Background
Methods
Patients’ samples
Characteristics | Discovery cohort | Internal validation cohort | GSE31312 cohort | GSE10846 cohort | GSE4475 cohort |
---|---|---|---|---|---|
No. of patients | 213 | 213 | 426 | 350 | 129 |
Age, year | |||||
>60 | 121 | 123 | 244 | 196 | 72 |
≤60 | 92 | 90 | 182 | 154 | 57 |
Gender | |||||
Female | 101 | 82 | 183 | 152 | 54 |
Male | 112 | 131 | 243 | 184 | 74 |
Unknown | 14 | 1 | |||
Stage | |||||
I/II | 97 | 106 | 203 | 160 | 36 |
III/IV | 116 | 107 | 223 | 184 | 48 |
Unknown | 6 | 45 | |||
No. of extranodal sites | |||||
<2 | 167 | 170 | 337 | 299 | |
≥2 | 46 | 43 | 89 | 26 | |
Unknown | 25 | ||||
LDH | |||||
0 | 72 | 61 | 133 | 140 | |
1 | 120 | 133 | 253 | 156 | |
Unknown | 21 | 19 | 40 | 54 | |
ECOG | |||||
<2 | 168 | 171 | 339 | 256 | |
≥2 | 45 | 42 | 87 | 74 | |
Unknown | 20 | ||||
Subtype | |||||
GCB | 106 | 121 | 227 | 183 | 74 |
ABC | 107 | 92 | 199 | 167 | 55 |
Unclassified | |||||
Survival status | |||||
Dead | 80 | 74 | 154 | 143 | 51 |
Alive | 133 | 139 | 272 | 207 | 42 |
Unknown | 36 |
Acquisition and analysis of lncRNA expression profiles
Statistical analysis for subtype classification and prognosis prediction
Analysis of lncRNA expression profiles
Formulation of lncRNA-based molecular signature
Identification of lncRNA biomarkers associated with clinically molecular subtype and prognosis
Survival analysis
Functional enrichment analysis
Results
Identification of lncRNA biomarkers associated with clinically molecular subtype
Ensembl id | Gene symbol | Chromosomal position |
p-value | FDR | signal-to-noise ratio |
---|---|---|---|---|---|
ENSG00000226688.5 | ENTPD1-AS1 | Chr 10: 95,753,206-96,090,238 (−) | 5.34E-10 | 1.78E-07 | 0.453 |
ENSG00000229558.2 | SACS-AS1 | Chr 13: 23,418,971-23,428,869 (+) | 2.2E-07 | 3.94E-05 | 0.404 |
ENSG00000224660.1 | SH3BP5-AS1 | Chr 3: 15,254,184-15,264,493 (+) | 4.93E-12 | 3.83E-09 | 0.502 |
ENSG00000231090.1 | RP11-101C11.1 | Chr 1: 55,217,861-55,234,177 (+) | 3.88E-09 | 1.13E-06 | 0.421 |
ENSG00000224730.1 | AC009892.10 | Chr 19: 54,635,722-54,638,892 (−) | 1.03E-07 | 2.36E-05 | 0.38 |
ENSG00000255443.1 | RP1-68D18.4 | Chr 11: 35,210,343-35,214,985 (−) | 3.48E-07 | 5.8E-05 | 0.361 |
ENSG00000236901.4 | MIR600HG | Chr 9: 123,109,494-123,115,477 (−) | 9.02E-07 | 1.4E-04 | 0.359 |
ENSG00000279130.1 | RP11-278 J6.4 | Chr 5: 143,406,959-143,407,420 (+) | 2.57E-06 | 3.737E-04 | 0.341 |
ENSG00000260303.1 | RP11-203B7.2 | Chr 4: 146,052,604-146,056,762 (−) | 1.33E-07 | 2.57E-05 | 0.395 |
