Introduction
Methods
Identification of parity-related gene expression signature
Study population and sample handling
Data analysis
Expression of identified parity signature in tumor and paired adjacent normal tissues
Study population and sample handling
Data analysis
Comparison with previously published parity signatures
Results
Comparison of sample sets
Study demographics | PVLSI | SHLb[12] | UICHb[24] | PBCS cancer-adjacent normal tissue | PBCS tumor tissue |
---|---|---|---|---|---|
Cancer status | Cancer-free | Cancer-free | Cancer-free | Breast cancer | Breast cancer |
Tissue source | Fresh whole tissue | Core needle biopsies | Microdissected FFPE tissue | Fresh whole tissue | Fresh whole tissue |
Tissue enrichment | Stroma | Epithelial and stromal | Epithelial | Stroma | Epithelial |
Gene expression platform | Agilent 4 × 44K | GeneChip U133Plus 2.0 | RT-PCR of 64 genes | Agilent 4 × 44K | Illumina |
Samples | |||||
Total | 130 | 107 | 24 | 150 | |
ER+, n (%) | N/A | N/A | N/A | 117 (78%) | |
Parous, n (%) | 76 (58%) | 67 (63%) | 11 (46%) | 119 (79%) | |
Premenopausal, n (%) | 84 (65%) | 0 (0%) | 24 (100%) | 41 (27%) | |
Mean age (±SD), yr | 37 (13) | 60 (5) | 29 (6) | 56 (10) | |
Mean BMI (±SD) | 30c (6) | 25 (4) | – | 28 (5) |
Discovery of parity signature in PVLSI mammoplasty specimens
GO category | Gene names | Total | Up | P-value | FDR |
---|---|---|---|---|---|
[GO: 0002376] Immune system process | KLHL6, HCLS1, LAT2, CD93, SLC7A7, DOK2, NCF4, PTPRC, VNN1, CD38, MAFB, CCL2, ITK, ATP6V0A2, HCK, BLNK, TBX21, FCGR2B, FYB, BPGM, SCIN, CLEC4A, CD244, CD247, TFEB, SNCA, CD48, TNFSF13B, IL6R, TLR3, CDKN2A, P2RX7, SYK, LCP1, C3AR1, ENPP3, ANXA3, VAV1, LCP2, NDFIP1, CD14, TLR1, CD83, CSF1, TLR7, ITGAM, BST1, HLA-DMA, CYBB, EPB42, PRG4, NCF1, WAS, SIX1, TLR6, CCR1, IL1R2, EDA, ITGB2, NCF2, CD28, CCL3 | 1,040 | 62 | 5.3E-19 | < 0.001 |
[GO: 0006955] Immune response | KLHL6, ENPP3, ANXA3, LAT2, LCP2, NDFIP1, NCF4, PTPRC, CD14, VNN1, CD38, TLR1, CD83, CCL2, TLR7, ITK, ATP6V0A2, BLNK, TBX21, FCGR2B, FYB, BST1, CLEC4A, HLA-DMA, CYBB, PRG4, CD247, NCF1, TFEB, SNCA, WAS, TNFSF13B, IL6R, TLR3, TLR6, CCR1, IL1R2, EDA, ITGB2, SYK, P2RX7, NCF2, LCP1, CD28, CCL3, C3AR1 | 611 | 46 | 8.9E-18 | < 0.001 |
[GO: 0006952] Defense response | RNASE6, ANXA3, ADORA3, C1ORF38, ESR2, NDFIP1, PTPRC, CD14, VNN1, NLRC4, TLR1, CD83, CCL2, TLR7, ITK, HCK, BLNK, NOX4, HRH1, CLEC4A, CYBB, CD247, NCF1, SNCA, WAS, CD48, IL6R, LILRB3, TLR3, ALOX5AP, TLR6, AIF1, CCR1, ITGB2, P2RX7, LILRA3, NCF2, CD28, CCL3, C3AR1 | 578 | 40 | 3.1E-14 | < 0.001 |
