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Drautz-Moses DI, Luhung I, Gusareva ES, Kee C, Gaultier NE, Premkrishnan BNV, Lee CF, Leong ST, Park C, Yap ZH, Heinle CE, Lau KJX, Purbojati RW, Lim SBY, Lim YH, Kutmutia SK, Aung NW, Oliveira EL, Ng SG, Dacanay J, Ang PN, Spence S, Phung WJ, Wong A, Kennedy RJ, Kalsi N, Sasi SP, Chandrasekaran L, Uchida A, Junqueira ACM, Kim HL, Hankers R, Feuerle T, Corsmeier U, Schuster SC. Vertical stratification of the air microbiome in the lower troposphere. Proc Natl Acad Sci U S A 2022; 119:e2117293119. [PMID: 35131944 PMCID: PMC8851546 DOI: 10.1073/pnas.2117293119] [Citation(s) in RCA: 3] [Impact Index Per Article: 1.5] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/20/2021] [Accepted: 12/11/2021] [Indexed: 12/11/2022] Open
Abstract
The troposphere constitutes the final frontier of global ecosystem research due to technical challenges arising from its size, low biomass, and gaseous state. Using a vertical testing array comprising a meteorological tower and a research aircraft, we conducted synchronized measurements of meteorological parameters and airborne biomass (n = 480) in the vertical air column up to 3,500 m. The taxonomic analysis of metagenomic data revealed differing patterns of airborne microbial community composition with respect to time of day and height above ground. The temporal and spatial resolution of our study demonstrated that the diel cycle of airborne microorganisms is a ground-based phenomenon that is entirely absent at heights >1,000 m. In an integrated analysis combining meteorological and biological data, we demonstrate that atmospheric turbulence, identified by potential temperature and high-frequency three-component wind measurements, is the key driver of bioaerosol dynamics in the lower troposphere. Multivariate regression analysis shows that at least 50% of identified airborne microbial taxa (n = ∼10,000) are associated with either ground or height, allowing for an understanding of dispersal patterns of microbial taxa in the vertical air column. Due to the interconnectedness of atmospheric turbulence and temperature, the dynamics of microbial dispersal are likely to be impacted by rising global temperatures, thereby also affecting ecosystems on the planetary surface.
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Affiliation(s)
- Daniela I Drautz-Moses
- Singapore Centre for Environmental Life Sciences Engineering, Nanyang Technological University, Singapore 637551
| | - Irvan Luhung
- Singapore Centre for Environmental Life Sciences Engineering, Nanyang Technological University, Singapore 637551
| | - Elena S Gusareva
- Singapore Centre for Environmental Life Sciences Engineering, Nanyang Technological University, Singapore 637551
- The Asian School of the Environment, Nanyang Technological University, Singapore 637459
| | - Carmon Kee
- Singapore Centre for Environmental Life Sciences Engineering, Nanyang Technological University, Singapore 637551
| | - Nicolas E Gaultier
- Singapore Centre for Environmental Life Sciences Engineering, Nanyang Technological University, Singapore 637551
| | | | - Choou Fook Lee
- Singapore Centre for Environmental Life Sciences Engineering, Nanyang Technological University, Singapore 637551
| | - See Ting Leong
- Singapore Centre for Environmental Life Sciences Engineering, Nanyang Technological University, Singapore 637551
| | - Changsook Park
- Singapore Centre for Environmental Life Sciences Engineering, Nanyang Technological University, Singapore 637551
| | - Zhei Hwee Yap
- Singapore Centre for Environmental Life Sciences Engineering, Nanyang Technological University, Singapore 637551
| | - Cassie E Heinle
- Singapore Centre for Environmental Life Sciences Engineering, Nanyang Technological University, Singapore 637551
| | - Kenny J X Lau
- Singapore Centre for Environmental Life Sciences Engineering, Nanyang Technological University, Singapore 637551
| | - Rikky W Purbojati
- Singapore Centre for Environmental Life Sciences Engineering, Nanyang Technological University, Singapore 637551
| | - Serene B Y Lim
- Singapore Centre for Environmental Life Sciences Engineering, Nanyang Technological University, Singapore 637551
| | - Yee Hui Lim
- Singapore Centre for Environmental Life Sciences Engineering, Nanyang Technological University, Singapore 637551
| | - Shruti Ketan Kutmutia
- Singapore Centre for Environmental Life Sciences Engineering, Nanyang Technological University, Singapore 637551
| | - Ngu War Aung
- Singapore Centre for Environmental Life Sciences Engineering, Nanyang Technological University, Singapore 637551
| | - Elaine L Oliveira
