#METABOLOMICS WORKBENCH Giovanni_DAngelo_20210129_093257 DATATRACK_ID:2436 STUDY_ID:ST001673 ANALYSIS_ID:AN002731 PROJECT_ID:PR001076 VERSION 1 CREATED_ON February 2, 2021, 10:15 am #PROJECT PR:PROJECT_TITLE Targeted Sphingolipid analysis of HeLa silenced for or overexpressing GOLPH3 or PR:PROJECT_TITLE LCS PR:PROJECT_SUMMARY A group of sequentially-acting enzymes operating at the branchpoint among PR:PROJECT_SUMMARY sphingolipid synthetic pathways binds the Golgi-localised oncoprotein GOLPH3. PR:PROJECT_SUMMARY GOLPH3 sorts these enzymes into vesicles for intra-Golgi retro-transport, acting PR:PROJECT_SUMMARY as a component of the cisternae inter-conversion mechanisms. Through these PR:PROJECT_SUMMARY effects, GOLPH3 controls the sub-Golgi localisation, and the lysosomal PR:PROJECT_SUMMARY degradation rate of specific enzymes. Here we evaluated the impact of PR:PROJECT_SUMMARY overexpressing or silencing GOLPH3 or its client enzyme lactosylceramide PR:PROJECT_SUMMARY synthase (LCS) on the sphingolipid composition of HeLa cells by targeted lipid PR:PROJECT_SUMMARY analysis. PR:INSTITUTE École polytechnique fédérale de Lausanne (EPFL) PR:DEPARTMENT IBI PR:LABORATORY UPDANGELO PR:LAST_NAME D'Angelo PR:FIRST_NAME Giovanni PR:ADDRESS Station 15, Lausanne, Vaud, 1015, Switzerland PR:EMAIL giovanni.dangelo@epfl.ch PR:PHONE +41 216934276 #STUDY ST:STUDY_TITLE Targeted Sphingolipid analysis of HeLa silenced for or overexpressing GOLPH3 or ST:STUDY_TITLE LCS ST:STUDY_SUMMARY A group of sequentially-acting enzymes operating at the branchpoint among ST:STUDY_SUMMARY sphingolipid synthetic pathways binds the Golgi-localised oncoprotein GOLPH3. ST:STUDY_SUMMARY GOLPH3 sorts these enzymes into vesicles for intra-Golgi retro-transport, acting ST:STUDY_SUMMARY as a component of the cisternae inter-conversion mechanisms. Through these ST:STUDY_SUMMARY effects, GOLPH3 controls the sub-Golgi localisation, and the lysosomal ST:STUDY_SUMMARY degradation rate of specific enzymes. Here we evaluated the impact of ST:STUDY_SUMMARY overexpressing or silencing GOLPH3 or its client enzyme lactosylceramide ST:STUDY_SUMMARY synthase (LCS) on the sphingolipid composition of HeLa cells by targeted lipid ST:STUDY_SUMMARY analysis. ST:INSTITUTE École polytechnique fédérale de Lausanne (EPFL) ST:DEPARTMENT IBI ST:LABORATORY UPDANGELO ST:LAST_NAME D'Angelo ST:FIRST_NAME Giovanni ST:ADDRESS Station 15, Lausanne, Vaud, 1015, Switzerland ST:EMAIL giovanni.dangelo@epfl.ch ST:PHONE +41 216934276 #SUBJECT SU:SUBJECT_TYPE Cultured cells SU:SUBJECT_SPECIES Homo sapiens SU:TAXONOMY_ID 9606 #SUBJECT_SAMPLE_FACTORS: