korea
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94
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Shanmugasundaram M, Senthilvelan A, Kore AR. An Efficient Synthesis of 5-Aminopropargyl-Pyrimidine-5'-O-Triphosphates Through Palladium-Catalyzed Sonogashira Coupling. ACTA ACUST UNITED AC 2019; 77:e81. [PMID: 30883045 DOI: 10.1002/cpnc.81] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/10/2022]
Abstract
The utilization of 5-aminopropargyl nucleotide serves as a versatile molecular biology tool for the introduction of functional groups into a nucleic acid target of interest by using in-vitro enzymatic incorporation method. This article describes a simple, reliable, general, and efficient two-step chemical method for the synthesis of 5-(3-aminopropargyl)-2'-deoxycytidine-5'-O-triphosphate, 5-(3-aminopropargyl)-cytidine-5'-O-triphosphate, 5-(3-aminopropargyl)-2'-deoxyuridine-5'-O-triphosphate, and 5-(3-aminopropargyl)-uridine-5'-O-triphosphate, starting from the corresponding pyrimidine triphosphate. The first step involves regioselective C-5 iodination of pyrimidine triphosphate using N-iodosuccinimide and sodium azide. In the second step, propargylamine is coupled to the iodo-pyrimidine using the palladium-catalyzed Sonogashira reaction, producing good yields of highly pure (>99.5% HPLC) 5-aminopropargyl-pyrimidine-5'-O-triphosphate. In this approach, the palladium-catalyzed Sonogashira coupling reaction is highly chemoselective and does not involve protection and deprotection. © 2019 by John Wiley & Sons, Inc.
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Affiliation(s)
| | | | - Anilkumar R Kore
- Life Sciences Solutions Group, Thermo Fisher Scientific, Austin, Texas
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95
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Zhou R, Yang Y, Park SY, Seo YW, Jung SC, Kim KK, Kim K, Kim H. p300/CBP-associated factor promotes autophagic degradation of δ-catenin through acetylation and decreases prostate cancer tumorigenicity. Sci Rep 2019; 9:3351. [PMID: 30833716 PMCID: PMC6399259 DOI: 10.1038/s41598-019-40238-w] [Citation(s) in RCA: 10] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/19/2018] [Accepted: 02/12/2019] [Indexed: 01/21/2023] Open
Abstract
δ-Catenin shares common binding partners with β-catenin. As acetylation and deacetylation regulate β-catenin stability, we searched for histone acetyltransferases (HATs) or histone deacetylases (HDACs) affecting δ-catenin acetylation status and protein levels. We showed that p300/CBP-associated factor (PCAF) directly bound to and acetylated δ-catenin, whereas several class I and class II HDACs reversed this effect. Unlike β-catenin, δ-catenin was downregulated by PCAF-mediated acetylation and upregulated by HDAC-mediated deacetylation. The HDAC inhibitor trichostatin A attenuated HDAC1-mediated δ-catenin upregulation, whereas HAT or autophagy inhibitors, but not proteasome inhibitors, abolished PCAF-mediated δ-catenin downregulation. The results suggested that PCAF-mediated δ-catenin acetylation promotes its autophagic degradation in an Atg5/LC3-dependent manner. Deletions or point mutations identified several lysine residues in different δ-catenin domains involved in PCAF-mediated δ-catenin downregulation. PCAF overexpression in prostate cancer cells markedly reduced δ-catenin levels and suppressed cell growth and motility. PCAF-mediated δ-catenin downregulation inhibited E-cadherin processing and decreased the nuclear distribution of β-catenin, resulting in the suppression of β-catenin/LEF-1-mediated downstream effectors. These data demonstrate that PCAF downregulates δ-catenin by promoting its autophagic degradation and suppresses δ-catenin-mediated oncogenic signals.
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Affiliation(s)
- Rui Zhou
- College of Pharmacy and Research Institute of Life and Pharmaceutical Sciences, Sunchon National University, Sunchon, Republic of Korea
| | - Yi Yang
- College of Pharmacy and Research Institute of Life and Pharmaceutical Sciences, Sunchon National University, Sunchon, Republic of Korea
| | - So-Yeon Park
- College of Pharmacy and Research Institute of Life and Pharmaceutical Sciences, Sunchon National University, Sunchon, Republic of Korea
| | - Young-Woo Seo
- Korea Basic Science Institute, Gwangju Center, Gwangju, Republic of Korea
| | - Sang-Chul Jung
- Department of Environmental Engineering, Sunchon National University, Sunchon, Republic of Korea
| | - Kyung Keun Kim
- Department of Pharmacology, Chonnam National University Medical School, Gwangju, Republic of Korea
| | - Kwonseop Kim
- College of Pharmacy and Research Institute for Drug Development, Chonnam National University, Gwangju, Republic of Korea
| | - Hangun Kim
- College of Pharmacy and Research Institute of Life and Pharmaceutical Sciences, Sunchon National University, Sunchon, Republic of Korea.