- Singapore Centre for Environmental Life Sciences Engineering, Nanyang Technological University, Singapore 637551
| | - Soo Guek Ng
- Singapore Centre for Environmental Life Sciences Engineering, Nanyang Technological University, Singapore 637551
| | - Justine Dacanay
- Singapore Centre for Environmental Life Sciences Engineering, Nanyang Technological University, Singapore 637551
| | - Poh Nee Ang
- Singapore Centre for Environmental Life Sciences Engineering, Nanyang Technological University, Singapore 637551
| | - Sam Spence
- Singapore Centre for Environmental Life Sciences Engineering, Nanyang Technological University, Singapore 637551
| | - Wen Jia Phung
- Singapore Centre for Environmental Life Sciences Engineering, Nanyang Technological University, Singapore 637551
| | - Anthony Wong
- Singapore Centre for Environmental Life Sciences Engineering, Nanyang Technological University, Singapore 637551
| | - Ryan J Kennedy
- Singapore Centre for Environmental Life Sciences Engineering, Nanyang Technological University, Singapore 637551
| | - Namrata Kalsi
- Singapore Centre for Environmental Life Sciences Engineering, Nanyang Technological University, Singapore 637551
| | - Santhi Puramadathil Sasi
- Singapore Centre for Environmental Life Sciences Engineering, Nanyang Technological University, Singapore 637551
| | - Lakshmi Chandrasekaran
- Singapore Centre for Environmental Life Sciences Engineering, Nanyang Technological University, Singapore 637551
| | - Akira Uchida
- Singapore Centre for Environmental Life Sciences Engineering, Nanyang Technological University, Singapore 637551
| | - Ana Carolina M Junqueira
- Departamento de Genética, Instituto de Biologia, Universidade Federal do Rio de Janeiro, Rio de Janeiro 21941-590, Brazil
| | - Hie Lim Kim
- Singapore Centre for Environmental Life Sciences Engineering, Nanyang Technological University, Singapore 637551
- The Asian School of the Environment, Nanyang Technological University, Singapore 637459
| | - Rudolf Hankers
- Institute of Flight Guidance, Technische Universität, 38108 Braunschweig, Germany
| | - Thomas Feuerle
- Institute of Flight Guidance, Technische Universität, 38108 Braunschweig, Germany
| | - Ulrich Corsmeier
- Institute of Meteorology and Climate Research, Karlsruhe Institute of Technology, 76021 Karlsruhe, Germany
| | - Stephan C Schuster
- Singapore Centre for Environmental Life Sciences Engineering, Nanyang Technological University, Singapore 637551;
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2
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Chew EGY, Lim TC, Leong MF, Liu X, Sia YY, Leong ST, Yan-Jiang BC, Stoecklin C, Borhan R, Heilmann-Heimbach S, Nöthen MM, Viasnoff V, Shyh-Chang N, Wan ACA, Philpott MP, Hillmer AM. Observations that suggest a contribution of altered dermal papilla mitochondrial function to androgenetic alopecia. Exp Dermatol 2022; 31:906-917. [PMID: 35119146 DOI: 10.1111/exd.14536] [Citation(s) in RCA: 7] [Impact Index Per Article: 3.5] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/01/2020] [Revised: 01/25/2022] [Accepted: 01/30/2022] [Indexed: 11/28/2022]
Abstract
Androgenetic alopecia (AGA) is a prevalent hair loss condition in males that develops due to the influence of androgens and genetic predisposition. With the aim of elucidating genes involved in AGA pathogenesis, we modelled AGA with three-dimensional culture of keratinocyte-surrounded dermal papilla (DP) cells. We co-cultured immortalised balding and non-balding human DP cells (DPC) derived from male AGA patients with epidermal keratinocyte (NHEK) using multi-interfacial polyelectrolyte complexation technique. We observed up-regulated mitochondria-related gene expression in balding compared to non-balding DP aggregates which indicated altered mitochondria metabolism. Further observation of significantly reduced electron transport chain complex activity (complex I, IV and V), ATP levels and ability to uptake metabolites for ATP generation demonstrated compromised mitochondria function in balding DPC. Balding DP was also found to be under significantly higher oxidative stress than non-balding DP. Our experiments suggest that application of antioxidants lowers oxidative stress levels and improve metabolite uptake in balding DPC. We postulate that the observed up-regulation of mitochondria-related genes in balding DP aggregates resulted from an over-compensatory effort to rescue decreased mitochondrial function in balding DP through the attempted production of new functional mitochondria. In all, our three-dimensional co-culturing revealed mitochondrial dysfunction in balding DPC, suggesting a metabolic component in the etiology of AGA.
