WO2003057918A1 - Light-directed molecular analysis for cancer prognosis and diagnosis - Google Patents
Light-directed molecular analysis for cancer prognosis and diagnosis Download PDFInfo
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- WO2003057918A1 WO2003057918A1 PCT/US2002/032073 US0232073W WO03057918A1 WO 2003057918 A1 WO2003057918 A1 WO 2003057918A1 US 0232073 W US0232073 W US 0232073W WO 03057918 A1 WO03057918 A1 WO 03057918A1
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Classifications
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- C—CHEMISTRY; METALLURGY
- C12—BIOCHEMISTRY; BEER; SPIRITS; WINE; VINEGAR; MICROBIOLOGY; ENZYMOLOGY; MUTATION OR GENETIC ENGINEERING
- C12Q—MEASURING OR TESTING PROCESSES INVOLVING ENZYMES, NUCLEIC ACIDS OR MICROORGANISMS; COMPOSITIONS OR TEST PAPERS THEREFOR; PROCESSES OF PREPARING SUCH COMPOSITIONS; CONDITION-RESPONSIVE CONTROL IN MICROBIOLOGICAL OR ENZYMOLOGICAL PROCESSES
- C12Q1/00—Measuring or testing processes involving enzymes, nucleic acids or microorganisms; Compositions therefor; Processes of preparing such compositions
- C12Q1/68—Measuring or testing processes involving enzymes, nucleic acids or microorganisms; Compositions therefor; Processes of preparing such compositions involving nucleic acids
- C12Q1/6876—Nucleic acid products used in the analysis of nucleic acids, e.g. primers or probes
- C12Q1/6883—Nucleic acid products used in the analysis of nucleic acids, e.g. primers or probes for diseases caused by alterations of genetic material
- C12Q1/6886—Nucleic acid products used in the analysis of nucleic acids, e.g. primers or probes for diseases caused by alterations of genetic material for cancer
Definitions
- This invention relates to a combined method for the early location and prognosis of tissue containing potentially invasive cancer cells, before the normal
- the invention relates to a combined method for location and
- tissue containing such potentially invasive cancer cells the normal visual appearance of which is anomalous, which may lead to delay in obtaining a diagnosis
- prognosis or diagnosis the mortality rate risks of cancer would be reduced. Accordingly, I provide prognostic and diagnostic methods for early prediction of eventual development of invasive cancer or for definitive diagnosis, which are stepwise, rapid, conclusive, and readily adaptable as a clinical protocol.
- tumors require two separate mutational events. One of these events may occur in the germline and be inherited. The second then occurs somatically. Alternatively, the two mutational events may occur only in the somatic cell of an individual.
- Saliva contains exfoliated cells that originate from the head and neck region — a large surface area ⁇ that is a common origin of cancer cells, especially in patients who expose these areas to nicotine,
- Tissue containing tumor phenotypes which may indicate the eventual
- Lonky's light source radiates in the visible green, blue, and red
- Lonky can be applied to the surfaces of body cavities, such as mucousal tissues and as well as epithelial discharges.
- the advantages of using the chemilummescent light source include the elimination of a hot light source which can cause the patient discomfort, cellular damage, reduction of visual interference, such as shadowing, and, most importantly, the selective coloration of abnormal tissue which readily distinguishes it from adjacent normal tissue.
- Chemilummescent solutions and the processes for manufacture of the solutions and devices have been described by United States Patents 5,122,306 and 5,194,666.
- Mutations generally result from intramolecular gene reorganization, such as a
- Tumor suppressor genes are often associated with the loss of one chromosome or a part of a chromosome, resulting in a reduction to homozygosity, through elimination of one allele of a tumor suppressor gene as well as surrounding markers. The remaining tumor suppressor allele is inactivated by either an inherited or a somatic mutation.
- Adenomatous polyposis of the colon gene APC
- Familial breast/ovarian cancer genes 1 and 2 BRCA1 and BRCA2
- Cadherin 1 epidermal cadherin or E- cadherin
- CDH1 Cadherin 1 (epithelial cadherin or E- cadherin) gene
- MEM Multiple endocrine neoplasia type 1 gene
- NF1 Neurofibromatosis type 1 gene
- PRKAR1 A Retinoblastoma gene
- RBI Serine/threonine kinase 11
- chromosome loci are predictors of the probable onset of invasive cancer.
