Background
Methods
Study subjects
Characteristic | pSS patient |
---|---|
Sex, no. male/female | 0/30 |
Age, mean ± SD years | 47.63 ± 13.50 |
Dry mouth, VAS. mean ± SD | 6.57 ± 2.12 |
Dry eyes, VAS. mean ± SD | 2.90 ± 2.95 |
Parotid swelling, VAS. mean ± SD | 4.00 ± 2.40 |
Rose bengal score, no. +/− | 20/10 |
Saxon test (g/2 min). mean ± SD | 1.44 ± 0.62 |
Grading of labial salivary gland biopsies, no. | |
Nonspecific chronic sialadenitis | 1 |
Grade 1 (<50 periductal lymphocytes) | 1 |
Grade 2 (>50 periductal lymphocytes) | |
Nonsegregated | 6 |
Segregated aggregates | 6 |
Grade 3 (>50 periductal lymphocytes, with GC-like structures) | 16 |
Ro (SSA), no. +/− | 24/6 |
La (SSB), no. +/− | 10/20 |
Anti-centromere antibodies (ACA), no. +/− | 6/24 |
ESR (mm/hr). mean ± SD | 21.77 ± 12.95 |
RF (IU/ml). mean ± SD | 146.21 ± 195.12 |
IgG (g/L). mean ± SD | 19.12 ± 4.10 |
IgA (g/L). mean ± SD | 3.22 ± 0.84 |
IgE (IU/ml). mean ± SD | 78.54 ± 68.92 |
IgM (g/L). mean ± SD | 1.73 ± 0.74 |
Course of disease (month). mean ± SD | 35.53 ± 26.04 |
CRP (mg/L). mean ± SD | 4.46 ± 2.15 |
C3 (g/L). mean ± SD | 1.10 ± 0.19 |
C4 (g/L). mean ± SD | 0.26 ± 0.07 |
β2 microglobulin(mg/L). mean ± SD | 2.80 ± 0.88 |
Microarray
LncRNA-mRNA co-expression network
Screening of differentially expressed genes for validation
Real-time PCR
Immunohistochemistry
EBV-encoded RNA (EBER) in situ hybridization
Bioinformatics analysis
Results
Overview of aberrantly expressed lncRNAs and mRNAs in pSS
Upregulated | Downregulated | ||||
---|---|---|---|---|---|
lncRNAs |
P value | Fold change | lncRNAs |
P value | Fold change |
lnc-UTS2D-1:1 | 0.001 | 24.377 | NR_026839.1 | 0.010 | −7.135 |
NR_002712 | 0.018 | 20.057 | TCONS_l2_00013113 | 0.007 | −6.244 |
n341833 | 0.001 | 16.933 | NR_026842.1 | 0.022 | −5.943 |
lnc-MMP3-1:1 | 0.023 | 11.056 | TCONS_l2_00004830 | 0.033 | −5.319 |
lnc-LGALS14-1:2 | 0.000 | 9.526 | NR_046443.1 | 0.033 | −5.280 |
NR_034176.1 | 0.005 | 8.737 | lnc-CYR61-2:1 | 0.008 | −4.783 |
n333136 | 0.026 | 7.420 | NR_037839 | 0.001 | −4.760 |
n336199 | 0.031 | 6.893 | NR_037839 | 0.022 | −4.747 |
NR_073198.1 | 0.012 | 6.880 | n333443 | 0.031 | −4.633 |
lnc-MAGEA12-2:1 | 0.013 | 6.866 | NR_026838 | 0.012 | −4.358 |
lnc-ADAM2-1:1 | 0.020 | 6.853 | NR_026838.1 | 0.025 | −4.358 |
n337610 | 0.005 | 6.654 | TCONS_l2_00019075 | 0.006 | −4.350 |
n334829 | 0.007 | 6.628 | ENST00000495382.1 | 0.014 | −4.313 |
ENST00000577557.1 | 0.024 | 6.626 | NR_036580 | 0.028 | −4.308 |
XR_111691 | 0.010 | 6.482 | lnc-OBP2B-2:1 | 0.011 | −4.294 |
XR_111691 | 0.011 | 6.384 | n333418 | 0.003 | −4.256 |
lnc-KATNAL1-3:14 | 0.009 | 6.336 | ENST00000508179.1 | 0.005 | −4.180 |
n336575 | 0.017 | 6.215 | n334464 | 0.004 | −4.117 |
ENST00000578280.1 | 0.013 | 6.183 | TCONS_l2_00010194 | 0.022 | −4.005 |
lnc-BRD1-4:1 | 0.002 | 6.101 | lnc-ZNF572-1:15 | 0.012 | −3.962 |
Upregulated | Downregulated | ||||
---|---|---|---|---|---|
mRNAs |
P value | Fold change | mRNAs |
P value | Fold change |
EGFL6 | 0.018 | 26.237 | ITLN1 | 0.003 | −104.642 |
SCGB1D2 | 0.020 | 17.197 | TRH | 0.001 | −26.423 |
SCGB2A2 | 0.033 | 16.941 | C4orf40 | 0.036 | −9.826 |
CXCL13 | 0.018 | 16.911 | LCE5A | 0.001 | −7.139 |
