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Association between CHFR and PARP-1, and Their Roles in Regulation of Proliferation and Apoptosis of B Cell Lymphoma. Anal Cell Pathol (Amst) 2023. [DOI: 10.1155/2023/7940316] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 03/06/2023] Open
Abstract
Background. Aberrant methylation of checkpoint with forkhead and ring finger domains (CHFR) was found in B-cell non-Hodgkin lymphoma (NHL), whereas its role in carcinogenesis is not clear. CHFR can control poly (ADP-ribose) polymerase levels by causing its degradation. The study was aimed to explore the roles and mechanisms of CHFR in the pathogenesis of B-cell NHL. Methods. Short hairpin ribonucleic acid (ShRNAs) targeting CHFR and poly (ADP-ribose) polymerase 1 (PARP-1) were transduced into Raji cells, and real-time polymerase chain reaction (PCR) and western blotting were carried out to determine their expression. Afterwards, the CCK-8 assay and flow cytometry were used to evaluate the cell growth and apoptosis. Tumor size and weight were determined using a xenograft model, and decitabine (5-Aza-dC) was used to further determine the methylation status of CHFR through a methylation specificity-PCR assay. Results. 5-Aza-dC-treatment promoted the expression of CHFR and decreased the expression of PARP-1 at both messenger ribonucleic acid (mRNA) and protein levels. 5-Aza-dC also accelerated Raji-cell apoptosis and restrained its growth in vitro and in vivo (
). These results were contrary to those observed in the shRNA-CHFR group but consistent with those observed in the shRNA-PARP-1 group. The expression profiles of CHFR and PARP-1 in the xenograft model were consistent with those in the cellular model. Treatment with 5-Aza-dC led to demethylation of CHFR in nude mice. Besides, there may be a negative correlation between CHFR and PARP-1 in B-cell NHL cells. Conclusion. Our findings indicated that 5-Aza-dC could lead to the demethylation of the CHFR promoter and suppress Raji cell growth.
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Li H, Zhang N, Wang Y, Xia S, Zhu Y, Xing C, Tian X, Du Y. DNA N6-Methyladenine Modification in Eukaryotic Genome. Front Genet 2022; 13:914404. [PMID: 35812743 PMCID: PMC9263368 DOI: 10.3389/fgene.2022.914404] [Citation(s) in RCA: 6] [Impact Index Per Article: 3.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/06/2022] [Accepted: 06/08/2022] [Indexed: 11/18/2022] Open
Abstract
DNA methylation is treated as an important epigenetic mark in various biological activities. In the past, a large number of articles focused on 5 mC while lacking attention to N6-methyladenine (6 mA). The presence of 6 mA modification was previously discovered only in prokaryotes. Recently, with the development of detection technologies, 6 mA has been found in several eukaryotes, including protozoans, metazoans, plants, and fungi. The importance of 6 mA in prokaryotes and single-celled eukaryotes has been widely accepted. However, due to the incredibly low density of 6 mA and restrictions on detection technologies, the prevalence of 6 mA and its role in biological processes in eukaryotic organisms are highly debated. In this review, we first summarize the advantages and disadvantages of 6 mA detection methods. Then, we conclude existing reports on the prevalence of 6 mA in eukaryotic organisms. Next, we highlight possible methyltransferases, demethylases, and the recognition proteins of 6 mA. In addition, we summarize the functions of 6 mA in eukaryotes. Last but not least, we summarize our point of view and put forward the problems that need further research.
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Affiliation(s)
- Hao Li
- School of Basic Medical Sciences, Anhui Medical University, Hefei, China
- First School of Clinical Medicine, Anhui Medical University, Hefei, China
- First Affiliated Hospital of Anhui Medical University, Hefei, China
| | - Ning Zhang
- School of Basic Medical Sciences, Anhui Medical University, Hefei, China
- First School of Clinical Medicine, Anhui Medical University, Hefei, China
- First Affiliated Hospital of Anhui Medical University, Hefei, China
| | - Yuechen Wang
- School of Basic Medical Sciences, Anhui Medical University, Hefei, China
- Second School of Clinical Medicine, Anhui Medical University, Hefei, China
| | - Siyuan Xia
- School of Basic Medical Sciences, Anhui Medical University, Hefei, China
- Second School of Clinical Medicine, Anhui Medical University, Hefei, China
| | - Yating Zhu
- School of Basic Medical Sciences, Anhui Medical University, Hefei, China
| | - Chen Xing
- School of Basic Medical Sciences, Anhui Medical University, Hefei, China
| | - Xuefeng Tian
- School of Basic Medical Sciences, Anhui Medical University, Hefei, China
- First School of Clinical Medicine, Anhui Medical University, Hefei, China
| | - Yinan Du
- School of Basic Medical Sciences, Anhui Medical University, Hefei, China
- *Correspondence: Yinan Du,
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Safarzadeh M, Pan G. Detection of a Double-Stranded MGMT Gene Using Electrochemically Reduced Graphene Oxide (ErGO) Electrodes Decorated with AuNPs and Peptide Nucleic Acids (PNA). BIOSENSORS 2022; 12:98. [PMID: 35200358 PMCID: PMC8869880 DOI: 10.3390/bios12020098] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Subscribe] [Scholar Register] [Received: 12/10/2021] [Revised: 01/30/2022] [Accepted: 02/01/2022] [Indexed: 11/16/2022]
Abstract
The ability to detect double-stranded DNA (dsDNA) as a biomarker without denaturing it to single-stranded DNA (ss-DNA) continues to be a major challenge. In this work, we report a sandwich biosensor for the detection of the ds-methylated MGMT gene, a potential biomarker for brain tumors and breast cancer. The purpose of this biosensor is to achieve simultaneous recognition of the gene sequence, as well as the presence of methylation. The biosensor is based on reduced graphene oxide (rGO) electrodes decorated with gold nanoparticles (AuNPs) and uses Peptide Nucleic Acid (PNA) that binds to the ds-MGMT gene. The reduction of GO was performed in two ways: electrochemically (ErGO) and thermally (TrGO). XPS and Raman spectroscopy, as well as voltammetry techniques, showed that the ErGO was more efficiently reduced, had a higher C/O ratio, showed a smaller crystallite size of the sp2 lattice, and was more stable during measurement. It was also revealed that the electro-deposition of the AuNPs was more successful on the ErGO surface due to the higher At% of Au on the ErGO electrode. Therefore, the ErGO/AuNPs electrode was used to develop biosensors to detect the ds-MGMT gene. PNA, which acts as a bio-recognition element, was used to form a self-assembled monolayer (SAM) on the ErGO/AuNPs surface via the amine-AuNPs interaction, recognizing the ds-MGMT gene sequence by its invasion of the double-stranded DNA and the formation of a triple helix. The methylation was then detected using biotinylated-anti-5mC, which was then measured using the amperometric technique. The selectivity study showed that the proposed biosensor was able to distinguish between blank, non-methylated, non-complementary, and target dsDNA spiked in mouse plasma. The LOD was calculated to be 0.86 pM with a wide linear range of 1 pM to 50 µM. To the best of our knowledge, this is the first report on using PNA to detect ds-methylated DNA. This sandwich design can be modified to detect other methylated genes, making it a promising platform to detect ds-methylated biomarkers.
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Affiliation(s)
- Mina Safarzadeh
- Wolfson Nanomaterials and Devices Laboratory, School of Engineering, Computing and Mathematics, Faculty of Science and Engineering, University of Plymouth, Plymouth PL4 8AA, UK;
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4
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Lee JY, Park JW. Modified cytosines versus cytosine in a DNA polymerase: retrieving thermodynamic and kinetic constants at the single molecule level. Analyst 2021; 147:341-348. [PMID: 34935781 DOI: 10.1039/d1an02108g] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/21/2022]
Abstract
DNA methylation plays key roles in various areas, such as gene expression, regulation, epigenetics, and cancers. Since 5-methylcytosine (5mC) is commonly present in methylated DNA, characterizing the binding kinetics and thermodynamics of the nucleotide to the enzymatic pocket can help to understand the DNA replication process. Furthermore, 5-carboxycytosine (5caC) is a form that appears through the iterative oxidation of 5mC, and its effect on the DNA replication process is still not well known. Here, we immobilized a DNA polymerase (DNAP) with an orientation control on a tip of an atomic force microscope (AFM), and observed the interaction between the immobilized deoxyguanosine triphosphate (dGTP) on the surface and the DNAP in the presence of a DNA duplex. The interaction probability increased as the concentration of the DNA strand, and the affinity constant between the DNAP and DNA was obtained by fitting the change. Increasing the concentration of dGTP in solution diminished the interaction probability, and a fitting allowed us to retrieve the affinity constant between dGTP and the DNAP holding the DNA in the reaction pocket. Because the dissociation constant could be obtained through the loading rate dependence of the unbinding force value, both affinity and kinetic constants for cytosine (C), 5mC, and 5caC in the DNAP were compared in the light of the steric and electronic effect of the substituents at 5-position of cytosine.
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Affiliation(s)
- Ji Yoon Lee
- Department of Chemistry, Pohang University of Science and Technology, 77 Cheongam-Ro, Nam-Gu, Pohang 37673, Republic of Korea.
| | - Joon Won Park
- Department of Chemistry, Pohang University of Science and Technology, 77 Cheongam-Ro, Nam-Gu, Pohang 37673, Republic of Korea. .,Institute of Convergence Science, Yonsei University, 50 Yonsei-ro Seodaemun-gu, Seoul, 03722, Republic of Korea
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Safarzadeh M, Suhail A, Sethi J, Sattar A, Jenkins D, Pan G. A Label-Free DNA-Immunosensor Based on Aminated rGO Electrode for the Quantification of DNA Methylation. NANOMATERIALS 2021; 11:nano11040985. [PMID: 33921234 PMCID: PMC8070590 DOI: 10.3390/nano11040985] [Citation(s) in RCA: 3] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Subscribe] [Scholar Register] [Received: 03/12/2021] [Revised: 04/05/2021] [Accepted: 04/07/2021] [Indexed: 02/06/2023]
Abstract
In this work, we developed a sandwich DNA-immunosensor for quantification of the methylated tumour suppressor gene O-6-methylguanine-DNA methyltransferase (MGMT), which is a potential biomarker for brain tumours and breast cancer. The biosensor is based on aminated reduced graphene oxide electrode, which is achieved by ammonium hydroxide chemisorption and anti-5-methylcytosine (anti-5mC) as a methylation bioreceptor. The target single-strand (ss) MGMT oligonucleotide is first recognised by its hybridisation with complementary DNA to form double-stranded (ds) MGMT, which is then captured by anti-5mC on the electrode surface due to the presence of methylation. Raman spectroscopy, X-ray photoelectron spectroscopy (XPS) and Scanning electron microscopy (SEM) techniques were used to characterise the electrode surface. Cyclic voltammetry (CV) and differential pulse voltammetry (DPV) techniques were used for electrochemical measurements. Under optimised conditions, the proposed biosensor is able to quantify a linear range of concentrations of the MGMT gene from 50 fM to 100 pM with a limit of detection (LOD) of 12 fM. The sandwich design facilitates the simultaneous recognition and quantification of DNA methylation, and the amination significantly improves the sensitivity of the biosensor. This biosensor is label-, bisulfite- and PCR-free and has a simple design for cost-efficient production. It can also be tailor-made to detect other methylated genes, which makes it a promising detection platform for DNA methylation-related disease diagnosis and prognosis.
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Affiliation(s)
- Mina Safarzadeh
- Wolfson Nanomaterials and Devices Laboratory, School of Engineering, Computing and Mathematics, Faculty of Science and Engineering, University of Plymouth, Devon PL4 8AA, UK; (A.S.); (J.S.); (D.J.); (G.P.)
