#METABOLOMICS WORKBENCH juliehaines_20251202_062515 DATATRACK_ID:6799 STUDY_ID:ST004412 ANALYSIS_ID:AN007379 PROJECT_ID:PR002788 VERSION 1 CREATED_ON December 2, 2025, 6:57 am #PROJECT PR:PROJECT_TITLE Altered Hepatic Metabolism in Down Syndrome PR:PROJECT_SUMMARY Trisomy 21 (T21) gives rise to Down syndrome (DS), the most commonly occurring PR:PROJECT_SUMMARY chromosomal abnormality in humans. T21 affects nearly every organ and tissue PR:PROJECT_SUMMARY system in the body, predisposing individuals with DS to congenital heart PR:PROJECT_SUMMARY defects, autoimmunity, and Alzheimer’s disease, among other co-occurring PR:PROJECT_SUMMARY conditions. Here, using multi-omic analysis of plasma from more than 400 people, PR:PROJECT_SUMMARY we report broad metabolic changes in the population with DS typified by PR:PROJECT_SUMMARY increased bile acid levels and protein signatures of liver dysfunction. In a PR:PROJECT_SUMMARY mouse model of DS, we demonstrate conservation of perturbed bile acid metabolism PR:PROJECT_SUMMARY accompanied by liver pathology. Bulk RNA-sequencing revealed widespread impacts PR:PROJECT_SUMMARY of the Dp16 model on hepatic metabolism and inflammation, while single-cell PR:PROJECT_SUMMARY transcriptomics highlighted cell types associated with these observations. PR:PROJECT_SUMMARY Modulation of dietary fat profoundly impacted gene expression, bile acids, and PR:PROJECT_SUMMARY liver pathology. Overall, these data represent evidence for altered hepatic PR:PROJECT_SUMMARY metabolism in DS that could be modulated by diet. PR:INSTITUTE University of Colorado Anschutz Medical Campus PR:LABORATORY Lab of Angelo D'Alessandro in collaboration with labs of Kelly Sullivan and PR:LABORATORY Joaquin Espinosa PR:LAST_NAME Haines PR:FIRST_NAME Julie PR:ADDRESS 12801 E 17th Ave, Room 1303, Aurora, Colorado, 80045, USA PR:EMAIL julie.haines@cuanschutz.edu PR:PHONE 3037243339 #STUDY ST:STUDY_TITLE Plasma lipidomics characterization of mouse models of Down syndrome Dp16 and ST:STUDY_TITLE Dp16-2xIfnrs versus WT mice ST:STUDY_SUMMARY Lipidomics of plasma at baseline from adult mice comparing WT, the Dp16 Down ST:STUDY_SUMMARY syndrome mouse model, and Dp16-2xIfnrs, where genome editing has been utilized ST:STUDY_SUMMARY to correct the dosage of the Ifnr locus within a mouse model of DS. ST:INSTITUTE University of Colorado Anschutz Medical Campus ST:LAST_NAME Haines ST:FIRST_NAME Julie ST:ADDRESS 12801 E 17th Ave, Room 1303, Aurora, Colorado, 80045, USA ST:EMAIL julie.haines@cuanschutz.edu ST:PHONE 3037243339 #SUBJECT SU:SUBJECT_TYPE Mammal SU:SUBJECT_SPECIES Mus musculus SU:GENDER Male and female #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 - F2-51-02- Chromosome 21 status:Dp16 | Sex:Female | Sample source:plasma RAW_FILE_NAME(raw file name)=F2-51-02.raw SUBJECT_SAMPLE_FACTORS - F2-51-03- Chromosome 21 status:Dp16 | Sex:Female | Sample source:plasma RAW_FILE_NAME(raw file name)=F2-51-03.raw SUBJECT_SAMPLE_FACTORS - F2-51-04- Chromosome 21 status:Dp16 | Sex:Female | Sample source:plasma RAW_FILE_NAME(raw file