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A Reconstructed View of Personalized Medicine

Posted in Amino acids, Anaerobic Glycolysis, Apoptosis, Autophagy, Biochemical pathways, Biological Networks, Gene Regulation and Evolution, CANCER BIOLOGY & Innovations in Cancer Therapy, Cell Biology, Signaling & Cell Circuits, Cell death pathways, Curation, Disease Biology, DNA repair, Enzymes and isoenzymes, Gene Regulation and Evolution, Genetics & Innovations in Treatment, Genetics & Pharmaceutical, Genome Biology, Genomic Expression, Human aging, Metabolism, Metabolomics, Micronutrients, Nitric Oxide in Health and Disease, Nutrition, Pharmaceutical Analytics, Pharmaceutical Discovery, Protein-energy malnutrition, Proteins, Proteomics, Pyridine nucleotides, Pyruvate Kinase, RNA Biology, Signaling, Signaling & Cell Circuits, Stress Disorders, Ubiquitinylation, Warburg effect, tagged "inhibiting" RNAs, Allosteric regulation, DNA discoveries, DNA methylation, intracellular and extracellular transport, isoenzymes, LDH isoenzymes, metabolic pathways, Personalized medicine, protein-protein interactions, signaling pathways on February 26, 2016| Leave a Comment »

A Reconstructed View of Personalized Medicine

Author: Larry H. Bernstein, MD, FCAP

There has always been Personalized Medicine if you consider the time a physician spends with a patient, which has dwindled. But the current recognition of personalized medicine refers to breakthrough advances in technological innovation in diagnostics and treatment that differentiates subclasses within diagnoses that are amenable to relapse eluding therapies. There are just a few highlights to consider:

We live in a world with other living beings that are adapting to a changing environmental stresses.
Nutritional resources that have been available and made plentiful over generations are not abundant in some climates.
Despite the huge impact that genomics has had on biological progress over the last century, there is a huge contribution not to be overlooked in epigenetics, metabolomics, and pathways analysis.

A Reconstructed View of Personalized Medicine

There has been much interest in ‘junk DNA’, non-coding areas of our DNA are far from being without function. DNA has two basic categories of nitrogenous bases: the purines (adenine [A] and guanine [G]), and the pyrimidines (cytosine [C], thymine [T], and no uracil [U]), while RNA contains only A, G, C, and U (no T). The Watson-Crick proposal set the path of molecular biology for decades into the 21^st century, culminating in the Human Genome Project.

There is no uncertainty about the importance of “Junk DNA”. It is both an evolutionary remnant, and it has a role in cell regulation. Further, the role of histones in their relationship the oligonucleotide sequences is not understood. We now have a large output of research on noncoding RNA, including siRNA, miRNA, and others with roles other than transcription. This requires major revision of our model of cell regulatory processes. The classic model is solely transcriptional.

DNA-> RNA-> Amino Acid in a protein.

Redrawn we have

DNA-> RNA-> DNA and
DNA->RNA-> protein-> DNA.

Neverthess, there were unrelated discoveries that took on huge importance. For example, since the 1920s, the work of Warburg and Meyerhoff, followed by that of Krebs, Kaplan, Chance, and others built a solid foundation in the knowledge of enzymes, coenzymes, adenine and pyridine nucleotides, and metabolic pathways, not to mention the importance of Fe³⁺, Cu²⁺, Zn²⁺, and other metal cofactors. Of huge importance was the work of Jacob, Monod and Changeux, and the effects of cooperativity in allosteric systems and of repulsion in tertiary structure of proteins related to hydrophobic and hydrophilic interactions, which involves the effect of one ligand on the binding or catalysis of another, demonstrated by the end-product inhibition of the enzyme, L-threonine deaminase (Changeux 1961), L-isoleucine, which differs sterically from the reactant, L-threonine whereby the former could inhibit the enzyme without competing with the latter. The current view based on a variety of measurements (e.g., NMR, FRET, and single molecule studies) is a ‘‘dynamic’’ proposal by Cooper and Dryden (1984) that the distribution around the average structure changes in allostery affects the subsequent (binding) affinity at a distant site.

What else do we have to consider? The measurement of free radicals has increased awareness of radical-induced impairment of the oxidative/antioxidative balance, essential for an understanding of disease progression. Metal-mediated formation of free radicals causes various modifications to DNA bases, enhanced lipid peroxidation, and altered calcium and sulfhydryl homeostasis. Lipid peroxides, formed by the attack of radicals on polyunsaturated fatty acid residues of phospholipids, can further react with redox metals finally producing mutagenic and carcinogenic malondialdehyde, 4-hydroxynonenal and other exocyclic DNA adducts (etheno and/or propano adducts). The unifying factor in determining toxicity and carcinogenicity for all these metals is the generation of reactive oxygen and nitrogen species. Various studies have confirmed that metals activate signaling pathways and the carcinogenic effect of metals has been related to activation of mainly redox sensitive transcription factors, involving NF-kappaB, AP-1 and p53.

I have provided mechanisms explanatory for regulation of the cell that go beyond the classic model of metabolic pathways associated with the cytoplasm, mitochondria, endoplasmic reticulum, and lysosome, such as, the cell death pathways, expressed in apoptosis and repair. Nevertheless, there is still a missing part of this discussion that considers the time and space interactions of the cell, cellular cytoskeleton and extracellular and intracellular substrate interactions in the immediate environment.

There is heterogeneity among cancer cells of expected identical type, which would be consistent with differences in phenotypic expression, aligned with epigenetics. There is also heterogeneity in the immediate interstices between cancer cells. Integration with genome-wide profiling data identified losses of specific genes on 4p14 and 5q13 that were enriched in grade 3 tumors with high microenvironmental diversity that also substratified patients into poor prognostic groups. In the case of breast cancer, there is interaction with estrogen , and we refer to an androgen-unresponsive prostate cancer.

Finally, the interaction between enzyme and substrates may be conditionally unidirectional in defining the activity within the cell. The activity of the cell is dynamically interacting and at high rates of activity. In a study of the pyruvate kinase (PK) reaction the catalytic activity of the PK reaction was reversed to the thermodynamically unfavorable direction in a muscle preparation by a specific inhibitor. Experiments found that in there were differences in the active form of pyruvate kinase that were clearly related to the environmental condition of the assay – glycolitic or glyconeogenic. The conformational changes indicated by differential regulatory response were used to present a dynamic conformational model functioning at the active site of the enzyme. In the model, the interaction of the enzyme active site with its substrates is described concluding that induced increase in the vibrational energy levels of the active site decreases the energetic barrier for substrate induced changes at the site. Another example is the inhibition of H₄ lactate dehydrogenase, but not the M₄, by high concentrations of pyruvate. An investigation of the inhibition revealed that a covalent bond was formed between the nicotinamide ring of the NAD⁺ and the enol form of pyruvate. The isoenzymes of isocitrate dehydrogenase, IDH1 and IDH2 mutations occur in gliomas and in acute myeloid leukemias with normal karyotype. IDH1 and IDH2 mutations are remarkably specific to codons that encode conserved functionally important arginines in the active site of each enzyme. In this case, there is steric hindrance by Asp279 where the isocitrate substrate normally forms hydrogen bonds with Ser94.

Personalized medicine has been largely viewed from a lens of genomics. But genomics is only the reading frame. The living activities of cell processes are dynamic and occur at rapid rates. We have to keep in mind that personalized in reference to genotype is not complete without reconciliation of phenotype, which is the reference to expressed differences in outcomes.