- D ⁇ A analysis includes Microsatellite Analysis for determining
- Microsatellites are short repetitive sequences of D ⁇ A that have been observed to
- nucleotide mispairs contain nucleotide mispairs, misalignments, or nucleotide slippage (looping or shortening). Mutations, such as these, are termed microsatellite instability and have
- Sequence detection was accomplished on oligonucleotide microarrays, using a target-directed DNA ligation step coupled to a Rolling Circle Amplification (RCA)
- the DNA ligation step is adaptable to the detection of mRNAs containing point mutations.
- Telomeres are the DNA sequences, which are the specialized complexes at the
- telomeres ends of chromosomes. Telomerase, the ribonucleoprotein that helps maintain telomeres, is inactive in many adult human cell types, but is highly activated in most human cancers. It has been determined that a disruption or mutation in either the
- telomeric DNA or telomerase can uncap the telomere
- telomeres detect either abnormal telomeric nucleotides or abnormal enzymatic activity of telomerase, which are equally associated with the proliferation of pre-cancerous cells.
- Aberrant promoter methylation was recently discovered to be a fundamental molecular abnormality leading to transcriptional silencing of tumor suppressor genes, DNA repair genes and metastasis inhibitor genes, and is linked to the predisposition of genetic alterations of other cancer-associated genes.
- Somatic epigenetic alterations in DNA methylation are tightly linked to development, cell differentiation and neoplastic transformation. For instance,
- methylation alteration provides identification of epigenetic alterations associated with cell differentiation and cancer.
- DNA mutation or loss of heterogeneity can be alternatively detected by measuring DNA methylation. SeeYamamoto, F., Ph.D., "Technology to Detect Genome-wide DNA Methylation Changes", Burnham Institute, http://otir.cancer.gov/tech/imat_awards.html, (November 28, 2001).
- mtDNA mitchondrial DNA
- point mutations in mtDNA by PNA-directed PCR clamping permitted analysis of the presence or absence of, e.g., the A8344G, A3253G and T414G, point mutations in
- mutant mtDNA bands that were detected using a sensitive oligonucleotide-mismatch
- chromosomal expression associated with cancer, can be detected with common
- diagnostic techniques such as genetic, epigenetic, or mitochondrial molecular analysis are not effective early cancer detection methods, because the effectiveness of these techniques directly depend on obtaining tissue samples from the specific tissue sites containing cells which are propagating cancer.
- diagnostic techniques such as genetic, epigenetic, or mitochondrial molecular analysis are not effective early cancer detection methods, because the effectiveness of these techniques directly depend on obtaining tissue samples from the specific tissue sites containing cells which are propagating cancer.
- some of the prior art screening methods are capable of identifying specific sites of suspect cancerous and precancerous tissue, the location and identification of such suspect tissue was, heretofore, generally followed by conventional histological examination of the suspect tissue such as lighted microscopy.
- PCR chain reaction
- Yet another embodiment of the invention includes conducting a saliva screening test to determine whether the patient may or has developed head/neck
- suspect sites to confirm whether the specifically identified suspect tissue contains cells which exhibit characteristics associated with cancer or the eventual development
- molecular analysis means a procedure for identifiying cellular abnormalities which indicate cancer or the probable eventual
- these procedures include those which identify such abnormalities in the genetic code, i.e. DNA or RNA, in epi-genetic patterns, or in
- mtDNA mitochondrial DNA
- Steps 2 - 3 can be applied to any cells capable of visual inspection in
- My method comprises sequentially examining cells to first locate and identify
- Tumor phenotypes include any combination of tumor cells, tumor cells, and tumor cells, and tumor phenotypes.
- Tumor phenotypes include any combination
- mutation e.g. allelic loss, loss of heterogeneity, mutation of tumor suppressor genes, abnormal DNA methylation, or abnormal mtDNA, associated with cancer.
