Methods for artificial combinatorial control of biological systems

A therapeutic method against a hematological cancer, the method comprising:

• a) providing a biological sample from blood or bone marrow of a patient suffering from a hematological cancer, the sample comprising cells;
• b) providing a plurality of control molecules as a set of control molecules, wherein each control molecule of the set is independently selected from the group consisting of a microRNA, a small molecule, a peptide, a protein, a cytokine, and a metabolite;
• c) isolating cancer cells using density gradient centrifugation;
• d) obtaining RNA sequence data from the cancer cells and selecting a subset of control molecules from a measure of enrichment in differentially expressed genes in groups including targets of the control molecules and their neighbors within a network model of intracellular interactions, wherein the enrichment in differentially expressed genes is measured by measuring and comparing RNA expression data of the cancer cells and the control cells;
• e) assaying the subset of control molecules with the cells using an endpoint assay to obtain a set of assay results for a biological effect, wherein the endpoint assay is selected from the group consisting of an assay that determines growth, survival, or death of a living cell or an assay that determines differentiation from one cell type to another cell type under in vitro testing conditions providing a significant correlation between the effects of the same drugs in vitro and in vivo;
• f) executing a software platform that manages design of combinations with an algorithm, exchanges files between liquid handling and plate readout equipment, maps combinations to measured data, and compiles results;
• g) searching with a liquid handler, multi-well plates and a plate reader, an experimental space over iterations of measurements;
• h) retrieving and storing files from a database to identify reagents, track reagent combinations dispensed in wells of a series of multi-well plates, maintain assay data measured for each combination, and generate plate maps and files for interfacing liquid handlers and plate readers while searching the experimental space;
• i) searching the set of assay results to identify a subset of control molecules, wherein
• i) the subset of control molecules is composed of at least three of the plurality of control molecules,
• ii) each of the control molecules of the subset binds at least three targets,
• iii) each of the at least three targets binds at least three of the control molecules in the subset, and
• iv) at least three of the control molecules of the subset bind to one or more shared targets, wherein a shared target is a target that binds at least two of the control molecules;
• further wherein each target is a molecule independently selected from the group consisting of a cellular protein, an RNA, and a metabolite;
• j) providing the identified subset of control molecules as contributing to a combinatorial therapy for a patient having a same hematological cancer;
• and
• k) administering the subset of control molecules to the patient.