- Correspondence:
| | - Ahmed Suhail
- Wolfson Nanomaterials and Devices Laboratory, School of Engineering, Computing and Mathematics, Faculty of Science and Engineering, University of Plymouth, Devon PL4 8AA, UK; (A.S.); (J.S.); (D.J.); (G.P.)
| | - Jagriti Sethi
- Wolfson Nanomaterials and Devices Laboratory, School of Engineering, Computing and Mathematics, Faculty of Science and Engineering, University of Plymouth, Devon PL4 8AA, UK; (A.S.); (J.S.); (D.J.); (G.P.)
| | - Anas Sattar
- School of Biomedical and Healthcare Sciences, Peninsula Schools of Medicine and Dentistry, University of Plymouth, Devon PL4 8AA, UK;
| | - David Jenkins
- Wolfson Nanomaterials and Devices Laboratory, School of Engineering, Computing and Mathematics, Faculty of Science and Engineering, University of Plymouth, Devon PL4 8AA, UK; (A.S.); (J.S.); (D.J.); (G.P.)
| | - Genhua Pan
- Wolfson Nanomaterials and Devices Laboratory, School of Engineering, Computing and Mathematics, Faculty of Science and Engineering, University of Plymouth, Devon PL4 8AA, UK; (A.S.); (J.S.); (D.J.); (G.P.)
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Zhang S, Huang J, Lu J, Liu M, Chen X, Su S, Mo F, Zheng J. Electrochemical and Optical Biosensing Strategies for DNA Methylation Analysis. Curr Med Chem 2020; 27:6159-6187. [DOI: 10.2174/0929867326666190903161750] [Citation(s) in RCA: 3] [Impact Index Per Article: 0.8] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/05/2019] [Revised: 07/24/2019] [Accepted: 08/07/2019] [Indexed: 12/14/2022]
Abstract
DNA methylation is considered as a crucial part of epigenetic modifications and a popular
research topic in recent decades. It usually occurs with a methyl group adding to the fifth carbon
atom of cytosine while the base sequence of DNA remains unchanged. DNA methylation has significant
influences on maintaining cell functions, genetic imprinting, embryonic development and
tumorigenesis procedures and hence the analysis of DNA methylation is of great medical significance.
With the development of analytical techniques and further research on DNA methylation,
numerous DNA methylation detection strategies based on biosensing technology have been developed
to fulfill various study requirements. This article reviewed the development of electrochemistry
and optical biosensing analysis of DNA methylation in recent years; in addition, we also reviewed
some recent advances in the detection of DNA methylation using new techniques, such as
nanopore biosensors, and highlighted the key technical and biological challenges involved in these
methods. We hope this paper will provide useful information for the selection and establishment of
analysis of DNA methylation.
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Affiliation(s)
- Shu Zhang
- Department of Basic Clinical Laboratory Medicine, School of Clinical Laboratory Science, Guizhou Medical University, No. 9 Beijing Road, Yunyan District, Guiyang 550004, China
| | - Jian Huang
- Department of Clinical and Military Laboratory Medicine, College of Medical Laboratory Science, Army Medical University, 30 Gaotanyan Street, Shapingba District, Chongqing 400038, China
| | - Jingrun Lu
- Department of Basic Clinical Laboratory Medicine, School of Clinical Laboratory Science, Guizhou Medical University, No. 9 Beijing Road, Yunyan District, Guiyang 550004, China
| | - Min Liu
- Department of Basic Clinical Laboratory Medicine, School of Clinical Laboratory Science, Guizhou Medical University, No. 9 Beijing Road, Yunyan District, Guiyang 550004, China
| | - Xi Chen
- Department of Basic Clinical Laboratory Medicine, School of Clinical Laboratory Science, Guizhou Medical University, No. 9 Beijing Road, Yunyan District, Guiyang 550004, China
| | - Shasha Su
- Department of Basic Clinical Laboratory Medicine, School of Clinical Laboratory Science, Guizhou Medical University, No. 9 Beijing Road, Yunyan District, Guiyang 550004, China
| | - Fei Mo
- Department of Basic Clinical Laboratory Medicine, School of Clinical Laboratory Science, Guizhou Medical University, No. 9 Beijing Road, Yunyan District, Guiyang 550004, China
| | - Junsong Zheng
- Department of Clinical and Military Laboratory Medicine, College of Medical Laboratory Science, Army Medical University, 30 Gaotanyan Street, Shapingba District, Chongqing 400038, China
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Yang S, Wang Y, Chen Y, Dai Q. MASQC: Next Generation Sequencing Assists Third Generation Sequencing for Quality Control in N6-Methyladenine DNA Identification. Front Genet 2020; 11:269. [PMID: 32269589 PMCID: PMC7109398 DOI: 10.3389/fgene.2020.00269] [Citation(s) in RCA: 28] [Impact Index Per Article: 7.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/25/2019] [Accepted: 03/05/2020] [Indexed: 11/13/2022] Open
Abstract
DNA N6-methyladenine (6mA) modification has been discovered as the most prevalent DNA modification in prokaryotes and eukaryotes, involving gene expression, DNA replication and repair, and host-pathogen interactions. Single-molecule real-time sequencing (SMRT-seq) can detect 6mA events in prokaryotic and eukaryotic genomes at the single-nucleotide level. However, there are no strict and economical quality control methods for high false-positive 6mA events in eukaryotic genomes. Therefore, by analyzing the distribution of 6mA in eukaryotic and prokaryotes, we proposed a method named MASQC (MeDIP-seq assists SMRT-seq for quality control in 6mA identification), which can identify 6mA events without doing the whole genome amplification (WGA) sequencing. The proposed MASQC method was assessed on two eukaryotic genomes and six bacterial genomes, our results demonstrate that MASQC performs well in quality control of false positive 6mA identification for both eukaryotic and prokaryotic genomes.
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Affiliation(s)
- Siqian Yang
- College of Life Sciences and Medicine, Zhejiang Sci-Tech University, Hangzhou, China
| | - Yaoxin Wang
- College of Life Sciences and Medicine, Zhejiang Sci-Tech University, Hangzhou, China
| | - Ying Chen
- State Key Laboratory of Ophthalmology, Zhongshan Ophthalmic Center, Sun Yat-sen University, Guangzhou, China
| | - Qi Dai
- College of Life Sciences and Medicine, Zhejiang Sci-Tech University, Hangzhou, China
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Zehnbauer BA. The Journal of Molecular Diagnostics: 20 Years Defining Professional Practice. J Mol Diagn 2019; 21:938-942. [PMID: 31635797 DOI: 10.1016/j.jmoldx.2019.09.001] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.2] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/09/2019] [Accepted: 09/09/2019] [Indexed: 01/09/2023] Open
Abstract
This editorial highlights 20 years of JMD defining professional practice.
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Affiliation(s)
- Barbara A Zehnbauer
- Department of Pathology, Emory University School of Medicine, Atlanta, Georgia (Editor-in-Chief).
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Meronard K, Josowicz M, Saheb A. Voltammetric Label‐free Detection of DNA Hypermethylation Using Polypyrrole‐modified Microelectrode Array. ELECTROANAL 2019. [DOI: 10.1002/elan.201900278] [Citation(s) in RCA: 3] [Impact Index Per Article: 0.6] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/23/2023]
Affiliation(s)
- Kenton Meronard
- Department of Chemistry and Forensic ScienceAlbany State University Albany, GA USA
| | - Mira Josowicz
- School of Chemistry and BiochemistryGeorgia Institute of Technology Atlanta, GA USA
| | - Amir Saheb
- Department of Chemistry and Forensic ScienceAlbany State University Albany, GA USA
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Li L, Lim SF, Puretzky A, Riehn R, Hallen HD. DNA Methylation Detection Using Resonance and Nanobowtie-Antenna-Enhanced Raman Spectroscopy. Biophys J 2019; 114:2498-2506. [PMID: 29874601 DOI: 10.1016/j.bpj.2018.04.021] [Citation(s) in RCA: 14] [Impact Index Per Article: 2.8] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/01/2017] [Revised: 03/22/2018] [Accepted: 04/10/2018] [Indexed: 01/04/2023] Open
Abstract
We show that DNA carrying 5-methylcytosine modifications or methylated DNA (m-DNA) can be distinguished from DNA with unmodified cytosine by Raman spectroscopy enhanced by both a bowtie nanoantenna and excitation resonance. In particular, m-DNA can be identified by a peak near 1000 cm-1 and changes in the Raman peaks in the 1200-1700 cm-1 band that are enhanced by the ring-absorption resonance. The identification is robust to the use of resonance Raman and nanoantenna excitation used to obtain significant signal improvement. The primary differences are three additional Raman peaks with methylation at 1014, 1239, and 1639 cm-1 and spectral intensity inversion at 1324 (C5=C6) and 1473 cm-1 (C4=N3) in m-DNA compared to that of DNA with unmodified cytosine. We attribute this to the proximity of the methyl group to the antenna, which brings the (C5=C6) mode closer to experiencing a stronger near-field enhancement. We also show distinct Raman spectral features attributed to the transition of DNA from a hydrated state, when dissolved, to a dried/denatured state. We observe a general broadening of the larger lines and a transfer of spectral weight from the ∼1470 cm-1 vibration to the two higher-energy lines of the dried m-DNA solution. We attribute the new spectral characteristics to DNA softening under high salt conditions and find that the m-DNA is still distinguishable via the ∼1000 cm-1 peak and distribution of the signal in the 1200-1700 cm-1 band. The nanoantenna gain exceeds 20,000, whereas the real signal ratio is much less because of a low average enhanced region occupancy even with these relatively high DNA concentrations. It is improved when fixed DNA in a salt crystal lies near the nanoantenna. The Raman resonance gain profile is consistent with A-term expectations, and the resonance is found at ∼259 nm excitation wavelength.
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Affiliation(s)
- Ling Li
- Department of Physics, North Carolina State University, Raleigh, North Carolina
| | - Shuang Fang Lim
- Department of Physics, North Carolina State University, Raleigh, North Carolina
| | - Alexander Puretzky
- Center for Nanophase Materials Sciences, Oak Ridge National Laboratory, Oak Ridge, Tennessee
| | - Robert Riehn
- Department of Physics, North Carolina State University, Raleigh, North Carolina
| | - Hans D Hallen
- Department of Physics, North Carolina State University, Raleigh, North Carolina.
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Philipps G, de Vries S, Jennewein S. Development of a metabolic pathway transfer and genomic integration system for the syngas-fermenting bacterium Clostridium ljungdahlii. BIOTECHNOLOGY FOR BIOFUELS 2019; 12:112. [PMID: 31086564 PMCID: PMC6507227 DOI: 10.1186/s13068-019-1448-1] [Citation(s) in RCA: 28] [Impact Index Per Article: 5.6] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 09/17/2018] [Accepted: 04/22/2019] [Indexed: 05/15/2023]
Abstract
BACKGROUND Clostridium spp. can synthesize valuable chemicals and fuels by utilizing diverse waste-stream substrates, including starchy biomass, lignocellulose, and industrial waste gases. However, metabolic engineering in Clostridium spp. is challenging due to the low efficiency of gene transfer and genomic integration of entire biosynthetic pathways. RESULTS We have developed a reliable gene transfer and genomic integration system for the syngas-fermenting bacterium Clostridium ljungdahlii based on the conjugal transfer of donor plasmids containing large transgene cassettes (> 5 kb) followed by the inducible activation of Himar1 transposase to promote integration. We established a conjugation protocol for the efficient generation of transconjugants using the Gram-positive origins of replication repL and repH. We also investigated the impact of DNA methylation on conjugation efficiency by testing donor constructs with all possible combinations of Dam and Dcm methylation patterns, and used bisulfite conversion and PacBio sequencing to determine the DNA methylation profile of the C. ljungdahlii genome, resulting in the detection of four sequence motifs with N6-methyladenosine. As proof of concept, we demonstrated the transfer and genomic integration of a heterologous acetone biosynthesis pathway using a Himar1 transposase system regulated by a xylose-inducible promoter. The functionality of the integrated pathway was confirmed by detecting enzyme proteotypic peptides and the formation of acetone and isopropanol by C. ljungdahlii cultures utilizing syngas as a carbon and energy source. CONCLUSIONS The developed multi-gene delivery system offers a versatile tool to integrate and stably express large biosynthetic pathways in the industrial promising syngas-fermenting microorganism C. ljungdahlii. The simple transfer and stable integration of large gene clusters (like entire biosynthetic pathways) is expanding the range of possible fermentation products of heterologously expressing recombinant strains. We also believe that the developed gene delivery system can be adapted to other clostridial strains as well.
