51 results about "Aberrant methylation" patented technology

A molecular marker-based method for monitoring and detecting cancer in humans. Aberrant methylation of gene promoters is a marker for cancer risk in humans. A two-stage, or "nested" polymerase chain reaction method is disclosed for detecting methylated DNA sequences at sufficiently high levels of sensitivity to permit cancer screening in biological fluid samples, such as sputum, obtained non-invasively. The method is for detecting the aberrant methylation of the p16 gene, O 6-methylguanine-DNA methyltransferase gene, Death-associated protein kinase gene, RAS-associated family 1 gene, or other gene promoters. The method offers a potentially powerful approach to population-based screening for the detection of lung and other cancers.

The present invention provides a method for detecting pancreatic carcinoma in a subject. The method includes contacting a nucleic acid-containing specimen from the subject with an agent that provides a determination of the methylation state of at least one gene or associated regulatory region of the gene and identifying aberrant methylation of regions of the gene or regulatory region, wherein aberrant methylation is identified as being different when compared to the same regions of the gene or associated regulatory region in a subject not having the pancreatic carcinoma, thereby detecting pancreatic carcinoma in the subject.

Compounds and compositions of azacytosine analogs and derivatives are provided. In one aspect of the invention, analogs or derivatives of decitabine and azacitidine are provided with modification at the 2-, 4-, or 6-position of the triazine ring, at the 1′-6′position of the ribose ring, or combinations thereof. Methods of using, synthesizing and manufacturing these analogs and derivatives are also provided. These compounds can be formulated into pharmaceutical compositions that can be used for treating any disease associated with aberrant DNA methylation, or a disease or condition that is sensitive to the treatment with decitabine or azacitidine, such as hematological disorders, tumors and cancers.

Methods are provided for treating patients with epigenetic diseases, especially those associated with aberrant DNA methylation such as hematological disorders and cancer. By administering a DNA methylation inhibitor to the patients following unique dosing regimens, the disease can be efficaciously treated with reduced toxic side effects.

The present invention provides a method for detecting pancreatic carcinoma in a subject. The method includes contacting a nucleic acid-containing specimen from the subject with an agent that provides a determination of the methylation state of at least one gene or associated regulatory region of the gene and identifying aberrant methylation of regions of the gene or regulatory region, wherein aberrant methylation is identified as being different when compared to the same regions of the gene or associated regulatory region in a subject not having the pancreatic carcinoma, thereby detecting pancreatic carcinoma in the subject.

A molecular marker-based method for monitoring and detecting cancer in humans. Aberrant methylation of gene promoters is a marker for cancer risk in humans. A two-stage, or “nested” polymerase chain reaction method is disclosed for detecting methylated DNA sequences at sufficiently high levels of sensitivity to permit cancer screening in biological fluid samples, such as sputum, obtained non-invasively. The method is for detecting the aberrant methylation of the p16 gene, O 6-methylguanine-DNA methyltransferase gene, Death-associated protein kinase gene, RAS-associated family 1 gene, or other gene promoters. The method offers a potentially powerful approach to population-based screening for the detection of lung and other cancers.

In sporadic Alzheimer's disease, neurofibrillary lesion formation is preceded by extensive post-translational modification of the microtubule associated protein tau. Immunoassays have been developed recently that detect tau in biological specimens, thus providing a means for pre-mortem diagnosis of Alzheimer's disease, which has remained elusive. These assays have been improved by the analysis of relevant post-translational modifications, such as phosphorylation, however opportunity for improvement remains. The present invention addresses this issue by disclosing synthetic methylated peptides derived from the tau protein of paired helical filaments and non-diseased control brain. Alzheimer's disease specificity is provided by the presence or absence of methyl moieties on lysine residues and differences between mono-, di-, and tri-methylation. The methylated peptide is useful as an antigen and a binding partner for identifying compounds that interact with the peptide and the methylated tau protein, including antibodies that can distinguish non-diseased brain from that affected by Alzheimer's disease. The resulting antibodies are useful diagnostically and therapeutically. The compounds that specifically bind to methylated tau proteins are useful for eliminating abnormally methylated tau.