SUBJECT(optional)[tab]SAMPLE[tab]FACTORS(NAME:VALUE pairs separated by |)[tab]Raw file names and additional sample data SUBJECT_SAMPLE_FACTORS - CTRL_1 Treatment:no treatment RAW_FILE_NAME=CTRL_1.raw SUBJECT_SAMPLE_FACTORS - CTRL_2 Treatment:no treatment RAW_FILE_NAME=CTRL_2.raw SUBJECT_SAMPLE_FACTORS - CTRL_3 Treatment:no treatment RAW_FILE_NAME=CTRL_3.raw SUBJECT_SAMPLE_FACTORS - GOLPH3_OE_1 Treatment:GOLPH3 overexpression RAW_FILE_NAME=GOLPH3_OE_1.raw SUBJECT_SAMPLE_FACTORS - GOLPH3_OE_2 Treatment:GOLPH3 overexpression RAW_FILE_NAME=GOLPH3_OE_2.raw SUBJECT_SAMPLE_FACTORS - GOLPH3_OE_3 Treatment:GOLPH3 overexpression RAW_FILE_NAME=GOLPH3_OE_3.raw SUBJECT_SAMPLE_FACTORS - GOLPH3_KD_1 Treatment:GOLPH3 silencing RAW_FILE_NAME=GOLPH3_KD_1.raw SUBJECT_SAMPLE_FACTORS - GOLPH3_KD_2 Treatment:GOLPH3 silencing RAW_FILE_NAME=GOLPH3_KD_2.raw SUBJECT_SAMPLE_FACTORS - GOLPH3_KD_3 Treatment:GOLPH3 silencing RAW_FILE_NAME=GOLPH3_KD_3.raw SUBJECT_SAMPLE_FACTORS - LCS_OE_1 Treatment:LCS overexpression RAW_FILE_NAME=LCS_OE_1.raw SUBJECT_SAMPLE_FACTORS - LCS_OE_2 Treatment:LCS overexpression RAW_FILE_NAME=LCS_OE_2.raw SUBJECT_SAMPLE_FACTORS - LCS_OE_3 Treatment:LCS overexpression RAW_FILE_NAME=LCS_OE_3.raw SUBJECT_SAMPLE_FACTORS - LCS_KD_1 Treatment:LCS silencing RAW_FILE_NAME=LCS_KD_1.raw SUBJECT_SAMPLE_FACTORS - LCS_KD_2 Treatment:LCS silencing RAW_FILE_NAME=LCS_KD_2.raw SUBJECT_SAMPLE_FACTORS - LCS_KD_3 Treatment:LCS silencing RAW_FILE_NAME=LCS_KD_3.raw #COLLECTION CO:COLLECTION_SUMMARY Cells were washed in ice cold PBS and collected by scaling CO:SAMPLE_TYPE HeLa cells #TREATMENT TR:TREATMENT_SUMMARY Cells were treated to overexposes or down regulate GOLPH3 or LCS #SAMPLEPREP SP:SAMPLEPREP_SUMMARY Samples were fortified with an Internal standard Mix and lipids were extracted SP:SAMPLEPREP_SUMMARY twice with an extraction mix consisting of 85:15 Ethyl acetate 70% Isopropanol. SP:SAMPLEPREP_SUMMARY All lipids that were used in the Internal standard mix and in the Calibration SP:SAMPLEPREP_SUMMARY mixes were purchased from Avanti Polar Lipids Inc. After evaporating the cell SP:SAMPLEPREP_SUMMARY extract to dryness, the samples were reconstituted in the mobile phase. #CHROMATOGRAPHY CH:CHROMATOGRAPHY_SUMMARY Samples were analyzed with a Quantum Ultra triple quadrupole mass spectrometer CH:CHROMATOGRAPHY_SUMMARY connected to an Accela HPLC and Accela autosampler using a solvent gradient. CH:CHROMATOGRAPHY_SUMMARY Ceramides identity was achieved through MRM analysis with soft fragmentation. CH:CHROMATOGRAPHY_SUMMARY Quantitative analysis is based on calibration curves generated for each CH:CHROMATOGRAPHY_SUMMARY ceramide. J. Bielawski