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Affiliation(s)
- Gabriele Philipps
- Department for Industrial Biotechnology, Fraunhofer IME, Fraunhofer Institute for Molecular Biology and Applied Ecology IME, Forckenbeckstr. 6, 52074 Aachen, Germany
| | - Sebastian de Vries
- Department for Industrial Biotechnology, Fraunhofer IME, Fraunhofer Institute for Molecular Biology and Applied Ecology IME, Forckenbeckstr. 6, 52074 Aachen, Germany
- Present Address: Department of Intensive Care Medicine, University Hospital, RWTH Aachen University, Pauwelsstr. 30, 52074 Aachen, Germany
| | - Stefan Jennewein
- Department for Industrial Biotechnology, Fraunhofer IME, Fraunhofer Institute for Molecular Biology and Applied Ecology IME, Forckenbeckstr. 6, 52074 Aachen, Germany
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Review Article: The Role of Molecular Pathological Epidemiology in the Study of Neoplastic and Non-neoplastic Diseases in the Era of Precision Medicine. Epidemiology 2018; 27:602-11. [PMID: 26928707 DOI: 10.1097/ede.0000000000000471] [Citation(s) in RCA: 146] [Impact Index Per Article: 24.3] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/16/2022]
Abstract
Molecular pathology diagnostics to subclassify diseases based on pathogenesis are increasingly common in clinical translational medicine. Molecular pathological epidemiology (MPE) is an integrative transdisciplinary science based on the unique disease principle and the disease continuum theory. While it has been most commonly applied to research on breast, lung, and colorectal cancers, MPE can investigate etiologic heterogeneity in non-neoplastic diseases, such as cardiovascular diseases, obesity, diabetes mellitus, drug toxicity, and immunity-related and infectious diseases. This science can enhance causal inference by linking putative etiologic factors to specific molecular biomarkers as outcomes. Technological advances increasingly enable analyses of various -omics, including genomics, epigenomics, transcriptomics, proteomics, metabolomics, metagenomics, microbiome, immunomics, interactomics, etc. Challenges in MPE include sample size limitations (depending on availability of biospecimens or biomedical/radiological imaging), need for rigorous validation of molecular assays and study findings, and paucities of interdisciplinary experts, education programs, international forums, and standardized guidelines. To address these challenges, there are ongoing efforts such as multidisciplinary consortium pooling projects, the International Molecular Pathological Epidemiology Meeting Series, and the Strengthening the Reporting of Observational Studies in Epidemiology-MPE guideline project. Efforts should be made to build biorepository and biobank networks, and worldwide population-based MPE databases. These activities match with the purposes of the Big Data to Knowledge (BD2K), Genetic Associations and Mechanisms in Oncology (GAME-ON), and Precision Medicine Initiatives of the United States National Institute of Health. Given advances in biotechnology, bioinformatics, and computational/systems biology, there are wide open opportunities in MPE to contribute to public health.
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Neary JL, Perez SM, Peterson K, Lodge DJ, Carless MA. Comparative analysis of MBD-seq and MeDIP-seq and estimation of gene expression changes in a rodent model of schizophrenia. Genomics 2017; 109:204-213. [PMID: 28365388 PMCID: PMC5526217 DOI: 10.1016/j.ygeno.2017.03.004] [Citation(s) in RCA: 18] [Impact Index Per Article: 2.6] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/30/2016] [Revised: 03/14/2017] [Accepted: 03/26/2017] [Indexed: 12/11/2022]
Abstract
We conducted a comparative study of multiplexed affinity enrichment sequence methodologies (MBD-seq and MeDIP-seq) in a rodent model of schizophrenia, induced by in utero methylazoxymethanol acetate (MAM) exposure. We also examined related gene expression changes using a pooled sample approach. MBD-seq and MeDIP-seq identified 769 and 1771 differentially methylated regions (DMRs) between F2 offspring of MAM-exposed rats and saline control rats, respectively. The assays showed good concordance, with ~56% of MBD-seq-detected DMRs being identified by or proximal to MeDIP-seq DMRs. There was no significant overlap between DMRs and differentially expressed genes, suggesting that DNA methylation regulatory effects may act upon more distal genes, or are too subtle to detect using our approach. Methylation and gene expression gene ontology enrichment analyses identified biological processes important to schizophrenia pathophysiology, including neuron differentiation, prepulse inhibition, amphetamine response, and glutamatergic synaptic transmission regulation, reinforcing the utility of the MAM rodent model for schizophrenia research.
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Affiliation(s)
- Jennifer L Neary
- Department of Genetics, Texas Biomedical Research Institute, 7620 NW Loop 410, San Antonio, TX 78227, USA.
| | - Stephanie M Perez
- Department of Pharmacology, Center for Biomedical Neuroscience, University of Texas Health Science Center at San Antonio, 7703 Floyd Curl Drive, San Antonio, TX 78229, USA.
| | - Kara Peterson
- Department of Genetics, Texas Biomedical Research Institute, 7620 NW Loop 410, San Antonio, TX 78227, USA.
| | - Daniel J Lodge
- Department of Pharmacology, Center for Biomedical Neuroscience, University of Texas Health Science Center at San Antonio, 7703 Floyd Curl Drive, San Antonio, TX 78229, USA.
| | - Melanie A Carless
- Department of Genetics, Texas Biomedical Research Institute, 7620 NW Loop 410, San Antonio, TX 78227, USA.
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Ouyang L, Hu Y, Zhu L, Cheng GJ, Irudayaraj J. A reusable laser wrapped graphene-Ag array based SERS sensor for trace detection of genomic DNA methylation. Biosens Bioelectron 2017; 92:755-762. [DOI: 10.1016/j.bios.2016.09.072] [Citation(s) in RCA: 48] [Impact Index Per Article: 6.9] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/08/2016] [Revised: 09/01/2016] [Accepted: 09/21/2016] [Indexed: 10/21/2022]
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15
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Novel biotechnology approaches in colorectal cancer diagnosis and therapy. Biotechnol Lett 2017; 39:785-803. [DOI: 10.1007/s10529-017-2303-8] [Citation(s) in RCA: 15] [Impact Index Per Article: 2.1] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/01/2016] [Accepted: 02/07/2017] [Indexed: 12/17/2022]
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16
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Hossain T, Mahmudunnabi G, Masud MK, Islam MN, Ooi L, Konstantinov K, Hossain MSA, Martinac B, Alici G, Nguyen NT, Shiddiky MJA. Electrochemical biosensing strategies for DNA methylation analysis. Biosens Bioelectron 2017; 94:63-73. [PMID: 28259051 DOI: 10.1016/j.bios.2017.02.026] [Citation(s) in RCA: 49] [Impact Index Per Article: 7.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/18/2016] [Revised: 02/15/2017] [Accepted: 02/16/2017] [Indexed: 12/31/2022]
Abstract
DNA methylation is one of the key epigenetic modifications of DNA that results from the enzymatic addition of a methyl group at the fifth carbon of the cytosine base. It plays a crucial role in cellular development, genomic stability and gene expression. Aberrant DNA methylation is responsible for the pathogenesis of many diseases including cancers. Over the past several decades, many methodologies have been developed to detect DNA methylation. These methodologies range from classical molecular biology and optical approaches, such as bisulfite sequencing, microarrays, quantitative real-time PCR, colorimetry, Raman spectroscopy to the more recent electrochemical approaches. Among these, electrochemical approaches offer sensitive, simple, specific, rapid, and cost-effective analysis of DNA methylation. Additionally, electrochemical methods are highly amenable to miniaturization and possess the potential to be multiplexed. In recent years, several reviews have provided information on the detection strategies of DNA methylation. However, to date, there is no comprehensive evaluation of electrochemical DNA methylation detection strategies. Herein, we address the recent developments of electrochemical DNA methylation detection approaches. Furthermore, we highlight the major technical and biological challenges involved in these strategies and provide suggestions for the future direction of this important field.
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Affiliation(s)
- Tanvir Hossain
- Department of Biochemistry & Molecular Biology, Shahjalal University of Science & Technology, Sylhet 3114, Bangladesh
| | - Golam Mahmudunnabi
- Department of Genetic Engineering and Biotechnology, Shahjalal University of Science & Technology, Sylhet 3114, Bangladesh
| | - Mostafa Kamal Masud
- Department of Biochemistry & Molecular Biology, Shahjalal University of Science & Technology, Sylhet 3114, Bangladesh; Institute for Superconducting and Electronic Materials, Australian Institute for Innovative Materials (AIIM), University of Wollongong, Squires Way, Innovation Campus, North Wollongong, NSW 2519, Australia; Queensland Micro- and Nanotechnology Centre, Griffith University, Nathan, QLD 4111, Australia
| | - Md Nazmul Islam
- Queensland Micro- and Nanotechnology Centre, Griffith University, Nathan, QLD 4111, Australia; School of Natural Sciences, Griffith University (Nathan Campus), Nathan, QLD 4111, Australia
| | - Lezanne Ooi
- Illawarra Health and Medical Research Institute, School of Biological Sciences, University of Wollongong, Northfields Avenue, Wollongong, NSW 2522, Australia
| | - Konstantin Konstantinov
- Institute for Superconducting and Electronic Materials, Australian Institute for Innovative Materials (AIIM), University of Wollongong, Squires Way, Innovation Campus, North Wollongong, NSW 2519, Australia
| | - Md Shahriar Al Hossain
- Institute for Superconducting and Electronic Materials, Australian Institute for Innovative Materials (AIIM), University of Wollongong, Squires Way, Innovation Campus, North Wollongong, NSW 2519, Australia
| | - Boris Martinac
- Victor Chang Cardiac Research Institute, Darlinghurst, NSW 2010, Australia
| | - Gursel Alici
- ARC Centre of Excellence for Electromaterials Science, University of Wollongong, Northfields Avenue, Wollongong, NSW 2522, Australia
| | - Nam-Trung Nguyen
- Queensland Micro- and Nanotechnology Centre, Griffith University, Nathan, QLD 4111, Australia
| | - Muhammad J A Shiddiky
- Queensland Micro- and Nanotechnology Centre, Griffith University, Nathan, QLD 4111, Australia; School of Natural Sciences, Griffith University (Nathan Campus), Nathan, QLD 4111, Australia.
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17
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Huertas CS, Domínguez-Zotes S, Lechuga LM. Analysis of alternative splicing events for cancer diagnosis using a multiplexing nanophotonic biosensor. Sci Rep 2017; 7:41368. [PMID: 28120920 PMCID: PMC5264646 DOI: 10.1038/srep41368] [Citation(s) in RCA: 19] [Impact Index Per Article: 2.7] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/21/2016] [Accepted: 12/20/2016] [Indexed: 11/09/2022] Open
Abstract
Personalized medicine is a promising tool not only for prevention, screening and development of more efficient treatment strategies, but also for diminishing the side effects caused by current therapies. Deciphering gene regulation pathways provides a reliable prognostic analysis to elucidate the origin of grave diseases and facilitate the selection of the most adequate treatment for each individual. Alternative splicing of mRNA precursors is one of these gene regulation pathways and enables cells to generate different protein outputs from the same gene depending on their developmental or homeostatic status. Its deregulation is strongly linked to disease onset and progression constituting a relevant and innovative class of biomarker. Herein we report a highly selective and sensitive nanophotonic biosensor based on the direct monitoring of the aberrant alternative splicing of Fas gene. Unlike conventional methods, the nanobiosensor performs a real-time detection of the specific isoforms in the fM-pM range without any cDNA synthesis or PCR amplification requirements. The nanobiosensor has been proven isoform-specific with no crosshybridization, greatly minimizing detection biases. The demonstrated high sensitivity and specificity make our nanobiosensor ideal for examining significant tumor-associated expression shifts of alternatively spliced isoforms for the early and accurate theranostics of cancer.
