Cell-type-specific patterns of gene expression
Among the methods, compositions, combinations and kits provided herein are those for determining gene expression levels in one or more cell types in heterogeneous cell samples, for identifying genes differentially expressed in different cell types, and for detecting a cell type in a sample from a subject. Also provided herein are methods, compositions, combinations and kits for determining gene expression levels in cells corresponding to phenotypes, and for identifying a phenotype of a subject by detecting differentially expressed genes.
1. A method of determining gene expression levels in prostate tissue samples from subjects diagnosed as having prostate cancer, comprising the steps of:
(a) assaying the relative content of malignant and non-malignant cells within each of two or more heterogeneous prostate tissue samples from subjects diagnosed as having prostate cancer, wherein at least two of the samples do not contain the same relative content of malignant and non-malignant cells, and wherein the assaying is done without physically separating the malignant from the non-malignant cells in the sample;
(b) measuring the overall level of each of a plurality of different RNA expression analytes extracted from each prostate tissue sample without physically separating the malignant from the non-malignant cells in the sample, such that each measured level corresponds to the combined expression of an RNA expression analyte in malignant and nonmalignant cells;
(c) determining a linear or non-linear regression relationship between the relative content of malignant and non-malignant cells in each sample and the measured overall levels of the plurality of different RNA analytes in each sample to provide a quantitative relationship therebetween;
(d) using the regression relationship determined in step (c) to calculate the level of each of the plurality of different RNA expression analytes in the malignant cells and in the non-malignant cells separately, wherein the calculated levels of analytes correspond to the gene expression levels; and
(e) outputting to a display information regarding the calculated levels of analytes.
2. The method of claim 1 , further comprising a step of identifying genes differentially expressed in malignant cells relative to non-malignant cells, or in non-malignant cells relative to malignant cells.
3. The method of claim 1 , wherein the step of determining the regression relationship further comprises determining the regression of overall levels of each RNA expression analyte on the proportion of malignant and non-malignant cells.
4. The method of claim 1 , wherein step (c) comprises determining a linear regression relationship between the relative content of malignant and non-malignant cells in each sample and the measured overall levels of the plurality of different RNA analytes in each sample to provide a quantitative relationship therebetween, using Equation 1:
G
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j
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β
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assuming that the contribution to gene expression of any one cell type depends only on the proportion of that cell type and its corresponding characteristic cell-type expression level, β ij , wherein G jk is the average expression level of gene j in a sample k, and is the average of β ij weighted by cell type fractions x ki .