Introduction
Materials and methods
Study cohort
RNA sequencing
Sample collection and RNA extraction
Bone and tissue
Plasma
RNA sequencing
Statistics
Sequencing data analysis
Western Blot
Protein extraction from bone
Western blot
Results
Patient demographics
Revision N = 24 | Primary N = 26 | p-value | |
---|---|---|---|
Age | 67 ± 2 | 72 ± 2 | 0.31 |
Sex | 6 male 18 female | 6 male 20 female | 0.81 |
Joint | 22 hip 2 knee | 16 hip 10 knee | 0.07 |
Height (m) | 1.62 ± 0.03 | 1.64 ± 0.03 | 0.78 |
Weight (kg) | 85.2 ± 6.4 | 74.5 ± 6.1 | 0.26 |
BMI (kg/m2) | 32.3 ± 2.4 | 27.7 ± 1.7 | 0.17 |
Charlson Comorbidity Index | 2.9 ± 0.5 | 2.7 ± 0.3 | 0.74 |
Cardiovascular disease | 12 | 14 | 0.79 |
Diabetes mellitus | 4 | 4 | 0.72 |
Autoimmune disease | 0 | 0 | N/A |
Cancer | 0 | 0 | N/A |
Respiratory disease | 4 | 3 | 0.45 |
Osteoporosis | 0 | 0 | N/A |
Renal impairment | 2 | 0 | 0.18 |
Immunomodulatory meds | 0 | 0 | 1.00 |
Blood tests | |||
Haemoglobin (g/L) | 130 ± 3 | 134 ± 3 | 0.36 |
Creatinine (µmol/L) | 74 ± 10 | 62 ± 5 | 0.87 |
eGFR | 74 ± 5 | 80 ± 3 | 0.94 |
Calcium (mmol/L) | 2.29 ± 0.05 | 2.29 ± 0.05 | 0.87 |
Phosphate (mmol/L) | 1.30 ± 0.30 | 1.36 ± 0.31 | 0.94 |
Magnesium (mmol/L) | 0.81 ± 0.04 | 0.72 ± 0.03 | 0.34 |
Potassium (mmol/L) | 4.69 ± 0.17 | 4.38 ± 0.10 | 0.20 |
The expression profile of miRNA in plasma of patients with aseptic loosening is significantly different compared to controls
The expression profile of mRNA in bone and tissue of patients with aseptic loosening is significantly different compared to controls
Location | Gene | logFC | AveExpr | t | P Value | adj.P.Val | B |
---|---|---|---|---|---|---|---|
Bone | DEFA1B | − 9.87323 | 10.52257 | − 5.89125 | 6.82E-06 | 0.00011 | 3.695094 |
DEFA1 | − 9.92204 | 10.51236 | − 5.88224 | 6.96E-06 | 0.000111 | 3.676803 | |
LTF | − 8.9081 | 8.370686 | − 5.57556 | 1.42E-05 | 0.000161 | 3.187831 | |
COMP | 8.113538 | 1.880959 | 5.378271 | 2.27E-05 | 0.000213 | 2.709947 | |
DEFA3 | − 9.98611 | 8.880224 | − 5.01815 | 5.34E-05 | 0.000376 | 1.835942 | |
Tissue | LINC02154 | 5.085439 | −2.17528 | 5.23428 | 8.12E-06 | 0.000152 | 2.337842 |
APOC2 | 5.065549 | 0.516944 | 4.13716 | 0.000213 | 0.001447 | 0.577554 | |
CHIT1 | 8.470192 | 3.545606 | 4.022007 | 0.000297 | 0.001844 | 0.334267 | |
HP | − 5.8447 | 1.932185 | -3.85548 | 0.000479 | 0.00265 | − 0.08945 | |
DNASE2B | 5.064432 | − 0.82393 | 3.731657 | 0.000681 | 0.00347 | − 0.55021 |
In-silico disease gene-set enrichment analysis reveals disease associations with inflammation, osteolysis and osteoporosis
Target prediction reveals plasma miRNA targets mRNA genes in bone and tissue leading to bone resorption
miRNA | GeneRatio | Adj-P | Genes | |
---|---|---|---|---|
Bone | miR-3960 | 15/4286 | 0.00000 | PCDHA3/PCDHA10/PCDHA6/PCDHA7/PCDHAC2/PCDHA1 2/PCDHA13/PCDHA2/PCDHA9/PCDHA8/PCDHA11/PCDHAC1/PCDHA5/PCDHA1/PCDHA4 |
miR-574-5p | 29/4286 | 0.00014 | EPHA3/RGMA/LARP6/RERGL/EVX1/DPP4/IGDCC4/NRN1/C11orf96/TEADl/MDGAl/NEBL/THRB/FOSLl/FOXI2/ADGRB2/MYCBP/SEMA7A/NSUN5/CCDCgsc/RSC1A1/GALNT3/MKRN1/CD9 6/D G KG/ N S D 2/S 0X6/1L5 RA/S10 0 A12 | |
