Introduction
Materials and methods
Microarray data
Metagenes for feature reduction
Assessment of ER, HER2, proliferative status and tumors with stem-cell-like characteristics of the samples
Immunohistochemistry
Statistical analyses
Results
Metagene | Incorporated genesa |
---|---|
IgG | Most of the genes in this cluster represent genes of immunoglobulins of the immunoglobulin gamma type mainly associated with B lymphocytes |
HCK | This cluster encompasses genes specific for macrophages and cells of the monocyte/myeloid lineage such as hemopoietic cell kinase, CD163, Chemokine (C-C motif) receptor 1 (CCR1), complement receptors, and B7-2 |
MHC-II | This cluster contains the HLA-DP, HLA-DQ, HLA-DR genes of the major histocompatability class II complex expressed on the surface of professional antigen-presenting cells for their interaction with T cells |
LCK | Genes in this cluster contain T-cell-specific markers such as CD3, T-cell receptor α, T-cell receptor β, lymphocyte-specific kinase, IL-7 receptor |
MHC-I | This cluster contains HLA-A, HLA-B, HLA-C, HLA-F and HLA-G genes of the major histocompatability class I complex common to all cell types for the presentation of intracellular antigens |
STAT1 | The genes in this cluster are associated with interferon signal transduction (like signal transducer and activator of transcription 1 and interferon regulatory factor 1 (IRF1)) and are also interferon inducible |
Interferon | All genes in this cluster represent genes known to be interferon inducible and that are associated with the interferon response of cells |
Expression of the metagene clusters in different immunological cell types
Relationship of expression of immune-system-related metagenes with ER status, HER2 status and presence of stem-cell-like markers and lymphocyte infiltration
Prognostic value of immune-system-related metagenes in subgroups of breast cancer patients
Parameter | Stratification |
n
1
a
|
n
2
a
| P valueb | Hazard ratio | 95% confidence interval |
---|---|---|---|---|---|---|
Lymphocyte-specific kinase metagene | Low vs. high | 60 | 64 |
0.017
| 2.16 | 1.15 to 4.03 |
Lymph node status | LNN vs. N1 | 89 | 35 | 0.059 | 1.84 | 0.98 to 3.47 |
Age | >50 years vs. ≤ 50 years | 71 | 53 | 0.91 | 0.97 | 0.53 to 1.78 |
Pathological grading | Poor vs. well/intermediate | 83 | 41 | 0.97 | 1.01 | 0.53 to 1.95 |
Tumor size | >2 cm vs. ≤ 2 cm | 76 | 48 | 0.078 | 1.85 | 0.93 to 3.66 |
Human epidermal growth factor receptor 2 status | Positive vs. negative | 45 | 79 | 0.78 | 1.09 | 0.58 to 2.05 |
Parameter |
n
1
a
|
n
2
a
| P valueb | Hazard ratio | 95% confidence interval | |
---|---|---|---|---|---|---|
Lymphocyte-specific kinase metagene | Low vs. high | 21 | 16 |
0.011
| 4.17 | 1.38 to 12.6 |
Lymph node status | LNN vs. N1 | 24 | 13 | 0.438 | 0.69 | 0.27 to 1.77 |
Age | >50 years vs. ≤ 50 years | 18 | 19 | 0.558 | 1.38 | 0.47 to 4.09 |
Pathological grading | Poor vs. well/intermediate | 19 | 18 | 0.097 | 2.27 | 0.86 to 5.99 |
Tumor size | >2 cm vs. ≤ 2 cm | 15 | 22 | 0.405 | 1.63 | 0.52 to 5.12 |