1
|
Kolkman R, Michel-Souzy S, Wasserberg D, Segerink LI, Huskens J. Density Control over MBD2 Receptor-Coated Surfaces Provides Superselective Binding of Hypermethylated DNA. ACS APPLIED MATERIALS & INTERFACES 2022; 14:40579-40589. [PMID: 36052432 PMCID: PMC9478954 DOI: 10.1021/acsami.2c09641] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Figures] [Subscribe] [Scholar Register] [Received: 05/30/2022] [Accepted: 08/26/2022] [Indexed: 06/15/2023]
Abstract
Using the biomarker hypermethylated DNA (hmDNA) for cancer detection requires a pretreatment to isolate or concentrate hmDNA from nonmethylated DNA. Affinity chromatography using a methyl binding domain-2 (MBD2) protein can be used, but the relatively low enrichment selectivity of MBD2 limits its clinical applicability. Here, we developed a superselective, multivalent, MBD2-coated platform to improve the selectivity of hmDNA enrichment. The multivalent platform employs control over the MBD2 surface receptor density, which is shown to strongly affect the binding of DNA with varying degrees of methylation, improving both the selectivity and the affinity of DNAs with higher numbers of methylation sites. Histidine-10-tagged MBD2 was immobilized on gold surfaces with receptor density control by tuning the amount of nickel nitrilotriacetic acid (NiNTA)-functionalized thiols in a thiol-based self-assembled monolayer. The required MBD2 surface receptor densities for DNA surface binding decreases for DNA with higher degrees of methylation. Both higher degrees of superselectivity and surface coverages were observed upon DNA binding at increasing methylation levels. Adopting the findings of this study into hmDNA enrichment of clinical samples has the potential to become more selective and sensitive than current MBD2-based methods and, therefore, to improve cancer diagnostics.
Collapse
Affiliation(s)
- Ruben
W. Kolkman
- Molecular
Nanofabrication Group, Department for Molecules & Materials, MESA+
Institute, Faculty of Science and Technology, University of Twente, P.O. Box 217, 7500 AE Enschede, The Netherlands
- BIOS
Lab on a Chip Group, MESA+ Institute and TechMed Centre, Max Planck
Institute for Complex Fluid Dynamics, Faculty of Electrical Engineering,
Mathematics and Computer Science, University
of Twente, P.O. Box 217, 7500 AE Enschede, The Netherlands
| | - Sandra Michel-Souzy
- Biomolecular
Nanotechnology Group, Department for Molecules & Materials, MESA+
Institute, Faculty of Science and Technology, University of Twente, P.O. Box 217, 7500 AE Enschede, The Netherlands
| | - Dorothee Wasserberg
- BIOS
Lab on a Chip Group, MESA+ Institute and TechMed Centre, Max Planck
Institute for Complex Fluid Dynamics, Faculty of Electrical Engineering,
Mathematics and Computer Science, University
of Twente, P.O. Box 217, 7500 AE Enschede, The Netherlands
| | - Loes I. Segerink
- BIOS
Lab on a Chip Group, MESA+ Institute and TechMed Centre, Max Planck
Institute for Complex Fluid Dynamics, Faculty of Electrical Engineering,
Mathematics and Computer Science, University
of Twente, P.O. Box 217, 7500 AE Enschede, The Netherlands
| | - Jurriaan Huskens
- Molecular
Nanofabrication Group, Department for Molecules & Materials, MESA+
Institute, Faculty of Science and Technology, University of Twente, P.O. Box 217, 7500 AE Enschede, The Netherlands
| |
Collapse
|
2
|
Shim WC, Woo S, Park JW. Nanoscale Force-Mapping-Based Quantification of Low-Abundance Methylated DNA. NANO LETTERS 2022; 22:1324-1330. [PMID: 35080393 DOI: 10.1021/acs.nanolett.1c04637] [Citation(s) in RCA: 2] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 06/14/2023]
Abstract
Methylation changes at cytosine-guanine dinucleotide (CpG) sites in genes are closely related to cancer development. Thus, detection and quantification of low-abundance methylated DNA is critical for early diagnosis. Here, we report an atomic force microscopy (AFM)-based quantification method for DNA that contains methyl-CpG at a specific site, without any treatment to the target DNA such as chemical labeling, fluorescence tagging, or amplification. We employed AFM-tip-tethered methyl-CpG-binding proteins to probe surface-captured methylated DNA. We observed a linear correlation (R2 = 0.982) between the input copy number and detected copy number, in the low copy number regime (10 or fewer; subattomolar concentrations). For a mixture of methylated and nonmethylated DNA that resembles clinical samples, we were still able to quantify the methylated DNA. These results highlight the potential of our force-mapping-based quantification method for wide applications in early detection of diseases associated with methylated DNA.