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Affiliation(s)
- César S. Huertas
- Nanobiosensors and Bioanalytical Applications Group, Catalan Institute of Nanoscience and Nanotechnology (ICN2), CSIC, The Barcelona Institute of Science and Technology, and CIBER-BBN, Campus UAB, Bellaterra, 08193 Barcelona, Spain
| | - Santos Domínguez-Zotes
- Nanobiosensors and Bioanalytical Applications Group, Catalan Institute of Nanoscience and Nanotechnology (ICN2), CSIC, The Barcelona Institute of Science and Technology, and CIBER-BBN, Campus UAB, Bellaterra, 08193 Barcelona, Spain
| | - Laura M. Lechuga
- Nanobiosensors and Bioanalytical Applications Group, Catalan Institute of Nanoscience and Nanotechnology (ICN2), CSIC, The Barcelona Institute of Science and Technology, and CIBER-BBN, Campus UAB, Bellaterra, 08193 Barcelona, Spain
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18
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Kim S, Hwang SH, Im SG, Lee MK, Lee CH, Son SJ, Oh HB. Upconversion Nanoparticle-Based Förster Resonance Energy Transfer for Detecting DNA Methylation. SENSORS 2016; 16:s16081259. [PMID: 27517925 PMCID: PMC5017424 DOI: 10.3390/s16081259] [Citation(s) in RCA: 12] [Impact Index Per Article: 1.5] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Subscribe] [Scholar Register] [Received: 06/07/2016] [Revised: 08/03/2016] [Accepted: 08/04/2016] [Indexed: 01/02/2023]
Abstract
Aberrant methylation of a crucial CpG island is the main mechanism for the inactivation of CDKN2A in the early stages of carcinogenesis. Therefore, the detection of DNA methylation with high sensitivity and specificity is important, and various detection methods have been developed. Recently, upconversion nanoparticles (UCNPs) have been found to display a high signal-to-noise ratio and no photobleaching, making them useful for diagnostic applications. In this pilot study, we applied UCNPs to the detection of CDKN2A methylation and evaluated the feasibility of this system for use in molecular diagnostics. DNA PCR was performed using biotinylated primers, and the PCR amplicon was then intercalated with SYTOX Orange dye, followed by incubation with streptavidin-conjugated UCNPs. Fluorescence detection of the Förster resonance energy transfer (FRET) of the UCNPs (MS-UC-FRET) was then performed, and the results were compared to those from real-time PCR (RQ-PCR) and pyrosequencing. Detection by MS-UC-FRET was more sensitive than that by either RQ-PCR or pyrosequencing. Our results confirmed the success of our MS-UC-FRET system for detecting DNA methylation and demonstrated the potential application of this system in molecular diagnostics.
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Affiliation(s)
- Seockjune Kim
- Department of Laboratory Medicine, University of Ulsan College of Medicine and Asan Medical Center, Seoul 05505, Korea.
| | - Sang-Hyun Hwang
- Department of Laboratory Medicine, Center for Diagnostic Oncology, Research Institute and Hospital, National Cancer Center, Goyang-si 10408, Korea.
- Hematologic Malignancy Branch, Research Institute and Hospital, National Cancer Center, Goyang-si 10408, Korea.
| | - Su-Gyeong Im
- Department of Laboratory Medicine, Center for Diagnostic Oncology, Research Institute and Hospital, National Cancer Center, Goyang-si 10408, Korea.
| | - Min-Ki Lee
- Department of Internal Medicine, Pusan National University School of Medicine and Biomedical Research Institute, Pusan National University Hospital, 179 Gudeok-ro, Seo-gu, Busan 602-739, Korea.
| | - Chang-Hun Lee
- Department of Pathology, Pusan National University School of Medicine and Biomedical Research Institute, Pusan National University Hospital, 179 Gudeok-ro, Seo-gu, Busan 602-739, Korea.
| | - Sang Jun Son
- Department of Chemistry, Gachon University, Seongnam, Gyeonggi, and Gachon Medical Research Institute, Gil Medical Center, Inchon 461-701, Korea.
| | - Heung-Bum Oh
- Department of Laboratory Medicine, University of Ulsan College of Medicine and Asan Medical Center, Seoul 05505, Korea.
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19
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Quantitative comparison of DNA methylation assays for biomarker development and clinical applications. Nat Biotechnol 2016; 34:726-37. [PMID: 27347756 DOI: 10.1038/nbt.3605] [Citation(s) in RCA: 223] [Impact Index Per Article: 27.9] [Reference Citation Analysis] [Abstract] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/14/2015] [Accepted: 05/10/2016] [Indexed: 02/08/2023]
Abstract
DNA methylation patterns are altered in numerous diseases and often correlate with clinically relevant information such as disease subtypes, prognosis and drug response. With suitable assays and after validation in large cohorts, such associations can be exploited for clinical diagnostics and personalized treatment decisions. Here we describe the results of a community-wide benchmarking study comparing the performance of all widely used methods for DNA methylation analysis that are compatible with routine clinical use. We shipped 32 reference samples to 18 laboratories in seven different countries. Researchers in those laboratories collectively contributed 21 locus-specific assays for an average of 27 predefined genomic regions, as well as six global assays. We evaluated assay sensitivity on low-input samples and assessed the assays' ability to discriminate between cell types. Good agreement was observed across all tested methods, with amplicon bisulfite sequencing and bisulfite pyrosequencing showing the best all-round performance. Our technology comparison can inform the selection, optimization and use of DNA methylation assays in large-scale validation studies, biomarker development and clinical diagnostics.
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20
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Pimson C, Ekalaksananan T, Pientong C, Promthet S, Putthanachote N, Suwanrungruang K, Wiangnon S. Aberrant methylation of PCDH10 and RASSF1A genes in blood samples for non-invasive diagnosis and prognostic assessment of gastric cancer. PeerJ 2016; 4:e2112. [PMID: 27330867 PMCID: PMC4906662 DOI: 10.7717/peerj.2112] [Citation(s) in RCA: 29] [Impact Index Per Article: 3.6] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/09/2016] [Accepted: 05/17/2016] [Indexed: 12/15/2022] Open
Abstract
Background. Assessment of DNA methylation of specific genes is one approach to the diagnosis of cancer worldwide. Early stage detection is necessary to reduce the mortality rate of cancers, including those occurring in the stomach. For this purpose, tumor cells in circulating blood offer promising candidates for non-invasive diagnosis. Transcriptional inactivation of tumor suppressor genes, like PCDH10 and RASSF1A, by methylation is associated with progression of gastric cancer, and such methylation can therefore be utilized as a biomarker. Methods. The present research was conducted to evaluate DNA methylation in these two genes using blood samples of gastric cancer cases. Clinicopathological data were also analyzed and cumulative survival rates generated for comparison. Results. High frequencies of PCDH10 and RASSF1A methylations in the gastric cancer group were noted (94.1% and 83.2%, respectively, as compared to 2.97% and 5.45% in 202 matched controls). Most patients (53.4%) were in severe stage of the disease, with a median survival time of 8.4 months after diagnosis. Likewise, the patients with metastases, or RASSF1A and PCDH10 methylations, had median survival times of 7.3, 7.8, and 8.4 months, respectively. A Kaplan–Meier analysis showed that cumulative survival was significantly lower in those cases positive for methylation of RASSF1A than in their negative counterparts. Similarly, whereas almost 100% of patients positive for PCDH10 methylation had died after five years, none of the negative cases died over this period. Notably, the methylations of RASSF1A and PCDH10 were found to be higher in the late-stage patients and were also significantly correlated with metastasis and histology. Conclusions.PCDH10 and RASSF1A methylations in blood samples can serve as potential non-invasive diagnostic indicators in blood for gastric cancer. In addition to RASSF1A methylation, tumor stage proved to be a major prognostic factor in terms of survival rates.
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Affiliation(s)
- Charinya Pimson
- Biomedical Science Programme, Graduate School, Khon Kaen University, Khon Kaen, Thailand
| | - Tipaya Ekalaksananan
- Department of Microbiology, Faculty of Medicine, Khon Kaen University,Khon Kaen,Thailand; HPV & EBV and Carcinogenesis Research Group, Khon Kaen University,Khon Kaen,Thailand
| | - Chamsai Pientong
- Department of Microbiology, Faculty of Medicine, Khon Kaen University,Khon Kaen,Thailand; HPV & EBV and Carcinogenesis Research Group, Khon Kaen University,Khon Kaen,Thailand
| | - Supannee Promthet
- Department of Epidemiology, Faculty of Public Health, Khon Kaen University, Khon Kaen, Thailand
| | - Nuntiput Putthanachote
- Department of Epidemiology, Faculty of Public Health, Khon Kaen University, Khon Kaen, Thailand
| | - Krittika Suwanrungruang
- Cancer Unit, Srinagarind Hospital, Faculty of Medicine, Khon Kaen University, Khon Kaen, Thailand
| | - Surapon Wiangnon
- Department of Pediatrics, Faculty of Medicine, Khon Kaen University, Khon Kaen, Thailand
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21
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Recent advances in electrochemical detection of important sulfhydryl-containing compounds. MONATSHEFTE FUR CHEMIE 2016. [DOI: 10.1007/s00706-016-1757-z] [Citation(s) in RCA: 4] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 02/07/2023]
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22
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Moison C, Assemat F, Daunay A, Arimondo PB, Tost J. DNA Methylation Analysis of ChIP Products at Single Nucleotide Resolution by Pyrosequencing®. Methods Mol Biol 2016; 1315:315-33. [PMID: 26103908 DOI: 10.1007/978-1-4939-2715-9_22] [Citation(s) in RCA: 4] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Abstract] [MESH Headings] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/13/2022]
Abstract
Interaction and co-occurrence of protein and DNA-based epigenetic modifications have become a topic of interest for many fundamental and biomedical questions. We describe within this chapter a protocol that combines two techniques in order to determine the methylation status of the DNA specifically associated with a protein of interest. First, DNA that directly interacts with the selected protein (such as a specific histone modification, a transcription factor, or any other DNA-associated protein) is purified by standard chromatin immunoprecipitation (ChIP). Second, the level of DNA methylation of this immunoprecipitated DNA is measured by bisulfite conversion and Pyrosequencing, a quantitative sequencing-by-synthesis method. This procedure allows determining the methylation status of genomic DNA associated to a specific protein at single nucleotide resolution.
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Affiliation(s)
- Céline Moison
- Unité de Service et de Recherche CNRS-Pierre Fabre n°3388, Epigenetic Targeting of Cancer (ETaC), Toulouse, France
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Grasso C, Trevisan M, Fiano V, Tarallo V, De Marco L, Sacerdote C, Richiardi L, Merletti F, Gillio-Tos A. Performance of Different Analytical Software Packages in Quantification of DNA Methylation by Pyrosequencing. PLoS One 2016; 11:e0150483. [PMID: 26934703 PMCID: PMC4775062 DOI: 10.1371/journal.pone.0150483] [Citation(s) in RCA: 3] [Impact Index Per Article: 0.4] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/16/2015] [Accepted: 02/14/2016] [Indexed: 12/18/2022] Open
Abstract
BACKGROUND Pyrosequencing has emerged as an alternative method of nucleic acid sequencing, well suited for many applications which aim to characterize single nucleotide polymorphisms, mutations, microbial types and CpG methylation in the target DNA. The commercially available pyrosequencing systems can harbor two different types of software which allow analysis in AQ or CpG mode, respectively, both widely employed for DNA methylation analysis. OBJECTIVE Aim of the study was to assess the performance for DNA methylation analysis at CpG sites of the two pyrosequencing software which allow analysis in AQ or CpG mode, respectively. Despite CpG mode having been specifically generated for CpG methylation quantification, many investigations on this topic have been carried out with AQ mode. As proof of equivalent performance of the two software for this type of analysis is not available, the focus of this paper was to evaluate if the two modes currently used for CpG methylation assessment by pyrosequencing may give overlapping results. METHODS We compared the performance of the two software in quantifying DNA methylation in the promoter of selected genes (GSTP1, MGMT, LINE-1) by testing two case series which include DNA from paraffin embedded prostate cancer tissues (PC study, N = 36) and DNA from blood fractions of healthy people (DD study, N = 28), respectively. RESULTS We found discrepancy in the two pyrosequencing software-based quality assignment of DNA methylation assays. Compared to the software for analysis in the AQ mode, less permissive criteria are supported by the Pyro Q-CpG software, which enables analysis in CpG mode. CpG mode warns the operators about potential unsatisfactory performance of the assay and ensures a more accurate quantitative evaluation of DNA methylation at CpG sites. CONCLUSION The implementation of CpG mode is strongly advisable in order to improve the reliability of the methylation analysis results achievable by pyrosequencing.