SCGB1D1 | 0.019 | 15.752 | CYP2F1 | 0.013 | −6.398 |
FCRL4 | 0.010 | 14.227 | FXYD2 | 0.000 | −6.070 |
MMP12 | 0.028 | 11.131 | CADPS | 0.002 | −5.823 |
IDO1 | 0.024 | 9.307 | ASTN1 | 0.038 | −5.735 |
CD1A | 0.007 | 8.942 | CABS1 | 0.022 | −5.372 |
CXCL11 | 0.018 | 8.175 | GABRG3 | 0.005 | −5.303 |
KLHDC7B | 0.008 | 8.152 | FGF12 | 0.039 | −5.231 |
CXCL9 | 0.028 | 7.876 | CSN3 | 0.008 | −4.829 |
TIMD4 | 0.001 | 7.647 | DACH2 | 0.048 | −4.709 |
UTS2D | 0.029 | 7.368 | LEFTY1 | 0.027 | −4.709 |
SLC26A4 | 0.014 | 7.037 | NA | 0.048 | −4.652 |
ZBTB32 | 0.011 | 6.793 | XLOC_002852 | 0.011 | −4.508 |
TIMD4 | 0.004 | 6.746 | NA | 0.012 | −4.375 |
EXOC3L4 | 0.003 | 6.281 | PPP1R17 | 0.033 | −4.332 |
IFNG | 0.018 | 6.201 | ABO | 0.012 | −4.272 |
CTLA4 | 0.011 | 6.177 | SLC35G1 | 0.024 | −4.215 |
Real-time PCR: lncRNA expression profiles and correlations with clinical characteristics
Functional prediction of DE mRNAs
Relational analyses of lncRNAs and mRNAs
mRNA gene symbol |
P value | Fold change | Regulation | Correlated lncRNA gene name |
r value |
P value |
---|---|---|---|---|---|---|
ACY3 | 0.028 | 2.221 | up | n340599 | 0.9996 | 0.0004 |
AGAP2 | 0.016 | 2.618 | up | ENST00000420219.1, n336161 | 0.9995 0.9992 | 0.0005 0.0008 |
ARHGAP30 | 0.019 | 2.377 | up | n336161, ENST00000455309.1 | 0.9993 0.9991 | 0.0007 0.0009 |
CCL20 | 0.013 | 4.295 | up | TCONS_l2_00014794 | 0.9991 | 0.0009 |
CCR5 | 0.003 | 4.040 | up | ENST00000455309.1 | 0.9993 | 0.0007 |
CD19 | 0.033 | 5.657 | up | n340599 | 0.9992 | 0.0008 |
CD6 | 0.002 | 2.604 | up | ENST00000420219.1 | 09990 | 0.0009 |
CFP | 0.011 | 2.089 | up | ENST00000546086.1, TCONS_l2_00014794 | 0.9995 0.9996 | 0.0005 0.0004 |
CXCR4 | 0.028 | 5.527 | up | ENST00000546086.1, TCONS_l2_00014794 | 0.9998 0.9997 | 0.0002 0.0003 |
CYTH4 | 0.015 | 2.151 | up | n340599 | 0.9996 | 0.0004 |
GIMAP4 | 0.004 | 2.905 | up | ENST00000455309.1 | 0.9997 | 0.0003 |
GNGT2 | 0.011 | 3.857 | up | ENST00000455309.1, n336161 | 0.9991 0.9999 | 0.0009 0.0001 |
HCST | 0.005 | 3.011 | up | ENST00000546086.1, TCONS_l2_00014794 | 0.9998 0.9995 | 0.0002 0.0005 |
HIST1H2AI | 0.033 | 3.800 | up | ENST00000455309.1 | 0.9995 | 0.0005 |
ICAM1 | 0.008 | 2.385 | up | ENST00000455309.1 n336161 | 0.9991 0.9994 | 0.0009 0.0006 |
KIF20B | 0.007 | 2.118 | up | ENST00000455309.1, | 0.9992 | 0.0008 |
LAPTM5 | 0.022 | 3.223 | up | ENST00000546086.1 | 0.9997 | 0.0003 |
LEF1 | 0.020 | 3.743 | up | TCONS_l2_00014794 | 0.9999 | 0.0001 |
LILRB1 | 0.003 | 3.180 | up | ENST00000420219.1, ENST00000455309.1, n336161 | 0.9994 0.9998 0.9997 | 0.0006 0.00020.0003 |
PRKCQ | 0.025 | 2.969 | up | ENST00000455309.1 | 0.9994 | 0.0006 |
RABGAP1L | 0.010 | 2.149 | up | n340599 | 0.9997 | 0.0003 |
RAC2 | 0.006 | 3.169 | up | n340599 | 0.9992 | 0.0008 |
RLTPR | 0.016 | 2.094 | up | ENST00000420219.1, n336161 | 0.9994 0.9993 | 0.0006 0.0007 |
SUSD3 | 0.010 | 2.587 | up | ENST00000546086.1, TCONS_l2_00014794 | 0.9998, 0.9999 | 0.0002 0.0001 |
TLR9 | 0.043 | 2.029 | up | n340599 | 0.9992 | 0.0008 |
TRAF1 | 0.014 | 2.530 | up | n340599 | 0.9998 | 0.0002 |
WDFY4 | 0.014 | 3.251 | up | n340599 | 0.9995 | 0.0005 |
ZNF831 | 0.014 | 4.663 | up | ENST00000455309.1 | 0.9997 | 0.0003 |