- Step 1 Saliva Screening for Head and Neck Cancer Saliva samples can be collected in a number of ways. It is most important that
- the collection apparatus complies with the requirements of polymerase chain reaction
- the PCR analysis detect an increase or decrease in short repetitive sequences
- microsatellite DNA The microsatellite DNA correspond to an allele because of their location on the DNA. Mutations in microsatellite DNA are found to be most
- PCR is considered a method for nucleic acid amplification which allows for DNA and RNA sequencing
- Step 2 Location by Selective Light Examination
- Step 2 enables a practitioner to precisely locate and select suspect cells in vivo
- Step 3 enabling the practitioner to select suspect tissues from surrounding normal tissue to direct the biopsy procedure for obtaining cells for the molecular analysis, Step 3.
- Another embodiment of the invention employs the in vivo Mashberg Protocol or similar dye-staining selective location protocols as a further adjuct to the initial selective light location step. These selective dye-staining protocols are
- Patent 6,086,852 The protocol employs toluidine blue O (TBO) dye to selectively
- Patent 5,372,801 to Tucci et al incorporated herein by reference.
- Other cationic dyes e.g. Azure B, Azure C and Brilliant Cresyl Blue, have been identified as useful for
- Step3 Molecular Analysis Diagnosis-Prognosis
- Step 3 Molecular Analysis Diagnosis-Prognosis
- Cell samples for molecular analysis are derived from a variety of biopsy techniques, which, in general terms, involve the removal of a small piece of suspect tissue for molecular analysis.
- the method of tissue removal or extraction varies with the various types of biopsies.
- the biopsy sample can comprise portions or skin lesions or isolated blood cells, e.g., erythrocytes, leukocytes, and lymphocytes, parathyroid tissue; salivary gland tissue; nasal mucosal tissue, oropharynx tissue, open lung tissue, small bowel tissues, etc.
- Molecular analysis is then performed to confirm whether the biopsy sample of suspect tissue is cancerous or precancerous.
- the target of molecular analysis i.e., DNA, mRNA, DNA methylation, telemorase activity, or mtDNA analysis is selected based on access to instrumentation, qualified analysts, or the nature of the cell sample.
- the molecular analysis of the cell sample entails a choice among various procedures. Gel electrophoresis, the polymerase chain reaction (PCR) based chemistry, Rolling Circle Amplification (RCA) unimolecular detection system, flourescence tagging, immunohistochemical staining, mass spectroscopy, and colorimetry are representative examples of effective molecular analysis procedures.
- PCR polymerase chain reaction
- RCA Rolling Circle Amplification
- PCR Polymerase Chain Reaction
- MSI Microsatellite Instability
- MSI is identified by electrophoretic resolution of amplified microsatellite DNA sequences.
- blocks of surgically resected tumor tissue either a fresh frozen specimen or a formalin-fixed, parafiin-embedded specimen is obtained.
- the tumor tissue is microdissected to separate neoplastic tissue from normal tissue, and DNA is extracted from both. Samples of genomic DNA from these samples are amplified for a panel of specific mono- and di-nucleotide microsatellite loci using PCR.
- PCR products are then analyzed by electrophoresis. Additional bands in the PCR products of the tumor DNA not observed in the normal DNA is scored as instability at that locus (or specific site).
- MSI analyses require the use of five MS markers, two mononucleotide repeats and three di- nucleotide repeats. According to the National Cancer Institute's consensus statement on MSI testing, any pair of samples that display instability at two or more of five different loci is scored as high MSI.
- Nucleic acid strands are first selectively digested and then subjected to
- electrophoresis in which molecules (as proteins and nucleic acids) migrate through a gel (e.g., a polyacrylamide gel) and separate into bands according to size.
- a gel e.g., a polyacrylamide gel
- Rolling circle amplification is a surface-anchored DNA replication reaction that can display single molecular recognition events. RCA successfully
- Each amplified DNA molecule generated by RCA may be localized and
- Expression profiles may be generated as histograms of single molecule counts
- Southern blotting can identify differences between normal and mutant alleles and identify genes that are related in other genomes.
