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Supplementary Table 2: Differential pathway genes (DPGs) Supplementary Table 2: Contd... between retinoblastoma and controls No. Genes No. Genes No. Genes No. Genes No. Genes No. Genes No. Genes No. Genes 67 MRPS18A 254 LPAR3 441 LAMC3 628 NTRK1 1 NUDT9 188 YARS 375 HDDC3 562 PGF 68 TARSL2 255 POLR1B 442 PDE6C 629 TPM3 2 MRPS2 189 WNT16 376 RPL30 563 VEGFC 69 GSK3B 256 MRPL16 443 FN1 630 TPR 3 EARS2 190 HLA‑DOA 377 GNG2 564 TGFA 70 C2 257 LPAR4 444 PDE6D 631 TFG 4 DCC 191 ENTPD6 378 PRUNE 565 EGF 71 APRT 258 ZNRD1 445 ITGA2 632 RASSF1 5 FGG 192 RPS27 379 RPL31 566 EGFR 72 MRPS21 259 MRPL17 446 PDE6G 633 RASSF5 6 ADPRM 193 YARS2 380 GNG3 567 ERBB2 73 SARS2 260 LPAR5 447 ITGA2B 634 STK4 7 MRPS5 194 FZD1 381 RPL32 568 PDGFA 74 TCF7 261 TWISTNB 448 PDE6H 635 DAPK1 8 EPRS 195 HLA‑DOB 382 GNG4 569 PDGFB 75 C5 262 MRPL18 449 ITGA3 636 DAPK3 9 CASP3 196 NUDT16 383 RPL34 570 PDGFRA 76 NT5C2 263 LPAR6 450 PDE9A 637 DAPK2 10 C3 197 RPS27L 384 GNG5 571 PDGFRB 77 RPS2 264 POLR1E 451 ITGA6 638 PLCG1 11 NUDT5 198 WARS2 385 RPL35 572 IGF1 78 SARS 265 MRPL19 452 PDE10A 639 PLCG2 12 MRPS6 199 FZD7 386 GNG7 573 IGF1R 79 TCF7L1 266 AGTR1 453 ITGAV 640 RALGDS 13 QRSL1 200 HLA‑DPA1 387 RPL35A 574 KITLG 80 C3AR1 267 POLR2A 454 PDE11A 641 RALA 14 CASP9 201 ITPA 388 GNG8 575 KIT 81 NT5C1A 268 MRPL20 455 ITGB1 642 RALB 15 CFB 202 RPS27A 389 RPL36 576 FLT3LG 82 RPS3 269 GNA12 456 ADSSL1 643 RALBP1 16 PGM1 203 WARS 390 GNG11 577 FLT3 83 PSTK 270 POLR2B 457 PTK2 644 CDC42 17 MRPS7 204 FZD2 391 RPL37 578 HGF 84 TCF7L2 271 MRPL21 458 ADSS 645 RAC1 18 GATB 205 HLA‑DPB1 392 GNG12 579 MET 85 C5AR1 272 GNA13 459 PIK3CA 646 RAC2 19 APPL1 206 XDH 393 RPL37A 580 FGF1 86 NT5E 273 POLR2C 460 AMPD2 647 RAC3 20 CFD 207 RPS28 394 GNG13 581 FGF2 87 RPS4Y1 274 MRPL22 461 PIK3CD 648 MAPK8 21 PGM2 208 FZD3 395 RPL38 582 FGF3 88 SEPSECS 275 ARHGEF12 462 AMPD3 649 MAPK10 22 MRPS9 209 HLA‑DQA1 396 GNGT1 583 FGF4 89 LEF1 276 POLR2D 463 PIK3CB 650 MAPK9 23 GATC 210 NUDT2 397 RPL39 584 FGF17 90 FCGR1A 277 MRPL23 464 AMPD1 651 PAX8 24 CDH1 211 RPS29 398 GNGT2 585 FGF6 91 NT5C 278 ARHGEF11 465 PIK3CG 652 PPARG 25 CFH 212 FZD4 399 ADCY10 586 FGF7 92 RPS4X 279 POLR2E 466 ADK 653 RXRA 26 PRPS1L1 213 HLA‑DQB1 400 UBA52 587 FGF8 93 CARS 280 MRPL24 467 PIK3R1 654 RXRB 27 MRPS10 214 GMPS 401 COL4A2 588 FGF9 94 BIRC5 281 ARHGEF1 468 DCK 655 RXRG 28 AARS2 215 FAU 