The invention belongs to the technical field of biomedicine. Based on the fact that the abnormal methylation of genes are involved in the generation and development of tumors, the invention aims to overcome the defects of a methylation sensitive restriction enzyme method, a bisulfite sequencing method and a methylation specificity PCR (Polymerase Chain Reaction) method, and provide a methylation quantitative detection method of the PCDH8 (Protocadherin-8) gene, with simple and convenient operation and high sensitivity. The detection method comprises the steps of: taking pancreatic cancer tissues, extracting DNA to prepare a standard curve sample of ACTB (Actin, Beta), and preparing a standard curve sample of PCDH8; extracting the DNA of a tissue to be detected, carrying out chemical decoration, designing a methylation primer and a probe for a CPG island in a human PCDH8 gene promoter area, and designing a BSP primer and a probe for a CPG island in a human reference gene ACTB promoter area, carrying out real-time quantitative PCR on the DNA subjected to the sulfite treatment by using a Taqman-MGB real-time quantitative PCR method, and calculating out a quantitative value on the methylation degree of a PCDH8 gene. The method has the advantages of rapidness, correctness and high sensitivity.

The present invention provides a method for analysis methylation patterns in DNA and identifying aberrantly methylated genes in disease tissue. The invention also provides a method of identifying novel targets for therapeutic intervention and disease markers. Novel cancer targets are provided.

The invention is directed to a method of diagnosing a cell proliferative disorder of breast tissue by determining the methylation status of nucleic acids obtained from a subject. Aberrant methylation of several genes including TWIST, HOXA5, NES-1, retinoic acid receptor beta (RARβ), estrogen receptor (ER), cyclin D2, WT-1, 14.3.3 sigma, HIN-1, RASSF1A, and combinations of such genes serve as markers of breast malignancy.

Methods for detecting the methylation status of a target genomic locus are provided. Methods described allow for simultaneous assay of multiple cytosines in a target genomic locus. Assays of multiple cytosines in a target genomic locus provide detection of an aggregate cytosine methylation state of the target genomic locus. Methods to detect methylation of a genomic locus associated with a disease or disorder characterized by aberrant methylation of the genomic locus, such as, but not limited to, Fragile X mental retardation syndrome, Prader-Willi syndrome, Angelman sydrome, Beckwith-Wiedemann syndrome, and Russell-Silverman syndrome, diabetes, cancer, multiple sclerosis or schizophrenia are described herein.

The invention belongs to the technical field of biomedicine. The abnormal methylation of genes participates in the occurrence and the development of tumors. The invention aims at overcoming the defects of the methylation sensitivity restriction enzyme method, the bisulfite sequencing method and the methylation specificity PCR (Polymerase Chain Reaction) method and providing an LRRC55 gene methylation quantitative detection method with easy and simple operation and high sensitivity. The method comprises the following steps of: taking a pancreatic cancer tissue, extracting DNA, preparing a standard curve sample of ACTB (Actin, Beta), and preparing a standard curve sample of LRRC55 by using a complete methylation template; extracting the DNA of a tissue to be tested, performing chemical modification, designing a methylation primer and probe aiming at the CpG island of a promoter region of the human LRRC55 gene, designing a BSP primer and probe aiming at the CPG island of a promoter region of human reference gene ACTB, performing real-time quantitative PCR on the DNA treated by sulfite by using the Tagman-MGB real-time quantitative PCR method, and calculating the quantitative value of the methylation degree of the LRRC55 gene. The method is rapid and accurate and is high in sensitivity.

The present invention provides a method for detecting a cellular proliferative disorder in a subject. The method includes contacting a nucleic acid-containing specimen from the subject with an agent that provides a determination of the methylation state of at least one gene or associated regulatory region of the gene and identifying aberrant methylation of regions of the gene or regulatory region, wherein aberrant methylation is identified as being different when compared to the same regions of the gene or associated regulatory region in a subject not having said cellular proliferative, thereby detecting a cellular proliferative disorder in the subject.

This application describes methods and compositions for detecting and treating C6Orf150-associated neoplasia. Differential methylation of the C6Orf150 nucleotide sequences has been observed in C6Orf150-associated neoplasia such as colon neoplasia.

The present invention provides a method and single-tube assay for identification and quantitative analysis of differentially methylated MLH1 promoter sequences that are associated with certain types of cancer in an individual by obtaining a biological sample comprising DNA from the individual, detecting the presence of and measuring the level of methylated MLH1 promoter sequences, and comparing the presence of and level of methylation in the sample to a normalization reference of “normal” beta-actin gene promoters, wherein a difference in the level or pattern of MLH1 methylation of the sample compared to the Actin gene reference level identifies abnormally methylated MLH1 promoter sequences associated with cancer.

Compositions and methods are provided for facilitating the enrichment of single-stranded DNA containing methylated CpG in a mixture containing methylated and unmethylated DNA. The compositions relate to methylation-binding protein domains that selectively bind to methylated single strand DNA. In embodiments of the invention, the methylated DNA is eluted in 0.4M-0.6M NaCl while the unmethylated single strand DNA is eluted in less than 0.4M salt. The ability to readily enrich for methylated DNA permits high throughput sequencing of the methylated DNA and identification of abnormal methylation patterns associated with disease.