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Affiliation(s)
- Elaine G Y Chew
- Cancer Therapeutics & Stratified Oncology, Genome Institute of Singapore, Singapore.,Lee Kong Chian School of Medicine, Nanyang Technological University, Singapore
| | - Tze Chiun Lim
- Cell and Tissue Engineering, Institute of Bioengineering and Nanotechnology, Singapore
| | - Meng Fatt Leong
- Cell and Tissue Engineering, Institute of Bioengineering and Nanotechnology, Singapore.,School of Applied Science, Temasek Polytechnic, Singapore
| | - Xingliang Liu
- Cancer Therapeutics & Stratified Oncology, Genome Institute of Singapore, Singapore
| | - Yee Yen Sia
- Cancer Therapeutics & Stratified Oncology, Genome Institute of Singapore, Singapore
| | - See Ting Leong
- Cancer Therapeutics & Stratified Oncology, Genome Institute of Singapore, Singapore
| | - Benjamin C Yan-Jiang
- Cancer Stem Cell Biology, Genome Institute of Singapore, Singapore.,NUS Graduate School for Integrative Sciences and Engineering, National University of Singapore, Singapore
| | - Celine Stoecklin
- Mechanobiology Institute, National University of Singapore, Singapore
| | - Rosa Borhan
- Centre for Cell Biology and Cutaneous Research, Blizard Institute Barts and The London School of Medicine and Dentistry, Queen Mary College, London, UK
| | - Stefanie Heilmann-Heimbach
- Institute of Human Genetics, University of Bonn, School of Medicine &, University Hospital of Bonn, Bonn, Germany.,Department of Genomics, Life & Brain Center, University of Bonn, Bonn, Germany
| | - Markus M Nöthen
- Institute of Human Genetics, University of Bonn, School of Medicine &, University Hospital of Bonn, Bonn, Germany.,Department of Genomics, Life & Brain Center, University of Bonn, Bonn, Germany
| | - Virgile Viasnoff
- Mechanobiology Institute, National University of Singapore, Singapore
| | - Ng Shyh-Chang
- Institute of Zoology, Institute of Stem Cell & Regeneration, Chinese Academy of Sciences, Beijing, China
| | - Andrew C A Wan
- Cell and Tissue Engineering, Institute of Bioengineering and Nanotechnology, Singapore.,Institute of Food and Biotechnology Innovation, Singapore
| | - M P Philpott
- Centre for Cell Biology and Cutaneous Research, Blizard Institute Barts and The London School of Medicine and Dentistry, Queen Mary College, London, UK
| | - Axel M Hillmer
- Cancer Therapeutics & Stratified Oncology, Genome Institute of Singapore, Singapore.,Institute of Pathology, Faculty of Medicine, University Hospital Cologne, University of Cologne, Cologne, Germany.,Center for Molecular Medicine Cologne, University of Cologne, Cologne, Germany
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3
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Chan M, Smirnov A, Mulawadi F, Lim P, Lim WH, Leong ST, Low HM, Yee MQ, Yeo YQ, Zhou X, Lee C, Huang W, Welebob L, Wu M. A Novel System Control for Quality Control of Diagnostic Tests Based on Next-Generation Sequencing. J Appl Lab Med 2016; 1:25-35. [PMID: 33626812 DOI: 10.1373/jalm.2016.020131] [Citation(s) in RCA: 4] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/19/2016] [Accepted: 05/06/2016] [Indexed: 11/06/2022]
Abstract
