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Ferrarini A, Forcato C, Buson G, Tononi P, del Monaco V, Terracciano M, Bolognesi C, Fontana F, Medoro G, Neves R, Möhlendick B, Rihawi K, Ardizzoni A, Sumanasuriya S, Flohr P, Lambros M, de Bono J, Stoecklein NH, Manaresi N. A streamlined workflow for single-cells genome-wide copy-number profiling by low-pass sequencing of LM-PCR whole-genome amplification products. PLoS One 2018; 13:e0193689. [PMID: 29494651 PMCID: PMC5832318 DOI: 10.1371/journal.pone.0193689] [Citation(s) in RCA: 15] [Impact Index Per Article: 2.5] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/23/2017] [Accepted: 02/19/2018] [Indexed: 11/23/2022] Open
Abstract
Chromosomal instability and associated chromosomal aberrations are hallmarks of cancer and play a critical role in disease progression and development of resistance to drugs. Single-cell genome analysis has gained interest in latest years as a source of biomarkers for targeted-therapy selection and drug resistance, and several methods have been developed to amplify the genomic DNA and to produce libraries suitable for Whole Genome Sequencing (WGS). However, most protocols require several enzymatic and cleanup steps, thus increasing the complexity and length of protocols, while robustness and speed are key factors for clinical applications. To tackle this issue, we developed a single-tube, single-step, streamlined protocol, exploiting ligation mediated PCR (LM-PCR) Whole Genome Amplification (WGA) method, for low-pass genome sequencing with the Ion Torrent™ platform and copy number alterations (CNAs) calling from single cells. The method was evaluated on single cells isolated from 6 aberrant cell lines of the NCI-H series. In addition, to demonstrate the feasibility of the workflow on clinical samples, we analyzed single circulating tumor cells (CTCs) and white blood cells (WBCs) isolated from the blood of patients affected by prostate cancer or lung adenocarcinoma. The results obtained show that the developed workflow generates data accurately representing whole genome absolute copy number profiles of single cell and allows alterations calling at resolutions down to 100 Kbp with as few as 200,000 reads. The presented data demonstrate the feasibility of the Ampli1™ WGA-based low-pass workflow for detection of CNAs in single tumor cells which would be of particular interest for genome-driven targeted therapy selection and for monitoring of disease progression.
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Affiliation(s)
| | | | - Genny Buson
- Menarini Silicon Biosystems spa, Bologna, Italy
| | | | | | | | | | | | | | - Rui Neves
- Department of General, Visceral and Pediatric Surgery, Medical Faculty, University Hospital of the Heinrich- Heine-University Düsseldorf, Düsseldorf, Germany
| | - Birte Möhlendick
- Department of General, Visceral and Pediatric Surgery, Medical Faculty, University Hospital of the Heinrich- Heine-University Düsseldorf, Düsseldorf, Germany
| | - Karim Rihawi
- Unità Operativa di Oncologia Medica, Policlinico Sant’Orsola – Malpighi, Bologna, Italy
| | - Andrea Ardizzoni
- Unità Operativa di Oncologia Medica, Policlinico Sant’Orsola – Malpighi, Bologna, Italy
| | - Semini Sumanasuriya
- The Institute of Cancer Research and Royal Marsden NHS Foundation Trust, London, United Kingdom
| | - Penny Flohr
- The Institute of Cancer Research and Royal Marsden NHS Foundation Trust, London, United Kingdom
| | - Maryou Lambros
- The Institute of Cancer Research and Royal Marsden NHS Foundation Trust, London, United Kingdom
| | - Johann de Bono
- The Institute of Cancer Research and Royal Marsden NHS Foundation Trust, London, United Kingdom
| | - Nikolas H. Stoecklein
- Department of General, Visceral and Pediatric Surgery, Medical Faculty, University Hospital of the Heinrich- Heine-University Düsseldorf, Düsseldorf, Germany
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Li Y, Wu Z, Jin Y, Wu A, Cao M, Sun K, Jia X, Chen M. Analysis of hippocampal gene expression profile of Alzheimer's disease model rats using genome chip bioinformatics. Neural Regen Res 2015; 7:332-40. [PMID: 25774171 PMCID: PMC4350114 DOI: 10.3969/j.issn.1673-5374.2012.05.002] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.2] [Reference Citation Analysis] [Abstract] [Key Words] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/27/2011] [Accepted: 12/20/2011] [Indexed: 02/06/2023] Open
Abstract
In this study, an Alzheimer's disease model was established in rats through stereotactic injection of condensed amyloid beta 1–40 into the bilateral hippocampus, and the changes of gene expression profile in the hippocampus of rat models and sham-operated rats were compared by genome expression profiling analysis. Results showed that the expression of 50 genes was significantly up-regulated (fold change ≥ 2), while 21 genes were significantly down-regulated in the hippocampus of Alzheimer's disease model rats (fold change ≤ 0.5) compared with the sham-operation group. The differentially expressed genes are involved in many functions, such as brain nerve system development, neuronal differentiation and functional regulation, cellular growth, differentiation and apoptosis, synaptogenesis and plasticity, inflammatory and immune responses, ion channels/transporters, signal transduction, cell material/energy metabolism. Our findings indicate that several genes were abnormally expressed in the metabolic and signal transduction pathways in the hippocampus of amyloid beta 1–40-induced rat model of Alzheimer's disease, thereby affecting the hippocampal and brain functions.