402 GUCY1A2 589 FGF10 95 FCGR2A 282 POLR2F 469 PIK3R5 656 RARB 29 CTNNB1 216 FZD5 403 RPL41 590 FGF11 96 NT5M 283 MRPL27 470 ADA 657 PPARD 30 MBL2 217 HLA‑DRA 404 COL4A4 591 FGF12 97 RPS5 284 RHOA 471 PIK3R2 658 JUP 31 PRPS2 218 GMPR 405 GUCY1A3 592 FGF13 98 CARS2 285 POLR2G 472 AK7 659 ZBTB16 32 MRPS11 219 MRPL1 406 RPL36AL 593 FGF14 99 MYC 286 MRPL28 473 PIK3R3 660 PML 33 AARS 220 FZD6 407 COL4A6 594 FGF16 100 FCGR2B 287 ROCK1 474 AK4 661 RARA 34 CTNNA3 221 HLA‑DRB4 408 GUCY1B3 595 FGF5 101 NT5C3A 288 POLR2H 475 PTEN 662 RUNX1T1 35 MASP1 222 GMPR2 409 RPL36A 596 FGF18 102 RPS6 289 MRPL30 476 AK5 663 SPI1 36 PRPS1 223 MRPL2 410 COL4A1 597 FGF19 103 MARS2 290 ROCK2 477 NKX3‑1 664 CEBPA 37 MRPS12 224 FZD10 411 GUCY2C 598 FGF20 104 CCND1 291 POLR2I 478 AK2 665 CSF2RA 38 DARS2 225 PTAFR 412 RPLP0 599 FGF21 105 FCGR2C 292 MRPL32 479 AKT1 666 CSF3R 39 CTNNA1 226 GDA 413 COL4A5 600 FGF22 106 NT5C3B 293 CXCL12 480 AK1 667 CSF1R 40 MASP2 227 MRPL3 414 GUCY2D 601 FGF23 107 RPS7 294 POLR2L 481 AKT2 668 IL6 41 PPAT 228 FZD9 415 RPLP1 602 FGFR1 108 MTFMT 295 MRPL33 482 AK8 669 CDKN2A 42 MRPS14 229 IL10 416 COL4A3 603 FGFR2 109 WNT1 296 CXCR4 483 AKT3 670 E2F1 43 DARS 230 GUK1 417 GUCY2F 604 FGFR3 110 FCGR3B 297 POLR2J 484 AK6 671 E2F2 44 CTNNA2 231 MRPL4 418 RPLP2 605 GRB2 111 PNP 298 MRPL34 485 CHUK 672 E2F3 45 C1QA 232 DVL3 419 LAMA1 606 SOS1 112 RPS8 299 GNAI1 486 AK3 673 MAX 46 GART 233 KRT10 420 NPR1 607 SOS2 113 VARS2 300 POLR2K 487 IKBKB 674 PIAS2 47 MRPS15 234 PKM 421 LAMA2 608 HRAS 114 WNT2 301 MRPL35 488 ENTPD2 675 CDKN2B 48 NARS2 235 MRPL12 422 NPR2 609 KRAS 115 FCAR 302 GNAI3 489 IKBKG 676 CDK6 49 AXIN1 236 DVL2 423 LAMA3 610 NRAS 116 HPRT1 303 POLR3A 490 NTPCR 677 CKS1B 50 C1QB 237 PKLR 424 PDE1A 611 ARAF 117 RPS9 304 MRPL36 491 NFKBIA 678 CKS2 51 PFAS 238 MRPL9 425 LAMA5 612 BRAF 118 VARS 305 GNAI2 492 PNPT1 679 SKP2 52 MRPS16 239 DVL1 426 PDE1B 613 RAF1 119 WNT2B 306 POLR3B 493 NFKB1 680 CDK2 53 NARS 240 RRM1 427 LAMA4 614 MAP2K1 120 FPR3 307 RPL3L 494 PDE4A 681 CCNE1 54 AXIN2 241 MRPL10 428 PDE1C 615 MAP2K2 121 IMPDH1 308 PTGER1 495 NFKB2 682 CCNE2 55 C1QC 242 F2R 429 LAMB1 616 MAPK1 122 RPS10 309 POLR3C 496 PDE4B 683 RB1 56 PAICS 243 RRM2B 430 PDE2A 617 MAPK3 123 LARS 310 RPL3 497 RELA 684 MITF 57 MRPS17 244 MRPL11 431 LAMB2 618 JUN 124 WNT4 311 PTGER2 498 PDE4D 685 TGFB1 58 GARS 245 F2RL3 432 PDE3A 619 FOS 125 FPR2 312 POLR3D 499 PTGS2 686 TGFB2 