BACKGROUND We describe a novel system control (SC) implemented in an automated AmpliSeq™-based next-generation sequencing (NGS)2 run that simultaneously acts as (a) an external positive/sensitivity control, (b) a spike-in QC for DNA extraction, and (c) a nontemplate control to detect exogenous DNA contamination. METHODS Plasmids carrying wild-type tobacco mosaic virus sequence and a sequence with three designed mutations were synthesized and mixed, such that the mutations are present at 5% variant frequency in the mixture designated as SC. SC was used as a stand-alone sample and spiked into each sample in each run. A cell line-derived reference material, in both a formalin-fixed paraffin-embedded (FFPE) sample and genomic DNA (gDNA), was sequenced in the same runs. RESULTS By interpolation, 100 fg SC spiked in FFPE sample produced sequencing coverage equivalent to approximately 3 fg in the gDNA. In the SC-only sample, all three designed mutations were recovered around 5% as expected, while no significant reads of human genome were present. In samples with a common PCR inhibitor, coverage for both SC and target amplicons were eliminated. An inverse relationship between the coverage of SC and DNA input was observed. In clinical samples, the ratio of SC to the median coverage of sample can be used to indicate insufficient DNA input. CONCLUSIONS The SC is an elegant and comprehensive QC concept for NGS-based diagnostic tests.
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4
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Yao F, Kausalya JP, Sia YY, Teo ASM, Lee WH, Ong AGM, Zhang Z, Tan JHJ, Li G, Bertrand D, Liu X, Poh HM, Guan P, Zhu F, Pathiraja TN, Ariyaratne PN, Rao J, Woo XY, Cai S, Mulawadi FH, Poh WT, Veeravalli L, Chan CS, Lim SS, Leong ST, Neo SC, Choi PSD, Chew EGY, Nagarajan N, Jacques PÉ, So JBY, Ruan X, Yeoh KG, Tan P, Sung WK, Hunziker W, Ruan Y, Hillmer AM. Recurrent Fusion Genes in Gastric Cancer: CLDN18-ARHGAP26 Induces Loss of Epithelial Integrity. Cell Rep 2015; 12:272-85. [PMID: 26146084 DOI: 10.1016/j.celrep.2015.06.020] [Citation(s) in RCA: 98] [Impact Index Per Article: 10.9] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/26/2014] [Revised: 04/21/2015] [Accepted: 06/06/2015] [Indexed: 12/21/2022] Open
Abstract
Genome rearrangements, a hallmark of cancer, can result in gene fusions with oncogenic properties. Using DNA paired-end-tag (DNA-PET) whole-genome sequencing, we analyzed 15 gastric cancers (GCs) from Southeast Asians. Rearrangements were enriched in open chromatin and shaped by chromatin structure. We identified seven rearrangement hot spots and 136 gene fusions. In three out of 100 GC cases, we found recurrent fusions between CLDN18, a tight junction gene, and ARHGAP26, a gene encoding a RHOA inhibitor. Epithelial cell lines expressing CLDN18-ARHGAP26 displayed a dramatic loss of epithelial phenotype and long protrusions indicative of epithelial-mesenchymal transition (EMT). Fusion-positive cell lines showed impaired barrier properties, reduced cell-cell and cell-extracellular matrix adhesion, retarded wound healing, and inhibition of RHOA. Gain of invasion was seen in cancer cell lines expressing the fusion. Thus, CLDN18-ARHGAP26 mediates epithelial disintegration, possibly leading to stomach H(+) leakage, and the fusion might contribute to invasiveness once a cell is transformed.