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Affiliation(s)
- Yinghong Li
- First Affiliated Hospital of Shenzhen University/Second People's Hospital of Shenzhen City, Shenzhen 518035, Guangdong Province, China
| | - Zhengzhi Wu
- First Affiliated Hospital of Shenzhen University/Second People's Hospital of Shenzhen City, Shenzhen 518035, Guangdong Province, China ; Second Clinical Medical College of Jinan University/Shenzhen Institute of Geriatrics, Shenzhen 518020, Guangdong Province, China
| | - Yu Jin
- First Affiliated Hospital of Shenzhen University/Second People's Hospital of Shenzhen City, Shenzhen 518035, Guangdong Province, China
| | - Anmin Wu
- First Affiliated Hospital of Shenzhen University/Second People's Hospital of Shenzhen City, Shenzhen 518035, Guangdong Province, China
| | - Meiqun Cao
- Second Clinical Medical College of Jinan University/Shenzhen Institute of Geriatrics, Shenzhen 518020, Guangdong Province, China
| | - Kehuan Sun
- First Affiliated Hospital of Shenzhen University/Second People's Hospital of Shenzhen City, Shenzhen 518035, Guangdong Province, China
| | - Xiuqin Jia
- First Affiliated Hospital of Shenzhen University/Second People's Hospital of Shenzhen City, Shenzhen 518035, Guangdong Province, China
| | - Manyin Chen
- First Affiliated Hospital of Shenzhen University/Second People's Hospital of Shenzhen City, Shenzhen 518035, Guangdong Province, China
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Li YH, Wu ZZ, Cao MQ, Li M, Sun KH, Yang M, Chen MY, Huang ACJ. Effect of Tiantai No.1 on gene expression profiles in hippocampus of Alzheimer's disease rats by bioinformatic analysis. Chin J Integr Med 2014; 21:123-31. [PMID: 25081895 DOI: 10.1007/s11655-014-1773-3] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.1] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/20/2012] [Indexed: 11/28/2022]
Abstract
OBJECTIVE To study the effect of Tiantai No. 1 [symbol in text] on gene expression profile in hippocampus of Alzheimer's disease (AD) rat, molecular genetic target points of the effect of this drug were defined, its molecular genetic pharmacodynamic mechanism of anti-AD was further explored at molecular gene level, and a scientific basis was provided for its clinical availability and promotion. METHODS Thirty male Sprague-Dawley rats were divided into three groups with 10 rats per group: sham-operation group, model group and Tiantai No. 1 group. Sterile surgical procedure was applied, the model group with bilateral hippocampal injection of Aβ1-40 was established, and normal saline was used instead of Aβ1-40 in the sham-operation group. One week after the models was made, rats were administered by gastric lavage once every day for three consecutive weeks. The rats of the sham-operation group and the model group were daily fed with purified water by lavage; the rats of the Tiantai No.1 group treated group were administered with Tiantai No.1 by lavage. Total RNAs of hippocampus tissues were extracted with Trizol, the changes of hippocampus gene expression profiles in the above three groups were analyzed by using Affymetrix rat whole genome expression profile microarray. RESULTS Microarray analysis showed that, compared with the sham-operation group, the hippocampus of the model group had 50 up-regulated genes with significant difference (fold change >2), and 21 down-regulated genes with significant difference (fold change <0.5); compared with the hippocampus of the model group, the hippocampus of the Tiantai No. 1 group was found to have 5 up-regulated genes with significant difference (fold change >2) and 20 down-regulated genes with significant difference (fold change <0.5). The functions of differentially expressed genes of the groups were involved in nervous system's development, neuronic differentiation and function-regulation, cellular growth and differentiation and apoptosis, synaptic occurrence and plasticity, inflammation and immune response, ion channels/transporters, cellular signal transduction, cellular material/energy metabolism and so on. CONCLUSION Tiantai No. 1 can regulate hippocampal function, and further regulate the brain function of animals in multiple gene target points by a number of ways.