Collapse
Affiliation(s)
- Woo Cheol Shim
- Department of Chemistry, Pohang University of Science and Technology, 77 Cheongam-Ro, Nam-Gu, Pohang 37673, Republic of Korea
| | - Sungwook Woo
- 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
| |
Collapse
|
3
|
Meanor JN, Keung AJ, Rao BM. Modified Histone Peptides Linked to Magnetic Beads Reduce Binding Specificity. Int J Mol Sci 2022; 23:ijms23031691. [PMID: 35163614 PMCID: PMC8836101 DOI: 10.3390/ijms23031691] [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] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/28/2021] [Revised: 01/20/2022] [Accepted: 01/29/2022] [Indexed: 12/03/2022] Open
Abstract
Histone post-translational modifications are small chemical changes to the histone protein structure that have cascading effects on diverse cellular functions. Detecting histone modifications and characterizing their binding partners are critical steps in understanding chromatin biochemistry and have been accessed using common reagents such as antibodies, recombinant assays, and FRET-based systems. High-throughput platforms could accelerate work in this field, and also could be used to engineer de novo histone affinity reagents; yet, published studies on their use with histones have been noticeably sparse. Here, we describe specific experimental conditions that affect binding specificities of post-translationally modified histones in classic protein engineering platforms and likely explain the relative difficulty with histone targets in these platforms. We also show that manipulating avidity of binding interactions may improve specificity of binding.
Collapse
Affiliation(s)
- Jenna N. Meanor
- Department of Chemical and Biomolecular Engineering, North Carolina State University, Campus Box 7905, Raleigh, NC 27606, USA;
| | - Albert J. Keung
- Department of Chemical and Biomolecular Engineering, North Carolina State University, Campus Box 7905, Raleigh, NC 27606, USA;
- Correspondence: (A.J.K.); (B.M.R.)
| | - Balaji M. Rao
- Department of Chemical and Biomolecular Engineering, North Carolina State University, Campus Box 7905, Raleigh, NC 27606, USA;
- Golden LEAF Biomanufacturing Training and Education Center (BTEC), North Carolina State University, Raleigh, NC 27695, USA
- Correspondence: (A.J.K.); (B.M.R.)
| |
Collapse
|
4
|
Effects of SCFA on the DNA methylation pattern of adiponectin and resistin in high-fat-diet-induced obese male mice. Br J Nutr 2018; 120:385-392. [PMID: 29925443 DOI: 10.1017/s0007114518001526] [Citation(s) in RCA: 28] [Impact Index Per Article: 4.7] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/15/2022]
Abstract
Specific adipokines, such as adiponectin and resistin, are secreted from adipose tissue and are associated with the development of obesity. Supplementation of dietary SCFA can prevent and reverse high-fat-diet (HFD)-induced obesity. However, it is not clear whether SCFA ameliorate abnormal expression of adiponectin and resistin in the obese state. The aim of this study was to investigate the effects of SCFA on adiponectin and resistin's expressions in diet-induced obese mice, as well as the potential mechanisms associated with DNA methylation. C57BL/6J male mice were fed for 16 weeks with five types of HFD (34·9 % fat by wt., 60 % kJ) - a control HFD and four HFD with acetate (HFD-A), propionate (HFD-P), butyrate (HFD-B) and their admixture (HFD-SCFA). Meanwhile, a low-fat diet (4·3 % fat by wt., 10 % kJ) was used as the control group. The reduced mRNA levels of adiponectin and resistin in the adipose tissue of the HFD-fed mice were significantly reversed by dietary supplementation of acetate, propionate, butyrate or their admixture to the HFD. Moreover, the expressional changes of adiponectin and resistin induced by SCFA were associated with alterations in DNA methylation at their promoters, which was mediated by reducing the expressions of enzyme-catalysed DNA methyltransferase (DNMT1, 3a, 3b) and the methyl-CpG-binding domain protein 2 (MBD2) and suppressing the binding of these enzymes to the promoters of adiponectin and resistin. Our results indicate that SCFA may correct aberrant expressions of adiponectin and resistin in obesity by epigenetic regulation.