et al. / Methods 39 (2006) 82–91 CH:CHROMATOGRAPHY_TYPE Normal phase CH:INSTRUMENT_NAME Thermo Accela 1250 CH:COLUMN_NAME Thermo Accucore C18 (100 x 2.1mm, 2.6um) #ANALYSIS AN:ANALYSIS_TYPE MS #MS MS:INSTRUMENT_NAME Thermo Quantum Ultra MS:INSTRUMENT_TYPE Triple quadrupole MS:MS_TYPE ESI MS:ION_MODE POSITIVE MS:MS_COMMENTS Samples were analyzed with a Quantum Ultra triple quadrupole mass spectrometer MS:MS_COMMENTS connected to an Accela HPLC and Accela autosampler using a solvent gradient. MS:MS_COMMENTS Ceramides identity was achieved through MRM analysis with soft fragmentation. MS:MS_COMMENTS Quantitative analysis is based on calibration curves generated for each MS:MS_COMMENTS ceramide. J. Bielawski et al. / Methods 39 (2006) 82–91 #MS_METABOLITE_DATA MS_METABOLITE_DATA:UNITS pmoles MS_METABOLITE_DATA_START Samples CTRL_1 CTRL_2 CTRL_3 GOLPH3_OE_1 GOLPH3_OE_2 GOLPH3_OE_3 GOLPH3_KD_1 GOLPH3_KD_2 GOLPH3_KD_3 LCS_OE_1 LCS_OE_2 LCS_OE_3 LCS_KD_1 LCS_KD_2 LCS_KD_3 Factors Treatment:no treatment Treatment:no treatment Treatment:no treatment Treatment:GOLPH3 overexpression Treatment:GOLPH3 overexpression Treatment:GOLPH3 overexpression Treatment:GOLPH3 silencing Treatment:GOLPH3 silencing Treatment:GOLPH3 silencing Treatment:LCS overexpression Treatment:LCS overexpression Treatment:LCS overexpression Treatment:LCS silencing Treatment:LCS silencing Treatment:LCS silencing C14-Cer 10.524 12.143 12.777 10.117 10.099 9.014 18.467 18.560 20.692 10.103 9.377 7.842 16.024 14.685 14.985 C16-Cer 35.906 36.190 36.694 28.833 28.387 25.984 53.758 53.089 57.076 29.387 27.554 25.172 75.411 73.090 71.370 C18_1-Cer 5.293 6.152 6.728 6.669 6.475 5.055 6.503 7.185 8.165 5.860 5.768 4.900 4.583 4.410 4.411 C18-Cer 13.798 15.603 16.262 15.493 16.009 12.584 17.953 20.969 22.146 15.895 15.164 12.767 18.391 16.905 17.239 C20_1-Cer 2.632 2.999 3.182 3.596 3.200 2.790 4.749 4.917 5.433 3.462 2.935 2.590 2.557 2.223 2.339 C20-Cer 9.482 11.319 12.694 13.820 13.627 9.976 18.895 21.744 22.659 14.649 13.215 11.997 16.946 16.661 16.850 C22_1-Cer 43.438 46.563 45.329 44.384 42.803 34.036 77.131 84.648 91.685 42.912 41.757 36.849 30.979 30.198 30.714 C22-Cer 62.867 70.874 69.509 80.418 77.723 58.186 121.018 147.954 153.871 81.274 75.751 70.839 102.673 99.196 100.853 C24_1-Cer 222.961 254.854 265.953 345.490 347.029 253.424 530.947 588.672 637.582 364.076 341.059 311.230 442.159 444.161 427.374 C24-Cer 95.721 118.484 120.586 135.123 125.782 94.763 155.677 185.417 212.313 124.616 115.035 103.970 143.610 142.984 150.300 C26_1-Cer 3.185 3.834 3.817 5.034 4.817 3.697 6.466 8.330 9.349 4.793 4.697 3.950 5.126 5.167 5.076 C26-Cer 