Introduction
Materials and methods
Functional and co‑expression analyses
TCGA
KM plotter online database
Nomogram
Stratified analyses
Immunohistochemistry
Genome-wide co-expression analysis and functional enrichment of type II CST prognostic genes
Statistical analyses
Results
Functional enrichment of type II CST genes and co-expression analysis
Survival analysis in the TCGA
Gene expression status | Patients (n = 351) | Events, n (%) | MST (days) | Crude HR (95% CI) | Crude P-value | Adjusted HRa (95% CI) | Adjusted P-valuea |
---|---|---|---|---|---|---|---|
CST1 | 0.913 | 0.094 | |||||
Low | 176 | 73 (41.5) | 940 | Ref. | Ref. | ||
High | 175 | 71 (40.6) | 782 | 1.02 (0.74–1.41) | 1.42 (0.94–2.13) | ||
CST2 | 0.018 | 0.030 | |||||
Low | 176 | 66 (37.5) | 1407 | Ref. | Ref. | ||
High | 175 | 78 (44.6) | 669 | 1.48 (1.07–2.06) | 1.57 (1.05–2.35) | ||
CST3 | 0.161 | 0.130 | |||||
Low | 176 | 69 (39.2) | 1294 | Ref. | Ref. | ||
High | 175 | 75 (42.9) | 792 | 1.26 (0.91–1.75) | 1.37 (0.91–2.05) | ||
CST4 | 0.018 | 0.010 | |||||
Low | 176 | 63 (35.8) | 1686 | Ref. | Ref. | ||
High | 175 | 81 (46.3) | 675 | 1.48 (1.07–2.06) | 1.69 (1.13–2.51) | ||
CST5 | 0.010 | 0.001 | |||||
Low | 176 | 64 (36.4) | 1407 | Ref. | Ref. | ||
High | 175 | 80 (45.7) | 661 | 1.53 (1.10–2.13) | 1.94 (1.29–2.91) | ||
CST6 | 0.030 | 0.515 | |||||
Low | 176 | 66 (37.5) | 1095 | Ref. | Ref. | ||
High | 175 | 78 (44.6) | 669 | 1.43 (1.03–1.99) | 1.15 (0.76–1.72) | ||
CST7 | 0.327 | 0.284 | |||||
Low | 176 | 73 (41.5) | 832 | Ref. | Ref. | ||
High | 175 | 71 (40.6) | 1095 | 0.85 (0.61–1.18) | 0.81 (0.54–1.20) |
Validation of the CST cohort using the KM plotter online database
Nomogram and stratified analysis
Variables | Total (n = 351) | Low CST2 (n) | High CST2 (n) | HR (95%CI) | Log-rank P-value |
---|---|---|---|---|---|
Gender | |||||
Male | 226 | 113 | 113 | 1.26 (0.85–1.86) | 0.249 |
Female | 125 | 63 | 62 | 1.59 (0.87–2.88) | 0.122 |
Age (years) | |||||
< 60 | 108 | 54 | 54 | 1.50 (0.78–2.89) | 0.220 |
≥ 60 | 240 | 120 | 120 | 1.27 (0.87–1.85) | 0.219 |
Missing | 3 | ||||
Location | |||||
Gastroesophageal junction | 84 | 42 | 42 | 1.60 (0.83–3.10) | 0.154 |
Body/fundus | 123 | 62 | 61 | 1.71 (0.98–2.98) | 0.057 |
Antrum | 130 | 65 | 65 | 1.19 (0.69–2.06) | 0.052 |
Missing | 14 | ||||
Hp infection | |||||
Positive | 18 | 9 | 9 | 1.31 (0.26–6.60) | 0.735 |
Negative | 143 | 72 | 71 | 1.46 (0.88–2.42) | 0.142 |
Missing | 190 | ||||