[GO: 0045321] Leukocyte activation | ANXA3, VAV1, LAT2, CD93, LCP2, NDFIP1, PTPRC, VNN1, TLR1, CD38, CD83, CSF1, TLR7, BLNK, ITGAM, TBX21, HLA-DMA, CD247, SNCA, WAS, CD48, TNFSF13B, TLR3, CDKN2A, TLR6, P2RX7, SYK, LCP1, CD28 | 336 | 29 | 7.5E-13 | < 0.001 |
[GO: 0006954] Inflammatory response | CYBB, ADORA3, C1ORF38, NDFIP1, CD14, IL6R, VNN1, NLRC4, TLR1, TLR3, ALOX5AP, CCL2, TLR7, AIF1, TLR6, CCR1, ITGB2, BLNK, P2RX7, NOX4, HRH1, C3AR1, CCL3 | 265 | 23 | 1.9E-10 | < 0.001 |
[GO: 0002682] Regulation of immune system process | KLHL6, VAV1, LAT2, LCP2, NDFIP1, PTPRC, VNN1, CD38, CD83, MAFB, CSF1, TLR7, ITK, HCK, TBX21, FCGR2B, FYB, SCIN, HLA-DMA, CD247, SNCA, TNFSF13B, WAS, IL6R, TLR3, CDKN2A, TLR6, ITGB2, SYK, P2RX7, CD28, C3AR1 | 513 | 32 | 2.5E-10 | < 0.001 |
[GO: 0002274] Myeloid leukocyte activation | TLR1, TLR3, ANXA3, CSF1, LAT2, CD93, TLR7, TLR6, LCP2, SYK, SNCA, CD48 | 63 | 12 | 6.9E-10 | < 0.001 |
[GO: 0009611] Response to wounding | VAV1, IL10RA, SLC7A7, ADORA3, C1ORF38, LCP2, DOK2, NDFIP1, CD14, GATM, VNN1, TLR1, NLRC4, CCL2, TLR7, BLNK, ITGAM, NOX4, HRH1, CYBB, CD244, WAS, CD48, IL6R, TLR3, ALOX5AP, TLR6, AIF1, CCR1, ITGB2, SYK, P2RX7, LAMP2, PIK3CG, CCL3, C3AR1 | 671 | 36 | 1.1E-09 | < 0.001 |
[GO: 0001775] Cell activation | ANXA3, VAV1, LAT2, CD93, LCP2, NDFIP1, PTPRC, VNN1, CD38, TLR1, CD83, CSF1, TLR7, BLNK, ITGAM, TBX21, HLA-DMA, CD247, SNCA, WAS, CD48, TNFSF13B, TLR3, CDKN2A, TLR6, P2RX7, SYK, LAMP2, LCP1, CD28, PIK3CG | 520 | 31 | 1.5E-09 | < 0.001 |
[GO: 0050896] Response to stimulus | HCLS1, KLHL6, FPR3, ANG, LAT2, IL10RA, SLC7A7, CACNA2D4, C1ORF38, PTGIS, DOK2, NCF4, PTPRC, VNN1, PTPRO, CD38, NLRC4, FGF1, CCL2, ITK, ATP6V0A2, HCK, PTGS1, BLNK, TBX21, NOX4, HRH1, FCGR2B, FYB, CLEC4A, HTR2B, CD244, CD247, TFEB, SNCA, TNFSF13B, CD48, IL6R, LILRB3, TLR3, ALOX5AP, CDKN2A, AIF1, SYK, P2RX7, LILRA3, LCP1, CRY1, LAMP2, C3AR1, ENPP3, ANXA3, RNASE6, VAV1, ADORA3, LCP2, ESR2, NDFIP1, CD14, GATM, DYNLRB1, TLR1, CD83, TBXAS1, KCNQ1, CYP4V2, C20ORF39, HSPA6, TLR7, CYB5R4, MAOB, ITGAM, ATP6V1F, BST1, HLA-DMA, CYBB, PRG4, NCF1, WAS, ABLIM2, GDF10, TLR6, CCR1, CNGA1, AGPS, IL1R2, EDA, ITGB2, NCF2, CD28, TFEC, PIK3CG, CCL3 | 3,121 | 93 | 2.0E-09 | < 0.001 |
Assessment of three parity signatures in mammoplasty samples, cancer-adjacent tissues and cancer tissues
PVLSI signature | SHL signature | UICH signature | ||||
---|---|---|---|---|---|---|
PVLSI normal tissues | ||||||