Collapse
|
5
|
Kumar N, Hori Y, Kikuchi K. Live-Cell Imaging of DNA Methylation Based on Synthetic-Molecule/Protein Hybrid Probe. CHEM REC 2018; 18:1672-1680. [PMID: 29863802 DOI: 10.1002/tcr.201800039] [Citation(s) in RCA: 8] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/05/2018] [Accepted: 05/18/2018] [Indexed: 12/15/2022]
Abstract
The epigenetic modification of DNA involves the conversion of cytosine to 5-methylcytosine, also known as DNA methylation. DNA methylation is important in modulating gene expression and thus, regulating genome and cellular functions. Recent studies have shown that aberrations in DNA methylation are associated with various epigenetic disorders or diseases including cancer. This stimulates great interest in the development of methods that can detect and visualize DNA methylation. For instance, fluorescent proteins (FPs) in conjugation with methyl-CpG-binding domain (MBD) have been employed for live-cell imaging of DNA methylation. However, the FP-based approach showed fluorescence signals for both the DNA-bound and -unbound states and thus differentiation between these states is difficult. Synthetic-molecule/protein hybrid probes can provide an alternative to overcome this restriction. In this article, we discuss the synthetic-molecule/protein hybrid probe that we developed recently for live-cell imaging of DNA methylation, which exhibited fluorescence enhancement only after binding to methylated DNA.
Collapse
Affiliation(s)
- Naresh Kumar
- Graduate School of Engineering, Osaka University Suita, Osaka, 565-0871, Japan
| | - Yuichiro Hori
- Graduate School of Engineering, Osaka University Suita, Osaka, 565-0871, Japan.,Immunology Fontier Research Center, Osaka University Suita, Osaka, 565-0871, Japan
| | - Kazuya Kikuchi
- Graduate School of Engineering, Osaka University Suita, Osaka, 565-0871, Japan.,Immunology Fontier Research Center, Osaka University Suita, Osaka, 565-0871, Japan
| |
Collapse
|
6
|
Sperlazza MJ, Bilinovich SM, Sinanan LM, Javier FR, Williams DC. Structural Basis of MeCP2 Distribution on Non-CpG Methylated and Hydroxymethylated DNA. J Mol Biol 2017; 429:1581-1594. [PMID: 28450074 DOI: 10.1016/j.jmb.2017.04.009] [Citation(s) in RCA: 26] [Impact Index Per Article: 3.7] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/22/2016] [Revised: 04/03/2017] [Accepted: 04/18/2017] [Indexed: 10/19/2022]
Abstract
The Rett-syndrome-associated methyl-CpG-binding protein 2 (MeCP2) selectively binds methylated DNA to regulate transcription during the development of mature neurons. Like other members of the methyl-CpG-binding domain (MBD) family, MeCP2 functions through the recognition of symmetrical 5-methylcytosines in CpG (mCG) dinucleotides. Advances in base-level resolution epigenetic mapping techniques have revealed, however, that MeCP2 can bind asymmetrically methylated and hydroxymethylated CpA dinucleotides and that this alternative binding selectivity modifies gene expression in the developing mammalian brain. The structural determinants of binding to methylated CpA (mCA) and hydroxymethylated DNA have not been previously investigated. Here, we employ isothermal titration calorimetry and NMR spectroscopy to characterize MeCP2 binding to methylated and hydroxymethylated mCG and mCA DNA, examine the effects of Rett-syndrome-associated missense mutations, and make comparisons to the related and evolutionarily most ancient protein, MBD2. These analyses reveal that MeCP2 binds mCA with high affinity in a strand-specific and orientation-dependent manner. In contrast, MBD2 does not show high affinity or methyl-specific binding to mCA. The Rett-associated missense mutations (T158M, R106W, and P101S) destabilize the MeCP2 MBD and disrupt the recognition of mCG and mCA equally. Finally, hydroxymethylation of a high-affinity mCA site does not alter the binding properties, whereas hemi-hydroxylation of the equivalent cytosine in an mCG site decreases affinity and specificity. Based on these findings, we suggest that MeCP2 recognition of methylated/hydroxymethylated CpA dinucleotides functions as an epigenetic switch redistributing MeCP2 among mCG and mCA loci.
Collapse
Affiliation(s)
- M Jeannette Sperlazza
- Department of Pathology and Laboratory Medicine, University of North Carolina School of Medicine, Chapel Hill, NC 27599, USA.
| | - Stephanie M Bilinovich
- Department of Pathology and Laboratory Medicine, University of North Carolina School of Medicine, Chapel Hill, NC 27599, USA.
| | - Leander M Sinanan
- Department of Pathology and Laboratory Medicine, University of North Carolina School of Medicine, Chapel Hill, NC 27599, USA
| | - Fatima R Javier
- Department of Physiology and Biophysics, Case Western Reserve University, Cleveland, OH 44106, USA.
