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Differentially methylated sequences in pancreatic cancer

a differential methylation and pancreatic cancer technology, applied in the field of gene expression regulation, can solve the problems of not well understood whether this global aberrant methylation is global, unclear role of abnormal dna methylation in human tumorigenesis, and inability to fully understand the global aberrant methylation. , to achieve the effect of increasing the likelihood of finding genes methylated in a particular cancer, increasing the sensitivity and specificity of methylation detection, and increasing the likelihood o

Inactive Publication Date: 2005-03-31
THE JOHNS HOPKINS UNIVERSITY SCHOOL OF MEDICINE
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  • Summary
  • Abstract
  • Description
  • Claims
  • Application Information

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Benefits of technology

[0014] The present invention is based on the finding that several genes are newly identified as being differentially methylated in cancer. This seminal discovery is useful for cancer screening, risk-assessment, prognosis, minimal-residual disease identification, staging and identification of therapeutic targets. The identification of new genes that are methylated in cancer, aging or diseases associated with aging increases the likelihood of finding genes methylated in a particular cancer; increases the sensitivity and specificity of methylation detection; allows methylation profiling using multiple genes; and allows identification of new targets for therapeutic intervention. The invention also provides a newly identified gene that is a target for hypermethylation in human tumors.

Problems solved by technology

However, the precise role of abnormal DNA methylation in human tumorigenesis has not been established.
However, an understanding of aberrant methylation in CRC has been somewhat limited by the small number of CGIs analyzed to date.
In fact, previous studies have suggested that large numbers of CGIs are methylated in immortalized cell lines, and it is not well understood whether this global aberrant methylation is caused by the cell culture conditions or whether they are an integral part of the pathogenesis of cancer.
Genomic sequencing protocols which identify a 5-MeC residue in genomic DNA as a site that is not cleaved by any of the Maxam Gilbert sequencing reactions have also been used, but still suffer disadvantages such as the requirement for large amount of genomic DNA and the difficulty in detecting a gap in a sequencing ladder which may contain bands of varying intensity.
This method provides an assessment of the overall methylation status of CpG islands, including some quantitative analysis, but is relatively insensitive and requires large amounts of high molecular weight DNA.
However, this method is technically difficult, labor intensive and without cloning amplified products, it is less sensitive than Southern analysis, requiring approximately 10% of the alleles to be methylated for detection.

Method used

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Examples

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example 1

Collection and Preparation of Pancreatic Cell Lines

[0096] The following pancreatic adenocarcinoma cell lines were used: PL3 and PL8 (both CIMP-cell lines (CpG island methylator phenotype) were from Dr. Elizabeth Jaffe, John Hopkins University); CAPAN1, CAPAN2, Panc1, Hs766T, and MiaPaca2 (from the American Type Culture Collection, Rockville, Md.) and Colo357 (from the European Collection of Animal Cell Cultures, Salisbury, United Kingdom). In addition, seventeen pancreatic cancer xenografts were selected at random from a total of 90 xenografts, which were established from the primary carcinomas as described in Ueki, et al., Cancer Res., 60:1835-1839, 2000. Forty-seven primary pancreatic adenocarcinomas, 15 normal pancreata, 5 pancreata from patients with chronic pancreatitis, and a panel of normal tissues were obtained from the resected surgical specimens at The Johns Hopkins Medical Institutions, Baltimore, Md. Frozen tissues or paraffin-embedded tissues were microdissected to obt...

example 2

Methylated CpG Island Amplification / Representational Difference Analysis (MCA / RDA)

[0097] MCA / RDA was performed as described by Toyota et al., Cancer Res., 59:2307-2312, 1999, modifying such procedure to increase the efficiency by digesting 5 μg of DNA with SmaI and XmaI (New England Biolabs). The restriction fragments were then ligated to RMCA adapter and amplified by PCR in 10 mM Tris-HCl (pH 8.3), 1.5 mM MgCl2, 50 mM KCl, 0.5 M betaine, 2% DMSO, 200 μM each deoxynucleotide triphosphate, 100 μmol of RMCA 24mer primer and 15 units of Taq polymerase (Life Technologies, Inc.) in a final reaction volume of 100 μl. The reaction mixture was then incubated at 72° C. for 5 min and at 95° C. for 3 min, and then subjected to 25 cycles of 1 min at 95° C. and 3 min at 77° C. followed by a final extension of 10 min at 77° C. Betaine was included in the PCR reaction to help amplify the methylated templates at a higher annealing temperature (77° C.). The combination of betaine and DMSO can unifo...

example 3

DNA Sequencing of Clones and Dot Blot Hybridization

[0098] The clones recovered from each cell line after MCA / RDA were amplified with T3 and T7 primers and then sequenced using KS primer as recommended by the manufacturer (Sequitherm Excel; Epicentre Technologies). To determine the methylation status of MCA / RDA MICPs in pancreatic cancer and normal pancreas, MICPs were screened by hybridizing them to a dot blot of MCA products of pancreatic cancers and normal pancreata. Plasmid DNA containing each independent clone was prepared and digested with SmaI. DNA fragments were recovered from agarose gel and used as a probe for dot blot hybridization. Aliquots (1 μl) of the mixture of 10×SSC and MCA products from the driver and from the tester (PL3 and PL8) both before and after each of the three rounds of RDA competitive hybridization / selective amplification were blotted onto nylon membranes in duplicate. Similarly, MCA products from six pancreatic cell lines (CAPAN1, CAPAN2, Panc1, Hs766T...

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Abstract

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.

Description

RELATED APPLICATIONS [0001] This application claims priority under 35 U.S.C. §119(e) to U.S. Provisional Application Ser. No. 60 / 271,268, filed Feb. 23, 2001, which is herein incorporated by reference in its entirety.FIELD OF THE INVENTION [0002] The present invention relates generally to the regulation of gene expression and more specifically to a method of determining the DNA methylation status of CpG sites in a given locus and correlating the methylation status with the presence of a cell proliferative disorder. BACKGROUND OF THE INVENTION [0003] DNA methylases transfer methyl groups from the universal methyl donor S-adenosyl methionine to specific sites on the DNA. Several biological functions have been attributed to the methylated bases in DNA. The most established biological function for methylated DNA is the protection of DNA from digestion by cognate restriction enzymes. The restriction modification phenomenon has, so far, been observed only in bacteria. Mammalian cells, how...

Claims

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Application Information

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Patent Type & Authority Applications(United States)
IPC IPC(8): G01N33/50C07H21/04C07K14/00C07K14/47C12N9/10C12N9/22C12N15/09C12P19/34C12Q1/68C12Q1/6886
CPCC12Q2600/156C12Q1/6886
Inventor GOGGINS, MICHAELUEKI, TAKASHI
Owner THE JOHNS HOPKINS UNIVERSITY SCHOOL OF MEDICINE
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