The invention is directed to a method of diagnosing a cell proliferative disorder of breast tissue by determining the methylation status of nucleic acids obtained from a subject. Aberrant methylation of several genes including TWIST, HOXA5, NES-1, retinoic acid receptor beta (RARβ), estrogen receptor (ER), cyclin D2, WT-1, 14.3.3 sigma, HIN-1, RASSF1A, and combinations of such genes serve as markers of breast malignancy.

The invention is directed to a method of diagnosing a cell proliferative disorder of breast tissue by determining the methylation status of nucleic acids obtained from a subject. Aberrant methylation of several genes including TWIST, HOXA5, NES-1, retinoic acid receptor beta (RARβ), estrogen receptor (ER), cyclin D2, WT-1, 14.3.3 sigma, HIN-1, RASSF1A, and combinations of such genes serve as markers of breast malignancy.

The invention belongs to the technical field of biomedical sciences. Abnormal methylation of genes participates in the development of tumors. The invention aims at overcoming the defects of a methylation-sensitive restrictive endonuclease method, a bisulfite sequencing method and a methylation-specific PCR (Polymerase Chain Reaction) method and provides a methylated quantitative detection method of a GSH2 (glutathione 2) gene, which has simple and convenient operation and high senibilitiy. The method comprises the following steps of: taking pancreatic cancer tissues, extracting DNA and preparing an ACTB (Actin, Beta) standard curve sample, and preparing a GSH2 (Glutathione 2) standard curve sample by utilizing a full methylation template; extracting DNA of tissues to be detected, and carrying out chemical modification; designing methylation primers and probes aiming at CPG islands at a human GSH2 gene promoter region, designing BSP (Bisulfite) primers and probes aiming at CPG islands at a human reference gene ACTB promoter region, carrying out real-time quantitive PCR on DNA after bisulfite treatment by adopting a Taqman-MGB real-time quantitive PCR method, and calculating a quantitive value of the GSH2 gene methylation degree. The method is rapid, accurate and high in sensitivity.

The invention discloses a method for setting a primer used in a detection method of abnormal methylation of upstream CpG island of fragile X chromosome syndrome FMR1 gene. The designed position of an amplification primer does not cover any CG dinucleotide to ensure that PCR amplification treated by a hydrosulphite has no bias. The method is specifically as follows: a pair of amplification primers designed for the upstream CpG island area of the FMR1 gene: PyroAF: TGAGTGTATTTTTGTAGAAATGGG, PyroAR: TCTCTCTTCAAATAACCTAAAAAC. The invention further provides a method for detecting fragile X syndrome by quantitatively comparing the methylation level of the CpG island stably and quickly. By adopting the method, the defects that the existing method for quantitatively detecting abnormal methylation of a FMR1 promoter is still not mature and especially cannot achieve quantitative detection of a single CpG site are solved.

The present invention provides a method for detecting a cellular proliferative disorder in a subject. The method includes contacting a nucleic acid-containing specimen from the subject with an agent that provides a determination of the methylation state of at least one gene or associated regulatory region of the gene and identifying aberrant methylation of regions of the gene or regulatory region, wherein aberrant methylation is identified as being different when compared to the same regions of the gene or associated regulatory region in a subject not having said cellular proliferative, thereby detecting a cellular proliferative disorder in the subject.

The invention relates to the field of biotechnology, in particular to a macrophage polarization inhibitor and application thereof. A macrophage polarization inhibitor Dnmt3aos, a kit containing the inhibitor Dnmt3aos claimed in Claim 1 and the application of the macrophage polarization inhibitor Dnmt3aos are provided. The Dnmt3aos plays a crucial role in macrophage polarization, Dnmt3aos-Dnmt3a axis-mediated DNA aberrant methylation may play a key role in the macrophage polarization, and the inhibitor enriches the understanding of the macrophage polarization mechanism and provides theoreticaldata support for studying the macrophage polarization.

Compositions and methods are provided for facilitating the enrichment of single-stranded DNA containing methylated CpG in a mixture containing methylated and unmethylated DNA. The compositions relate to methylation-binding protein domains that selectively bind to methylated single strand DNA. In embodiments of the invention, the methylated DNA is eluted in 0.4M-0.6M NaCl while the unmethylated single strand DNA is eluted in less than 0.4M salt. The ability to readily enrich for methylated DNA permits high throughput sequencing of the methylated DNA and identification of abnormal methylation patterns associated with disease.