Histological_type | |||||
Intestinal | 160 | 80 | 80 | 1.46 (0.89–2.41) | 0.121 |
Diffuse Type | 61 | 31 | 30 | 1.10 (0.49–2.44) | 0.820 |
Signet Ring Type | 11 | 6 | 5 | 5.2 (0.79–34.09) | 0.005 |
Other | 118 | 59 | 59 | 1.05 (0.60–1.85) | 0.862 |
Missing | 1 | ||||
Histologic grade | |||||
G1 | 9 | 5 | 4 | 4.33 (0.12–151.0) | 0.197 |
G2 | 127 | 64 | 63 | 1.21 (0.69–2.14) | 0.505 |
G3 | 206 | 103 | 103 | 1.34 (0.88–2.02) | 0.171 |
Missing | 9 | ||||
MMS | |||||
MSI-H | 240 | 120 | 120 | 1.41 (0.95–2.10) | 0.084 |
MSI-L | 51 | 26 | 25 | 1.30 (0.56–2.99) | 0.542 |
MMS | 59 | 30 | 29 | 1.16 (0.51–2.63) | 0.722 |
Missing | 1 | ||||
Tumor stage | |||||
I | 47 | 24 | 23 | 1.83 (0.56–5.96) | 0.328 |
II | 109 | 55 | 54 | 1.78 (0.91–3.51) | 0.091 |
III | 147 | 74 | 73 | 1.26 (0.79–2.03) | 0.331 |
IV | 35 | 18 | 17 | 1.01 (0.43–2.37) | 0.001 |
Missing | 13 | ||||
Cancer status | |||||
Tumor free | 206 | 103 | 103 | 1.59 (0.82–3.09) | 0.171 |
With tumor | 118 | 59 | 59 | 1.39 (0.91–2.14) | 0.117 |
Missing | 27 | ||||
Residual_tumor | |||||
R1 | 14 | 7 | 7 | 1.13 (0.30–4.22) | 0.856 |
R2 | 14 | 7 | 7 | 0.76 (0.25–2.36) | 0.617 |
R0 | 287 | 144 | 143 | 1.76 (1.19–2.62) | 0.004 |
Missing | 36 | ||||
Radiotherapy | |||||
Yes | 62 | 31 | 31 | 3.17 (1.29–7.79) | 0.019 |
No | 266 | 133 | 133 | 1.27 (0.88–1.82) | 0.199 |
Missing | 23 | ||||
Targeted Therapy | |||||
Yes | 151 | 76 | 75 | 2.09 (1.23–3.56) | 0.005 |
No | 175 | 88 | 87 | 1.02 (0.66–1.59) | 0.010 |
Missing | 25 |
Variables | Total (n = 351) | Low CST2 (n) | High CST2 (n) | HR (95%CI) | Log-rank P-value |
---|---|---|---|---|---|
Gender | |||||
Male | 226 | 113 | 113 | 1.16 (0.78–1.71) | 0.461 |
Female | 125 | 63 | 62 | 2.33 (1.28–4.27) | 0.005 |
Age (years) | |||||
< 60 | 108 | 54 | 54 | 1.31 (0.68–2.52) | 0.661 |
≥ 60 | 240 | 120 | 120 | 1.51 (1.03–2.20) | 0.034 |
Missing | 3 | ||||
Location | |||||
Gastroesophageal junction | 84 | 42 | 42 | 1.15 (0.60–2.22) | 0.669 |
Body/fundus | 123 | 62 | 61 | 1.48 (0.85–2.58) | 0.167 |
Antrum | 130 | 65 | 65 | 1.45 (0.84–2.50) | 0.176 |
Missing | 14 | ||||
Hp infection | |||||
Positive | 18 | 9 | 9 | 1.06 (0.21–5.27) | 0.940 |
Negative | 143 | 72 | 71 | 1.62 (0.97–2.68) | 0.064 |
Missing | 190 | ||||
Histological_type | |||||
Intestinal | 160 | 80 | 80 | 1.58 (0.96–2.58) | 0.065 |
Diffuse Type | 61 | 31 | 30 | 1.89 (0.85–4.22) | 0.119 |
Signet Ring Type | 11 | 6 | 5 | 1.54 (0.37–6.35) | 0.484 |
Other | 118 | 59 | 59 | 1.49 (0.85–2.62) | 0.170 |