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96
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Abstract
In infectious disease epidemiology, the laboratory plays a critical role in diagnosis, outbreak investigations, surveillance, and characterizing biologic properties of microbes associated with their transmissibility, resistance to anti-infectives, and pathogenesis. The laboratory can inform and refine epidemiologic study design and data analyses. In public health, the laboratory functions to assess effect of an intervention. In addition to research laboratories, the new-generation molecular microbiology technology has been adapted into clinical and public health laboratories to simplify, accelerate, and make precise detection and identification of infectious disease pathogens. This technology is also being applied to subtype microbes to conduct investigations that advance our knowledge of epidemiology of old and emerging infectious diseases. Because of the recent explosive progress in molecular microbiology technology and the vast amount of data generated from the applications of this technology, this Microbiology Spectrum Curated Collection: Advances in Molecular Epidemiology of Infectious Diseases describes these methods separately for bacteria, viruses, and parasites. This review discusses past and current advancements made in laboratory methods used to conduct epidemiologic studies of bacterial infections. It describes methods used to subtype bacterial organisms based on molecular microbiology techniques, following a discussion on what is meant by bacterial "species" and "clones." Discussions on past and new genotyping tests applied to epidemiologic investigations focus on tests that compare electrophoretic band patterns, hybridization matrices, and nucleic acid sequences. Applications of these genotyping tests to address epidemiologic issues are detailed elsewhere in other reviews of this series. *This article is part of a curated collection.
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97
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Troumbis AY, Hatziantoniou M, Vasios GK. Nutritional Culturomics and Big Data: Macroscopic Patterns of Change in Food, Nutrition and Diet Choices. Curr Pharm Biotechnol 2019; 20:895-908. [PMID: 30747060 DOI: 10.2174/1389201020666190211125550] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/29/2018] [Revised: 09/11/2018] [Accepted: 12/10/2018] [Indexed: 11/22/2022]
Abstract
BACKGROUND & OBJECTIVE Nutritional culturomics (NCs) is a specific focus area of culturomics epistemology developing digital humanities and computational linguistics approaches to search for macro-patterns of public interest in food, nutrition and diet choice as a major component of cultural evolution. Cultural evolution is considered as a driver at the interface of environmental and food science, economy and policy. METHODS The paper presents an epistemic programme that builds on the use of big data from webbased services such as Google Trends, Google Adwords or Google Books Ngram Viewer. RESULTS A comparison of clearly defined NCs in terms of geography, culture, linguistics, literacy, technological setups or time period might be used to reveal variations and singularities in public's behavior in terms of adaptation and mitigation policies in the agri-food and public health sectors. CONCLUSION The proposed NC programme is developed along major axes: (1) the definition of an NC; (2) the reconstruction of food and diet histories; (3) the nutrition related epidemiology; (4) the understanding of variability of NCs; (5) the methodological diversification of NCs; (6) the quantifiable limitations and flaws of NCs. A series of indicative examples are presented regarding these NC epistemology components.
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Affiliation(s)
- Andreas Y Troumbis
- Biodiversity Conservation Laboratory, Department of Environmental Studies, University of the Aegean, Greece
| | - Maria Hatziantoniou
- Section of Environmental Social Sciences, Department of Environmental Studies, University of the Aegean, Greece
| | - Georgios K Vasios
- Department of Food Science and Nutrition; School of the Environment, University of the Aegean, Greece
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98
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You X, Xu M, Li Q, Zhang K, Hao G, Xu H. Discovery of potential transcriptional biomarkers in broiler chicken for detection of amantadine abuse based on RNA sequencing technology. Food Addit Contam Part A Chem Anal Control Expo Risk Assess 2019; 36:254-269. [PMID: 30650025 DOI: 10.1080/19440049.2018.1562232] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.4] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/13/2022]
Abstract
The aim of this study was to identify candidate transcriptional biomarkers so as to provide a new method for monitoring amantadine residues during the feeding of broiler chicken. RNA sequencing (RNA-seq) and bioinformatic analyses were conducted to examine the transcriptomic changes and screen differentially expressed genes (DEGs) in broiler chicken breast muscle and liver tissues treated with amantadine. The results indicated that a total of 170 DEGs were screened from broiler chicken breast muscle tissues after amantadine was fed. Among the genes, 120 were up-regulated and 50 were down-regulated. The gene ontology (GO) terms for these genes mainly existed in the areas of hydrolase activity, immune reaction and chemokine activity. The significantly enriched pathways in the Kyoto Encyclopedia for Genes and Genomes (KEGG) were in phagosomes, cell adhesion molecules (CAMs), lysosomes and extracellular matrix (ECM) receptors. From the broiler chicken liver tissues, 172 DEGs were screened, among which 116 were up-regulated and 56 were down-regulated. The GO terms of these DEGs were related to functions such as catalytic activities, metabolic activities, oxidation-reduction activities, immune reactions and cofactor binding. The significantly enriched KEGG pathways existed in metabolism, CAM, ECM receptor reaction and drug metabolism-cytochrome P450. According to the fold-change (FC), significance levels, functional annotations and possible biological processes of DEGs, 11 and 9 candidate DEGs related to amantadine treatment were further screened from broiler chicken breast muscle and liver tissues, respectively. In addition, the quantitative real-time polymerase chain reaction (qRT-PCR) verification showed exactly concordant results with the RNA-seq data. Principal components analysis (PCA) on the qRT-PCR data resulted in the separation of treated samples from the control samples in both tissues. The results provided a basis for identification of transcriptional biomarkers for detecting amantadine residues in broiler chicken breast muscle and liver tissues.