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Affiliation(s)
- Chiara Grasso
- Cancer Epidemiology Unit – C.E.R.M.S, Department of Medical Sciences, University of Turin, Turin, Italy
| | - Morena Trevisan
- Cancer Epidemiology Unit – C.E.R.M.S, Department of Medical Sciences, University of Turin, Turin, Italy
| | - Valentina Fiano
- Cancer Epidemiology Unit – C.E.R.M.S, Department of Medical Sciences, University of Turin, Turin, Italy
| | - Valentina Tarallo
- Cancer Epidemiology Unit – C.E.R.M.S, Department of Medical Sciences, University of Turin, Turin, Italy
| | - Laura De Marco
- Cancer Epidemiology Unit – C.E.R.M.S, Department of Medical Sciences, University of Turin, Turin, Italy
- Cancer Epidemiology Unit, Department of Medical Sciences, City of Health and Science Hospital, Turin, Italy
| | - Carlotta Sacerdote
- Cancer Epidemiology Unit, Department of Medical Sciences, City of Health and Science Hospital, Turin, Italy
| | - Lorenzo Richiardi
- Cancer Epidemiology Unit – C.E.R.M.S, Department of Medical Sciences, University of Turin, Turin, Italy
| | - Franco Merletti
- Cancer Epidemiology Unit – C.E.R.M.S, Department of Medical Sciences, University of Turin, Turin, Italy
- Cancer Epidemiology Unit, Department of Medical Sciences, City of Health and Science Hospital, Turin, Italy
| | - Anna Gillio-Tos
- Cancer Epidemiology Unit – C.E.R.M.S, Department of Medical Sciences, University of Turin, Turin, Italy
- * E-mail:
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Abstract
DNA methylation was the first epigenetic mark to be discovered, involving the addition of a methyl group to the 5' position of cytosine by DNA methyltransferases, and can be inherited through cell division. DNA methylation plays an important role in normal human development and is associated with the regulation of gene expression, tumorigenesis, and other genetic and epigenetic diseases. Differential methylation is now known to play a central role in the development and outcome of most if not all human malignancies.Bisulfite conversion is a commonly used approach for gene-specific DNA methylation analysis. Treatment of DNA with bisulfite converts cytosine to uracil while leaving 5-methylcytosine intact, allowing for single-nucleotide resolution information about the methylated areas of DNA. PCR-based methods are routinely used to study DNA methylation on a gene-specific basis, after bisulfite treatment. Variations of this method include bisulfite sequencing, methylation-specific PCR, real-time PCR-based MethyLight, and methylation-sensitive high-resolution melting PCR. Several whole-epigenome profiling technologies such as MethylC-seq reduced representation bisulfite sequencing (RRBS) and the Infinium Human methylation 450 K bead chip are now available allowing for the identification of epigenetic drivers of disease processes as well as biomarkers that could potentially be integrated into clinical practice.
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Nishi A, Milner DA, Giovannucci EL, Nishihara R, Tan AS, Kawachi I, Ogino S. Integration of molecular pathology, epidemiology and social science for global precision medicine. Expert Rev Mol Diagn 2015; 16:11-23. [PMID: 26636627 PMCID: PMC4713314 DOI: 10.1586/14737159.2016.1115346] [Citation(s) in RCA: 74] [Impact Index Per Article: 8.2] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/12/2022]
Abstract
The precision medicine concept and the unique disease principle imply that each patient has unique pathogenic processes resulting from heterogeneous cellular genetic and epigenetic alterations and interactions between cells (including immune cells) and exposures, including dietary, environmental, microbial and lifestyle factors. As a core method field in population health science and medicine, epidemiology is a growing scientific discipline that can analyze disease risk factors and develop statistical methodologies to maximize utilization of big data on populations and disease pathology. The evolving transdisciplinary field of molecular pathological epidemiology (MPE) can advance biomedical and health research by linking exposures to molecular pathologic signatures, enhancing causal inference and identifying potential biomarkers for clinical impact. The MPE approach can be applied to any diseases, although it has been most commonly used in neoplastic diseases (including breast, lung and colorectal cancers) because of availability of various molecular diagnostic tests. However, use of state-of-the-art genomic, epigenomic and other omic technologies and expensive drugs in modern healthcare systems increases racial, ethnic and socioeconomic disparities. To address this, we propose to integrate molecular pathology, epidemiology and social science. Social epidemiology integrates the latter two fields. The integrative social MPE model can embrace sociology, economics and precision medicine, address global health disparities and inequalities, and elucidate biological effects of social environments, behaviors and networks. We foresee advancements of molecular medicine, including molecular diagnostics, biomedical imaging and targeted therapeutics, which should benefit individuals in a global population, by means of an interdisciplinary approach of integrative MPE and social health science.
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Affiliation(s)
- Akihiro Nishi
- Yale Institute for Network Science, New Haven, CT, USA (AN); Department of Sociology, Yale University, New Haven, CT, USA (AN); Department of Pathology, Brigham and Women's Hospital and Harvard Medical School, Boston, MA, USA (DAM, SO); Department of Immunology and Infectious Diseases, Harvard T.H. Chan School of Public Health, Boston, MA, USA (DAM); Department of Epidemiology, Harvard T.H. Chan School of Public Health, Boston, MA, USA (ELG, RN, SO); Department of Nutrition, Harvard T.H. Chan School of Public Health, Boston, MA, USA (ELG, RN); Channing Division of Network Medicine, Department of Medicine, Brigham and Women's Hospital and Harvard Medical School, Boston, MA, USA (ELG); Department of Biostatistics, Harvard T.H. Chan School of Public Health, Boston, MA, USA (RN); Department of Medical Oncology, Dana-Farber Cancer Institute, Boston, MA, USA (RN, AST, SO); Department of Social and Behavioral Sciences, Harvard T.H. Chan School of Public Health, Boston, MA, USA (AST, IK)
| | - Danny A Milner
- Yale Institute for Network Science, New Haven, CT, USA (AN); Department of Sociology, Yale University, New Haven, CT, USA (AN); Department of Pathology, Brigham and Women's Hospital and Harvard Medical School, Boston, MA, USA (DAM, SO); Department of Immunology and Infectious Diseases, Harvard T.H. Chan School of Public Health, Boston, MA, USA (DAM); Department of Epidemiology, Harvard T.H. Chan School of Public Health, Boston, MA, USA (ELG, RN, SO); Department of Nutrition, Harvard T.H. Chan School of Public Health, Boston, MA, USA (ELG, RN); Channing Division of Network Medicine, Department of Medicine, Brigham and Women's Hospital and Harvard Medical School, Boston, MA, USA (ELG); Department of Biostatistics, Harvard T.H. Chan School of Public Health, Boston, MA, USA (RN); Department of Medical Oncology, Dana-Farber Cancer Institute, Boston, MA, USA (RN, AST, SO); Department of Social and Behavioral Sciences, Harvard T.H. Chan School of Public Health, Boston, MA, USA (AST, IK)
| | - Edward L. Giovannucci
- Yale Institute for Network Science, New Haven, CT, USA (AN); Department of Sociology, Yale University, New Haven, CT, USA (AN); Department of Pathology, Brigham and Women's Hospital and Harvard Medical School, Boston, MA, USA (DAM, SO); Department of Immunology and Infectious Diseases, Harvard T.H. Chan School of Public Health, Boston, MA, USA (DAM); Department of Epidemiology, Harvard T.H. Chan School of Public Health, Boston, MA, USA (ELG, RN, SO); Department of Nutrition, Harvard T.H. Chan School of Public Health, Boston, MA, USA (ELG, RN); Channing Division of Network Medicine, Department of Medicine, Brigham and Women's Hospital and Harvard Medical School, Boston, MA, USA (ELG); Department of Biostatistics, Harvard T.H. Chan School of Public Health, Boston, MA, USA (RN); Department of Medical Oncology, Dana-Farber Cancer Institute, Boston, MA, USA (RN, AST, SO); Department of Social and Behavioral Sciences, Harvard T.H. Chan School of Public Health, Boston, MA, USA (AST, IK)
| | - Reiko Nishihara
- Yale Institute for Network Science, New Haven, CT, USA (AN); Department of Sociology, Yale University, New Haven, CT, USA (AN); Department of Pathology, Brigham and Women's Hospital and Harvard Medical School, Boston, MA, USA (DAM, SO); Department of Immunology and Infectious Diseases, Harvard T.H. Chan School of Public Health, Boston, MA, USA (DAM); Department of Epidemiology, Harvard T.H. Chan School of Public Health, Boston, MA, USA (ELG, RN, SO); Department of Nutrition, Harvard T.H. Chan School of Public Health, Boston, MA, USA (ELG, RN); Channing Division of Network Medicine, Department of Medicine, Brigham and Women's Hospital and Harvard Medical School, Boston, MA, USA (ELG); Department of Biostatistics, Harvard T.H. Chan School of Public Health, Boston, MA, USA (RN); Department of Medical Oncology, Dana-Farber Cancer Institute, Boston, MA, USA (RN, AST, SO); Department of Social and Behavioral Sciences, Harvard T.H. Chan School of Public Health, Boston, MA, USA (AST, IK)
| | - Andy S. Tan
- Yale Institute for Network Science, New Haven, CT, USA (AN); Department of Sociology, Yale University, New Haven, CT, USA (AN); Department of Pathology, Brigham and Women's Hospital and Harvard Medical School, Boston, MA, USA (DAM, SO); Department of Immunology and Infectious Diseases, Harvard T.H. Chan School of Public Health, Boston, MA, USA (DAM); Department of Epidemiology, Harvard T.H. Chan School of Public Health, Boston, MA, USA (ELG, RN, SO); Department of Nutrition, Harvard T.H. Chan School of Public Health, Boston, MA, USA (ELG, RN); Channing Division of Network Medicine, Department of Medicine, Brigham and Women's Hospital and Harvard Medical School, Boston, MA, USA (ELG); Department of Biostatistics, Harvard T.H. Chan School of Public Health, Boston, MA, USA (RN); Department of Medical Oncology, Dana-Farber Cancer Institute, Boston, MA, USA (RN, AST, SO); Department of Social and Behavioral Sciences, Harvard T.H. Chan School of Public Health, Boston, MA, USA (AST, IK)
| | - Ichiro Kawachi
- Yale Institute for Network Science, New Haven, CT, USA (AN); Department of Sociology, Yale University, New Haven, CT, USA (AN); Department of Pathology, Brigham and Women's Hospital and Harvard Medical School, Boston, MA, USA (DAM, SO); Department of Immunology and Infectious Diseases, Harvard T.H. Chan School of Public Health, Boston, MA, USA (DAM); Department of Epidemiology, Harvard T.H. Chan School of Public Health, Boston, MA, USA (ELG, RN, SO); Department of Nutrition, Harvard T.H. Chan School of Public Health, Boston, MA, USA (ELG, RN); Channing Division of Network Medicine, Department of Medicine, Brigham and Women's Hospital and Harvard Medical School, Boston, MA, USA (ELG); Department of Biostatistics, Harvard T.H. Chan School of Public Health, Boston, MA, USA (RN); Department of Medical Oncology, Dana-Farber Cancer Institute, Boston, MA, USA (RN, AST, SO); Department of Social and Behavioral Sciences, Harvard T.H. Chan School of Public Health, Boston, MA, USA (AST, IK)
| | - Shuji Ogino
- Yale Institute for Network Science, New Haven, CT, USA (AN); Department of Sociology, Yale University, New Haven, CT, USA (AN); Department of Pathology, Brigham and Women's Hospital and Harvard Medical School, Boston, MA, USA (DAM, SO); Department of Immunology and Infectious Diseases, Harvard T.H. Chan School of Public Health, Boston, MA, USA (DAM); Department of Epidemiology, Harvard T.H. Chan School of Public Health, Boston, MA, USA (ELG, RN, SO); Department of Nutrition, Harvard T.H. Chan School of Public Health, Boston, MA, USA (ELG, RN); Channing Division of Network Medicine, Department of Medicine, Brigham and Women's Hospital and Harvard Medical School, Boston, MA, USA (ELG); Department of Biostatistics, Harvard T.H. Chan School of Public Health, Boston, MA, USA (RN); Department of Medical Oncology, Dana-Farber Cancer Institute, Boston, MA, USA (RN, AST, SO); Department of Social and Behavioral Sciences, Harvard T.H. Chan School of Public Health, Boston, MA, USA (AST, IK)
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Ogino S, Campbell PT, Nishihara R, Phipps AI, Beck AH, Sherman ME, Chan AT, Troester MA, Bass AJ, Fitzgerald KC, Irizarry RA, Kelsey KT, Nan H, Peters U, Poole EM, Qian ZR, Tamimi RM, Tchetgen Tchetgen EJ, Tworoger SS, Zhang X, Giovannucci EL, van den Brandt PA, Rosner BA, Wang M, Chatterjee N, Begg CB. Proceedings of the second international molecular pathological epidemiology (MPE) meeting. Cancer Causes Control 2015; 26:959-72. [PMID: 25956270 DOI: 10.1007/s10552-015-0596-2] [Citation(s) in RCA: 34] [Impact Index Per Article: 3.8] [Reference Citation Analysis] [Abstract] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/09/2015] [Accepted: 04/27/2015] [Indexed: 02/07/2023]
Abstract
Disease classification system increasingly incorporates information on pathogenic mechanisms to predict clinical outcomes and response to therapy and intervention. Technological advancements to interrogate omics (genomics, epigenomics, transcriptomics, proteomics, metabolomics, metagenomics, interactomics, etc.) provide widely open opportunities in population-based research. Molecular pathological epidemiology (MPE) represents integrative science of molecular pathology and epidemiology. This unified paradigm requires multidisciplinary collaboration between pathology, epidemiology, biostatistics, bioinformatics, and computational biology. Integration of these fields enables better understanding of etiologic heterogeneity, disease continuum, causal inference, and the impact of environment, diet, lifestyle, host factors (including genetics and immunity), and their interactions on disease evolution. Hence, the Second International MPE Meeting was held in Boston in December 2014, with aims to: (1) develop conceptual and practical frameworks; (2) cultivate and expand opportunities; (3) address challenges; and (4) initiate the effort of specifying guidelines for MPE. The meeting mainly consisted of presentations of method developments and recent data in various malignant neoplasms and tumors (breast, prostate, ovarian and colorectal cancers, renal cell carcinoma, lymphoma, and leukemia), followed by open discussion sessions on challenges and future plans. In particular, we recognized need for efforts to further develop statistical methodologies. This meeting provided an unprecedented opportunity for interdisciplinary collaboration, consistent with the purposes of the Big Data to Knowledge, Genetic Associations and Mechanisms in Oncology, and Precision Medicine Initiative of the US National Institute of Health. The MPE meeting series can help advance transdisciplinary population science and optimize training and education systems for twenty-first century medicine and public health.