miR-423-5p | 40/4286 | 0.00091 | RIMS4/CADM3/CSMD2/COL1A1/CPEB1/LHX6/ARHGEF4/ TSPAN11/RGMA/KCNIP3/DNAL11/S100A16/NNAT/EVC/C1QTNF6/SYP/ROR2/NAV1/NRSN2/LZTS3/SLC52A3/SLC20A2/CLDN23/ADGRL1/TMEM150A/OBSL1/KLK4/DUSP8/L0C730098/0DC1/CRIP3/C20Orf27/NECTIN1/ATG4D/UBE20/SLC6A9/RAC2/PHOSPHO1/TCLIB/DMTN | |
miR-1290 | 65/4286 | 0.00166 | OGN/KCNK2/DPT/TMEM255A/ANTXR1/COLEC12/ANK2/EFNA5/TGFB 2/COL8A1/SYNP02/THS D7A/RGS5/EGFR/SGIP1/SORCS1/PCDH7/TEAD3/ACKR4/EMP2/PRRG1/RASAL2/CSTB/NAALADL2/VEGFD/GALNT15/PREX2/SRGAP1/ASXL3/ZFHX3/EBF1/ARHGEF26/SEMA6A/AGAP1/ERBB4/KCNAB1/MSR1/LRRTM2/CALCR/DYNC1|1/RASGRF2/TAFA5/CAPN2/HYDIN/MGME1/CAMK4/CBFA2T3/ADARB2/USP15/SMC4/FBN2/SLAIN1/AMMECR1/ITGA4/PIP5K1B/BEND 4/EPCAM/IL5RA/MN D1/PLCH1/SG 01 /TCN1/ MS4A3/SPT A1/TSP02 | |
miR-122-5p | 28/4286 | 0.00188 | STMN2/MYOCD/CPEB1/LALMC1/RANBP3L/MECOM/RBMS2/MAP3K12/DDR2/FLNB/CTNNA3/CLIC5/MIPOL1/KCNN3/MICU3/SLC25A34/CLIC4/ADGRB2/CO40LG/TBC1D22B/S E MA4 D/G6PD/S LC7A1/RBL1/S LC05A1/ PRR11/C21orf62/KIF11 | |
Tissue | miR-3960 | 7/881 | 0.00046 | PCDHA11/PCDHA2/PCOHA12/PCDHA1/PCDHA10/PCDHAC2/pou3p3 |
miR-1290 | 20/881 | 0.02309 | TMEM255A/CSTB/KLHL6/MS4A3/PLCH1/ARHGEF26/ASXL3/BTG2/THRSP/SORCS1/VEGFD/WNK2/SYN2/GREM2/BEGAIN/CNTN6/ERBB4/SYT4/TRHDE/NRXN1 |
miRNA | Bone/tissue | Gene | Direction | Adj-P | logFC |
---|---|---|---|---|---|
miR-1246 | Tissue | C7 | Down | 0.0003 | −3.6 |
Bone | LINC00346 | Up | 0.0008 | 3.3 | |
Bone | PPP1R3C | Up | 0.0008 | 3.6 | |
Bone | HOXC10 | Up | 0.0008 | 4.0 | |
Bone | KIAA0930 | Up | 0.0008 | 3.6 | |
Bone | PCDHB2 | Up | 0.0009 | 3.3 | |
Bone | THBS2 | Up | 0.0009 | 3.6 | |
Bone | SIX4 | Up | 0.0009 | 3.5 | |
Bone | LINC00346 | Up | 0.0008 | 3.3 | |
Bone | DIXDC1 | Up | 0.0008 | 4.0 | |
Bone | KLHL30 | Up | 0.0008 | 3.2 | |
Bone | ANTXR1 | Up | 0.0008 | 3.3 | |
Bone | APLN | Up | 0.0008 | 3.3 | |
Bone | KIAA0930 | Up | 0.0008 | 3.6 | |
Bone | CLDN1 | Up | 0.0009 | 3.1 | |
Bone | PCDHB2 | Up | 0.0009 | 3.3 | |
miR-3960_8072 | Bone | NTN1 | Up | 0.0008 | 3.7 |
miR-423-5p | Bone | NTN1 | Up | 0.0008 | 3.7 |
miR-574-3p | Tissue | MMP3 | Down | 0.0005 | -3.5 |
miR-6089 | Bone | PPP1R3C | Up | 0.0008 | 3.6 |
Bone | ACE | Up | 0.0008 | 3.2 | |
Bone | DIXDC1 | Up | 0.0008 | 4.0 | |
Bone | KLHL30 | Up | 0.0008 | 3.2 | |
Bone | PPIC | Up | 0.0008 | 3.1 | |
Bone | NTN1 | Up | 0.0008 | 3.7 | |
Bone | APLN | Up | 0.0008 | 3.3 | |
Bone | KIAA0930 | Up | 0.0008 | 3.6 | |
Bone | CCDC3 | Up | 0.0008 | 3.9 |
miRNA | Target tissue | Pathway | Gene | Direction | Adj-P | logFC |
---|---|---|---|---|---|---|
miR-1246 | Bone | Wnt | FZD7 | Up | 0.0038 | 2.1 |
Bone | Wnt | PRKCB | Down | 0.0032 | -2.5 | |
Bone | Wnt | DIXDC1 | Up | 0.0007 | 4.0 | |
Bone | Wnt | SFRP4 | Up | 0.0014 | 3.6 | |
Bone | Inflammation | TGFB3 | Up | 0.0014 | 2.4 | |
Bone | TGFB | TGFB3 | Up | 0.0014 | 2.4 | |
Bone | Wnt | FSTL1 | Up | 0.0037 | 2.4 | |
miR-574-3p | Bone | JAK-STAT | IL6 | Up | 0.0080 | 2.4 |
miR-6089 | Bone | Wnt | RAC2 | Down | 0.0089 | − 2.3 |
Bone | Wnt | FRAT2 | Down | 0.0059 | − 2.2 | |
Bone | Wnt | DIXDC1 | Up | 0.0008 | 4.0 | |
Bone | Wnt | WNT9A | Up | 0.0021 | 2.4 |