0.519 0.756 0.713 1.212 0.805 0.590 0.972 1.339 1.352 0.773 0.927 0.737 0.965 0.861 1.339 C14-SM 125.989 124.486 117.335 119.393 123.423 87.996 158.879 172.220 191.950 120.992 116.105 104.653 131.338 126.754 126.789 C16-SM 2189.630 2160.857 2171.885 2273.539 2314.236 1671.577 2541.305 2998.993 3180.184 2238.547 2270.450 1948.984 2953.994 2961.602 2761.761 C18_1-SM 60.593 58.002 56.037 65.187 62.212 55.020 60.336 63.861 65.415 62.046 60.300 57.506 50.576 48.620 52.123 C18-SM 196.435 188.565 187.946 221.096 219.259 190.059 250.601 250.205 272.089 213.609 210.508 208.144 240.290 242.502 235.196 C20_1-SM 26.175 24.180 25.393 30.744 28.933 24.702 39.004 41.390 42.977 28.516 27.575 27.788 20.993 19.657 21.102 C20-SM 57.936 55.959 52.021 70.342 67.992 52.491 85.369 84.106 96.504 58.543 60.646 59.618 58.183 63.313 57.461 C22_1-SM 364.891 343.716 333.969 379.379 385.383 312.193 521.290 538.664 590.070 346.405 349.420 335.217 210.657 196.203 204.957 C22-SM 272.917 269.672 268.882 291.876 275.171 240.530 340.334 363.971 402.325 249.701 267.316 241.777 211.192 202.985 209.654 C24_1-SM 2552.009 2452.597 2442.822 2717.197 2489.529 2243.303 3732.953 3584.005 3880.436 2434.598 2451.226 2286.429 2132.060 2093.137 2115.014 C24-SM 235.420 227.654 237.527 204.753 194.967 189.821 272.453 272.515 283.615 170.912 184.293 157.975 166.493 171.659 164.654 C26_1-SM 17.332 16.806 17.882 14.327 13.226 13.145 28.571 23.060 28.466 11.825 12.989 13.071 11.987 12.539 12.858 C26-SM 2.528 2.471 2.623 2.500 2.201 2.183 2.741 2.799 2.918 2.308 2.220 2.319 2.294 2.381 2.367 C14Lact-Cer 0.551 BQL BQL BQL BQL BQL BQL BQL BQL BQL BQL BQL 0.489 0.487 BQL C14HexosylCer 3.127 3.622 3.522 4.246 4.226 3.720 5.931 6.010 6.670 3.514 3.196 3.182 10.524 9.775 8.758 C16Lact-Cer 38.100 43.091 43.928 70.063 67.540 49.720 52.277 55.532 65.711 88.354 86.098 77.279 29.670 27.331 28.698 C18_1Lact-Cer 0.736 0.744 0.801 0.922 0.883 0.831 1.151 0.940 1.075 1.157 1.159 0.943 0.703 0.658 0.724 C16HexosylCer 75.348 88.958 84.562 110.325 111.280 91.754 132.145 144.953 150.342 81.072 78.255 71.280 443.144 426.484 367.825 C18_1HexosylCer 1.435 1.513 1.504 1.554 1.583 1.486 1.589 1.673 1.630 1.500 1.496 1.502 1.447 1.687 1.557 C18Lact-Cer 6.074 7.236 7.331 9.415 9.186 8.200 10.617 9.966 10.973 14.157 13.964 12.671 4.968 4.075 4.384 C20_1Lact-Cer 1.063 1.126 1.019 1.145 1.185 1.111 1.534 1.549 1.503 1.813 1.620 1.617 0.845 0.740 0.767 C18HexosylCer 7.531 7.650 7.701 10.252 9.712 9.729 10.838 11.506 11.028 8.136 7.891 7.658 36.649 35.823 31.098 C20_1HexosylCer 1.994 2.090 1.970 2.837 2.596 2.473 4.095 3.863 3.864 2.284 2.293 2.161 3.529 3.441 3.189 C20Lact-Cer 