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Affiliation(s)
- Fei Yao
- Cancer Therapeutics and Stratified Oncology, Genome Institute of Singapore, Singapore 138672, Singapore; The Singapore Gastric Cancer Consortium, National University of Singapore, Singapore 119228, Singapore
| | - Jaya P Kausalya
- Epithelial Cell Biology Laboratory, Institute of Molecular and Cell Biology, Singapore 138673, Singapore
| | - Yee Yen Sia
- Cancer Therapeutics and Stratified Oncology, Genome Institute of Singapore, Singapore 138672, Singapore; The Singapore Gastric Cancer Consortium, National University of Singapore, Singapore 119228, Singapore
| | - Audrey S M Teo
- Cancer Therapeutics and Stratified Oncology, Genome Institute of Singapore, Singapore 138672, Singapore; The Singapore Gastric Cancer Consortium, National University of Singapore, Singapore 119228, Singapore
| | - Wah Heng Lee
- Computational and Systems Biology, Genome Institute of Singapore, Singapore 138672, Singapore
| | - Alicia G M Ong
- Epithelial Cell Biology Laboratory, Institute of Molecular and Cell Biology, Singapore 138673, Singapore
| | - Zhenshui Zhang
- Human Genetics, Genome Institute of Singapore, Singapore 138672, Singapore
| | - Joanna H J Tan
- Cancer Therapeutics and Stratified Oncology, Genome Institute of Singapore, Singapore 138672, Singapore
| | - Guoliang Li
- National Key Laboratory of Crop Genetic Improvement, Center for Bioinformatics, College of Informatics, Huazhong Agricultural University, Wuhan 430070, China
| | - Denis Bertrand
- Computational and Systems Biology, Genome Institute of Singapore, Singapore 138672, Singapore
| | - Xingliang Liu
- Cancer Therapeutics and Stratified Oncology, Genome Institute of Singapore, Singapore 138672, Singapore
| | - Huay Mei Poh
- Cancer Therapeutics and Stratified Oncology, Genome Institute of Singapore, Singapore 138672, Singapore
| | - Peiyong Guan
- Computational and Systems Biology, Genome Institute of Singapore, Singapore 138672, Singapore; School of Computing, National University of Singapore, Singapore 117417, Singapore
| | - Feng Zhu
- The Singapore Gastric Cancer Consortium, National University of Singapore, Singapore 119228, Singapore; Department of Medicine, Yong Loo Lin School of Medicine, National University of Singapore, Singapore 119228, Singapore
| | - Thushangi Nadeera Pathiraja
- Cancer Therapeutics and Stratified Oncology, Genome Institute of Singapore, Singapore 138672, Singapore; The Singapore Gastric Cancer Consortium, National University of Singapore, Singapore 119228, Singapore
| | - Pramila N Ariyaratne
- Computational and Systems Biology, Genome Institute of Singapore, Singapore 138672, Singapore
| | - Jaideepraj Rao
- Department of General Surgery, Tan Tock Seng Hospital, Singapore 308433, Singapore
| | - Xing Yi Woo
- Personal Genomic Solutions, Genome Institute of Singapore, Singapore 138672, Singapore
| | - Shaojiang Cai
- Computational and Systems Biology, Genome Institute of Singapore, Singapore 138672, Singapore
| | - Fabianus H Mulawadi
- Computational and Systems Biology, Genome Institute of Singapore, Singapore 138672, Singapore
| | - Wan Ting Poh
- Personal Genomic Solutions, Genome Institute of Singapore, Singapore 138672, Singapore
| | - Lavanya Veeravalli
- Research Computing, Genome Institute of Singapore, Singapore 138672, Singapore
| | - Chee Seng Chan
- Research Computing, Genome Institute of Singapore, Singapore 138672, Singapore
| | - Seong Soo Lim
- Human Genetics, Genome Institute of Singapore, Singapore 138672, Singapore
| | - See Ting Leong
- Genome Technology and Biology, Genome Institute of Singapore, Singapore 138672, Singapore
| | - Say Chuan Neo
- Genome Technology and Biology, Genome Institute of Singapore, Singapore 138672, Singapore
| | - Poh Sum D Choi
- Genome Technology and Biology, Genome Institute of Singapore, Singapore 138672, Singapore
| | - Elaine G Y Chew
- Cancer Therapeutics and Stratified Oncology, Genome Institute of Singapore, Singapore 138672, Singapore
| | - Niranjan Nagarajan
- Computational and Systems Biology, Genome Institute of Singapore, Singapore 138672, Singapore
| | | | - Jimmy B Y So
