Patient classification
View Patent ↗Clinical patient tissue samples are classified according to the physiological status of cells present in the sample. In some embodiments of the invention, such cells are classified according to their ability to respond to therapeutic agents and treatments. In other embodiments, the cells or tissue samples are classified according to their status with respect to the activity of pathways of interest. The information thus derived is useful in prognosis and diagnosis, and can further be used develop surrogate markers for disease states, and to investigate the effect of genetic polymorphisms in the responsiveness and state of cells involved in disease.
1. A method of preparing a biomap for the classification of a patient sample according to the physiological status of cells or constituents present in the sample, the method comprising:
contacting a patient sample in a test cell culture with at least two factors acting on said cells in an amount and incubating for a time sufficient to induce a plurality of pathways active in said cell culture;
recording changes in at least two parameter readouts associated with said plurality of pathways;
deriving a biomap from said changes in parameter readouts, wherein said biomap comprises data normalized to be a ratio of test to control data on the sample type under control conditions; and
analyzing said biomap by a pattern recognition algorithm to quantify relatedness of said biomap to reference biomaps that include one or more of biomaps of normal cells, cells from similarly diseased tissue, or from cell lines with responses induced by assay combinations involving known pathway stimuli or inhibitors, wherein the presence or absence of relatedness to said reference biomaps provides a characterization of the physiological status of cells or constituents present in the sample.
2. The method according to claim 1 , wherein said cell culture comprises patient cells, non-patient indicator cells, or a mixture thereof.
3. The method according to claim 1 , wherein said patient sample is distributed in a panel of cell culture assay combinations, wherein at least one of said assay combinations is a control cell culture differing in at least one component from said test cell culture; wherein said component can be a factor, a biologically active agent or other environmental condition.
4. A method for characterization of a cellular patient sample as to the ability of cells in the sample to respond to a therapeutic agent, the method comprising:
contacting the therapeutic agent with a patient sample comprising cells in a test cell culture with at least two factors acting on said cells in an amount and incubating for a time sufficient to induce a plurality of pathways active in said cell culture;
recording changes in at least four parameter readouts associated with said plurality of pathways as a result of introduction of the therapeutic agent;
deriving a biomap from said changes in parameter readouts, wherein said biomap comprises data normalized to be a ratio of test to control data on the sample under control conditions in the absence of the therapeutic agent; and
analyzing said biomap by a pattern recognition algorithm to quantify relatedness of said biomap to reference biomaps that include one or more of biomaps of normal cells, cells from similarly diseased tissue, or from cell lines with responses induced by assay combinations involving known pathway stimuli or inhibitors, wherein the presence or absence of relatedness to said reference biomaps provides a characterization of the signaling pathway responsiveness of said patient sample to said therapeutic agent.
5. The method according to claim 4 , wherein said patient sample comprises two or more distinct types of cells.
6. The method according to claim 5 , wherein said distinct types of cells are selected from the group consisting of endothelial cells, tumor cells, lymphocytes, monocytes, epithelial cells, neoplastic cells and mast cells.
7. The method according to claim 5 , wherein cells in said patient sample are separated according to phenotype prior to said contacting step.
8. The method according to claim 1 , further comprising the step of analyzing said cellular patient sample for the presence of nucleic acid polymorphisms.
9. The method according to claim 4 , further comprising the step of correlating said biomap with patient history and clinical diagnosis.
10. The method of claim 4 , wherein said method further comprises contacting the patient sample with a combination of therapeutic agents.
11. A method for characterization of an acellular patient sample for the activity of constituents in the sample, the method comprising:
contacting the acellular patient sample with cells in a test cell culture comprising at least two factors acting on said cells in an amount and incubated for a time sufficient to induce a plurality of pathways active in said cell culture;
recording changes in at least four parameter readouts associated with said plurality of pathways as a result of introduction of the acellular patient sample;
deriving a biomap from said changes in parameter readouts, wherein said biomap comprises data normalized to be a ratio of test to control data on the sample under control conditions in the absence of the acellular patient sample; and
analyzing said biomap by a pattern recognition algorithm to quantify relatedness of said biomap to reference biomaps that include one or more of biomaps of normal cells, cells from similarly diseased tissue, or from cell lines with responses induced by assay combinations involving known pathway stimuli or inhibitors, wherein the presence or absence of relatedness to said reference biomaps provides a characterization of the signaling pathway responsiveness of the cell culture to the acellular patient sample.