name)=F2-51-04.raw SUBJECT_SAMPLE_FACTORS - F2-51-05- Chromosome 21 status:Dp16 | Sex:Female | Sample source:plasma RAW_FILE_NAME(raw file name)=F2-51-05.raw SUBJECT_SAMPLE_FACTORS - F2-51-06- Chromosome 21 status:Dp16 | Sex:Female | Sample source:plasma RAW_FILE_NAME(raw file name)=F2-51-06.raw SUBJECT_SAMPLE_FACTORS - F2-51-07- Chromosome 21 status:Dp16 | Sex:Male | Sample source:plasma RAW_FILE_NAME(raw file name)=F2-51-07.raw SUBJECT_SAMPLE_FACTORS - F2-51-08- Chromosome 21 status:Dp16 | Sex:Male | Sample source:plasma RAW_FILE_NAME(raw file name)=F2-51-08.raw SUBJECT_SAMPLE_FACTORS - F2-51-09- Chromosome 21 status:Dp16 | Sex:Male | Sample source:plasma RAW_FILE_NAME(raw file name)=F2-51-09.raw SUBJECT_SAMPLE_FACTORS - F2-51-10- Chromosome 21 status:Dp16 | Sex:Male | Sample source:plasma RAW_FILE_NAME(raw file name)=F2-51-10.raw SUBJECT_SAMPLE_FACTORS - F2-51-11- Chromosome 21 status:Dp16 | Sex:Male | Sample source:plasma RAW_FILE_NAME(raw file name)=F2-51-11.raw SUBJECT_SAMPLE_FACTORS - F2-51-12- Chromosome 21 status:Dp16 | Sex:Male | Sample source:plasma RAW_FILE_NAME(raw file name)=F2-51-12.raw SUBJECT_SAMPLE_FACTORS - F2-51-13- Chromosome 21 status:Dp16 | Sex:Male | Sample source:plasma RAW_FILE_NAME(raw file name)=F2-51-13.raw SUBJECT_SAMPLE_FACTORS - F2-51-14- Chromosome 21 status:Dp16-2xIfnrs | Sex:Female | Sample source:plasma RAW_FILE_NAME(raw file name)=F2-51-14.raw SUBJECT_SAMPLE_FACTORS - F2-51-15- Chromosome 21 status:Dp16-2xIfnrs | Sex:Female | Sample source:plasma RAW_FILE_NAME(raw file name)=F2-51-15.raw SUBJECT_SAMPLE_FACTORS - F2-51-16- Chromosome 21 status:Dp16-2xIfnrs | Sex:Female | Sample source:plasma RAW_FILE_NAME(raw file name)=F2-51-16.raw SUBJECT_SAMPLE_FACTORS - F2-51-17- Chromosome 21 status:Dp16-2xIfnrs | Sex:Female | Sample source:plasma RAW_FILE_NAME(raw file name)=F2-51-17.raw SUBJECT_SAMPLE_FACTORS - F2-51-18- Chromosome 21 status:Dp16-2xIfnrs | Sex:Female | Sample source:plasma RAW_FILE_NAME(raw file name)=F2-51-18.raw SUBJECT_SAMPLE_FACTORS - F2-51-19- Chromosome 21 status:Dp16-2xIfnrs | Sex:Male | Sample source:plasma RAW_FILE_NAME(raw file name)=F2-51-19.raw SUBJECT_SAMPLE_FACTORS - F2-51-20- Chromosome 21 status:Dp16-2xIfnrs | Sex:Male | Sample source:plasma RAW_FILE_NAME(raw file name)=F2-51-20.raw SUBJECT_SAMPLE_FACTORS - F2-51-21- Chromosome 21 status:Dp16-2xIfnrs | Sex:Male | Sample source:plasma RAW_FILE_NAME(raw file name)=F2-51-21.raw SUBJECT_SAMPLE_FACTORS - F2-51-22- Chromosome 21 status:Dp16-2xIfnrs | Sex:Male | Sample source:plasma RAW_FILE_NAME(raw file name)=F2-51-22.raw SUBJECT_SAMPLE_FACTORS - F2-51-23- Chromosome 21 status:Dp16-2xIfnrs | Sex:Male | Sample source:plasma RAW_FILE_NAME(raw file name)=F2-51-23.raw SUBJECT_SAMPLE_FACTORS - F2-51-24- Chromosome 21 status:WT | Sex:Female | Sample source:plasma RAW_FILE_NAME(raw file name)=F2-51-24.raw SUBJECT_SAMPLE_FACTORS - F2-51-25- Chromosome 21 status:WT | Sex:Female | Sample source:plasma RAW_FILE_NAME(raw file name)=F2-51-25.raw SUBJECT_SAMPLE_FACTORS - F2-51-26- Chromosome 21 status:WT | Sex:Female | Sample source:plasma