- The Singapore Gastric Cancer Consortium, National University of Singapore, Singapore 119228, Singapore; Department of Surgery, Yong Loo Lin School of Medicine, National University of Singapore, Singapore 119228, Singapore; National University Health System, Singapore 119228, Singapore
| | - Xiaoan Ruan
- Personal Genomic Solutions, Genome Institute of Singapore, Singapore 138672, Singapore; Genome Technology and Biology, Genome Institute of Singapore, Singapore 138672, Singapore
| | - Khay Guan Yeoh
- The Singapore Gastric Cancer Consortium, National University of Singapore, Singapore 119228, Singapore; Department of Medicine, Yong Loo Lin School of Medicine, National University of Singapore, Singapore 119228, Singapore; National University Health System, Singapore 119228, Singapore
| | - Patrick Tan
- Cancer Therapeutics and Stratified Oncology, Genome Institute of Singapore, Singapore 138672, Singapore; The Singapore Gastric Cancer Consortium, National University of Singapore, Singapore 119228, Singapore; Duke-NUS Graduate Medical School, Singapore 169857, Singapore; Cancer Science Institute of Singapore, Yong Loo Lin School of Medicine, National University of Singapore, Singapore 117599, Singapore
| | - Wing-Kin Sung
- Computational and Systems Biology, Genome Institute of Singapore, Singapore 138672, Singapore; School of Computing, National University of Singapore, Singapore 117417, Singapore
| | - Walter Hunziker
- Epithelial Cell Biology Laboratory, Institute of Molecular and Cell Biology, Singapore 138673, Singapore; Department of Physiology, National University of Singapore, Singapore 117597, Singapore.
| | - Yijun Ruan
- The Jackson Laboratory for Genomic Medicine, Farmington, CT 06032, USA.
| | - Axel M Hillmer
- Cancer Therapeutics and Stratified Oncology, Genome Institute of Singapore, Singapore 138672, Singapore; The Singapore Gastric Cancer Consortium, National University of Singapore, Singapore 119228, Singapore.
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5
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Yao F, Ariyaratne PN, Hillmer AM, Lee WH, Li G, Teo ASM, Woo XY, Zhang Z, Chen JP, Poh WT, Zawack KFB, Chan CS, Leong ST, Neo SC, Choi PSD, Gao S, Nagarajan N, Thoreau H, Shahab A, Ruan X, Cacheux-Rataboul V, Wei CL, Bourque G, Sung WK, Liu ET, Ruan Y. Long span DNA paired-end-tag (DNA-PET) sequencing strategy for the interrogation of genomic structural mutations and fusion-point-guided reconstruction of amplicons. PLoS One 2012; 7:e46152. [PMID: 23029419 PMCID: PMC3461012 DOI: 10.1371/journal.pone.0046152] [Citation(s) in RCA: 11] [Impact Index Per Article: 0.9] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/04/2012] [Accepted: 08/28/2012] [Indexed: 01/23/2023] Open
Abstract
Structural variations (SVs) contribute significantly to the variability of the human genome and extensive genomic rearrangements are a hallmark of cancer. While genomic DNA paired-end-tag (DNA-PET) sequencing is an attractive approach to identify genomic SVs, the current application of PET sequencing with short insert size DNA can be insufficient for the comprehensive mapping of SVs in low complexity and repeat-rich genomic regions. We employed a recently developed procedure to generate PET sequencing data using large DNA inserts of 10–20 kb and compared their characteristics with short insert (1 kb) libraries for their ability to identify SVs. Our results suggest that although short insert libraries bear an advantage in identifying small deletions, they do not provide significantly better breakpoint resolution. In contrast, large inserts are superior to short inserts in providing higher physical genome coverage for the same sequencing cost and achieve greater sensitivity, in practice, for the identification of several classes of SVs, such as copy number neutral and complex events. Furthermore, our results confirm that large insert libraries allow for the identification of SVs within repetitive sequences, which cannot be spanned by short inserts. This provides a key advantage in studying rearrangements in cancer, and we show how it can be used in a fusion-point-guided-concatenation algorithm to study focally amplified regions in cancer.