Missing | 1 | ||||
Histologic grade | |||||
G1 | 9 | 5 | 4 | 0.20 (0.00–11.57) | 0.439 |
G2 | 127 | 64 | 63 | 1.76 (1.00–3.11) | 0.046 |
G3 | 206 | 103 | 103 | 1.53 (1.02–2.32) | 0.044 |
Missing | 9 | ||||
MMS | |||||
MSI-H | 240 | 120 | 120 | 1.40 (0.94–2.08) | 0.090 |
MSI-L | 51 | 26 | 25 | 2.14 (0.92–4.95) | 0.078 |
MMS | 59 | 30 | 29 | 1.56 (0.69–3.55) | 0.281 |
Missing | 1 | ||||
Tumor stage | |||||
I | 47 | 24 | 23 | 2.68 (0.80–8.99) | 0.084 |
II | 109 | 55 | 54 | 1.69 (0.86–3.34) | 0.122 |
III | 147 | 74 | 73 | 1.42 (0.88–2.27) | 0.149 |
IV | 35 | 18 | 17 | 0.81 (0.35–1.86) | 0.613 |
Missing | 13 | ||||
Cancer status | |||||
Tumor free | 206 | 103 | 103 | 1.21 (0.62–2.35) | 0.573 |
With tumor | 118 | 59 | 59 | 1.71 (1.11–2.62) | 0.010 |
Missing | 27 | ||||
Residual_tumor | |||||
R1 | 14 | 7 | 7 | 6.00 (1.55–23.24) | 0.009 |
R2 | 14 | 7 | 7 | 0.45 (0.14–1.45) | 0.149 |
R0 | 287 | 144 | 143 | 1.61 (1.09–2.38) | 0.018 |
Missing | 36 | ||||
Radiotherapy | |||||
Yes | 62 | 31 | 31 | 3.50 (1.42–8.65) | 0.010 |
No | 266 | 133 | 133 | 1.37 (0.95–1.98) | 0.087 |
Missing | 23 | ||||
Target Therapy | |||||
Yes | 151 | 76 | 75 | 2.15 (1.27–3.63) | 0.005 |
No | 175 | 88 | 87 | 1.19 (0.76–1.85) | 0.450 |
Missing | 25 |
Variables | Patients (n = 875) | HR (95%CI) | Log-rank P-value |
---|---|---|---|
Gender | |||
Female | 236 | 2.04 (1.43–2.91) | 6.3e-05 |
Male | 544 | 1.64 (1.32–2.03) | 5.9e-06 |
Missing | 95 | ||
Stage | |||
I | 67 | 1.52 (0.56–4.11) | 0.400 |
II | 140 | 1.33 (0.72–2.45) | 0.360 |
III | 305 | 1.61 (1.21–2.15) | 0.001 |
IV | 148 | 1.59 (1.08–2.34) | 0.017 |
Missing | 215 | ||
Lauren classification | |||
Intestinal | 320 | 2.08 (1.51–2.87) | 5.8e-06 |
Diffuse | 241 | 1.60 (1.13–2.25) | 0.007 |
Mixed | 32 | 1.44 (0.51–4.01) | 0.490 |
Missing | 282 | ||
Differentiation | |||
Poorly | 165 | 1.50 (1.01–2.24) | 0.044 |
Moderately | 67 | 1.76 (0.91–3.41) | 0.092 |
Well | 32 | 2.32 (0.95–5.65) | 0.056 |
Missing | 611 | ||
Treatment | |||
Surgery alone | 380 | 1.36 (1.02–1.82) | 0.035 |
5-Fu based adjuvant | 152 | 1.01 (0.72–1.43) | 0.940 |
Other adjuvant | 76 | 0.69 (0.28–1.69) | 0.410 |
Missing | 267 | ||
HER2 status | |||
Negative | 532 | 1.57 (1.25–1.96) | 9.1e-05 |
Positive | 343 | 1.52 (1.17–1.98) | 0.002 |
Variables | Patients (n = 875) | HR (95%CI) | Log-rank P-value |
---|---|---|---|
Gender | |||
Female | 236 | 1.51 (1.06–2.14) | 0.021 |
Male | 544 | 1.40 (1.13–1.74) | 0.002 |
