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Precision Medicine: The Coolest Part of Medicine

QuellosOne size rarely fits all. Most medical knowledge is derived from studying groups of subjects, subjects who may be different in some way from the individual who walks into the doctor’s office. Basing medicine only on randomized controlled studies can lead to over-simplified “cookbook” medicine. A good clinician interprets study results and puts them into context, considering the whole patient and using clinical judgment to apply current scientific knowledge appropriately to the individual.

CAM practitioners claim to be providing individualized treatments. Homeopaths look up symptoms like “dreams of robbers,” “sensation of coldness in the heart,” and “chills between 9 and 11 AM” in their books, and naturopaths quiz patients in great depth about their habits and preferences; but they don’t have a plausible rationale for interpreting the information they gather. And they have not been able to demonstrate better patient outcomes from using that information.

A new concept, “precision medicine,” was recently featured in UW Medicine, the alumni magazine of my alma mater, the University of Washington School of Medicine. Precision medicine strives to provide truly individualized care based on good science. It identifies the individual variations in people that make a difference in our ability to diagnose and treat accurately. Peter Byers, MD, director of the new Center for Precision Diagnostics at the University of Washington, calls it “the coolest part of medicine.”

The “omic” tool set

It’s not enough to map the DNA; knowing that a patient has a gene doesn’t tell us whether that gene will be active, how it will interact with other genes or the environment, or what effects it will have. We need to understand how genes are expressed, what controls gene expression (what turns a gene on or off, or modifies its rate of function), and how RNA transcription molecules, proteins, and metabolic processes are involved. The 4-part “omic” tool set consists of:

  • Genomics: DNA sequencing and analysis. We have gone far beyond the methods of the Human Genome Project and can now sequence all the genes at the same time.
  • Transcriptomics: study of RNA transcript molecules.
  • Proteomics: study of the complete array of proteins produced by genes.
  • Metabolomics: study of small-molecule metabolites that fingerprint cellular processes resulting from gene expression.

The UW-Oncoplex cancer gene panel

Want personalized information about your cancer? Your surgeon can submit a sample of your tumor for a UW-Oncoplex cancer gene panel. It uses genetic sequencing to detect mutations in tumor tissue and identifies 194 cancer-related genes. It looks for “actionable” mutations, those we can do something about, for instance those that tell us one drug will work better than another. Potentially, it might some day be able to pick out cancers that are slow-growing and unlikely to metastasize, identifying patients who can safely avoid the risks and discomforts of radiation and chemotherapy.

Oncoplex uses next-generation “deep sequencing.” I don’t understand what that means, but apparently it can identify more kinds of mutations – not just single nucleotide variants, but also small insertions and deletions, gene amplifications, and selected gene-fusions. In an example given by Dr. Byers, a patient with metastatic lung cancer was found to have a gene fusion that had been missed by other genetic testing panels. Based on this new information, the patient was switched to crizotinib and had a complete symptomatic and radiographic response.

Quellos High-Throughput Screening Core

Researchers used to work with single test tubes. The process has been automated and miniaturized (see the picture above). Scientists can now work with plates that have as many as 1,536 compartments (“wells,” essentially tiny test tubes) that a machine automatically fills with as little as 50 nanoliters from tiny dispensing nozzles. The Quellos High-throughput Screening Core has a library of 120,000 compounds, including FDA-approved drugs, drugs in the testing stage, and candidates for future testing. Diseased cell samples can be simultaneously exposed to a multitude of compounds in various concentrations to see which ones damage or kill the cells, identifying drugs that merit further study. The system has both clinical uses (guiding treatment) and basic science applications like studying what happens downstream in cell metabolic processes when a specific gene is knocked out.

Precision medicine research at UW

Cancer researcher Pam Becker has been testing cells donated by her acute myeloid leukemia patients, and in almost every case the screening has suggested an alternate treatment that would not have been next in line.

Tony Blau, director of the UW Medicine Center for Cancer Innovation, and his wife, oncologist Sibel Blau, are using these techniques to test biopsy samples from women with metastatic triple-negative breast cancer, investigating how the tumor cells respond to 180 compounds and trying to incorporate the positive responses into the patient’s treatment regime.

Ophthalmologist Jennifer Chao is using Quellos to study macular degeneration. Stem cells are prodded into transforming into retinal pigment epithelium and the resulting cells are bombarded with factors that are thought to cause macular degeneration (the death of retinal cells), then they are exposed to 2,000 different medical compounds to see if any of them prevent cell death.

Neuropathologist Tom Montine is using precision medicine tools to study Alzheimer’s disease, which he compares to arthritis of the brain. A damaged joint can be further damaged by the body’s immune response, and immune regulation in the brain seems to play a key role in Alzheimer’s disease. He is attempting not just to identify the genetic drivers of the disease but to track the molecular pathways that provide the mechanisms for genetic influence.

The Act Smart initiative at the Institute for Prostate Cancer Research is a multi-million-dollar effort to understand and target prostate cancer tumors in ways specific to each patient, using the new tools of precision medicine.

Conclusion

This is an exciting time in medical science. We are just beginning to see authentic science-based individualized medical care. Accept no substitutes.

Posted in: Basic Science, Cancer, Diagnostic tests & procedures

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