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Affiliation(s)
- Fei Yao
- Genome Institute of Singapore, Agency for Science, Technology and Research, Singapore, Singapore
- Department of Epidemiology and Public Health, Yong Loo Lin School of Medicine, National University of Singapore, Singapore, Singapore
| | - Pramila N. Ariyaratne
- Genome Institute of Singapore, Agency for Science, Technology and Research, Singapore, Singapore
| | - Axel M. Hillmer
- Genome Institute of Singapore, Agency for Science, Technology and Research, Singapore, Singapore
| | - Wah Heng Lee
- Genome Institute of Singapore, Agency for Science, Technology and Research, Singapore, Singapore
| | - Guoliang Li
- Genome Institute of Singapore, Agency for Science, Technology and Research, Singapore, Singapore
| | - Audrey S. M. Teo
- Genome Institute of Singapore, Agency for Science, Technology and Research, Singapore, Singapore
| | - Xing Yi Woo
- Genome Institute of Singapore, Agency for Science, Technology and Research, Singapore, Singapore
| | - Zhenshui Zhang
- Genome Institute of Singapore, Agency for Science, Technology and Research, Singapore, Singapore
| | - Jieqi P. Chen
- Genome Institute of Singapore, Agency for Science, Technology and Research, Singapore, Singapore
| | - Wan Ting Poh
- Genome Institute of Singapore, Agency for Science, Technology and Research, Singapore, Singapore
| | - Kelson F. B. Zawack
- Genome Institute of Singapore, Agency for Science, Technology and Research, Singapore, Singapore
| | - Chee Seng Chan
- Genome Institute of Singapore, Agency for Science, Technology and Research, Singapore, Singapore
| | - See Ting Leong
- Genome Institute of Singapore, Agency for Science, Technology and Research, Singapore, Singapore
| | - Say Chuan Neo
- Genome Institute of Singapore, Agency for Science, Technology and Research, Singapore, Singapore
| | - Poh Sum D. Choi
- Genome Institute of Singapore, Agency for Science, Technology and Research, Singapore, Singapore
| | - Song Gao
- Graduate School for Integrative Sciences and Engineering, Centre for Life Sciences, National University of Singapore, Singapore, Singapore
| | - Niranjan Nagarajan
- Genome Institute of Singapore, Agency for Science, Technology and Research, Singapore, Singapore
| | - Hervé Thoreau
- Genome Institute of Singapore, Agency for Science, Technology and Research, Singapore, Singapore
| | - Atif Shahab
- Genome Institute of Singapore, Agency for Science, Technology and Research, Singapore, Singapore
| | - Xiaoan Ruan
- Genome Institute of Singapore, Agency for Science, Technology and Research, Singapore, Singapore
| | - Valère Cacheux-Rataboul
- Genome Institute of Singapore, Agency for Science, Technology and Research, Singapore, Singapore
| | - Chia-Lin Wei
- Genome Institute of Singapore, Agency for Science, Technology and Research, Singapore, Singapore
| | - Guillaume Bourque
- Genome Institute of Singapore, Agency for Science, Technology and Research, Singapore, Singapore
| | - Wing-Kin Sung
- Genome Institute of Singapore, Agency for Science, Technology and Research, Singapore, Singapore
| | - Edison T. Liu
- Genome Institute of Singapore, Agency for Science, Technology and Research, Singapore, Singapore
| | - Yijun Ruan
- Genome Institute of Singapore, Agency for Science, Technology and Research, Singapore, Singapore
- Department of Biochemistry, Yong Loo Lin School of Medicine, National University of Singapore, Singapore, Singapore
- * E-mail:
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6
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Hillmer AM, Yao F, Inaki K, Lee WH, Ariyaratne PN, Teo ASM, Woo XY, Zhang Z, Zhao H, Ukil L, Chen JP, Zhu F, So JBY, Salto-Tellez M, Poh WT, Zawack KFB, Nagarajan N, Gao S, Li G, Kumar V, Lim HPJ, Sia YY, Chan CS, Leong ST, Neo SC, Choi PSD, Thoreau H, Tan PBO, Shahab A, Ruan X, Bergh J, Hall P, Cacheux-Rataboul V, Wei CL, Yeoh KG, Sung WK, Bourque G, Liu ET, Ruan Y. Comprehensive long-span paired-end-tag mapping reveals characteristic patterns of structural variations in epithelial cancer genomes. Genome Res 2011; 21:665-75. [PMID: 21467267 DOI: 10.1101/gr.113555.110] [Citation(s) in RCA: 70] [Impact Index Per Article: 5.4] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/13/2022]
Abstract
Somatic genome rearrangements are thought to play important roles in cancer development. We optimized a long-span paired-end-tag (PET) sequencing approach using 10-Kb genomic DNA inserts to study human genome structural variations (SVs). The use of a 10-Kb insert size allows the identification of breakpoints within repetitive or homology-containing regions of a few kilobases in size and results in a higher physical coverage compared with small insert libraries with the same sequencing effort. We have applied this approach to comprehensively characterize the SVs of 15 cancer and two noncancer genomes and used a filtering approach to strongly enrich for somatic SVs in the cancer genomes. Our analyses revealed that most inversions, deletions, and insertions are germ-line SVs, whereas tandem duplications, unpaired inversions, interchromosomal translocations, and complex rearrangements are over-represented among somatic rearrangements in cancer genomes. We demonstrate that the quantitative and connective nature of DNA-PET data is precise in delineating the genealogy of complex rearrangement events, we observe signatures that are compatible with breakage-fusion-bridge cycles, and we discover that large duplications are among the initial rearrangements that trigger genome instability for extensive amplification in epithelial cancers.