- cloned or amplified DNA is digested with a restriction enzyme. The large variety of DNA
- fragments is separated according to size by electrophoresis and transferred onto a
- nitrocellulose filter The fragments are then hybridized with a probe, but only those DNA fragments containing sequences homologous, or identical in base sequence, to
- the probe are detected.
- Single-base differences between individuals are detected when
- D ⁇ A sequencing has been
- a probe is a stretch of D ⁇ A or other nucleic acid that has been tethered to a stable material.
- the probe is then exposed to a target of free nucleic acid whose identity is being detected (by the probe) through a hybridization reaction (for terminology, see Phimster B: Nat Genet 21[Suppl]:l-60, 1999).
- the probe is generally labeled with a radioactive isotope or a chemical than can be detected after the hybridization takes place.
- chemilummescent labels e.g. 1,2-dioxetanes, alkaline phosphate, or biotin, may be used as hybridization probes to detect nucleotide sequence ladders on membranes generated by the sequencing protocol of Church and Gilbert. See Church, G.M., Gilbert, W., Proc. Natl. Acad. Sci., USA 81, 1991-1995, (1984).
- D ⁇ A microarrays made of high-speed robotics on inert materials, such as glass
- microarrays such as genome chip
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Abstract
Description
Claims
Priority Applications (8)
Application Number | Priority Date | Filing Date | Title |
---|---|---|---|
JP2003558211A JP2005514040A (en) | 2001-12-14 | 2002-10-05 | Light-directed molecular analysis for cancer prognosis and diagnosis |
EP02784048A EP1463833A4 (en) | 2001-12-14 | 2002-10-05 | Light-directed molecular analysis for cancer prognosis and diagnosis |
US10/484,409 US20050014145A1 (en) | 2000-09-26 | 2002-10-05 | Light-directed molecular analysis for cancer prognosis and diagnosis |
IL15997402A IL159974A0 (en) | 2001-12-14 | 2002-10-05 | Light-directed molecular analysis for cancer prognosis and diagnosis |
CA002457407A CA2457407A1 (en) | 2001-12-14 | 2002-10-05 | Light-directed molecular analysis for cancer prognosis and diagnosis |
MXPA04002658A MXPA04002658A (en) | 2001-12-14 | 2002-10-05 | Light-directed molecular analysis for cancer prognosis and diagnosis. |
AU2002347835A AU2002347835A1 (en) | 2001-12-14 | 2002-10-05 | Light-directed molecular analysis for cancer prognosis and diagnosis |
NO20042472A NO20042472L (en) | 2001-12-14 | 2004-06-14 | Light-guided molecular analysis for cancer prognosis and diagnosis |
Applications Claiming Priority (2)
Application Number | Priority Date | Filing Date | Title |
---|---|---|---|
US1700701A | 2001-12-14 | 2001-12-14 | |
US10/017,007 | 2001-12-14 |
Publications (1)
Publication Number | Publication Date |
---|---|
WO2003057918A1 true WO2003057918A1 (en) | 2003-07-17 |
Family
ID=21780202
Family Applications (2)
Application Number | Title | Priority Date | Filing Date |
---|---|---|---|
PCT/US2002/032073 WO2003057918A1 (en) | 2000-09-26 | 2002-10-05 | Light-directed molecular analysis for cancer prognosis and diagnosis |
PCT/US2002/032067 WO2003072826A1 (en) | 2000-09-26 | 2002-10-05 | Stain-directed molecular analysis for cancer prognosis and diagnosis |
Family Applications After (1)
Application Number | Title | Priority Date | Filing Date |
---|---|---|---|
PCT/US2002/032067 WO2003072826A1 (en) | 2000-09-26 | 2002-10-05 | Stain-directed molecular analysis for cancer prognosis and diagnosis |