GSEA ESb | 0.98 | -0.52 | 0.71 | |||
GSEA FWERb | 0% (sig) | N/A | 3% (sig) | |||
Creighton analysisc | Negative | Positive | Negative | Positive | Negative | Positive |
Nulliparous | 37 (69%) | 17 (31%) | 22 (41%) | 32 (59%) | 33 (61%) | 21 (39%) |
Parous | 27 (36%) | 49 (64%) | 45 (59%) | 31 (41%) | 30 (39%) | 46 (61%) |
OR (95% CI)d | 3.95 (1.88 to 8.29) | 0.47 (0.23 to 0.96) | 2.4 (1.18 to 4.92) | |||
P-valuee | 0.0002 (sig) | N/A | 0.015 (sig) | |||
PBCS cancer-adjacent normal tissues | ||||||
GSEA ESb | 0.52 | 0.24 | 0.60 | |||
GSEA FWERb | 5% (sig) | 37% | 14% (sig) | |||
Creighton analysisc | Negative | Positive | Negative | Positive | Negative | Positive |
Nulliparous | 17 (57%) | 13 (43%) | 16 (53%) | 14 (47%) | 15 (50%) | 15 (50%) |
Parous | 58 (49%) | 61 (51%) | 62 (52%) | 57 (48%) | 62 (52%) | 57 (48%) |
OR (95% CI)d | 1.38 (0.61 to 3.08) | 1.05 (0.47 to 2.34) | 0.92 (0.41 to 2.05) | |||
P-valuee | 0.44 | 0.90 | 0.84 | |||
PBCS tumor tissues | ||||||
GSEA ESb | 0.47 | 0.40 | 0.58 | |||
GSEA FWERb | 18% | 24% | 21% | |||
Creighton analysisc | Negative | Positive | Negative | Positive | Negative | Positive |
Nulliparous | 16 (53%) | 14 (47%) | 14 (47%) | 16 (53%) | 21 (70%) | 9 (30%) |
Parous | 58 (49%) | 61 (51%) | 55 (46%) | 64 (54%) | 65 (55%) | 54 (45%) |
OR (95% CI)d | 1.20 (0.54 to 2.68) | 1.02 (0.56 to 2.27) | 1.94 (0.82 to 4.58) | |||
P-valuee | 0.65 | 0.96 | 0.13 |
Evaluation of parity signatures in benign cancer adjacent and cancer tissues by estrogen receptor status
Cancer-adjacent normal tissue, ER+ | Tumor tissue, ER+ | Cancer-adjacent normal tissue, ER- | Tumor tissue, ER- | |||||
---|---|---|---|---|---|---|---|---|
GSEA ESb | 0.45 | 0.50 | 0.37 | 0.31 | ||||
GSEA FWERb | 12% (sig) | 15% (sig) | 21% | 44% | ||||
Creighton analysisc | Negative | Positive | Negative | Positive | Negative | Positive | Negative | Positive |
Nulliparous | 16 (62%) | 10 (38%) | 15 (58%) | 11 (42%) | 1 (25%) | 3 (75%) | 1 (25%) | 3 (75%) |
Parous | 46 (51%) | 44 (49%) | 50 (56%) | 40 (44%) | 12 (43%) | 16 (57%) | 8 (29%) | 20 (71%) |
OR (95% CI)d | 1.53 (0.63 to 3.73) | 1.91 (0.45 to 2.6) | 0.44 (0.04 to 4.82) | 0.83 (0.07 to 9.25) | ||||
P-valuee | 0.35 | 0.85 | 0.63 | 1.00 |
Gene symbol | Gene name | FCb | P-valueb | FDRb |
---|---|---|---|---|
CD163L1 | Scavenger receptor cysteine-rich type 1 protein M160 | 1.50 | 0.00006 | 0 |
FCGR2A | Fc fragment of IgG, low affinity IIa, receptor for (CD32) | 1.61 | 0.00006 | 0 |