RAW_FILE_NAME(raw file name)=F2-51-26.raw SUBJECT_SAMPLE_FACTORS - F2-51-27- Chromosome 21 status:WT | Sex:Female | Sample source:plasma RAW_FILE_NAME(raw file name)=F2-51-27.raw SUBJECT_SAMPLE_FACTORS - F2-51-28- Chromosome 21 status:WT | Sex:Female | Sample source:plasma RAW_FILE_NAME(raw file name)=F2-51-28.raw SUBJECT_SAMPLE_FACTORS - F2-51-29- Chromosome 21 status:WT | Sex:Male | Sample source:plasma RAW_FILE_NAME(raw file name)=F2-51-29.raw SUBJECT_SAMPLE_FACTORS - F2-51-30- Chromosome 21 status:WT | Sex:Male | Sample source:plasma RAW_FILE_NAME(raw file name)=F2-51-30.raw SUBJECT_SAMPLE_FACTORS - F2-51-31- Chromosome 21 status:WT | Sex:Male | Sample source:plasma RAW_FILE_NAME(raw file name)=F2-51-31.raw SUBJECT_SAMPLE_FACTORS - F2-51-32- Chromosome 21 status:WT | Sex:Male | Sample source:plasma RAW_FILE_NAME(raw file name)=F2-51-32.raw SUBJECT_SAMPLE_FACTORS - F2-51-33- Chromosome 21 status:WT | Sex:Male | Sample source:plasma RAW_FILE_NAME(raw file name)=F2-51-33.raw #COLLECTION CO:COLLECTION_SUMMARY Blood was collected from WT, Dp16, or Dp16-2xIfnrs mice via a cardiac puncture CO:COLLECTION_SUMMARY post euthanasia into lithium heparin tubes (Sarstedt). Plasma was isolated from CO:COLLECTION_SUMMARY whole blood via centrifugation for 15 minutes at 700g, then the supernatant was CO:COLLECTION_SUMMARY isolated and spun again for 15 minutes at 2100g. CO:SAMPLE_TYPE Blood (plasma) CO:STORAGE_CONDITIONS -80℃ #TREATMENT TR:TREATMENT_SUMMARY No treatments were performed for this lipidomics study. The Dp16-2xIfnrs mouse TR:TREATMENT_SUMMARY model was previously described in PMID 37277650. #SAMPLEPREP SP:SAMPLEPREP_SUMMARY Plasma specimens were thawed on ice then a 10 uL aliquot was diluted with 240 uL SP:SAMPLEPREP_SUMMARY cold methanol. Samples were vortexed for 30 minutes at 4 degrees. Insoluble SP:SAMPLEPREP_SUMMARY material was then pelleted by centrifugation (18,000 g, 10 min) then SP:SAMPLEPREP_SUMMARY supernatants were diluted 1:1 with 5 mM ammonium acetate. SP:PROCESSING_STORAGE_CONDITIONS 4℃ SP:EXTRACT_STORAGE -80℃ #CHROMATOGRAPHY CH:CHROMATOGRAPHY_SUMMARY Positive C18 global lipidomics CH:CHROMATOGRAPHY_TYPE Reversed phase CH:INSTRUMENT_NAME Thermo Vanquish CH:COLUMN_NAME Waters ACQUITY UPLC HSS T3 (150 x 2.1mm,1.8um) CH:SOLVENT_A 75% water/25% acetonitrile; 5 mM ammonium acetate CH:SOLVENT_B 90% isopropanol/10% acetonitrile; 5 mM ammonium acetate CH:FLOW_GRADIENT 0–10 min 30–100% B and 0.325 mL/min; 10–12 min 100% B and 0.325 mL/min; CH:FLOW_GRADIENT 12–12.5 min 100–30% B and 0.4 mL/min; 12.5–14.9 min 30% B and 0.4 mL/min; CH:FLOW_GRADIENT 14.9–15 min 30% B and 0.325 mL/min CH:FLOW_RATE 0.3-0.4 ml/min CH:COLUMN_TEMPERATURE 45 CH:SAMPLE_INJECTION 10 uL #ANALYSIS AN:ANALYSIS_TYPE MS #MS MS:INSTRUMENT_NAME Thermo Q Exactive Orbitrap MS:INSTRUMENT_TYPE Orbitrap MS:MS_TYPE ESI MS:ION_MODE POSITIVE MS:MS_COMMENTS The Q Exactive was run independently in positive and negative ion mode, scanning MS:MS_COMMENTS using full MS from 125-1500 m/z at 70,000 resolution and top 10 data-dependent MS:MS_COMMENTS MS2 at 17,500 