The present invention provides a method for analysis methylation patterns in DNA and identifying aberrantly methylated genes in disease tissue. The invention also provides a method of identifying novel targets for therapeutic intervention and disease markers. Novel cancer targets are provided.

The invention belongs to the technical field of biomedicine. The abnormal methylation of the gene participates in the occurrence and the development of tumors, therefore, the invention aims at overcoming the defects of a methylation sensitive restriction enzyme method, a bisulfite sequencing method and a methylation specificity PCR method, and providing a quantitative detection method of HPP1 genemethylation with convenient operation and high sensitivity. The method comprises the steps of: taking pancreatic cancer tissue; extracting NDA to prepare a standard curve sample of ACTB; using a fullmethylated template to prepare a standard curve sample of HPP1; extracting the DNA of tissue to be tested, and chemically modifying; designing methylated primer and probe by aiming at the human HPP1gene promoter area CPG island; designing BSP primer and probe by aiming at the human reference gene ACTB promoter area CPG island; conducting real-time and quantitative polymerase chain reaction (PCR)to the DNA of processed sulfite by means of Taqman-MGB real-time quantitative PCR method; and counting the quantitative value of the HPP1 gene methylation degree. The method is fast and accurate, andhas high sensitivity.

Provided are systems and methods for cell-free nucleic acid sequencing to assess a condition.Generally, cell-free nucleic acid samples are used to perform methyl sequencing, targeting specific regions associated with abnormal methylation.The methylation of cell-free nucleic acid molecules can be evaluated based on sequencing results.Various features can be derived from methylation evaluation and used in computational models to assess cell-free nucleic acid samples for a condition.

The invention belongs to the technical field of bioinformatics, and particularly relates to a method for detecting abnormal DNA methylation fragments from cell free DNA (cell free DNA, cfDNA) and classifying the abnormal DNA methylation fragments from the cell free DNA, and the method comprises the following steps: based on a healthy cfDNA sample and a tumor cfDNA sample, selecting methylation haplotype regions (Methylation Haplotype Block, MHB) having significant difference between the two samples by adopting seven DNA methylation measurement indexes; on the basis of the selected methylated haplotype regions with significant differences, constructing total distribution of seven DNA methylation measurement indexes in the healthy cfDNA sample and the tumor cfDNA sample, and carrying out differential analysis; seven DNA methylation measurement indexes are adopted to construct classification models for abnormal DNA methylation fragments, and the classification models of the seven abnormal DNA methylation fragments are integrated on the basis of differential analysis results of overall distribution of the seven DNA methylation measurement indexes. According to the application, the abnormal DNA methylation fragments in the cell free DNA are detected by adopting seven DNA methylation measurement indexes, and the abnormal DNA methylation fragment classification model based on the seven DNA methylation measurement indexes is integrated, so that the improvement of the sensitivity of tumor early screening is facilitated.

The present invention provides systems and methods for sequencing cell free nucleic acids to assess a condition. Generally, methylation sequencing for specific regions associated with aberrant methylation is performed using a cell free nucleic acid sample. Based on the results of the sequencing, methylation of the cell free nucleic acid molecule can be assessed. Various features may be derived from methylation assessment and used within a computational model to assess a cell free nucleic acid sample for a condition.

The present invention discloses a method for screening non-small cell lung cancer markers based on enhancer methylation differences, as well as the markers and applications thereof. Abnormal DNA methylation in the enhancer regions of the human genome can lead to abnormal gene expression regulation in non-small cell lung cancer. The method for screening non-small cell lung cancer markers described in the present invention is based on this principle and further combines paired-end tag sequencing analysis of chromatin interaction technology (ChIA-PET) to screen out DNA methylation markers in the genomic enhancer regions that cause abnormal gene expression regulation in non-small cell lung cancer. This screening method has the advantages of accuracy, rapidity, and high throughput. The DNA methylation markers described in the present invention are cg00787780, cg16434331, cg21862081, and cg24327132. The markers have good diagnostic efficacy for non-small cell lung cancer, showing high accuracy, high sensitivity, and strong specificity, and can better help improve the detection rate of non-small cell lung cancer.

The present disclosure discloses a set of novel epigenetic biomarkers for early detection, prediction of treatment response and prognosis of lung cancer. Aberrant methylation of the epigenetic biomarkers can be detected in tumor tissues and plasma samples from lung cancer patients but not in normal individuals. The present disclosure also discloses primers and kits used herein.