2.062 2.208 2.099 2.705 2.472 2.265 2.713 2.657 2.396 4.024 4.110 3.503 1.482 1.403 1.518 C22_1Lact-Cer 6.127 5.785 6.172 7.895 6.526 6.711 10.419 9.822 9.851 13.491 11.900 12.188 3.528 3.553 3.618 C20HexosylCer 5.521 5.232 5.383 7.090 7.397 7.192 7.763 8.361 8.087 5.771 5.544 5.484 18.292 17.258 16.105 C22_1HexosylCer 13.494 15.214 15.497 23.720 23.931 21.868 41.887 39.407 41.357 17.882 17.987 16.937 31.812 29.859 26.668 C22Lact-Cer 30.934 34.347 36.028 36.460 34.082 33.514 44.877 44.596 51.805 59.259 57.279 54.881 13.072 13.359 13.436 C24_1Lact-Cer 105.750 107.947 112.621 148.376 135.023 133.263 177.886 174.459 183.727 243.061 219.416 213.961 56.490 53.871 59.014 C22HexosylCer 162.235 184.529 191.004 223.450 230.233 201.509 293.005 303.590 314.592 178.398 176.450 161.947 485.336 440.644 404.053 C24_1HexosylCer 454.074 501.389 512.099 705.367 695.840 607.689 878.620 931.960 961.134 584.663 566.360 525.635 1256.146 1172.306 1050.384 C24Lact-Cer 41.135 43.646 44.472 51.809 48.747 44.518 47.979 47.591 48.766 71.842 69.486 66.921 20.702 19.995 21.360 C26_1Lact-Cer 4.942 5.020 4.672 5.015 5.039 4.568 5.849 6.044 6.058 6.822 6.496 6.497 3.281 3.421 3.332 C24HexosylCer 253.848 324.527 330.981 369.630 363.637 287.918 445.579 464.222 499.899 281.578 277.578 242.540 724.827 648.820 571.066 C26_1HexosylCer 20.396 23.607 22.593 23.189 23.723 19.608 32.433 33.722 35.256 18.992 18.996 17.562 35.502 33.050 27.579 C26Lact-Cer 2.156 2.282 2.301 2.319 2.307 2.257 2.379 2.624 2.579 2.493 2.489 2.375 2.092 2.094 2.063 C26HexosylCer 3.479 4.023 4.028 4.133 4.179 3.750 4.076 4.654 4.815 3.543 3.463 3.519 4.723 4.643 4.713 MS_METABOLITE_DATA_END #METABOLITES METABOLITES_START metabolite_name RT C14-Cer 15.053 C16-Cer 16.57993424 C18_1-Cer 17.0608333 C18-Cer 17.93720568 C20_1-Cer 18.62231951 C20-Cer 19.3108956 C22_1-Cer 19.94082869 C22-Cer 20.77011827 C24_1-Cer 20.97331072 C24-Cer 22.3756384 C26_1-Cer 22.87423635 C26-Cer 24.53351824 C14-SM 17.662 C16-SM 18.481 C18_1-SM 19.081 C18-SM 19.711 C20_1-SM 19.964 C20-SM 20.845 C22_1-SM 20.658 C22-SM 21.602 C24_1-SM 21.729 C24-SM 22.988 C26_1-SM 23.083 C26-SM 24.624 C14Lact-Cer 15.552 C14HexosylCer 15.979 C16Lact-Cer 16.742 C18_1Lact-Cer 16.744 C16HexosylCer 17.160 C18_1HexosylCer 17.550 C20_1Lact-Cer 17.808 C18Lact-Cer 17.804 C18HexosylCer 18.167 C20_1HexosylCer 18.170 C20Lact-Cer 18.814 C22_1Lact-Cer 19.037 C20HexosylCer 19.233 C22_1HexosylCer 19.455 C22Lact-Cer 19.875 C24_1Lact-Cer 20.046 C22HexosylCer 20.404 C24_1HexosylCer 20.576 C26_1Lact-Cer 21.109 C24Lact-Cer 21.866 C26_1HexosylCer 21.748 C24HexosylCer 22.562 C26Lact-Cer 22.561 C26HexosylCer 23.258 METABOLITES_END #END