resolution. Electrospray ionization was achieved with 45 Arb MS:MS_COMMENTS sheath gas, 25 Arb auxiliary gas, and 4 kV spray voltage. Calibration was MS:MS_COMMENTS performed prior to the run using the PierceTM Positive and Negative Ion MS:MS_COMMENTS Calibration Solutions (Thermo Fisher Scientific). Run order of samples was MS:MS_COMMENTS randomized and technical replicates were injected after every 4 samples to MS:MS_COMMENTS assess quality control. #MS_METABOLITE_DATA MS_METABOLITE_DATA:UNITS peak area MS_METABOLITE_DATA_START Samples F2-51-02- F2-51-03- F2-51-04- F2-51-05- F2-51-06- F2-51-07- F2-51-08- F2-51-09- F2-51-10- F2-51-11- F2-51-12- F2-51-13- F2-51-14- F2-51-15- F2-51-16- F2-51-17- F2-51-18- F2-51-19- F2-51-20- F2-51-21- F2-51-22- F2-51-23- F2-51-24- F2-51-25- F2-51-26- F2-51-27- F2-51-28- F2-51-29- F2-51-30- F2-51-31- F2-51-32- F2-51-33- Factors Chromosome 21 status:Dp16 | Sex:Female | Sample source:plasma Chromosome 21 status:Dp16 | Sex:Female | Sample source:plasma Chromosome 21 status:Dp16 | Sex:Female | Sample source:plasma Chromosome 21 status:Dp16 | Sex:Female | Sample source:plasma Chromosome 21 status:Dp16 | Sex:Female | Sample source:plasma Chromosome 21 status:Dp16 | Sex:Male | Sample source:plasma Chromosome 21 status:Dp16 | Sex:Male | Sample source:plasma Chromosome 21 status:Dp16 | Sex:Male | Sample source:plasma Chromosome 21 status:Dp16 | Sex:Male | Sample source:plasma Chromosome 21 status:Dp16 | Sex:Male | Sample source:plasma Chromosome 21 status:Dp16 | Sex:Male | Sample source:plasma Chromosome 21 status:Dp16 | Sex:Male | Sample source:plasma Chromosome 21 status:Dp16-2xIfnrs | Sex:Female | Sample source:plasma Chromosome 21 status:Dp16-2xIfnrs | Sex:Female | Sample source:plasma Chromosome 21 status:Dp16-2xIfnrs | Sex:Female | Sample source:plasma Chromosome 21 status:Dp16-2xIfnrs | Sex:Female | Sample source:plasma Chromosome 21 status:Dp16-2xIfnrs | Sex:Female | Sample source:plasma Chromosome 21 status:Dp16-2xIfnrs | Sex:Male | Sample source:plasma Chromosome 21 status:Dp16-2xIfnrs | Sex:Male | Sample source:plasma Chromosome 21 status:Dp16-2xIfnrs | Sex:Male | Sample source:plasma Chromosome 21 status:Dp16-2xIfnrs | Sex:Male | Sample source:plasma Chromosome 21 status:Dp16-2xIfnrs | Sex:Male | Sample source:plasma Chromosome 21 status:WT | Sex:Female | Sample source:plasma Chromosome 21 status:WT | Sex:Female | Sample source:plasma Chromosome 21 status:WT | Sex:Female | Sample source:plasma Chromosome 21 status:WT | Sex:Female | Sample source:plasma Chromosome 21 status:WT | Sex:Female | Sample source:plasma Chromosome 21 status:WT | Sex:Male | Sample source:plasma Chromosome 21 status:WT | Sex:Male | Sample source:plasma Chromosome 21 status:WT | Sex:Male | Sample source:plasma Chromosome 21 status:WT | Sex:Male | Sample source:plasma Chromosome 21 status:WT | Sex:Male | Sample source:plasma AcCa 8:1 19074 28270 42489 38955 63610 32222 25859 29079 37872 28853 35308 31552 50395 45087 43955 28113 48165 26106 32322 33880 34994 40958 20521 32477 44993 48578 35422 29671 24104 20720 35647 25642 