Missing | 95 | ||
Stage | |||
I | 67 | 2.00 (0.73–5.50) | 0.170 |
II | 140 | 1.26 (0.70–2.29) | 0.440 |
III | 305 | 1.68 (1.26–2.25) | < 0.001 |
IV | 148 | 1.52 (1.03–2.23) | 0.033 |
Missing | 215 | ||
Lauren classification | |||
Intestinal | 320 | 2.09 (1.52–2.89) | 4.3e-06 |
Diffuse | 241 | 1.60 (1.14–2.26) | 0.007 |
Mixed | 32 | 0.45 (0.15–1.33) | 0.140 |
Missing | 282 | ||
Differentiation | |||
Poorly | 165 | 1.35 (0.91–2.01) | 0.140 |
Moderately | 67 | 1.51 (0.78–2.90) | 0.210 |
Well | 32 | 3.21 (1.28–8.09) | 0.009 |
Missing | 611 | ||
Treatment | |||
Surgery alone | 380 | 1.51 (1.13–2.01) | 0.005 |
5-Fu based adjuvant | 152 | 0.92 (0.65–1.30) | 0.630 |
Other adjuvant | 76 | 1.12 (0.46–2.68) | 0.810 |
Missing | 267 | ||
HER2 status | |||
Negative | 532 | 1.29 (1.03–1.62) | 0.025 |
Positive | 343 | 1.62 (1.25–2.11) | < 0.001 |
Immunohistochemistry
Variable | Patients (n = 115) | No. of events (%) | MST (months) | HR (95% CI) | Log-rank P-value |
---|---|---|---|---|---|
Gender | 0.687 | ||||
Male | 75 | 49 (62.7) | 50.0 | Ref. | |
Female | 40 | 27 (60.0) | 32.5 | 1.10 (0.68–1.77) | |
Age (years) | 0.839 | ||||
< 60 | 69 | 43 (58.0) | 45.0 | Ref. | |
≥ 60 | 46 | 33 (67.4) | 52.0 | 1.05 (0.66–1.65) | |
Tumor location | 0.052 | ||||
Gastroesophageal junction | 12 | 10 (92.3) | 41.5 | Ref. | |
Gastric body/fundus | 31 | 25 (80.0) | 50 | 0.77 (0.37–1.61) | |
Antrum | 67 | 37 (49.3) | 61 | 0.48 (0.24–0.97) | |
Missing | 5 | ||||
Histologic grade | 0.106 | ||||
G2 | 17 | 9 (47.1) | 205.0 | Ref. | |
G3 | 86 | 59 (64.0) | 47.5 | 1.73 (0.97–3.11) | |
Missing | 9 | ||||
Tumor stage | < 0.001 | ||||
I | 21 | 6 (23.8) | 205 | Ref. | |
II | 16 | 12 (75.0) | 47.5 | 4.82 (1.69–13.72) | |
III | 32 | 20 (53.1) | 59 | 3.14 (1.18–8.37) | |
IV | 45 | 38 (81.8) | 26 | 7.00 (2.74–17.89) | |
Missing | 1 | ||||
Chemotherapy | 0.259 | ||||
Yes | 53 | 33 (56.6) | 55 | Ref. | |
No | 60 | 42 (66.7) | 43.5 | 1.29 (0.82–2.04) | |
Missing | 2 |
Gene expression status | Patients (n = 351) | Events, n (%) | MST (days) | Crude HR (95% CI) | Crude P-value | Adjusted HRa (95% CI) | Adjusted P-valuea |
---|---|---|---|---|---|---|---|
CST2 | 0.991 | 0.527 | |||||
Low | 23 | 15(61.1) | 50 | Ref. | Ref. | ||
High | 92 | 61(65.0) | 50 | 1.00 (0.57–1.76) | 1.20 (0.68–2.12) | ||
CST4 | 0.010 | 0.015 | |||||
Low | 60 | 34(51.7) | 57 | Ref. | Ref. | ||
High | 55 | 42(72.7) | 39 | 1.78 (1.13–2.81) | 1.76 (1.11–2.78) |
