Infrared Microscope Studies DNA Changes in Cancer

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Rich Murray: PNRI: Malins:
Highly capable IR studies of DNA damage in cancer 3.9.01 rmforall

This approach can quickly and accurately show cancer promoting DNA damage from aspartame, methanol, formaldehyde, MSG, fluoride, pesticides, and  toxins in dairy products, using tiny 1 microgram samples of DNA, even from apparently tumor-free tissues. They have already studied the effects of environmental chemicals, estrogens, and hydroxyl  radicals, especially in breast, ovarian,  and prostate cancers.

Rich Murray   Room For All   rmforall@earthlink.net
1943 Otowi Road   Santa Fe, NM 87505     505-986-9103

The development of an infrared microscope, used in conjunction with advanced computer software, makes it possible to obtain Fourier transform-infrared spectra of micrograms of DNA from biological specimens. Comparisons of statistically transformed spectra are the basis for discriminating between DNA from normal, primary and metastatic tumor tissues and establishing the probability of cancer occurring in apparently healthy tissues. The infrared models are presently being used in conjunction with other cancer predictive models based on DNA structure.

Proc Natl Acad Sci U S A 2000 Nov 7;97(23):12442-5
Single 8-oxo-guanine and 8-oxo-adenine lesions induce marked changes in the backbone structure of a 25-base DNA strand. Malins DC, Polissar NL, Ostrander GK, Vinson MA Molecular Epidemiology Program    206-726-1200 Pacific Northwest Research Institute, 720 Broadway, Seattle, WA 98122, USA.    dmalins@pnri.org    Donald C. Malins

Structural changes in a 25-base DNA strand, induced by single 8-oxo-guanine or 8-oxo-adenine substitutions, were shown by using Fourier transform-infrared spectroscopy with multivariate statistics. Pronounced differences were demonstrated between the parent and derivatives with respect to base interactions and changes in the phospho - deoxyribose backbone. The greatest degree of change in the backbone likely occurred immediately adjacent to the 8-oxo group, potentially altering the stereochemistry at a distance. The 8-oxo lesions, formed from reactive oxygen species (e.g., hydroxyl radicals), may appreciably alter the conformational properties of strands at the replication fork, thus affecting the selectivity of polymerases, the proofreading capability of repair enzymes, and the fidelity of the transcriptional machinery. PMID: 11058168

J Natl Cancer Inst Monogr 2000;(27):147-56
Factors critical to the design and execution of epidemiologic studies and description of an innovative technology to follow the progression from normal to cancer tissue. Garcia - Closas M, Hankinson SE, Ho S, Malins DC, Polissar NL, Schaefer SN, Su Y, Vinson MA Environmental Epidemiology Branch, National Cancer Institute, Bethesda, MD, USA.

The results obtained from experimental studies of estrogen carcinogenesis need validation in epidemiologic studies. Such studies present additional challenges, however, because variations in human populations are much greater than those in experimental systems and in animal models. Because epidemiologic studies are often used to evaluate modest differences in risk factors, it is essential to minimize sources of errors and to maximize sensitivity, reproducibility, and specificity. In the first part of this chapter, critical factors in designing and executing epidemiologic studies, as well as the influence of sample collection, processing, and storage on data reliability, are discussed. One of the most important requirements is attaining sufficient statistical power to assess small genetic effects and to evaluate interactions between genetic and environmental factors. The second part of this chapter describes innovative technology, namely, Fourier transform - infrared (FT-IR) spectra of DNA that reveal major structural differences at various stages of the progression from normal to cancer tissue. The structural differences become evident from wavenumber - by - wavenumber statistical comparisons of the mean FT-IR spectra of DNA from normal to cancer tissues. This analysis has allowed distinguishing benign tissues from cancer and metastatic tissues in human breast, prostate, and ovarian cancers. This analysis, which requires less than 1 microg of DNA, is predicted to be used for detecting early cancer-related changes at the level of DNA, rather than at the cellular level. PMID: 10963626

Proc Natl Acad Sci U S A 1998 Jun 23;95(13):7637-42
A unified theory of carcinogenesis based on order-disorder transitions in DNA structure as studied in the human ovary and breast. Malins DC, Polissar NL, Schaefer S, Su Y, Vinson M Molecular Epidemiology Program, Pacific Northwest Research Institute 720 Broadway, Seattle, WA 98122, USA.

Fourier transform-infrared/statistics models demonstrate that the malignant transformation of morphologically normal human ovarian and breast tissues involves the creation of a high degree of structural modification (disorder) in DNA, before restoration of order in distant metastases. Order-disorder transitions were revealed by methods including principal components analysis of infrared spectra in which DNA samples were represented by points in two-dimensional space. Differences between the geometric sizes of clusters of points and between their locations revealed the magnitude of the order-disorder transitions. Infrared spectra provided evidence for the types of structural changes involved. Normal ovarian DNAs formed a tight cluster comparable to that of normal human blood leukocytes. The DNAs of ovarian primary carcinomas, including those that had given rise to metastases, had a high degree of disorder, whereas the DNAs of distant metastases from ovarian carcinomas were relatively ordered. However, the spectra of the metastases were more diverse than those of normal ovarian DNAs in regions assigned to base vibrations, implying increased genetic changes. DNAs of normal female breasts were substantially disordered (e.g., compared with the human blood leukocytes) as were those of the primary carcinomas, whether or not they had metastasized. The DNAs of distant breast cancer metastases were relatively ordered. These findings evoke a unified theory of carcinogenesis in which the creation of disorder in the DNA structure is an obligatory process followed by the selection of ordered, mutated DNA forms that ultimately give rise to metastases. PMID: 9636202

Proc Natl Acad Sci U S A 1997 Apr 15;94(8):3611-5
Infrared spectral models demonstrate that exposure to environmental chemicals leads to new forms of DNA. Malins DC, Polissar NL, Gunselman SJ Molecular Epidemiology Program, Pacific Northwest Research Foundation, Seattle, WA 98122,  USA.

Environmental chemicals are known to induce a high degree of hydroxyl radical - mediated damage in DNA. Accordingly, we tested the hypothesis that this exposure leads to new forms of DNA using principal components analysis of Fourier transform infrared spectra. The hepatic DNA of English sole (controls) from an essentially clean environment was compared with that of sole inhabiting a chemically contaminated environment. All livers studied were cancer-free; however, a high incidence of liver cancer has been found in the exposed population. The exposed sole were sampled twice, 2 years apart, while the sediments in which they live were under remediation. After obtaining infrared spectra, the first three principal components (PC1, PC2, and PC3) were calculated and found to represent 97% of the total spectral variance. When the principal component scores were plotted in 3-dimensional space, clusters of points were obtained that represented the DNA from the control and exposed groups. Each of the points was derived from approximately 10(6) wavenumber-absorbance correlations. The spatial location of a point was a highly discriminating measure of DNA structure. The clusters of points were completely separated, demonstrating that the three groups could be 100% correctly classified. The points from the control group were tightly clustered whereas those from the exposed groups were highly diverse. The findings demonstrate that exposure to environmental chemicals results in new, structurally diverse forms of DNA that likely play an important role in carcinogenesis. PMID: 9108025
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