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Affiliation(s)
- Ying-hong Li
- The First Affiliated Hospital of Shenzhen University, Shenzhen, Guangdong Province, 518035, China
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Morlighem JÉ, Harbers M, Traeger-Synodinos J, Lezhava A. DNA amplification techniques in pharmacogenomics. Pharmacogenomics 2011; 12:845-60. [PMID: 21692615 DOI: 10.2217/pgs.11.10] [Citation(s) in RCA: 6] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/21/2022] Open
Abstract
The variable predisposition of patients, both to disease susceptibility and drug response, is well established. It is largely attributed to genetic, as well as epigenetic variations between individuals, which may be inherited or acquired. The most common variation in the human genome is the SNP, which occurs throughout the genome, both within coding and noncoding regions. Characterization of SNPs in the context of both inherited and acquired conditions, such as cancer, are a main focus of many genotyping procedures. The demand for identifying (diagnosing) targeted SNPs or other variations, as well as the application of genome-wide screens, is continuously directing the development of new technologies. In general, most methods require a DNA amplification step to provide the amounts of DNA needed for the SNP detection step. In addition, DNA amplification is an important step when investigating other types of genomic information, for instance when addressing repeat, deletion, copy number variation or epigenetic regulation by DNA methylation. Besides the widely used PCR technique, there are several alternative approaches for genomic DNA amplification suitable for supporting the detection of genomic variation. In this article, we describe and evaluate a number of techniques, and discuss possible future prospects of DNA amplification in the fields of pharmacogenetics and pharmacogenomics.
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Affiliation(s)
- Jean-Étienne Morlighem
- Omics Science Center, RIKEN Yokohama Institute, 1-7-22 Suehiro-cho, Tsurumi-ku, Yokohama 230-0045, Japan
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Soong YK, Wang TH, Lee YS, Chen CP, Chang CL, Ho SY, Chao AS, Cheng PJ, Chang SD. Genome-wide detection of uniparental disomy in a fetus with intrauterine growth restriction using genotyping microarrays. Taiwan J Obstet Gynecol 2009; 48:152-8. [PMID: 19574178 DOI: 10.1016/s1028-4559(09)60277-1] [Citation(s) in RCA: 10] [Impact Index Per Article: 0.7] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/17/2022] Open
Abstract
OBJECTIVE To present the clinical and molecular features of a fetus with confined trisomy 16 mosaicism with maternal uniparental disomy (UPD), using various prenatal diagnostic techniques. MATERIALS AND METHODS Chromosomal karyotyping was performed on samples of chorionic villi, amniotic fluid cells, amniotic membrane, umbilical cord, fetal skin, and placenta from a fetus with elevated nuchal translucency. Polymorphic short tandem repeat markers and Affymetrix single nucleotide polymorphism (SNP) mapping chips were used for molecular analyses. RESULTS Karyotypes from chorionic villi and amniocytes showed 47,XX,+16 and 46,XX, respectively. Short tandem repeat markers on chromosome 16 suggested maternal UPD for chromosome 16. Affymetrix 10K SNP mapping chips were used to simultaneously confirm the difference in karyotypes between the placenta and amniocytes and to diagnose UPD for chromosome 16. Fetal ultrasonography and magnetic resonance imaging identified severe intrauterine growth restriction (IUGR). Autopsy revealed IUGR, incomplete lobulation of bilateral lungs, and malrotation of the intestines. The karyotypes of umbilical cord, fetal skin and amniotic membrane were 46,XX, and the trisomy 16 karyotype appeared to be confined to the placenta. CONCLUSION UPD should be investigated as a possible etiology in all cases of unexplained IUGR. SNP microarrays can be useful for confirming this diagnosis.
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Affiliation(s)
- Yung-Kuei Soong
- Department of Obstetrics and Gynecology, Lin-Kou Medical Center, Chang Gung Memorial Hospital, Chang Gung University, Taoyuan, Taiwan.
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Imle A, Polzer B, Alexander S, Klein CA, Friedl P. Genomic instability of micronucleated cells revealed by single-cell comparative genomic hybridization. Cytometry A 2009; 75:562-8. [DOI: 10.1002/cyto.a.20733] [Citation(s) in RCA: 16] [Impact Index Per Article: 1.1] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/10/2022]
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