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Affiliation(s)
- Shuji Ogino
- Department of Pathology, Brigham and Women's Hospital, Harvard Medical School, 450 Brookline Ave., Room M422, Boston, MA, 02215, USA,
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Yang Y, Sebra R, Pullman BS, Qiao W, Peter I, Desnick RJ, Geyer CR, DeCoteau JF, Scott SA. Quantitative and multiplexed DNA methylation analysis using long-read single-molecule real-time bisulfite sequencing (SMRT-BS). BMC Genomics 2015; 16:350. [PMID: 25943404 PMCID: PMC4422326 DOI: 10.1186/s12864-015-1572-7] [Citation(s) in RCA: 53] [Impact Index Per Article: 5.9] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/17/2014] [Accepted: 04/23/2015] [Indexed: 02/08/2023] Open
Abstract
Background DNA methylation has essential roles in transcriptional regulation, imprinting, X chromosome inactivation and other cellular processes, and aberrant CpG methylation is directly involved in the pathogenesis of human imprinting disorders and many cancers. To address the need for a quantitative and highly multiplexed bisulfite sequencing method with long read lengths for targeted CpG methylation analysis, we developed single-molecule real-time bisulfite sequencing (SMRT-BS). Results Optimized bisulfite conversion and PCR conditions enabled the amplification of DNA fragments up to ~1.5 kb, and subjecting overlapping 625–1491 bp amplicons to SMRT-BS indicated high reproducibility across all amplicon lengths (r = 0.972) and low standard deviations (≤0.10) between individual CpG sites sequenced in triplicate. Higher variability in CpG methylation quantitation was correlated with reduced sequencing depth, particularly for intermediately methylated regions. SMRT-BS was validated by orthogonal bisulfite-based microarray (r = 0.906; 42 CpG sites) and second generation sequencing (r = 0.933; 174 CpG sites); however, longer SMRT-BS amplicons (>1.0 kb) had reduced, but very acceptable, correlation with both orthogonal methods (r = 0.836-0.897 and r = 0.892-0.927, respectively) compared to amplicons less than ~1.0 kb (r = 0.940-0.951 and r = 0.948-0.963, respectively). Multiplexing utility was assessed by simultaneously subjecting four distinct CpG island amplicons (702–866 bp; 325 CpGs) and 30 hematological malignancy cell lines to SMRT-BS (average depth of 110X), which identified a spectrum of highly quantitative methylation levels across all interrogated CpG sites and cell lines. Conclusions SMRT-BS is a novel, accurate and cost-effective targeted CpG methylation method that is amenable to a high degree of multiplexing with minimal clonal PCR artifacts. Increased sequencing depth is necessary when interrogating longer amplicons (>1.0 kb) and the previously reported bisulfite sequencing PCR bias towards unmethylated DNA should be considered when measuring intermediately methylated regions. Coupled with an optimized bisulfite PCR protocol, SMRT-BS is capable of interrogating ~1.5 kb amplicons, which theoretically can cover ~91% of CpG islands in the human genome. Electronic supplementary material The online version of this article (doi:10.1186/s12864-015-1572-7) contains supplementary material, which is available to authorized users.
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Affiliation(s)
- Yao Yang
- Department of Genetics and Genomic Sciences, Icahn School of Medicine at Mount Sinai, New York, NY, 10029, USA.
| | - Robert Sebra
- Department of Genetics and Genomic Sciences, Icahn School of Medicine at Mount Sinai, New York, NY, 10029, USA. .,Icahn Institute for Genomics and Multiscale Biology, Icahn School of Medicine at Mount Sinai, New York, NY, 10029, USA.
| | - Benjamin S Pullman
- Department of Genetics and Genomic Sciences, Icahn School of Medicine at Mount Sinai, New York, NY, 10029, USA.
| | - Wanqiong Qiao
- Department of Genetics and Genomic Sciences, Icahn School of Medicine at Mount Sinai, New York, NY, 10029, USA.
| | - Inga Peter
- Department of Genetics and Genomic Sciences, Icahn School of Medicine at Mount Sinai, New York, NY, 10029, USA.
| | - Robert J Desnick
- Department of Genetics and Genomic Sciences, Icahn School of Medicine at Mount Sinai, New York, NY, 10029, USA.
| | - C Ronald Geyer
- Cancer Stem Cell Research Group, University of Saskatchewan, Saskatoon, SK, S7N 4H4, Canada.
| | - John F DeCoteau
- Cancer Stem Cell Research Group, University of Saskatchewan, Saskatoon, SK, S7N 4H4, Canada.
| | - Stuart A Scott
- Department of Genetics and Genomic Sciences, Icahn School of Medicine at Mount Sinai, New York, NY, 10029, USA.
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Non AL, Thayer ZM. Epigenetics for anthropologists: An introduction to methods. Am J Hum Biol 2015; 27:295-303. [DOI: 10.1002/ajhb.22679] [Citation(s) in RCA: 24] [Impact Index Per Article: 2.7] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/08/2014] [Revised: 11/22/2014] [Accepted: 12/20/2014] [Indexed: 12/17/2022] Open
Affiliation(s)
- Amy L. Non
- Department of Anthropology; Vanderbilt University; Nashville Tennessee 37235-7703
| | - Zaneta M. Thayer
- Department of Anthropology; University of Colorado Denver; Denver Colorado 80217-3364
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Lochhead P, Chan AT, Nishihara R, Fuchs CS, Beck AH, Giovannucci E, Ogino S. Etiologic field effect: reappraisal of the field effect concept in cancer predisposition and progression. Mod Pathol 2015; 28:14-29. [PMID: 24925058 PMCID: PMC4265316 DOI: 10.1038/modpathol.2014.81] [Citation(s) in RCA: 145] [Impact Index Per Article: 16.1] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/20/2013] [Revised: 02/12/2014] [Accepted: 04/02/2014] [Indexed: 02/07/2023]
Abstract
The term 'field effect' (also known as field defect, field cancerization, or field carcinogenesis) has been used to describe a field of cellular and molecular alteration, which predisposes to the development of neoplasms within that territory. We explore an expanded, integrative concept, 'etiologic field effect', which asserts that various etiologic factors (the exposome including dietary, lifestyle, environmental, microbial, hormonal, and genetic factors) and their interactions (the interactome) contribute to a tissue microenvironmental milieu that constitutes a 'field of susceptibility' to neoplasia initiation, evolution, and progression. Importantly, etiological fields predate the acquisition of molecular aberrations commonly considered to indicate presence of filed effect. Inspired by molecular pathological epidemiology (MPE) research, which examines the influence of etiologic factors on cellular and molecular alterations during disease course, an etiologically focused approach to field effect can: (1) broaden the horizons of our inquiry into cancer susceptibility and progression at molecular, cellular, and environmental levels, during all stages of tumor evolution; (2) embrace host-environment-tumor interactions (including gene-environment interactions) occurring in the tumor microenvironment; and, (3) help explain intriguing observations, such as shared molecular features between bilateral primary breast carcinomas, and between synchronous colorectal cancers, where similar molecular changes are absent from intervening normal colon. MPE research has identified a number of endogenous and environmental exposures which can influence not only molecular signatures in the genome, epigenome, transcriptome, proteome, metabolome and interactome, but also host immunity and tumor behavior. We anticipate that future technological advances will allow the development of in vivo biosensors capable of detecting and quantifying 'etiologic field effect' as abnormal network pathology patterns of cellular and microenvironmental responses to endogenous and exogenous exposures. Through an 'etiologic field effect' paradigm, and holistic systems pathology (systems biology) approaches to cancer biology, we can improve personalized prevention and treatment strategies for precision medicine.
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Affiliation(s)
- Paul Lochhead
- Gastrointestinal Research Group, Institute of Medical Sciences, University of Aberdeen, Aberdeen, UK
| | - Andrew T Chan
- 1] Division of Gastroenterology, Massachusetts General Hospital, Boston, MA, USA [2] Channing Division of Network Medicine, Department of Medicine, Brigham and Women's Hospital, Harvard Medical School, Boston, MA, USA
| | - Reiko Nishihara
- 1] Department of Medical Oncology, Dana-Farber Cancer Institute, Harvard Medical School, Boston, MA, USA [2] Department of Nutrition, Harvard School of Public Health, Boston, MA, USA
| | - Charles S Fuchs
- 1] Channing Division of Network Medicine, Department of Medicine, Brigham and Women's Hospital, Harvard Medical School, Boston, MA, USA [2] Department of Medical Oncology, Dana-Farber Cancer Institute, Harvard Medical School, Boston, MA, USA
| | - Andrew H Beck
- Department of Pathology, Beth Israel Deaconess Medical Center, Harvard Medical School, Boston, MA, USA
| | - Edward Giovannucci
- 1] Channing Division of Network Medicine, Department of Medicine, Brigham and Women's Hospital, Harvard Medical School, Boston, MA, USA [2] Department of Nutrition, Harvard School of Public Health, Boston, MA, USA [3] Department of Epidemiology, Harvard School of Public Health, Boston, MA, USA
| | - Shuji Ogino
- 1] Department of Medical Oncology, Dana-Farber Cancer Institute, Harvard Medical School, Boston, MA, USA [2] Department of Epidemiology, Harvard School of Public Health, Boston, MA, USA [3] Department of Pathology, Brigham and Women's Hospital, Harvard Medical School, Boston, MA, USA
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30
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Qiang-long Z, Shi L, Peng G, Fei-shi L. High-throughput Sequencing Technology and Its Application. ACTA ACUST UNITED AC 2014. [DOI: 10.1016/s1006-8104(14)60073-8] [Citation(s) in RCA: 3] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 02/07/2023]
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Lochhead P, Chan AT, Giovannucci E, Fuchs CS, Wu K, Nishihara R, O'Brien M, Ogino S. Progress and opportunities in molecular pathological epidemiology of colorectal premalignant lesions. Am J Gastroenterol 2014; 109:1205-14. [PMID: 24935274 PMCID: PMC4125459 DOI: 10.1038/ajg.2014.153] [Citation(s) in RCA: 50] [Impact Index Per Article: 5.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Received: 10/21/2013] [Accepted: 04/18/2014] [Indexed: 02/06/2023]
Abstract
Molecular pathological epidemiology (MPE) is an integrative molecular and population health science that addresses the molecular pathogenesis and heterogeneity of disease processes. The MPE of colonic and rectal premalignant lesions (including hyperplastic polyps, tubular adenomas, tubulovillous adenomas, villous adenomas, traditional serrated adenomas, sessile serrated adenomas/sessile serrated polyps, and hamartomatous polyps) can provide unique opportunities for examining the influence of diet, lifestyle, and environmental exposures on specific pathways of carcinogenesis. Colorectal neoplasia can provide a practical model by which both malignant epithelial tumor (carcinoma) and its precursor are subjected to molecular pathological analyses. KRAS, BRAF, and PIK3CA oncogene mutations, microsatellite instability, CpG island methylator phenotype, and LINE-1 methylation are commonly examined tumor biomarkers. Future opportunities include interrogation of comprehensive genomic, epigenomic, or panomic datasets, and the adoption of in vivo pathology techniques. Considering the colorectal continuum hypothesis and emerging roles of gut microbiota and host immunity in tumorigenesis, detailed information on tumor location is important. There are unique strengths and caveats, especially with regard to case ascertainment by colonoscopy. The MPE of colorectal premalignant lesions can identify etiologic exposures associated with neoplastic initiation and progression, help us better understand colorectal carcinogenesis, and facilitate personalized prevention, screening, and therapy.