Country Status (10)
Country | Link |
---|---|
US (1) | US20050014145A1 (en) |
EP (2) | EP1463838A4 (en) |
JP (2) | JP2005514040A (en) |
CN (1) | CN1558956A (en) |
AU (2) | AU2002347835A1 (en) |
CA (2) | CA2457907A1 (en) |
IL (2) | IL159974A0 (en) |
MX (2) | MXPA04002659A (en) |
NO (2) | NO20042471L (en) |
WO (2) | WO2003057918A1 (en) |
Cited By (2)
Publication number | Priority date | Publication date | Assignee | Title |
---|---|---|---|---|
EP1793727A1 (en) * | 2004-09-28 | 2007-06-13 | Zila Pharmaceuticals, Inc. | Methods for detecting abnormal epithelial tissue |
US7659057B2 (en) | 2000-09-26 | 2010-02-09 | Zila Biotechnology, Inc. | Stain-directed molecular analysis for cancer prognosis and diagnosis |
Families Citing this family (2)
Publication number | Priority date | Publication date | Assignee | Title |
---|---|---|---|---|
AU785490B2 (en) * | 2000-07-20 | 2007-11-15 | Zila Biotechnology, Inc. | Improved diagnostic method for detecting dysplastic epithelial tissue |
US20090023138A1 (en) * | 2007-07-17 | 2009-01-22 | Zila Biotechnology, Inc. | Oral cancer markers and their detection |
Citations (3)
Publication number | Priority date | Publication date | Assignee | Title |
---|---|---|---|---|
US5882627A (en) * | 1996-01-16 | 1999-03-16 | Zila Pharmaceuticals, Inc. | Methods and compositions for in-vivo detection of oral cancers precancerous conditions |
US6025127A (en) * | 1994-01-14 | 2000-02-15 | The Johns Hopkins University School Of Medicine | Nucleic acid mutation detection in histologic tissue |
US6291163B1 (en) * | 1996-08-28 | 2001-09-18 | The Johns Hopkins University School Of Medicine | Method for detecting cell proliferative disorders |
Family Cites Families (12)
Publication number | Priority date | Publication date | Assignee | Title |
---|---|---|---|---|
US4321251A (en) * | 1979-12-19 | 1982-03-23 | The United States Of America As Represented By The Department Of Health And Human Services | Detection of malignant lesions of the oral cavity utilizing toluidine blue rinse |
US5179938A (en) * | 1983-02-17 | 1993-01-19 | The Trylon Corporation | Apparatus for endoscopic examination of body cavity using chemiluminescent light source |
DK0565668T3 (en) * | 1991-10-31 | 2000-01-31 | Zila Inc | Biological dye composition, method of preparation thereof and for use in epithelial cancer signaling |
WO1994019492A1 (en) * | 1993-02-24 | 1994-09-01 | Mayo Foundation For Medical Education And Research | Tumor-specific genomic instability as a prognostic indicator |
US6235470B1 (en) * | 1993-11-12 | 2001-05-22 | The Johns Hopkins University School Of Medicine | Detection of neoplasia by analysis of saliva |
US5786227A (en) * | 1995-06-07 | 1998-07-28 | Biex, Inc. | Fluid collection kit and method |
KR19990067532A (en) * | 1995-11-13 | 1999-08-25 | 코텍스(유케이) 리미티드 | Diagnostic test device |
US6086852A (en) * | 1997-11-13 | 2000-07-11 | Zila, Inc. | In vivo stain composition, process of manufacture, and methods of use to identify dysplastic tissue |
US6405070B1 (en) * | 1998-06-16 | 2002-06-11 | Bhaskar Banerjee | Detection of cancer using cellular autofluorescence |
US6256530B1 (en) * | 1998-09-15 | 2001-07-03 | Denvu, L.L.C. | Optical instrument and technique for cancer diagnosis using in-vivo fluorescence emission of test tissue |
AU2000237154A1 (en) * | 2000-02-28 | 2001-09-12 | Zila, Inc. | Method for detecting and killing epithelial cancer cells |
