Table 1.
GRASP KO alters HS and CS synthesis enzymes at both the mRNA and protein levels
| Enzymes | Proteomics | RNA-seq | ||||||||
|---|---|---|---|---|---|---|---|---|---|---|
| Common enzymes | 55KO/WT | p-value | 65KO/WT | p-value | log2 (55KO/WT) | p-value | log2 (65KO/WT) | p-value | log2 (DKO/WT) | p-value |
| XylT1 | ND | ND | − 0.009 | NA | 6.511E-04 | NA | − 0.007 | NA | ||
| XylT2 | ND | ND | 0.100 | 0.770 | − 0.250 | 0.290 | − 0.100 | 0.740 | ||
| GalT1 (B4GALT7) | ND | ND | 0.210 | 0.440 | − 0.170 | 0.500 | 0.140 | 0.590 | ||
| GalT2 | ND | ND | − 0.850 | 0.020 | − 0.410 | 0.340 | − 0.110 | 0.840 | ||
| GlcAT1 (B3GAT3) | ND | ND | − 0.370 | 0.210 | − 0.110 | 0.750 | 0.020 | 0.960 | ||
| PAPSS 1 | 0.047 | 0.411 | − 0.093 | 0.082 | 3.733E-03 | 0.990 | − 0.060 | 0.790 | − 0.120 | 0.460 |
| PAPSS 2 | − 0.825 | 1.854E-05 | − 0.873 | 2.289E-06 | − 0.910 | 7.920E-10 | − 0.690 | 2.269E-06 | − 0.690 | 3.599E-06 |
| PAPST 1 (SLC35B2) | − 0.141 | 0.034 | − 0.069 | 0.256 | − 0.120 | 0.750 | 0.380 | 0.080 | 0.400 | 0.060 |
| PAPST 2 (SLC35B3) | ND | ND | 0.290 | 0.190 | 0.070 | 0.800 | 0.370 | 0.050 | ||
| Enzymes in HS synthesis | ||||||||||
| EXTL2 | ND | ND | − 0.170 | 0.420 | 0.320 | 0.030 | 0.090 | 0.670 | ||
| EXTL3 | ND | ND | 0.330 | 0.120 | 0.130 | 0.620 | 0.290 | 0.160 | ||
| EXTL1 | ND | ND | − 0.010 | NA | − 0.010 | NA | − 0.010 | NA | ||
| EXT1 | ND | ND | 0.200 | 0.420 | 0.660 | 3.090E-05 | 0.180 | 0.430 | ||
| EXT2 | ND | ND | − 0.080 | 0.790 | − 0.100 | 0.690 | − 0.230 | 0.240 | ||
| NDST 1 | ND | ND | 0.230 | 0.260 | 0.120 | 0.600 | − 0.170 | 0.400 | ||
| NDST 2 | ND | ND | 0.280 | 0.620 | − 0.030 | 0.960 | − 0.050 | 0.940 | ||
| NDST 3 | ND | ND | − 0.210 | 0.700 | − 0.460 | 0.200 | 0.100 | 0.850 | ||
| NDST 4 | ND | ND | ND | ND | ND | |||||
| HS C5-EP (HSGLCE) | ND | ND | ND | ND | ND | |||||
| H2ST | ND | ND | ND | ND | ND | |||||
| H3ST 1 | ND | ND | ND | ND | ND | |||||
| H3ST 2 | ND | ND | ND | ND | ND | |||||
| H3ST 3A | ND | ND | ND | ND | ND | |||||
| H3ST 3B | ND | ND | ND | ND | ND | |||||
| H3ST 4 | ND | ND | ND | ND | ND | |||||
| H3ST 5 | ND | ND | ND | ND | ND | |||||
| H3ST 6 | ND | ND | ND | ND | ND | |||||
| H6ST 1 | ND | ND | ND | ND | ND | |||||
| H6ST 2 | ND | ND | ND | ND | ND | |||||
| H6ST 3 | ND | ND | ND | ND | ND | |||||
| Enzymes in CS synthesis | ||||||||||
| GalNAcT1 (GALNT1) | − 0.404 | 8.206E-05 | − 0.521 | 1.34308E-05 | − 0.521 | 2.856E-09 | − 0.884 | 3.668E-26 | -1.135 | 7.254E-42 |
| GalNAcT2 (GALNT2) | − 0.095 | 0.094 | 0.096 | 0.111 | − 0.140 | 0.480 | 0.290 | 0.040 | − 0.290 | 0.040 |
| CHPF2 | 0.159 | 0.368 | 0.197 | 0.227 | 0.040 | 0.950 | − 0.050 | 0.910 | 0.200 | 0.540 |
| CHSY1 | ND | ND | − 0.880 | 8.023E-07 | − 0.693 | 9.417E-05 | − 0.579 | 1.442E-03 | ||
| CHSY2 | ND | ND | NA | NA | NA | |||||
| CHSY3 | ND | ND | − 0.110 | 0.790 | 0.050 | 0.900 | 0.110 | 0.740 | ||
| C4ST 1 (CHST11) | ND | ND | − 0.184 | 0.472 | 0.163 | 0.461 | − 0.177 | 0.424 | ||
| C4ST 2 (CHST12) | ND | ND | − 0.092 | 0.732 | − 0.022 | 0.935 | − 0.026 | 0.925 | ||
| C4ST 3 (CHST13) | ND | ND | − 0.270 | 0.635 | 0.480 | 0.240 | 0.903 | 0.008 | ||
| GalNAc4S-6ST (CHST15) | ND | ND | − 0.083 | 0.866 | − 0.734 | 0.003 | − 0.678 | 0.007 | ||
| C6ST 1 (CHST3) | ND | ND | − 0.242 | 0.471 | − 0.641 | 0.005 | − 0.839 | 1.600E-04 | ||
| C6ST 2 (CHST4) | ND | ND | 0 | NA | 0 | NA | 0.013 | NA | ||
| UST | ND | ND | ND | ND | ND | |||||
| DS-epi 1 (DSE) | ND | ND | − 0.715 | 6.146E-10 | − 1.274 | 3.265E-28 | − 0.788 | 7.330E-12 | ||
| DS-epi 2 (DSEL) | ND | ND | 0.721 | 8.811E-05 | 0.505 | 8.939E-03 | − 0.001 | 9.967E-01 | ||
| D4ST (CHST14) | ND | ND | ND | ND | ND | |||||
| Enzymes in HA synthesis | ||||||||||
| HAS1 | ND | ND | − 0.009 | NA | − 0.009 | NA | − 0.007 | NA | ||
| HAS2 | ND | ND | 0.131 | 0.850 | 0.088 | 0.888 | 0.390 | 0.356 | ||
| HAS3 | ND | ND | 0.009 | 0.992 | − 0.132 | 0.819 | 0.066 | 0.915 | ||
WT and GRASP KO cells were analyzed by proteomic and RNA-seq analyses. Shown are the fold changes of the indicated GAG synthesis enzymes in GRASP KO cells compared to that in WT cells. Enzymes in bold were further tested by Western blot. NA data not available; ND not detected