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Affiliation(s)
- Xinyong You
- a School of Biotechnology and Food Engineering , Anyang Institute of Technology , Anyang , Henan , China
| | - Meijuan Xu
- a School of Biotechnology and Food Engineering , Anyang Institute of Technology , Anyang , Henan , China
| | - Qiong Li
- a School of Biotechnology and Food Engineering , Anyang Institute of Technology , Anyang , Henan , China
| | - Kunpeng Zhang
- a School of Biotechnology and Food Engineering , Anyang Institute of Technology , Anyang , Henan , China
| | - Guizeng Hao
- a School of Biotechnology and Food Engineering , Anyang Institute of Technology , Anyang , Henan , China
| | - Huaide Xu
- b College of Food Science and Engineering , Northwest A & F University , Yangling , Shanxi , China
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99
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Liyanage T, Masterson AN, Oyem HH, Kaimakliotis H, Nguyen H, Sardar R. Plasmoelectronic-Based Ultrasensitive Assay of Tumor Suppressor microRNAs Directly in Patient Plasma: Design of Highly Specific Early Cancer Diagnostic Technology. Anal Chem 2019; 91:1894-1903. [DOI: 10.1021/acs.analchem.8b03768] [Citation(s) in RCA: 23] [Impact Index Per Article: 4.6] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/02/2023]
Affiliation(s)
- Thakshila Liyanage
- Department of Chemistry and Chemical Biology, Indiana University-Purdue University Indianapolis, 402 N. Blackford Street, Indianapolis, Indiana 46202, United States
| | - Adrianna N. Masterson
- Department of Chemistry and Chemical Biology, Indiana University-Purdue University Indianapolis, 402 N. Blackford Street, Indianapolis, Indiana 46202, United States
| | - Hector H. Oyem
- School of Chemistry, Newcastle University, Newcastle upon Tyne NE1 7RU, United Kingdom
| | - Hristos Kaimakliotis
- Department of Urology, Indiana University School of Medicine, 535 N. Barnhill Dr., Indianapolis, Indiana 46202, United States
| | - Hang Nguyen
- Department of Chemistry and Chemical Biology, Indiana University-Purdue University Indianapolis, 402 N. Blackford Street, Indianapolis, Indiana 46202, United States
| | - Rajesh Sardar
- Department of Chemistry and Chemical Biology, Indiana University-Purdue University Indianapolis, 402 N. Blackford Street, Indianapolis, Indiana 46202, United States
- Integrated Nanosystems Development Institute, Indiana University-Purdue University Indianapolis, 402 N. Blackford Street, Indianapolis, Indiana 46202, United States
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100
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ISOdb: A Comprehensive Database of Full-Length Isoforms Generated by Iso-Seq. Int J Genomics 2018; 2018:9207637. [PMID: 30581839 PMCID: PMC6276398 DOI: 10.1155/2018/9207637] [Citation(s) in RCA: 5] [Impact Index Per Article: 0.8] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/27/2018] [Revised: 08/13/2018] [Accepted: 09/02/2018] [Indexed: 01/12/2023] Open
Abstract
The accurate landscape of transcript isoforms plays an important role in the understanding of gene function and gene regulation. However, building complete transcripts is very challenging for short reads generated using next-generation sequencing. Fortunately, isoform sequencing (Iso-Seq) using single-molecule sequencing technologies, such as PacBio SMRT, provides long reads spanning entire transcript isoforms which do not require assembly. Therefore, we have developed ISOdb, a comprehensive resource database for hosting and carrying out an in-depth analysis of Iso-Seq datasets and visualising the full-length transcript isoforms. The current version of ISOdb has collected 93 publicly available Iso-Seq samples from eight species and presents the samples in two levels: (1) sample level, including metainformation, long read distribution, isoform numbers, and alternative splicing (AS) events of each sample; (2) gene level, including the total isoforms, novel isoform number, novel AS number, and isoform visualisation of each gene. In addition, ISOdb provides a user interface in the website for uploading sample information to facilitate the collection and analysis of researchers' datasets. Currently, ISOdb is the first repository that offers comprehensive resources and convenient public access for hosting, analysing, and visualising Iso-Seq data, which is freely available.
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