59 APC 246 RRM2 433 LAMB3 620 MMP1 126 IMPDH2 313 RPL6 500 PDE7A 687 TGFB3 60 C1R 247 MRPL13 434 PDE3B 621 MMP2 127 RPS11 314 PTGER3 501 NOS2 688 TGFBR1 61 ADSL 248 LPAR1 435 LAMB4 622 MMP9 128 LARS2 315 POLR3E 502 PDE7B 689 TGFBR2 62 MRPS18C 249 DGUOK 436 PDE5A 623 CXCL8 129 WNT5A 316 RPL7 503 BCL2 690 SMAD2 63 TARS 250 MRPL14 437 LAMC1 624 CDK4 130 FPR1 317 PTGER4 504 PDE8B 691 SMAD3 64 APC2 251 LPAR2 438 PDE6A 625 RET 131 NME6 318 POLR1C 505 BIRC2 692 SMAD4 65 C1S 252 POLR1A 439 LAMC2 626 CCDC6 132 RPS12 319 RPL8 506 PDE8A 693 MECOM 66 ATIC 253 MRPL15 440 PDE6B 627 NCOA4 133 IARS 320 GNAS 507 BIRC3 694 CTBP1 Contd... Contd... Supplementary Table 2: Contd... Supplementary Table 2: Contd... No. Genes No. Genes No. Genes No. Genes No. Genes No. Genes No. Genes No. Genes 134 WNT5B 321 POLR3K 508 FHIT 695 CTBP2 161 AK9 348 PRIM2 535 CBLC 722 ARNT 135 PLG 322 RPL9 509 XIAP 696 HDAC1 162 RPS18 349 RPL22L1 536 CBL 723 ARNT2 136 NME7 323 ADCY1 510 ENPP4 697 HDAC2 163 HARS 350 PRKACA 537 CBLB 724 CREBBP 137 RPS14 324 POLR1D 511 BIRC7 698 MLH1 164 WNT9A 351 POLD1 538 STAT5A 725 EP300 138 IARS2 325 RPL10L 512 PAPSS2 699 MSH2 165 ITGAM 352 RPL22 539 STAT5B 726 SLC2A1 139 WNT6 326 ADCY2 513 BCL2L1 700 MSH3 166 ENTPD3 353 PRKACB 540 BDKRB1 727 SHH 140 CFI 327 POLR3H 514 PAPSS1 701 MSH6 167 RPS19 354 POLD2 541 BDKRB2 728 PTCH1 141 NME4 328 RPL10A 515 TRAF1 702 BAX 168 HARS2 355 RPL23A 542 EDNRA 729 SMO 142 RPS15 329 ADCY3 516 ENPP1 703 BRCA2 169 WNT9B 356 PRKACG 543 EDNRB 730 STK36 143 KARS 330 POLR3GL 517 TRAF2 704 RAD51 170 ITGB2 357 POLD3 544 GNAQ 731 SUFU 144 WNT7A 331 RPL11 518 ENPP3 705 FASLG 171 ENTPD1 358 RSL24D1 545 GNA11 732 GLI1 145 SELPLG 332 ADCY4 519 TRAF3 706 FAS 172 RPS21 359 PRKX 546 PLCB1 733 GLI2 146 NME1 333 POLR3G 520 ALLC 707 FADD 173 FARSA 360 POLD4 547 PLCB2 734 GLI3 147 RPS15A 334 RPL12 521 TRAF4 708 CASP8 174 WNT10B 361 RPL24 548 PLCB3 735 BMP2 148 RARS2 335 ADCY5 522 TRAF5 709 BID 175 DSG1 362 GNB1 549 PLCB4 736 BMP4 149 WNT7B 336 POLR3F 523 TRAF6 710 CYCS 176 CANT1 363 POLE 550 PRKCA 737 HHIP 150 SELP 337 RPL14 524 MTOR 711 VHL 177 RPS23 364 RPL26L1 551 PRKCB 738 PTCH2 151 NME5 338 ADCY6 525 BAD 712 TCEB1 178 FARS2 365 GNB2 552 PRKCG 739 AR 152 RPS16 339 POLA1 526 FOXO1 713 TCEB2 179 WNT10A 366 POLE2 553 RASGRP1 740 HSP90AA1 153 RARS 340 RPL15 527 MDM2 714 RBX1 180 HLA‑DMA 367 RPL27 554 RASGRP2 741 HSP90AB1 154 WNT8A 341 ADCY7 528 TP53 