Genome-wide co-expression analysis and functional enrichment of type II CST prognostic genes
Term | Count | P-value | Genes |
---|---|---|---|
GO:0005925~focal adhesion | 27 | 6.47E-05 | TGFB1I1, DIXDC1, LPP, AKAP12, CNN1, CSRP2, CSRP1, FLRT1, FLNA, PGM5, FLNC, PIP5K1C, WASF1, PDLIM7, TNS1, SVIL, PPP1R12A, ACTN1, ITGA1, RHOB, NFASC, PALLD, DLC1, CSPG4, FERMT2, VCL, LIMS2 |
GO:0008285~negative regulation of cell proliferation | 27 | 6.71E-05 | HDAC4, BTG2, ATP8A2, TGFB1I1, SRF, DPT, GATA3, FGF2, ADRA1A, RERG, GLI3, NACC2, SPEG, KLF10, BCHE, ZBTB16, MAGI2, ITGA1, LDOC1, WNT9A, PHOX2B, AR, ZEB1, BCL6, DLC1, ROR2, FGF10 |
GO:0005916~fascia adherens | 4 | 0.002399344 | DES, ACTN1, CTNNA3, VCL |
GO:0007160~cell-matrix adhesion | 9 | 0.003997901 | SRF, ITGA1, ITGA7, NID1, PKD1, FERMT2, VCL, JAM3, TMEM8B |
GO:0010811~positive regulation of cell-substrate adhesion | 6 | 0.004158018 | HACD1, FOXF1, ABI3BP, NPY2R, VWC2, NID1 |
GO:0030336~negative regulation of cell migration | 8 | 0.018321255 | IGFBP5, CITED2, SRF, DLC1, TPM1, MAGI2, VCL, RHOB |
Term | Count | P-value | Genes |
---|---|---|---|
hsa04022:cGMP-PKG signaling pathway | 21 | 4.60E-09 | PPP1R12A, SRF, PDE2A, ATP1A4, ATP2B4, ADCY2, ATP1A2, CACNA1C, ADRA1A, SLC8A1, NFATC4, SLC8A2, MYLK, RGS2, PLN, KCNMB1, MRVI1, CALM1, SLC25A4, MYL9, PRKG1 |
hsa04020:Calcium signaling pathway | 20 | 2.04E-07 | CHRM2, PDE1C, CAMK2A, ATP2B4, TACR2, ADCY2, CACNA1C, GRPR, ADRA1A, CACNA1H, SLC8A1, RYR3, SLC8A2, MYLK, PLN, NOS1, CALM1, SLC25A4, PLCD4, CAMK2G |
hsa04270:Vascular smooth muscle contraction | 16 | 3.65E-07 | PPP1R12A, PLA2G2C, ADCY2, CACNA1C, ADRA1A, ACTG2, MYLK, ACTA2, MYL6, CALD1, KCNMB1, MRVI1, CALM1, PPP1R12C, MYL9, PRKG1 |
hsa04261:Adrenergic signaling in cardiomyocytes | 17 | 5.95E-07 | TPM2, TPM1, CAMK2A, ATP1A4, ATP2B4, CACNA2D3, ADCY2, ATP1A2, CACNA1C, ADRA1A, CACNB2, RPS6KA5, PLN, PPP1R1A, SCN7A, CALM1, CAMK2G |
hsa05414:Dilated cardiomyopathy | 13 | 1.76E-06 | TPM2, TPM1, ITGA1, CACNA2D3, ADCY2, CACNA1C, CACNB2, PLN, DES, SGCD, ITGA7, DMD, SGCG |
hsa05410:Hypertrophic cardiomyopathy (HCM) | 12 | 5.47E-06 | CACNB2, DES, PRKAA2, SGCD, TPM2, TPM1, ITGA1, CACNA2D3, ITGA7, DMD, CACNA1C, SGCG |
hsa04713:Circadian entrainment | 13 | 6.59E-06 | ADCYAP1R1, CAMK2A, ADCY2, CACNA1C, CACNA1H, RYR3, PER1, RPS6KA5, PER3, NOS1, CALM1, CAMK2G, PRKG1 |
hsa04921:Oxytocin signaling pathway | 16 | 8.75E-06 | PPP1R12A, PRKAA2, CAMK2A, CACNA2D3, ADCY2, CACNA1C, RYR3, NFATC4, MYLK, CACNB2, RGS2, MYL6, CALM1, CAMK2G, PPP1R12C, MYL9 |