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Affiliation(s)
- Paul Lochhead
- 1] Institute of Medical Sciences, University of Aberdeen, Aberdeen, UK [2] The first two authors contributed equally to this work
| | - Andrew T Chan
- 1] Division of Gastroenterology, Massachusetts General Hospital, Boston, Massachusetts, USA [2] Channing Division of Network Medicine, Department of Medicine, Brigham and Women's Hospital, and Harvard Medical School, Boston, Massachusetts, USA [3] The first two authors contributed equally to this work
| | - Edward Giovannucci
- 1] Channing Division of Network Medicine, Department of Medicine, Brigham and Women's Hospital, and Harvard Medical School, Boston, Massachusetts, USA [2] Department of Epidemiology, Harvard School of Public Health, Boston, Massachusetts, USA [3] Department of Nutrition, Harvard School of Public Health, Boston, Massachusetts, USA
| | - Charles S Fuchs
- 1] Channing Division of Network Medicine, Department of Medicine, Brigham and Women's Hospital, and Harvard Medical School, Boston, Massachusetts, USA [2] Department of Medical Oncology, Dana-Farber Cancer Institute and Harvard Medical School, Boston, Massachusetts, USA
| | - Kana Wu
- Department of Nutrition, Harvard School of Public Health, Boston, Massachusetts, USA
| | - Reiko Nishihara
- 1] Department of Nutrition, Harvard School of Public Health, Boston, Massachusetts, USA [2] Department of Medical Oncology, Dana-Farber Cancer Institute and Harvard Medical School, Boston, Massachusetts, USA
| | - Michael O'Brien
- Department of Pathology, Boston University Medical Center, Boston, Massachusetts, USA
| | - Shuji Ogino
- 1] Department of Epidemiology, Harvard School of Public Health, Boston, Massachusetts, USA [2] Department of Medical Oncology, Dana-Farber Cancer Institute and Harvard Medical School, Boston, Massachusetts, USA [3] Department of Pathology, Brigham and Women's Hospital, and Harvard Medical School, Boston, Massachusetts, USA
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Ogino S, Lochhead P, Giovannucci E, Meyerhardt JA, Fuchs CS, Chan AT. Discovery of colorectal cancer PIK3CA mutation as potential predictive biomarker: power and promise of molecular pathological epidemiology. Oncogene 2014; 33:2949-55. [PMID: 23792451 PMCID: PMC3818472 DOI: 10.1038/onc.2013.244] [Citation(s) in RCA: 104] [Impact Index Per Article: 10.4] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/21/2013] [Revised: 04/26/2013] [Accepted: 04/27/2013] [Indexed: 12/18/2022]
Abstract
Regular use of aspirin reduces incidence and mortality of various cancers, including colorectal cancer. Anticancer effect of aspirin represents one of the 'Provocative Questions' in cancer research. Experimental and clinical studies support a carcinogenic role for PTGS2 (cyclooxygenase-2), which is an important enzymatic mediator of inflammation, and a target of aspirin. Recent 'molecular pathological epidemiology' (MPE) research has shown that aspirin use is associated with better prognosis and clinical outcome in PIK3CA-mutated colorectal carcinoma, suggesting somatic PIK3CA mutation as a molecular biomarker that predicts response to aspirin therapy. The PI3K (phosphatidylinositol-4,5-bisphosphonate 3-kinase) enzyme has a pivotal role in the PI3K-AKT signaling pathway. Activating PIK3CA oncogene mutations are observed in various malignancies including breast cancer, ovarian cancer, brain tumor, hepatocellular carcinoma, lung cancer and colon cancer. The prevalence of PIK3CA mutations increases continuously from rectal to cecal cancers, supporting the 'colorectal continuum' paradigm, and an important interplay of gut microbiota and host immune/inflammatory reaction. MPE represents an interdisciplinary integrative science, conceptually defined as 'epidemiology of molecular heterogeneity of disease'. As exposome and interactome vary from person to person and influence disease process, each disease process is unique (the unique disease principle). Therefore, MPE concept and paradigm can extend to non-neoplastic diseases including diabetes mellitus, cardiovascular diseases, metabolic diseases, and so on. MPE research opportunities are currently limited by paucity of tumor molecular data in the existing large-scale population-based studies. However, genomic, epigenomic and molecular pathology testings (for example, analyses for microsatellite instability, MLH1 promoter CpG island methylation, and KRAS and BRAF mutations in colorectal tumors) are becoming routine clinical practices. In order for integrative molecular and population science to be routine practice, we must first reform education curricula by integrating both population and molecular biological sciences. As consequences, next-generation hybrid molecular biological and population scientists can advance science, moving closer to personalized precision medicine and health care.
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Affiliation(s)
- S Ogino
- 1] Department of Pathology, Brigham and Women's Hospital, Harvard Medical School, Boston, MA, USA [2] Department of Medical Oncology, Dana-Farber Cancer Institute, Boston, MA, USA [3] Department of Epidemiology, Harvard School of Public Health, Boston, MA, USA
| | - P Lochhead
- Institute of Medical Sciences, University of Aberdeen, Aberdeen, UK
| | - E Giovannucci
- 1] Department of Epidemiology, Harvard School of Public Health, Boston, MA, USA [2] Department of Nutrition, Harvard School of Public Health, Boston, MA, USA [3] Channing Division of Network Medicine, Department of Medicine, Brigham and Women's Hospital, Harvard Medical School, Boston, MA, USA
| | - J A Meyerhardt
- Department of Medical Oncology, Dana-Farber Cancer Institute, Boston, MA, USA
| | - C S Fuchs
- 1] Department of Medical Oncology, Dana-Farber Cancer Institute, Boston, MA, USA [2] Channing Division of Network Medicine, Department of Medicine, Brigham and Women's Hospital, Harvard Medical School, Boston, MA, USA
| | - A T Chan
- 1] Channing Division of Network Medicine, Department of Medicine, Brigham and Women's Hospital, Harvard Medical School, Boston, MA, USA [2] Division of Gastroenterology, Massachusetts General Hospital, Boston, MA, USA
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Kovalenko TF, Sorokina AV, Ozolinia LA, Patrushev LI. [Pseudogene PTENP1 5'-region methylation in endometrial cancer and hyperplasias]. RUSSIAN JOURNAL OF BIOORGANIC CHEMISTRY 2014; 39:445-53. [PMID: 24707726 DOI: 10.1134/s1068162013040109] [Citation(s) in RCA: 8] [Impact Index Per Article: 0.8] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 01/21/2023]
Abstract
Genetic mutations in tumor suppressor gene PTEN are often detected in malignant human cells and these genomic changes are especially characteristic ofendometrial cancer. In our previous researches we assumed that alternative epigenetic mechanism of PTEN inactivation trough promoter methylation may exist in endometrial cancer. Moreover, PTENP1 pseudogene has recently been shown to play a role in positive regulation of PTENgene expression. Taking into account these facts, we analyzed PTEN and PTENP1 methylation status in endometrial hyperplasia and cancer. It was demonstrated that PTENgene promoter was not methylated but PTENP1 was methylated in 11 of 18 endometrial cancers and in 5 of9 endometrial hyperplasias. We can assume that PTENP1 methylation may inhibit transcription of this gene and also PTEN gene transcription trough RNA interference in accordance with ceRNA theory. Thus, aberrant suppression of PTENP1 transcription can play a role in endometrial cancer pathogenesis.
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Nguyen HT, Tian G, Murph MM. Molecular epigenetics in the management of ovarian cancer: are we investigating a rational clinical promise? Front Oncol 2014; 4:71. [PMID: 24782983 PMCID: PMC3986558 DOI: 10.3389/fonc.2014.00071] [Citation(s) in RCA: 13] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/23/2014] [Accepted: 03/20/2014] [Indexed: 12/21/2022] Open
Abstract
Epigenetics is essentially a phenotypical change in gene expression without any alteration of the DNA sequence; the emergence of epigenetics in cancer research and mainstream oncology is fueling new hope. However, it is not yet known whether this knowledge will translate to improved clinical management of ovarian cancer. In this malignancy, women are still undergoing chemotherapy similar to what was approved in 1978, which to this day represents one of the biggest breakthroughs for treating ovarian cancer. Although liquid tumors are benefiting from epigenetically related therapies, solid tumors like ovarian cancer are not (yet?). Herein, we will review the science of molecular epigenetics, especially DNA methylation, histone modifications and microRNA, but also include transcription factors since they, too, are important in ovarian cancer. Pre-clinical and clinical research on the role of epigenetic modifications is also summarized. Unfortunately, ovarian cancer remains an idiopathic disease, for the most part, and there are many areas of patient management, which could benefit from improved technology. This review will also highlight the evidence suggesting that epigenetics may have pre-clinical utility in pharmacology and clinical applications for prognosis and diagnosis. Finally, drugs currently in clinical trials (i.e., histone deacetylase inhibitors) are discussed along with the promise for epigenetics in the exploitation of chemoresistance. Whether epigenetics will ultimately be the answer to better management in ovarian cancer is currently unknown; but we hope so in the future.
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Affiliation(s)
- Ha T Nguyen
- Department of Pharmaceutical and Biomedical Sciences, University of Georgia College of Pharmacy , Athens, GA , USA
| | - Geng Tian
- Department of Pharmaceutical and Biomedical Sciences, University of Georgia College of Pharmacy , Athens, GA , USA ; Department of Obstetrics and Gynecology, The Second Hospital of Jilin University , Changchun , China
| | - Mandi M Murph
- Department of Pharmaceutical and Biomedical Sciences, University of Georgia College of Pharmacy , Athens, GA , USA
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Head SR, Komori HK, LaMere SA, Whisenant T, Van Nieuwerburgh F, Salomon DR, Ordoukhanian P. Library construction for next-generation sequencing: overviews and challenges. Biotechniques 2014; 56:61-4, 66, 68, passim. [PMID: 24502796 DOI: 10.2144/000114133] [Citation(s) in RCA: 345] [Impact Index Per Article: 34.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/14/2014] [Accepted: 01/21/2014] [Indexed: 01/03/2023] Open
Abstract
High-throughput sequencing, also known as next-generation sequencing (NGS), has revolutionized genomic research. In recent years, NGS technology has steadily improved, with costs dropping and the number and range of sequencing applications increasing exponentially. Here, we examine the critical role of sequencing library quality and consider important challenges when preparing NGS libraries from DNA and RNA sources. Factors such as the quantity and physical characteristics of the RNA or DNA source material as well as the desired application (i.e., genome sequencing, targeted sequencing, RNA-seq, ChIP-seq, RIP-seq, and methylation) are addressed in the context of preparing high quality sequencing libraries. In addition, the current methods for preparing NGS libraries from single cells are also discussed.