AcCa 8:0 20589 51439 85093 129461 106976 45027 40915 56982 65794 75213 112119 48058 111849 98386 100944 44610 132043 41992 78351 66801 52880 116717 26563 51582 74671 85702 65430 60175 45155 44932 67847 44672 AcCa 6:0 32070 256533 337929 378442 411035 218402 204129 257239 442408 306209 395911 192553 381732 426057 411179 182134 476608 198169 512316 387508 306405 372334 216075 289755 250458 332047 247960 343329 189352 251891 310139 136267 AcCa 5:0-OH 260177 673869 402626 626917 757027 589301 464156 508019 639736 536139 539907 596801 485340 336569 411568 492403 674560 631044 408448 638257 592111 741978 441929 476331 689581 446216 470729 443932 543038 306519 692435 306408 AcCa 5:0 105540 118499 262314 231582 258718 195861 182135 197417 234492 214641 205459 178736 137088 189729 193924 108886 174239 125292 210185 239758 317388 227121 217765 147154 110555 187446 117445 178401 172046 108297 144764 114795 AcCa 4:0-OH 212781 822830 2422594 1726176 1023544 901771 601432 746762 852846 1754813 1778867 993094 3291118 1386588 2387563 1291045 2514808 994411 1049540 1161521 955846 2261980 426671 576214 1541898 1255545 1042241 1141908 1053300 987427 1577200 576846 AcCa 4:0 352866 2078853 2000278 2422292 1716381 1588068 1956988 1738706 2818043 2037632 2030104 1976888 2216866 2342304 2193789 1383813 2311631 2454572 2592358 2437292 1960241 1529158 1959491 1671343 1861326 2424237 2196577 2780207 1095416 1947555 1625003 1261532 AcCa 3:0 1611570 3250547 6030948 5473398 4510418 3821764 5108039 3940368 4629576 3231186 5065082 3706817 2763473 3403300 4169049 2963104 4522698 5233710 3883208 6832582 5297984 5321408 4380984 3118550 3284047 3009867 2902742 3943004 3798811 2626873 3345221 1942394 AcCa 20:4 168469 191490 292344 294307 283397 191235 136633 211785 137289 143500 187915 171876 369181 277140 280031 176302 326249 140117 172678 196226 153727 222241 114057 237063 191636 388316 199426 180537 139861 94103 244704 162431 AcCa 2:0 33700000 64100000 127000000 91900000 93300000 46200000 47600000 106000000 84600000 151000000 91900000 79200000 103000000 110000000 139000000 96000000 101000000 68500000 54600000 92800000 60200000 139000000 44100000 61500000 106000000 127000000 130000000 62200000 80500000 58900000 99200000 41900000 AcCa 18:2 287166 425859 846314 700295 841759 703792 480765 860748 606097 554786 825820 640980 1151509 721122 831880 468172 886024 535117 617598 733368 675998 1063594 222286 585507 526747 787230 478815 558044 567159 330415 671590 695654 AcCa 16:1 38561 56099 202311 262196 190458 90574 62413 117553 141106 154653 174182 115126 187098 284956 211203 136325 243562 75384 132113 136034 110407 254544 19698 74067 120683 139446 123443 157413 99495 81184 224201 101398 AcCa 16:0 708956 868571 1512248 1247188 1255680 1105690 826136 1378108 1218818 1184060 1108562 927485 1501306 1626716 1287039 982728 1303977 795825 1139251 1246751 970631 1823464 578696 824539 1028236 1655954 798744 1442190 1020351 752320 1733376 1214259 AcCa 14:1 70983 113484 161361 254470 243785 69624 63230 130826 78889 122742 197125 79877 275886 245735 250614 155226 270005 83123 