ALOX5AP | Arachidonate 5-lipoxygenase-activating protein | 1.52 | 0.00007 | 0 |
VNN1 | Vanin 1 | 1.62 | 0.00007 | 0 |
CD33 | CD33 antigen (gp67) | 1.54 | 0.00007 | 0 |
CD28 | CD28 antigen (Tp44) | 1.84 | 0.00007 | 0 |
FCGR2B | Fc fragment of IgG, low-affinity IIb, receptor for (CD32) | 1.92 | 0.00009 | 0 |
EAF2 | ELL-associated factor 2 | 1.27 | 0.00009 | 0 |
LCP2 | Lymphocyte cytosolic protein 2 | 1.25 | 0.00011 | 0 |
IL10RA | Interleukin 10 receptor, α | 1.32 | 0.00011 | 0 |
BLNK | B-cell linker | 1.34 | 0.00012 | 0 |
SAMSN1 | SAM domain, SH3 domain and nuclear localization, 1 | 1.43 | 0.00013 | 0 |
CYB5R4 | NADPH cytochrome B5 oxidoreductase | 1.33 | 0.00017 | 0 |
HTR2B | 5-hydroxytryptamine (serotonin) receptor 2B | 1.69 | 0.00031 | 0 |
TTC7A | Tetratricopeptide repeat domain 7A | 1.17 | 0.00032 | 0 |
ATP6V1F | ATPase, H + transporting, lysosomal 14 kDa, V1 subunit F | 1.20 | 0.00034 | 0 |
TLR7 | Toll-like receptor 7 | 1.28 | 0.00037 | 0 |
ANKRD27 | Ankyrin repeat domain 27 (VPS9 domain) | 1.19 | 0.00041 | 0 |
ITGAM | Integrin, α M | 1.55 | 0.00044 | 0 |
CCDC109B | Hypothetical protein FLJ20647 | 1.27 | 0.00045 | 0 |
CPVL | Carboxypeptidase, vitellogenic-like | 1.48 | 0.00048 | 0 |
LEPROTL1 | Leptin receptor overlapping transcript-like 1 | 1.19 | 0.00062 | 0.003 |
CCR1 | Chemokine (C-C motif) receptor 1 | 1.30 | 0.00068 | 0.004 |
S100A10 | S100 calcium binding protein A10 | 1.45 | 0.00073 | 0.004 |
ALG14 | Hypothetical protein MGC19780 | 1.26 | 0.00093 | 0.004 |
SLC7A7 | Solute carrier family 7, member 7 | 1.30 | 0.00093 | 0.004 |
CHRDL1 | Chordin-like 1 | 1.52 | 0.00095 | 0.004 |
S100A4 | S100 calcium binding protein A4 | 1.40 | 0.00098 | 0.004 |
ITGAE | Integrin α E | 1.27 | 0.00098 | 0.004 |
CCL2 | Chemokine (C-C motif) ligand 2 | 1.51 | 0.00102 | 0.004 |
CYP4X1 | Cytochrome P450, family 4, subfamily X, polypeptide 1 | 1.49 | 0.00128 | 0.004 |
CCNDBP1 | Cyclin D-type binding-protein 1 | 1.18 | 0.00144 | 0.006 |
TNFSF13B | Tumor necrosis factor (ligand) superfamily, member 13b | 1.30 | 0.00148 | 0.006 |
BLVRA | Biliverdin reductase A | 1.24 | 0.00163 | 0.006 |
C8orf40 | Hypothetical protein BC013035 | 1.15 | 0.00174 | 0.006 |
BIN2 | Bridging integrator 2 | 1.20 | 0.00185 | 0.006 |
CD48 | CD48 antigen (B-cell membrane protein) | 1.26 | 0.00188 | 0.006 |
TSG101 | Tumor susceptibility gene 101 | 1.13 | 0.00199 | 0.006 |
GLRX | Glutaredoxin (thioltransferase) | 1.40 | 0.00200 | 0.006 |
B3GALT4 | β 1,3-galactosyltransferase, polypeptide 4 | 1.25 | 0.00206 | 0.006 |