Differential expression and biological importance

Cure Arthritis Naturally

Cure Arthritis Naturally

Get Instant Access

Statistical measures determine the variability between samples. Intensity of signals and signal differences influence this measure. Signals reflect the abundance of

Figure 1

Signal log ratios (SLR) of expression comparison analysis between different normal donors (ND) or patients with rheumatoid arthritis (RA) using monocytes from peripheral blood (Mo) or synovial tissues (Syn). Expression was compared with MAS 5.0 software (Affymetrix). The distribution of SLR values by box-plots demonstrates that comparison of different cell types from the same donor group (ND Mo vs ND Syn) reveals more and higher differences than comparison between the same cell type (Mo or Syn) from different individuals from the same (ND vs ND or RA vs RA) or even different donor groups (RA vs ND).

Figure 1

Signal log ratios (SLR) of expression comparison analysis between different normal donors (ND) or patients with rheumatoid arthritis (RA) using monocytes from peripheral blood (Mo) or synovial tissues (Syn). Expression was compared with MAS 5.0 software (Affymetrix). The distribution of SLR values by box-plots demonstrates that comparison of different cell types from the same donor group (ND Mo vs ND Syn) reveals more and higher differences than comparison between the same cell type (Mo or Syn) from different individuals from the same (ND vs ND or RA vs RA) or even different donor groups (RA vs ND).

mRNA in a given sample. This abundance is related to the functional category to which a gene belongs. And functional importance does not always relate to the intensity of signal or signal differences. Figure 2 demonstrates such differences in

Figure 2

Expression signals of different genes in different cell types. Different molecular functions (extracellular or intracellular action, martrix production or signalling) require different absolute quantities, or changes of quantities upon activation. IgG, immunoglobulin G; MMP1, matrix metalloproteinase 1; HLA, human leukocyte antigen; CXCL12, chemokine SDF1; CXCR4, receptor for SDF1; TNF-a, tumor necrosis factor alpha; IL1-P, interleukin-1 beta; IL1R, receptor for IL1-P; STAT1, signal transducer and activator of transcription 1; FYB, FYN binding protein; RA, rheumatoid arthritis; ND, normal donor; OA, osteoarthritis; Mo, monocytes; CD4, CD4 positive T-cells; Syn, synovial tissue.

Figure 2

Expression signals of different genes in different cell types. Different molecular functions (extracellular or intracellular action, martrix production or signalling) require different absolute quantities, or changes of quantities upon activation. IgG, immunoglobulin G; MMP1, matrix metalloproteinase 1; HLA, human leukocyte antigen; CXCL12, chemokine SDF1; CXCR4, receptor for SDF1; TNF-a, tumor necrosis factor alpha; IL1-P, interleukin-1 beta; IL1R, receptor for IL1-P; STAT1, signal transducer and activator of transcription 1; FYB, FYN binding protein; RA, rheumatoid arthritis; ND, normal donor; OA, osteoarthritis; Mo, monocytes; CD4, CD4 positive T-cells; Syn, synovial tissue.

signal intensities related to function for representative genes of different categories, extracellular effectors and extra- and intracellular signalling.

Extracellular effector molecules like immunoglobulins and matrix molecules (collagens) are needed in high abundance and are therefore represented in the array with high signal intensities. Proteases involved in matrix turnover can cleave more than one matrix molecule. This may explain that expression levels are very low in normal tissue and are significantly increased only in exacerbating destructive processes like in RA.

Signalling molecules are expressed at different levels depending on 1) extracellular or intracellular location, 2) long or short distance action, 3) pre-formation and activation on the protein level or newly transcribed and synthesised as immediately active molecules. Chemokines like SDF1 are involved in extracellular long distance signalling and may become newly transcribed and highly expressed when needed. In contrast, the corresponding receptor CXCR4 is pre-formed on the surface of normal cells. High numbers of receptor molecules may compensate for smaller concentrations of signalling molecules which are diluted with increasing distance from the producer cell. Intensities measured for the receptor may even exceed those for the signalling molecule in a mixed sample. Short acting proinflammatory cytokines like TNF alpha and IL-1, which signal for danger and act in small concentrations, are strictly controlled. This may explain the low intensities and the difficulties to detect such important players in the inflammatory process. This problem may be aggravated by the analysis of mixtures of different cells, which may further dilute the concentration of low abundant messages. In contrast, intracellular signalling molecules like STAT1 or FYB are preformed molecules regulated on the protein level and may become transcribed higher only to a small extent as intracellular concentration will quickly increase and multiply intracellular effects.

These dependencies between biological importance and mathematical selection process are very critical and need to be considered for interpretation of expression results. They may explain why TNF inhibition is a successful therapy in arthritis although array results would not point to this cytokine as the key player [5]. Similarly, no interferon was identified in the SLE studies. In fact, the activity of such signalling molecules may be much easier identified by determining the signatures which are induced by these molecules [10].

Was this article helpful?

0 0
Arthritis Relief Now

Arthritis Relief Now

When you hear the word arthritis, images of painful hands and joints comes into play. Few people fully understand arthritis and this guide is dedicated to anyone suffering with this chronic condition and wants relief now.

Get My Free Ebook


Post a comment