715 CUL2 181 ENTPD4 368 GNB3 555 RASGRP3 742 HSP90B1 155 ICAM1 342 POLA2 529 CDKN1B 716 EGLN1 182 RPS24 369 POLE3 556 RASGRP4 743 KLK3 156 NME3 343 RPL18 530 CDKN1A 717 EGLN3 183 FARSB 370 RPL27A 557 JAK1 744 ETS1 157 RPS17 344 ADCY8 531 BCR 718 EGLN2 184 WNT11 371 GNB4 558 STAT3 745 GSTP1 158 PARS2 345 PRIM1 532 ABL1 719 FH 185 HLA‑DMB 372 POLE4 559 STAT1 746 PLD1 159 WNT8B 346 RPL19 533 CRK 720 HIF1A 186 ENTPD5 373 RPL29 560 VEGFA 747 CCNA1 160 ITGAL 347 ADCY9 534 CRKL 721 EPAS1 187 RPS25 374 GNB5 561 VEGFB Contd....
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  • Anti-MRPL11 Antibody (ARG41863)

    Anti-MRPL11 Antibody (ARG41863)

    Product datasheet [email protected] ARG41863 Package: 100 μl anti-MRPL11 antibody Store at: -20°C Summary Product Description Rabbit Polyclonal antibody recognizes MRPL11 Tested Reactivity Hu, Ms, Rat Tested Application IHC-P, WB Host Rabbit Clonality Polyclonal Isotype IgG Target Name MRPL11 Antigen Species Human Immunogen Recombinant fusion protein corresponding to aa. 1-192 of Human MRPL11. (NP_057134.1) Conjugation Un-conjugated Alternate Names MRP-L11; 39S ribosomal protein L11, mitochondrial; L11MT; L11mt; CGI-113 Application Instructions Application table Application Dilution IHC-P 1:50 - 1:100 WB 1:500 - 1:2000 Application Note * The dilutions indicate recommended starting dilutions and the optimal dilutions or concentrations should be determined by the scientist. Positive Control A549 Calculated Mw 21 kDa Observed Size ~ 19 kDa Properties Form Liquid Purification Affinity purified. Buffer PBS (pH 7.3), 0.02% Sodium azide and 50% Glycerol. Preservative 0.02% Sodium azide Stabilizer 50% Glycerol Storage instruction For continuous use, store undiluted antibody at 2-8°C for up to a week. For long-term storage, aliquot and store at -20°C. Storage in frost free freezers is not recommended. Avoid repeated freeze/thaw cycles. Suggest spin the vial prior to opening. The antibody solution should be gently mixed before use. www.arigobio.com 1/2 Note For laboratory research only, not for drug, diagnostic or other use. Bioinformation Gene Symbol MRPL11 Gene Full Name mitochondrial ribosomal protein L11 Background This nuclear gene encodes a 39S subunit component of the mitochondial ribosome. Alternative splicing results in multiple transcript variants. Pseudogenes for this gene are found on chromosomes 5 and 12.