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Affiliation(s)
- Steven R Head
- NGS and Microarray Core Facility, The Scripps Research Institute, La Jolla, CA
| | - H Kiyomi Komori
- Department of Molecular and Experimental Medicine, The Scripps Research Institute, La Jolla, CA
| | - Sarah A LaMere
- Department of Molecular and Experimental Medicine, The Scripps Research Institute, La Jolla, CA
| | - Thomas Whisenant
- Department of Molecular and Experimental Medicine, The Scripps Research Institute, La Jolla, CA
| | - Filip Van Nieuwerburgh
- Laboratory of Pharmaceutical Biotechnology, Faculty of Pharmaceutical Sciences, Ghent University, Ghent, Belgium
| | - Daniel R Salomon
- Department of Molecular and Experimental Medicine, The Scripps Research Institute, La Jolla, CA
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Andergassen U, Kölbl AC, Hutter S, Friese K, Jeschke U. Detection of Circulating Tumour Cells from Blood of Breast Cancer Patients via RT-qPCR. Cancers (Basel) 2013; 5:1212-20. [PMID: 24202442 PMCID: PMC3875936 DOI: 10.3390/cancers5041212] [Citation(s) in RCA: 13] [Impact Index Per Article: 1.2] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/10/2013] [Revised: 08/20/2013] [Accepted: 09/11/2013] [Indexed: 12/25/2022] Open
Abstract
Breast cancer is still the most frequent cause of cancer-related death in women worldwide. Often death is not caused only by the primary tumour itself, but also by metastatic lesions. Today it is largely accepted, that these remote metastases arise out of cells, which detach from the primary tumour, enter circulation, settle down at secondary sites in the body and are called Circulating Tumour Cells (CTCs). The occurrence of such minimal residual diseases in the blood of breast cancer patients is mostly linked to a worse prognosis for therapy outcome and overall survival. Due to their very low frequency, the detection of CTCs is, still a technical challenge. RT-qPCR as a highly sensitive method could be an approach for CTC-detection from peripheral blood of breast cancer patients. This assumption is based on the fact that CTCs are of epithelial origin and therefore express a different gene panel than surrounding blood cells. For the technical approach it is necessary to identify appropriate marker genes and to correlate their gene expression levels to the number of tumour cells within a sample in an in vitro approach. After that, samples from adjuvant and metastatic patients can be analysed. This approach may lead to new concepts in diagnosis and treatment.
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Affiliation(s)
- Ulrich Andergassen
- Department of Obstetrics and Gynaecology, Ludwig Maximilians University of Munich, Munich, Maistrasse 11, D-80337 Munich, Germany.
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Qu Y, Dang S, Hou P. Gene methylation in gastric cancer. Clin Chim Acta 2013; 424:53-65. [PMID: 23669186 DOI: 10.1016/j.cca.2013.05.002] [Citation(s) in RCA: 269] [Impact Index Per Article: 24.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/01/2013] [Revised: 05/03/2013] [Accepted: 05/03/2013] [Indexed: 02/07/2023]
Abstract
Gastric cancer is one of the most common malignancies and remains the second leading cause of cancer-related death worldwide. Over 70% of new cases and deaths occur in developing countries. In the early years of the molecular biology revolution, cancer research mainly focuses on genetic alterations, including gastric cancer. Epigenetic mechanisms are essential for normal development and maintenance of tissue-specific gene expression patterns in mammals. Disruption of epigenetic processes can lead to altered gene function and malignant cellular transformation. Recent advancements in the rapidly evolving field of cancer epigenetics have shown extensive reprogramming of every component of the epigenetic machinery in cancer, including DNA methylation, histone modifications, nucleosome positioning, noncoding RNAs, and microRNAs. Aberrant DNA methylation in the promoter regions of gene, which leads to inactivation of tumor suppressor and other cancer-related genes in cancer cells, is the most well-defined epigenetic hallmark in gastric cancer. The advantages of gene methylation as a target for detection and diagnosis of cancer in biopsy specimens and non-invasive body fluids such as serum and gastric washes have led to many studies of application in gastric cancer. This review focuses on the most common and important phenomenon of epigenetics, DNA methylation, in gastric cancer and illustrates the impact epigenetics has had on this field.
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Key Words
- 5-hmC
- 5-hydroxymethylcytosine
- 5-mC
- 5-methylcytosine
- ADAM metallopeptidase domain 23
- ADAM metallopeptidase with thrombospondin type 1 motif, 9
- ADAM23
- ADAMTS9
- AML
- APC
- ARID1A
- AT motif-binding factor 1
- AT rich interactive domain 1A (SWI-like)
- ATBF1
- Acute myelocytic leukemia
- Adenomatosis polyposis coli
- B-cell translocation gene 4
- BCL2/adenovirus E1B 19kDa interacting protein 3
- BMP-2
- BNIP3
- BS
- BTG4
- Biomarkers
- Bisulfite sequencing
- Bone morphogenetic protein 2
- C-MET
- CACNA1G
- CACNA2D3
- CD44
- CD44 molecule (Indian blood group)
- CDH1
- CDK4
- CDK6
- CDKN1C
- CDKN2A
- CDX2
- CGI
- CHD5
- CHFR
- CKLF-like MARVEL transmembrane domain containing 3
- CMTM3
- CNS
- CRBP1
- Cadherin 1 or E-cadherin
- Calcium channel, voltage-dependent, T type, alpha 1G subunit
- Calcium channel, voltage-dependent, alpha 2/delta subunit 3
- Caudal type homeobox 2
- Central nervous system
- Checkpoint with forkhead and ring finger domains, E3 ubiquitin protein ligase
- Chromodomain helicase DNA binding protein 5
- Chromosome 2 open reading frame 40
- Clinical outcomes
- CpG islands
- Cyclin-dependent kinase 4
- Cyclin-dependent kinase 6
- Cyclin-dependent kinase inhibitor 1A
- Cyclin-dependent kinase inhibitor 1B
- Cyclin-dependent kinase inhibitor 1C
- Cyclin-dependent kinase inhibitor 2A
- Cyclin-dependent kinase inhibitor 2B
- DAB2 interacting protein
- DACT1
- DAPK
- DNA
- DNA methylatransferases
- DNA mismatch repair
- DNMT
- Dapper, antagonist of beta-catenin, homolog 1 (Xenopus laevis)
- Death-associated protein kinase
- Deoxyribose Nucleic Acid
- Dickkopf 3 homolog (Xenopus laevis)
- Dkk-3
- EBV
- ECRG4
- EDNRB
- EGCG
- ERBB4
- Endothelin receptor type B
- Epigallocatechin gallate
- Epigenetics
- Epstein–Barr Virus
- FDA
- FLNc
- Filamin C
- Food and Drug Administration
- GC
- GDNF
- GI endoscopy
- GPX3
- GRIK2
- GSTP1
- Gastric cancer
- Gene methylation
- Glutamate receptor, ionotropic, kainate 2
- Glutathione S-transferase pi 1
- Glutathione peroxidase 3 (plasma)
- H. pylori
- HACE1
- HAI-2/SPINT2
- HECT domain and ankyrin repeat containing E3 ubiquitin protein ligase 1
- HGFA
- HLTF
- HOXA1
- HOXA10
- HRAS-like suppressor
- HRASLS
- Helicase-like transcription factor
- Helicobacter pylori
- Homeobox A1
- Homeobox A10
- Homeobox D10
- HoxD10
- IGF-1
- IGF-1R
- IGFBP3
- IL-1β
- ITGA4
- Insulin-like growth factor 1 (somatomedin C)
- Insulin-like growth factor I receptor
- Insulin-like growth factor binding protein 3
- Integrin, alpha 4 (antigen CD49D, alpha 4 subunit of VLA-4 receptor)
- Interleukin 1, beta
- KL
- KRAS
- Klotho
- LL3
- LMP2A
- LOX
- LRP1B
- Low density lipoprotein receptor-related protein 1B
- Lysyl oxidase
- MAPK
- MBPs
- MDS
- MGMT
- MINT25
- MLF1
- MLL
- MMR
- MSI
- MSP
- Matrix metallopeptidase 24 (membrane-inserted)
- Met proto-oncogene (hepatocyte growth factor receptor)
- Methyl-CpG binding proteins
- Methylation-specific PCR
- Microsatellite instability
- Myeloid leukemia factor 1
- Myeloid/lymphoid or mixed-lineage leukemia (trithorax homolog, Drosophila)
- Myeloid/lymphoid or mixed-lineage leukemia 3
- NDRG family member 2
- NDRG2
- NPR1
- NR3C1
- Natriuretic peptide receptor A/guanylate cyclase A
- Notch 1
- Nuclear receptor subfamily 3, group C, member 1 (glucocorticoid receptor)
- O-6-methylguanine-DNA methyltransferase
- PCDH10
- PCDH17
- PI3K/Akt
- PIK3CA
- PR domain containing 5
- PRDM5
- PTCH1
- Patched 1
- Phosphatidylethanolamine binding protein 1
- Protein tyrosine phosphatase, non-receptor type 6
- Protocadherin 10
- Protocadherin 17
- Q-MSP
- Quantitative methylation-specific PCR
- RAR-related orphan receptor A
- RARRES1
- RARß
- RAS/RAF/MEK/ERK
- RASSF1A
- RASSF2
- RBP1
- RKIP
- RORA
- ROS
- RUNX3
- Ras association (RalGDS/AF-6) domain family member 1
- Ras association (RalGDS/AF-6) domain family member 2
- Rb
- Retinoic acid receptor responder (tazarotene induced) 1
- Retinoic acid receptor, beta
- Retinol binding protein 1, cellular
- Runt-related transcription factor 3
- S-adenosylmethionine
- SAM
- SFRP2
- SFRP5
- SHP1
- SOCS-1
- STAT3
- SYK
- Secreted frizzled-related protein 2
- Secreted frizzled-related protein 5
- Serine peptidase inhibitor, Kunitz type, 2
- Spleen tyrosine kinase
- Suppressor of cytokine signaling 1
- TCF4
- TET
- TFPI2
- TGF-β
- TIMP metallopeptidase inhibitor 3
- TIMP3
- TNM
- TP73
- TSP1
- Thrombospondin 1
- Tissue factor pathway inhibitor 2
- Transcription factor 4
- Tumor Node Metastasis
- Tumor protein p73
- V-erb-a erythroblastic leukemia viral oncogene homolog 4
- ZFP82 zinc finger protein
- ZIC1
- ZNF545
- Zinc finger protein of the cerebellum 1
- gastrointestinal endoscopy
- glial cell derived neurotrophic factor
- hDAB2IP
- hMLH1
- hepatocyte growth factor activator
- latent membrane protein
- mutL homolog 1
- myelodysplastic syndromes
- p15
- p16
- p21
- p27
- p53
- p73
- phosphatidylinositol-4,5-bisphosphate 3-kinase, catalytic subunit alpha
- phosphoinositide 3-kinase (PI3K)/Akt
- reactive oxygen species
- retinoblastoma
- signal transducer and activator of transcription-3
- ten-eleven translocation
- transforming growth factor-β
- tumor protein p53
- tumor protein p73
- v-Ki-ras2 Kirsten rat sarcoma viral oncogene homolog
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Affiliation(s)
- Yiping Qu
- Department of Endocrinology, The First Affiliated Hospital of Xi'an Jiaotong University School of Medicine, Xi'an 710061, People's Republic of China
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In vivo imaging-based mathematical modeling techniques that enhance the understanding of oncogene addiction in relation to tumor growth. COMPUTATIONAL AND MATHEMATICAL METHODS IN MEDICINE 2013; 2013:802512. [PMID: 23573174 PMCID: PMC3616361 DOI: 10.1155/2013/802512] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Subscribe] [Scholar Register] [Received: 12/21/2012] [Accepted: 02/15/2013] [Indexed: 11/18/2022]
Abstract
The dependence on the overexpression of a single oncogene constitutes an exploitable weakness for molecular targeted therapy. These drugs can produce dramatic tumor regression by targeting the driving oncogene, but relapse often follows. Understanding the complex interactions of the tumor's multifaceted response to oncogene inactivation is key to tumor regression. It has become clear that a collection of cellular responses lead to regression and that immune-mediated steps are vital to preventing relapse. Our integrative mathematical model includes a variety of cellular response mechanisms of tumors to oncogene inactivation. It allows for correct predictions of the time course of events following oncogene inactivation and their impact on tumor burden. A number of aspects of our mathematical model have proven to be necessary for recapitulating our experimental results. These include a number of heterogeneous tumor cell states since cells following different cellular programs have vastly different fates. Stochastic transitions between these states are necessary to capture the effect of escape from oncogene addiction (i.e., resistance). Finally, delay differential equations were used to accurately model the tumor growth kinetics that we have observed. We use this to model oncogene addiction in MYC-induced lymphoma, osteosarcoma, and hepatocellular carcinoma.
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