| | - David C Williams
- Department of Pathology and Laboratory Medicine, University of North Carolina School of Medicine, Chapel Hill, NC 27599, USA.
| |
Collapse
|
7
|
Mei M, Zhou Y, Peng W, Yu C, Ma L, Zhang G, Yi L. Application of modified yeast surface display technologies for non-Antibody protein engineering. Microbiol Res 2017; 196:118-128. [DOI: 10.1016/j.micres.2016.12.002] [Citation(s) in RCA: 12] [Impact Index Per Article: 1.7] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/29/2016] [Revised: 10/21/2016] [Accepted: 12/09/2016] [Indexed: 02/07/2023]
|
8
|
Tarn BE, Sung KJ, Sikes HD. Engineering affinity agents for the detection of hemi-methylated CpG sites in DNA. MOLECULAR SYSTEMS DESIGN & ENGINEERING 2016; 1:273-277. [PMID: 28580176 PMCID: PMC5450655 DOI: 10.1039/c6me00073h] [Citation(s) in RCA: 3] [Impact Index Per Article: 0.4] [Reference Citation Analysis] [Abstract] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 06/07/2023]
Abstract
Wild-type methyl-CpG-binding domain (MBD) proteins specifically bind symmetrically methylated DNA sequences, and assays have been developed that use these proteins for profiling DNA methylation. Here, we use directed evolution in the yeast surface display format to identify a new protein variant that binds hemi-methylated CpG dinucleotides.
Collapse
Affiliation(s)
- B E Tarn
- Department of Chemical Engineering, Massachusetts Institute of Technology, 77 Massachusetts Avenue, Cambridge, MA, 02139, USA
| | - K-J Sung
- Department of Chemical Engineering, Massachusetts Institute of Technology, 77 Massachusetts Avenue, Cambridge, MA, 02139, USA
| | - H D Sikes
- Department of Chemical Engineering, Massachusetts Institute of Technology, 77 Massachusetts Avenue, Cambridge, MA, 02139, USA
| |
Collapse
|
9
|
McCarthy D, Pulverer W, Weinhaeusel A, Diago OR, Hogan DJ, Ostertag D, Hanna MM. MethylMeter(®): bisulfite-free quantitative and sensitive DNA methylation profiling and mutation detection in FFPE samples. Epigenomics 2016; 8:747-65. [PMID: 27337298 DOI: 10.2217/epi-2016-0004] [Citation(s) in RCA: 4] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Abstract] [Key Words] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/21/2022] Open
Abstract
AIM Development of a sensitive method for DNA methylation profiling and associated mutation detection in clinical samples. MATERIALS & METHODS Formalin-fixed and paraffin-embedded tumors received by clinical laboratories often contain insufficient DNA for analysis with bisulfite or methylation sensitive restriction enzymes-based methods. To increase sensitivity, methyl-CpG DNA capture and Coupled Abscription PCR Signaling detection were combined in a new assay, MethylMeter(®). Gliomas were analyzed for MGMT methylation, glioma CpG island methylator phenotype and IDH1 R132H. RESULTS MethylMeter had 100% assay success rate measuring all five biomarkers in formalin-fixed and paraffin-embedded tissue. MGMT methylation results were supported by survival and mRNA expression data. CONCLUSION MethylMeter is a sensitive and quantitative method for multitarget DNA methylation profiling and associated mutation detection. The MethylMeter-based GliomaSTRAT assay measures methylation of four targets and one mutation to simultaneously grade gliomas and predict their response to temozolomide. This information is clinically valuable in management of gliomas.
Collapse
Affiliation(s)
- David McCarthy
- Ribomed Biotechnologies Inc., 3469 Kurtz St., San Diego, CA 92110, USA
| | - Walter Pulverer
- Molecular Diagnostics, Health & Environment Department, Austrian Institute of Technology, Muthgasse 11, 1190 Vienna, Austria
| | - Andreas Weinhaeusel
- Molecular Diagnostics, Health & Environment Department, Austrian Institute of Technology, Muthgasse 11, 1190 Vienna, Austria
| | - Oscar R Diago
- Tocagen Inc., 3030 Bunker Hill Street, Suite 230; San Diego, CA 92109, USA
| | - Daniel J Hogan
- Tocagen Inc., 3030 Bunker Hill Street, Suite 230; San Diego, CA 92109, USA
| | - Derek Ostertag
- Tocagen Inc., 3030 Bunker Hill Street, Suite 230; San Diego, CA 92109, USA
| | - Michelle M Hanna
- Ribomed Biotechnologies Inc., 3469 Kurtz St., San Diego, CA 92110, USA
| |
Collapse
|