Methods for diagnosis, prognosis and methods of treatment

Abstract

This invention is directed to methods and compositions for diagnosis, prognosis and for determining methods of treatment. The physiological status of cells present in a sample (e.g. clinical sample) can be used in diagnosis or prognosis of a condition (e.g. Chronic Lymphocytic Leukemia), in patient selection for therapy, to monitor treatment and to modify or optimize therapeutic regimens. The physiological status of a cell can be determined by comparing the intracellular status of one or more activation elements (e.g. the phosphorylation status of a signaling molecule) in a cell (e.g. a cancer cell) to that of another cell (e.g. a normal cell). The physiological status of a cell can be further classified by adding one or more modulators (e.g. an inhibitor or activator) to the cell in question. In some embodiments, the invention is directed to methods of determining a phenotypic profile of a population of cells.

1 - 50 . (canceled) 
     
     
         51 . A method of treating an individual suffering from chronic lymphocytic leukemia (CLL) comprising treating the individual based on the outcome of a test comprising
 (i) contacting cells from the individual with a modulator;   (ii) determining the level of one or more activatable elements in the cells on a single cell basis; and   (iii) from the results of (ii), determining that the individual is suffering from an aggressive CLL, thereby requiring treatment.   
     
     
         52 . The method of  claim 51  wherein the cells are from a blood or blood-derived sample from the individual. 
     
     
         53 . The method of  claim 52  wherein the cells are from a peripheral blood mononuclear cell sample. 
     
     
         54 . The method of  claim 51  wherein the modulator comprises F(ab)2 IgM, H 2 O 2 , PMA, BAFF, April, SDF1a, CD40L, IGF-1, Imiquimod, polyCpG, IL-7, IL-6, IL-10, IL-27, IL-4, IL-2, IL-3, thapsigargin or a combination thereof. 
     
     
         55 . The method of  claim 51  wherein the modulator is selected from the group consisting off F(ab)2 IgM, H 2 O 2 , PMA, BAFF, April, SDF1a, and combinations thereof. 
     
     
         56 . The method of  claim 51  wherein the modulator comprises F(ab)2IgM. 
     
     
         57 . The method of  claim 51  further comprising determining a cell surface marker on the cells, wherein the cell surface marker is selected from the group consisting of CD1, CD2, CD3, CD4, CD5, CD8, CD10, CD14, CD19, CD20, CD22, CD23, CD40, CD52, CD100, CD280, CD281, CD282, CD283, CD284, and CD289 and combinations thereof. 
     
     
         58 . The method of  claim 51  wherein the cell surface marker is selected from the group consisting of CD3, CD5, CD19, CD20, and combinations thereof. 
     
     
         59 . The method of  claim 51  wherein the activatable element is selected from the group consisting of Akt1, Akt2, Akt3, SAPK/JNK1,2,3, p38s, Erk1/2, Syk, ZAP70, Btk, BLNK, Lck, PLCγ, PLC1γ 2 , STAT1, STAT 3, STAT 4, STAT 5, STAT 6, CREB, Lyn, p-S6, Cbl, NF-κB, GSK3β, CARMA/Bcl10 and Tcl-1. 
     
     
         60 . The method of  claim 59  wherein the activatable element is selected from the group consisting of Akt1, Akt2, Akt3, Syk, Erk 1/2, and combinations thereof. 
     
     
         61 . The method of  claim 59  wherein the activatable element is selected from the group consisting of Syk, Erk 1/2, and a combination thereof. 
     
     
         62 . A kit comprising
 a modulator selected from the group consisting of F(ab)2 IgM, H 2 O 2 , PMA, BAFF, April, SDF1a, CD40L, IGF-1, Imiquimod, polyCpG, IL-7, IL-6, IL-10, IL-27, IL-4, IL-2, IL-3, thapsigargin and a combination thereof;   an antibody specific for is a protein selected from the group consisting of Akt1, Akt2, Akt3, SAPK/JNK1,2,3, p38s, Erk1/2, Syk, ZAP70, Btk, BLNK, Lck, PLCγ, PLC1γ 2 , STAT1, STAT 3, STAT 4, STAT 5, STAT 6, CREB, Lyn, p-S6, Cbl, NF-κB, GSK3β, CARMA/Bcl10 and Tcl-1; and   an antibody specific for a surface marker selected from the group consisting of CD1, CD2, CD3, CD4, CD5, CD8, CD10, CD14, CD19, CD20, CD22, CD23, CD40, CD52, CD100, CD280, CD281, CD282, CD283, CD284, and CD289 and combinations thereof.   
     
     
         63 . The kit of  claim 62  wherein the modulator is selected from the group consisting of F(ab)2 IgM, H 2 O 2 , PMA, BAFF, April, SDF1a, and combinations thereof. 
     
     
         64 . The kit of  claim 62  wherein the modulator comprises F(ab)2IgM. 
     
     
         65 . The kit of  claim 62  wherein the antibody specific for a protein is specific for a protein selected from the group consisting of Akt1, Akt2, Akt3, Syk, Erk 1/2, and combinations thereof. 
     
     
         66 . The kit of  claim 62  wherein the antibody specific for a protein is specific for a protein selected from the group consisting of Syk, Erk 1/2, and a combination thereof. 
     
     
         67 . The kit of  claim 62  wherein the antibody specific for a protein is specific for Erk ½. 
     
     
         68 . The kit of  claim 62  wherein the antibody specific for a cell marker is specific for a cell marker selected from the group consisting of CD3, CD5, CD19, CD20, and combinations thereof. 
     
     
         69 . The kit of  claim 62  wherein the antibody specific for a cell marker is specific for a cell marker selected from the group consisting of CD19, CD20, and a combination thereof. 
     
     
         70 . The kit of  claim 62  further comprising instructions for use. 
     
     
         71 . The kit of  claim 62  further comprising one or more of a buffering agents, a stabilizing agent, agents for reducing background interference in a test, control reagents, or apparatus for conducting a test, or a combination thereof. 
     
     
         72 . The kit of  claim 62  wherein the components are packaged together.