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Affiliation(s)
- Axel M Hillmer
- Genome Technology and Biology, Genome Institute of Singapore, Singapore 138672, Singapore
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7
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McLachlan CS, Almsherqi ZA, Mossop P, Suzuki J, Leong ST, Deng Y. Down regulation of immuno-detectable cardiac connexin-43 in BALB/c mice following acute fasting. Int J Cardiol 2008; 136:99-102. [PMID: 18606469 DOI: 10.1016/j.ijcard.2008.03.098] [Citation(s) in RCA: 6] [Impact Index Per Article: 0.4] [Reference Citation Analysis] [What about the content of this article? (0)] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Received: 01/13/2008] [Accepted: 03/30/2008] [Indexed: 11/18/2022]
Abstract
Acute starvation effects for connexin-43 protein expression, in the heart, had not been previously explored. Hence we examined acute fasting on the myocardial immuno-histochemical expression of connexin-43 in 3 groups of 8-week old female BALB/c mice. Groups consisted of control mice (n=5), fasting for 24 h (N=5) and 48 h (N=3). Under light microscopy all control fed cases revealed the presence of some immuno-detectable staining for connexin-43 that is either present or weakly observed in some or all of the regions of interest, that include the cross-sectional left ventricular sub-endocardium, mid-myocardium and papillary muscle. Whereas mice that underwent 24 or 48 h of acute starvation, connexin-43 expression was either difficult to detect visually (N=3) or was completely absent (N=5) at 40x magnification using a light microscope. In starved mice with no membrane staining for connexin-43 we observed an increase in the intracellular accumulation of cytoplasmic connexin-43 expression.
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8
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Abstract
The use of unleaded gasoline, together with an increase in the number of vehicles in Bangkok, has significantly influenced benzene and toluene concentrations in vehicular emissions and contributes to the air pollution problem. As a matter of practical necessity, a quick test program is done for the measurement of emission concentrations/rates for vehicles driven on the road. Exhaust emission measurement at idle mode was conducted in a fleet of 12 vehicles of different model years and manufacturers. The study revealed that the benzene and toluene concentrations in the exhaust effluent averaged 4.4-22.02 and 12.24-44.75 mg/m3, respectively for 1990-1992 cars and decreased to 0.76-4.14 and 0.89-6.26 mg/m3, respectively for 1994-1995 cars. In another study, exhaust emission measurement on a chassis dynamometer was carried out in a fleet of nine selected, in-use cars. It was observed that benzene and toluene emission rates were considerably higher-in the range of 70.84-85.82 and 354.15- 429.00 mg/km, respectively, for 1990-1991 model year cars. Lower benzene and toluene emission rates of 0.43-95.07 and 2. 15-475.35 mg/km, respectively, were represented by newer cars with model years 1994-1995. These results indicated that there was a significant increase in benzene and toluene emission concentrations and rates with increasing car mileage and model year. The finding also revealed that only 28% of the tested vehicles complied to the approved emission standard.
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Affiliation(s)
- S Muttamara
- Environmental Engineering Program, School of Environment, Resource and Development, Asian Institute of Technology, Klong Luang, Pathumthani, 12120, Thailand
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