Customized molecular phenotyping by quantitative gene expression and pattern recognition analysis

Abstract

Description of the molecular phenotypes of pathobiological processes in vivo is a pressing need in genomic biology. We have implemented a high-throughput real-time PCR strategy to establish quantitative expression profiles of a customized set of target genes. It enables rapid, reproducible data acquisition from limited quantities of RNA, permitting serial sampling of mouse blood during disease progression. We developed an easy to use statistical algorithm--Global Pattern Recognition--to readily identify genes whose expression has changed significantly from healthy baseline profiles. This approach provides unique molecular signatures for rheumatoid arthritis, systemic lupus erythematosus, and graft versus host disease, and can also be applied to defining the molecular phenotype of a variety of other normal and pathological processes.

Figure 1

Reproducibility and sensitivity of the ImmunoQuantArray. Raw Ct values for each of the 96 genes in the IQA are plotted. The linear regression best-fit line is shown and its correlation coefficient indicated. (A) Spleen cDNAs (left panel) or blood cDNAs (middle panel) from two C57BL/6J males. The average of the two spleen cDNA Cts is compared with the average two blood cDNA Cts (right panel). (B) The average spleen cDNA Cts of five BALB/cJ (left), three 129X1/SvJ (middle), or five BXSB/MpJ-Yaa⁺ (right) males was compared with the average spleen cDNA Cts of five C57BL/6J males. The point lying closest to the ordinate is 18S rRNA.

Figure 2

Serial molecular phenotyping of BXSB-Yaa SLE. Spleen cDNAs from cohorts of three to five BXSB/MpJ-Yaa males and age-matched BXSB.B6-Yaa⁺ controls were subjected to IMQ/GPR analysis at weeks 4, 6, 8, and 14. The fold changes (normalized to 18S rRNA) of genes that received a GPR score ≥0.4 and were significant after normalization to 18S rRNA are plotted.

Figure 3

Molecular phenotype of GVHD progression. Bone marrow and splenocytes from C57BL/6J females were used to induce GVHD in five allogenic 129P3/J males (C57BL6/J → 129P3/J). Five syngeneic transplant recipients (C57BL6/J → C57BL6/J) were used as controls. cDNAs were prepared from samples collected on days 7 and 9 after the transplant and were subjected to IMQ/GPR analysis. The fold changes of genes that received a GPR score ≥0.4 and were significant after normalization to 18S rRNA are shown.