82057 108077 88195 215385 34806 147349 158584 204371 157064 111715 100218 79553 135371 99765 AcCa 14:0 77551 124232 291533 281072 253169 123933 93692 198299 162209 171810 206592 135182 376927 267213 298331 165193 302097 100519 169625 177633 130404 289927 69422 96968 171577 197482 161975 189501 125190 87266 211865 157890 AcCa 12:1 29241 58550 48955 69353 95536 12244 12968 17897 14977 24377 36307 17083 76003 57173 72555 56267 92111 11285 14268 16187 13976 43541 42698 53229 64097 63061 75032 16256 16960 14368 21560 12657 AcCa 12:0 26067 43845 81057 112935 102562 34296 28131 58773 45884 68964 81973 40357 127239 98961 117169 46878 141917 34559 59683 54106 49933 90412 17615 45083 69338 80298 58669 55299 43726 29979 58554 48329 AcCa 10:1 21384 28878 41051 36944 55102 94165 34242 32982 99629 36382 70829 69922 61970 32168 43281 25643 55814 52050 65825 98448 125408 61664 17817 33456 42809 41988 35172 15273 20639 14681 23849 19228 AcCa 10:0 31363 70007 134908 203029 149411 67408 54156 78429 63933 141449 171861 72150 129530 186362 134003 83590 237454 57066 90535 86538 90053 233255 22257 84015 134789 147054 92634 83546 82615 71391 123943 76456 Sphingosine 49122 29109 52169 61332 61179 47679 54366 35395 35443 47204 46359 29999 47605 50759 46552 44429 47901 42691 39455 61952 54374 53194 36812 43793 44129 49501 42319 45199 46571 32186 62408 46299 Sphinganine 20255 77401 98210 31223 39633 40627 41824 155873 221137 45844 23137 110684 78035 112904 45991 26135 49738 38419 182509 148695 125732 43439 43126 28687 41400 86554 44145 185381 97497 20786 112375 160201 MS_METABOLITE_DATA_END #METABOLITES METABOLITES_START metabolite_name KEGG ID Pathway/class m/z r.t. AcCa 8:1 ac111 Carnitine and fatty acid metabolism 286.2013 1.39 AcCa 8:0 HMDB00791 Carnitine and fatty acid metabolism 288.2168 1.63 AcCa 6:0 HMDB00756 Carnitine and fatty acid metabolism 260.1857 1.25 AcCa 5:0-OH ac107 Carnitine and fatty acid metabolism 262.1647 0.98 AcCa 5:0 C20826 Carnitine and fatty acid metabolism 246.1700 1.23 AcCa 4:0-OH HMDB13127 Carnitine and fatty acid metabolism 248.1491 0.97 AcCa 4:0 C02862 Carnitine and fatty acid metabolism 232.1540 0.98 AcCa 3:0 C03017 Carnitine and fatty acid metabolism 218.1386 0.98 AcCa 20:4 ac125 Carnitine and fatty acid metabolism 448.3410 5.52 AcCa 2:0 C02571 Carnitine and fatty acid metabolism 204.1229 0.97 AcCa 18:2 HMDB01064 Carnitine and fatty acid metabolism 424.3428 5.51 AcCa 16:1 HMDB06317 Carnitine and fatty acid metabolism 398.3260 5.22 AcCa 16:0 C02990 Carnitine and fatty acid metabolism 400.3426 5.95 AcCa 14:1 HMDB13329 Carnitine and fatty acid metabolism 370.2948 4.19 AcCa 14:0 HMDB05066 Carnitine and fatty acid metabolism 372.3123 4.83 AcCa 12:1 HMDB13326 Carnitine and fatty acid metabolism 342.2637 3.03 AcCa 12:0 HMDB02250 Carnitine and fatty acid metabolism 344.2794 3.63 AcCa 10:1 CID57357170 Carnitine and fatty acid metabolism 314.2324 1.89 AcCa 10:0 HMDB00651 Carnitine and fatty acid metabolism 316.2481 2.47 Sphingosine C00319 Oxylipins 300.2892 7.06 Sphinganine C00836 Oxylipins 302.3049 6.55 METABOLITES_END #END