hsa05412:Arrhythmogenic right ventricular cardiomyopathy (ARVC) | 10 | 5.94E-05 | CACNB2, DES, SGCD, ITGA1, CACNA2D3, ITGA7, DMD, CTNNA3, CACNA1C, SGCG |
hsa04970:Salivary secretion | 11 | 8.14E-05 | ATP1A4, ATP2B4, ADCY2, ATP1A2, NOS1, CALM1, ADRA1A, CST5, RYR3, PRKG1, CST4 |
hsa04024:cAMP signaling pathway | 15 | 7.23E-04 | CHRM2, ADCYAP1R1, PPP1R12A, CAMK2A, ATP1A4, ATP2B4, ADCY2, ATP1A2, CACNA1C, GLI3, PLN, CNGA3, CALM1, CAMK2G, MYL9 |
hsa04810:Regulation of actin cytoskeleton | 14 | 3.66E-03 | CHRM2, PPP1R12A, ACTN1, ITGA1, FGF2, MYLK, CFL2, ITGA7, PIP5K1C, WASF1, PPP1R12C, MYL9, VCL, FGF10 |
hsa04010:MAPK signaling pathway | 15 | 6.99E-03 | DUSP3, GADD45B, SRF, CACNA2D3, ARRB1, CACNA1C, HSPA2, FGF2, CACNA1H, CACNB2, RPS6KA5, FLNA, MAPT, FLNC, FGF10 |
hsa04911:Insulin secretion | 8 | 7.03E-03 | ADCYAP1R1, KCNMB1, CAMK2A, ATP1A4, ADCY2, ATP1A2, CACNA1C, CAMK2G |
hsa04725:Cholinergic synapse | 9 | 8.95E-03 | CHRM2, SLC5A7, CHRNB4, CAMK2A, KCNQ4, ADCY2, CACNA1C, CAMK2G, SLC18A3 |
hsa04971:Gastric acid secretion | 7 | 1.24E-02 | CAMK2A, ATP1A4, ADCY2, ATP1A2, CALM1, CAMK2G, MYLK |
hsa04514:Cell adhesion molecules (CAMs) | 10 | 1.27E-02 | NLGN1, NFASC, NLGN4X, NEGR1, NRXN1, LRRC4, NCAM2, LRRC4C, JAM2, JAM3 |
hsa04260:Cardiac muscle contraction | 7 | 1.41E-02 | CACNB2, TPM2, TPM1, ATP1A4, CACNA2D3, ATP1A2, CACNA1C |
hsa04925:Aldosterone synthesis and secretion | 7 | 1.99E-02 | PDE2A, CAMK2A, ADCY2, CACNA1C, CALM1, CAMK2G, CACNA1H |
hsa04114:Oocyte meiosis | 8 | 2.74E-02 | AR, CPEB1, PTTG2, CAMK2A, PGR, ADCY2, CALM1, CAMK2G |
hsa04080:Neuroactive ligand-receptor interaction | 14 | 3.17E-02 | CHRM2, ADCYAP1R1, CHRNB4, GRIK5, MLNR, NPY2R, TACR2, GRIK2, GRPR, ADRA1A, GLRB, CNR1, GALR1, NMUR1 |
hsa05205:Proteoglycans in cancer | 11 | 3.91E-02 | PPP1R12A, HPSE2, CAMK2A, FLNA, ANK2, WNT9A, FLNC, CAMK2G, ESR1, FGF2, PPP1R12C |
hsa04510:Focal adhesion | 11 | 4.62E-02 | PPP1R12A, ACTN1, ITGA1, CHAD, FLNA, ITGA7, FLNC, PPP1R12C, MYL9, VCL, MYLK |
hsa04922:Glucagon signaling pathway | 7 | 4.68E-02 | PRKAA2, CAMK2A, ADCY2, PYGM, CALM1, ACACB, CAMK2G |
hsa04710:Circadian rhythm | 4 | 4.76E-02 | PER1, PRKAA2, PER3, CRY2 |
hsa04530:Tight junction | 6 | 8.00E-02 | ACTN1, MYH11, AMOTL1, MYL9, JAM2, JAM3 |
hsa05031:Amphetamine addiction | 5 | 9.66E-02 | MAOB, CAMK2A, CACNA1C, CALM1, CAMK2G |
hsa04720:Long-term potentiation | 5 | 0.096645635 | PPP1R1A, CAMK2A, CACNA1C, CALM1, CAMK2G |