ENSG00000231163.4 | CSMD2-AS1 | Chr 1: 33,868,953-33,885,458 (+) | 2.76E-10 | 1.29E-07 | 0.493 |
ENSG00000245864.2 | CTC-467 M3.1 | Chr 5: 88,676,218-88,722,831 (+) | 1.12E-07 | 2.36E-05 | 0.379 |
ENSG00000223479.3 | RP4-788P17.1 | Chr 1: 73,635,216-73,715,214 (+) | 2.91E-12 | 3.39E-09 | 0.514 |
ENSG00000259976.1 | RP11-553 L6.5 | Chr 3: 114,314,501-114,316,179 (−) | 6.09E-08 | 1.58E-05 | 0.386 |
ENSG00000245694.7 | CRNDE | Chr 16: 54,918,863-54,929,189 (−) | 3.49E-06 | 4.71E-04 | 0.328 |
ENSG00000259354.4 | RP11-519G16.3 | Chr 15: 45,448,427-45,513,767 (+) | 3.7E-10 | 1.44E-07 | 0.494 |
ENSG00000254418.1 | RP11-21 L19.1 | Chr 11: 14,262,846-14,273,691 (−) | 2.96E-11 | 1.73E-08 | 0.507 |
ENSG00000240666.2 | MME-AS1 | Chr 3: 155,158,370-155,183,285 (−) | 4.33E-15 | 1.01E-11 | 0.666 |
A lncRNA-based molecular signature for subtype classification and prognosis prediction in DLBCL patients
Further validation of lncRNA-based molecular signature in the internal validation cohort and entire GSE31312 cohort
Variables | Univariate analysis | Multivariate analysis | ||||
---|---|---|---|---|---|---|
HR | 95% CI of HR |
P value | HR | 95% CI of HR |
P value | |
GSE31312 cohort (n = 426) | ||||||
SubSigLnc-17 (ABC vs. GCB) | 1.638 | 1.19-2.254 | 0.002 | 1.422 | 0.997-2.028 | 0.052 |
Age (> = 60 vs. <60) | 2.01 | 1.41-2.864 | 1.12E-04 | 1.946 | 1.315-2.881 | 8.79E-04 |
Gender (Male vs. Female) | 0.959 | 0.697-1.32 | 0.798 | 0.843 | 0.597-1.189 | 0.331 |
Stage (III/IV vs. I/II) | 2.314 | 1.646-3.251 | 1.35E-06 | 1.707 | 1.135-2.567 | 0.01 |
LDH (High vs. Normal) | 2.035 | 1.362-3.04 | 5.19 E-04 | 1.475 | 0.973-2.236 | 0.067 |
No. of extranodal sites (≥2 vs. < 2) | 2.247 | 1.598-3.16 | 3.23E-06 | 1.778 | 1.213-2.605 | 0.003 |
ECOG (≥2 vs. < 2) | 2.195 | 1.556-3.097 | 7.48E-06 | 1.584 | 1.065-2.355 | 0.023 |
GSE10846 cohort (n = 350) | ||||||
SubSigLnc-17 (ABC vs. GCB) | 2.364 | 1.673-3.341 | 1.10E-06 | 2.093 | 1.391-3.149 | 3.94E-04 |
Age (> = 60 vs. <60) | 2.099 | 1.464-3.009 | 5.50E-05 | 1.988 | 1.31-3.016 | 0.001 |
Gender (Male vs. Female) | 1.017 | 0.724-1.429 | 0.922 | 0.993 | 0.676-1.46 | 0.972 |
Stage (III/IV vs. I/II) | 1.747 | 1.239-2.464 | 0.001 | 1.147 | 0.762-1.727 | 0.51 |
LDH (High vs. Normal) | 2.643 | 1.791-3.899 | 9.72E-07 | 2.038 | 1.341-3.096 | 8.59E-04 |
No. of extranodal sites (≥2 vs. < 2) | 1.899 | 1.087-3.317 | 0.024 | 1.183 | 0.58-2.415 | 0.644 |
ECOG (≥2 vs. < 2) | 2.968 | 2.091-4.214 | 1.19E-09 | 1.907 | 1.246-2.918 | 0.003 |