AU776256B2 (en) * | 2000-09-26 | 2004-09-02 | Zila Biotechnology, Inc. | Method for early prediction of the onset of invasive cancer |
-
2002
- 2002-10-05 EP EP02806902A patent/EP1463838A4/en not_active Ceased
- 2002-10-05 WO PCT/US2002/032073 patent/WO2003057918A1/en active Application Filing
- 2002-10-05 US US10/484,409 patent/US20050014145A1/en not_active Abandoned
- 2002-10-05 CN CNA028187016A patent/CN1558956A/en active Pending
- 2002-10-05 MX MXPA04002659A patent/MXPA04002659A/en not_active Application Discontinuation
- 2002-10-05 IL IL15997402A patent/IL159974A0/en unknown
- 2002-10-05 JP JP2003558211A patent/JP2005514040A/en active Pending
- 2002-10-05 JP JP2003571505A patent/JP2005518221A/en active Pending
- 2002-10-05 CA CA002457907A patent/CA2457907A1/en not_active Abandoned
- 2002-10-05 AU AU2002347835A patent/AU2002347835A1/en not_active Abandoned
- 2002-10-05 MX MXPA04002658A patent/MXPA04002658A/en not_active Application Discontinuation
- 2002-10-05 WO PCT/US2002/032067 patent/WO2003072826A1/en active Application Filing
- 2002-10-05 IL IL15997502A patent/IL159975A0/en unknown
- 2002-10-05 CA CA002457407A patent/CA2457407A1/en not_active Abandoned
- 2002-10-05 EP EP02784048A patent/EP1463833A4/en not_active Withdrawn
- 2002-10-05 AU AU2002367731A patent/AU2002367731B2/en not_active Ceased
-
2004
- 2004-06-14 NO NO20042471A patent/NO20042471L/en not_active Application Discontinuation
- 2004-06-14 NO NO20042472A patent/NO20042472L/en not_active Application Discontinuation
Patent Citations (3)
Publication number | Priority date | Publication date | Assignee | Title |
---|---|---|---|---|
US6025127A (en) * | 1994-01-14 | 2000-02-15 | The Johns Hopkins University School Of Medicine | Nucleic acid mutation detection in histologic tissue |
US5882627A (en) * | 1996-01-16 | 1999-03-16 | Zila Pharmaceuticals, Inc. | Methods and compositions for in-vivo detection of oral cancers precancerous conditions |
US6291163B1 (en) * | 1996-08-28 | 2001-09-18 | The Johns Hopkins University School Of Medicine | Method for detecting cell proliferative disorders |
Non-Patent Citations (1)
Title |
---|
See also references of EP1463833A4 * |
Cited By (3)
Publication number | Priority date | Publication date | Assignee | Title |
---|---|---|---|---|
US7659057B2 (en) | 2000-09-26 | 2010-02-09 | Zila Biotechnology, Inc. | Stain-directed molecular analysis for cancer prognosis and diagnosis |
EP1793727A1 (en) * | 2004-09-28 | 2007-06-13 | Zila Pharmaceuticals, Inc. | Methods for detecting abnormal epithelial tissue |
EP1793727A4 (en) * | 2004-09-28 | 2009-01-07 | Zila Pharm Inc | Methods for detecting abnormal epithelial tissue |
Also Published As
Publication number | Publication date |
---|---|
JP2005518221A (en) | 2005-06-23 |
MXPA04002659A (en) | 2004-06-18 |
IL159974A0 (en) | 2004-06-20 |
IL159975A0 (en) | 2004-06-20 |
AU2002367731B2 (en) | 2008-11-13 |
NO20042472L (en) | 2004-06-14 |
CA2457407A1 (en) | 2003-07-17 |
MXPA04002658A (en) | 2004-06-18 |
NO20042471L (en) | 2004-06-14 |
JP2005514040A (en) | 2005-05-19 |
EP1463838A4 (en) | 2006-06-07 |
EP1463833A1 (en) | 2004-10-06 |
CA2457907A1 (en) | 2003-09-04 |
US20050014145A1 (en) | 2005-01-20 |
WO2003072826A1 (en) | 2003-09-04 |
AU2002347835A1 (en) | 2003-07-24 |
AU2002367731A1 (en) | 2003-09-09 |
EP1463838A1 (en) | 2004-10-06 |
CN1558956A (en) | 2004-12-29 |
EP1463833A4 (en) | 2006-06-07 |
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