from bc genome project--each persons' breast cancer is unique

[Lani]

Thus true individualization of treatment will be necessary. Will probably mean identifying the three or so most important pathways driving the cancer in any one patient and attacking those pathways with drugs, vaccines, etc. This is why there is no simple answer. The average bc tumor
has 81 mutated genes! Another reason to work for prevention in the first place!

Genome update defines landscape of breast and colon cancers: Represents next major step in cancer genome sequencing [Eureka News Service]
One year after completing the first large-scale report sequencing breast and colon cancer genes, Johns Hopkins Kimmel Cancer Center scientists have studied the vast majority of protein-coding genes which now suggest a landscape dominated by genes that each are mutated in relatively few cancers.
Their report, published online in the October 11 issue of Science Express, indicates that while little is known about these less-commonly mutated genes, they can be grouped into clusters according to their pathways.
"There are gene 'mountains' represented by those that are frequently altered and have been the focus of cancer research for years, in part because they were the only genes known to contribute to cancer," says Bert Vogelstein, M.D., an investigator at the Howard Hughes Medical Institute and co-director of the Ludwig Center at Johns Hopkins. "Now, we can see the whole picture, and it is clear that lower peaks or gene 'hills' are the predominant feature."
In a systematic search of 18,191 genes representing more than 90 percent of the protein-coding genes in the human genome — about 5,000 more than in the first screen — the Johns Hopkins scientists found that most cancer-causing gene mutations are quite diverse and can vary from person to person. They found that an average 77 genes are mutated in an individual colon cancer and 81 in breast cancer. Of these, about 15 are likely to contribute to a cancer's key characteristics, and most of these genes may be different for each patient.
"Fifteen years ago, we said the p53 gene was the most commonly mutated gene in cancer. It's amazing that this is still true," says Kenneth W. Kinzler, Ph.D., professor of oncology at Hopkins' Kimmel Cancer Center.
With no more higher-frequency mutations on the horizon, the investigators say that "personalized medicines" may now focus on the more complicated pathways that link these less-commonly mutated genes.
As an example, the Hopkins team charted the path of nine genes less frequently mutated in breast or colon cancers. Each of the genes' protein products interacted with an average of 25 other proteins, encoded by separate genes also found to be mutated in the cancers. It suggests that these genes converge in similar pathways. "The hard part used to be finding these mutant genes, now the challenge will be to link them to specific pathways and understand their function," says Victor Velculescu, M.D., Ph.D., associate professor of oncology at the Johns Hopkins Kimmel Cancer Center.
The scientists say that directing therapies at common pathways that are linked by both prevalent and rare gene mutations is a better approach than aiming treatments at specific genes. They also note that personalized cancer genomics paves the way for tailored therapies and diagnostics focusing on the alterations identified in a particular patient's cancer. Many of the mutations identified by scientists could be important in developing individualized cancer vaccines and monitoring patients for early recurrence of their disease.
For the study, the scientists screened the same set of tissue samples that were used for their first genome draft - 11 each of breast and colorectal cancers, removed from patients after surgery. Then, they evaluated all mutated genes in a second group of 24 samples from each cancer, and a subset of the most promising mutations were studied in a further 96 colorectal cancers. They compared the genetic sequence of these tumors with that of normal tissue samples from the same patients using computer software that matches up gene codes in cancer and normal cells.
Within each cell, chemicals called nucleotides pair up to form the rungs of a DNA ladder that carry genetic instructions guiding everything from cell-to-cell contact to eye color. Changes in the nucleotide arrangement can create errors in the proteins made from the DNA. Buildup of damaged proteins can turn a normal cell into a cancerous one.
Laura Wood, a postdoctoral fellow at Hopkins' Kimmel Cancer Center says that these results can help to direct the global race to map additional cancer genomes. For other cancers, she says scientists should expect to find a similar genetic landscape - "few mountains surrounded by many hills."
ABSTRACT: The Genomic Landscapes of Human Breast and Colorectal Cancers [Science]
Human cancer is caused by the accumulation of mutations in oncogenes and tumor suppressor genes. To catalogue the genetic changes that occur during tumorigenesis, we isolated DNA from 11 breast and 11 colorectal tumors and determined the sequences of the genes in the Reference Sequence database in these samples. Based on analysis of exons representing 20,857 transcripts from 18,191 genes, we conclude that the genomic landscapes of breast and colorectal cancers are composed of a handful of commonly mutated gene "mountains" and a much larger number of gene "hills" that are mutated at low frequency. We describe statistical and bioinformatic tools that may help identify mutations with a role in tumorigenesis. These results have implications for understanding the nature and heterogeneity of human cancers and for using personal genomics for tumor diagnosis and therapy.

[gdpawel]

In chemotherapy selection, Gene and Protein testing examine a single process within the cell or a relatively small number of processes. The aim is to tell if there is a theoretical predisposition to drug response.

Whole Cell Functional Profiling tests not only for the presence of genes and proteins but also for their functionality, for their interaction with other genes, proteins, and processes occurring within the cell, and for their response to anti-cancer drugs.

Genes create the blueprints for the production of proteins within the cell. A protein is a molecule that makes a cell behave in a certain way. It does so by interacting with other proteins in a complex series of steps.

The goal of Gene testing is to look for patterns of normal and abnormal gene expression which could suggest that certain proteins might or might not be produced within a cell. However, just because a gene is present it does not mean that an associated protein has been produced.

Protein testing goes one step further by testing to see if the relevant protein actually has been produced. However, even Protein testing cannot tell us if a protein is functional or how it will interact with other proteins in the presence of anti-cancer drugs.

Gene and Protein testing involve the use of dead, formaldehyde preserved cells that are never exposed to chemotherapy drugs. Gene and Protein tests cannot tells us anything about uptake of a certain drug into the cell or if the drug will be excluded before it can act or what changes will take place within the cell if the drug successfully enters the cell.

Gene and Protein tests cannot discriminate among the activities of different drugs within the same class. Instead, Gene and Protein tests assume that all drugs within a class will produce precisely the same effect, even though from clinical experience, this is not the case. Nor can Gene and Protein tests tell us anything about drug combinations.

"Whole Cell" Functional Tumor Cell Profiling tests living cancer cells. Functional Tumor Cell Profiling assesses the net result of all cellular processes, including interactions, occurring in real time when cancer cells actually are exposed to specific anti-cancer drugs. Functional Tumor Cell Profiling can discriminate differing anti-tumor effects of different drugs within the same class. Functional Profiling can also identify synergies in drug combinations.

Gene and Protein tests are better suited for ruling out "inactive" drugs than for identifying "active" drugs. When considering a cancer drug which is believed to act only upon cancer cells that have a specific genetic defect, it is useful to know if a patient's cancer cells do or do not have precisely that defect.

Although presence of a targeted defect does not necessarily mean that a drug will be effective, absence of the targeted defect may rule out use of the drug. Of course, this assumes that the mechanism of drug activity is known beyond any doubt, which is not always the case.

Although Gene and Protein testing currently are limited in their reliability as clinical tools, the tests can be important in research settings such as in helping to identify rational targets for development of new anti-cancer drugs.

As you can see, just selecting the right test to perform in the right situation is a very important step on the road to personalizing cancer therapy.

[hutchibk]

I know we are leaning a little this way already, and my onc always says that even with two identical DXes, no two cancers are alike. It is individual...

I love hearing "we are going to be able to..." but what I really want to hear is "we are now able to..."!

Hurry, Hurry, please!