  • Inhibition of the MID1 Protein Complex

    Inhibition of the MID1 Protein Complex

    Matthes et al. Cell Death Discovery (2018) 4:4 DOI 10.1038/s41420-017-0003-8 Cell Death Discovery ARTICLE Open Access Inhibition of the MID1 protein complex: a novel approach targeting APP protein synthesis Frank Matthes1,MoritzM.Hettich1, Judith Schilling1, Diana Flores-Dominguez1, Nelli Blank1, Thomas Wiglenda2, Alexander Buntru2,HannaWolf1, Stephanie Weber1,InaVorberg 1, Alina Dagane2, Gunnar Dittmar2,3,ErichWanker2, Dan Ehninger1 and Sybille Krauss1 Abstract Alzheimer’s disease (AD) is characterized by two neuropathological hallmarks: senile plaques, which are composed of amyloid-β (Aβ) peptides, and neurofibrillary tangles, which are composed of hyperphosphorylated tau protein. Aβ peptides are derived from sequential proteolytic cleavage of the amyloid precursor protein (APP). In this study, we identified a so far unknown mode of regulation of APP protein synthesis involving the MID1 protein complex: MID1 binds to and regulates the translation of APP mRNA. The underlying mode of action of MID1 involves the mTOR pathway. Thus, inhibition of the MID1 complex reduces the APP protein level in cultures of primary neurons. Based on this, we used one compound that we discovered previously to interfere with the MID1 complex, metformin, for in vivo experiments. Indeed, long-term treatment with metformin decreased APP protein expression levels and consequently Aβ in an AD mouse model. Importantly, we have initiated the metformin treatment late in life, at a time-point where mice were in an already progressed state of the disease, and could observe an improved behavioral phenotype. These 1234567890 1234567890 findings together with our previous observation, showing that inhibition of the MID1 complex by metformin also decreases tau phosphorylation, make the MID1 complex a particularly interesting drug target for treating AD.
  • Supplementary Dataset S2

    Supplementary Dataset S2

    mitochondrial translational termination MRPL28 MRPS26 6 MRPS21 PTCD3 MTRF1L 4 MRPL50 MRPS18A MRPS17 2 MRPL20 MRPL52 0 MRPL17 MRPS33 MRPS15 −2 MRPL45 MRPL30 MRPS27 AURKAIP1 MRPL18 MRPL3 MRPS6 MRPS18B MRPL41 MRPS2 MRPL34 GADD45GIP1 ERAL1 MRPL37 MRPS10 MRPL42 MRPL19 MRPS35 MRPL9 MRPL24 MRPS5 MRPL44 MRPS23 MRPS25 ITB ITB ITB ITB ICa ICr ITL original ICr ICa ITL ICa ITL original ICr ITL ICr ICa mitochondrial translational elongation MRPL28 MRPS26 6 MRPS21 PTCD3 MRPS18A 4 MRPS17 MRPL20 2 MRPS15 MRPL45 MRPL52 0 MRPS33 MRPL30 −2 MRPS27 AURKAIP1 MRPS10 MRPL42 MRPL19 MRPL18 MRPL3 MRPS6 MRPL24 MRPS35 MRPL9 MRPS18B MRPL41 MRPS2 MRPL34 MRPS5 MRPL44 MRPS23 MRPS25 MRPL50 MRPL17 GADD45GIP1 ERAL1 MRPL37 ITB ITB ITB ITB ICa ICr original ICr ITL ICa ITL ICa ITL original ICr ITL ICr ICa translational termination MRPL28 MRPS26 6 MRPS21 PTCD3 C12orf65 4 MTRF1L MRPL50 MRPS18A 2 MRPS17 MRPL20 0 MRPL52 MRPL17 MRPS33 −2 MRPS15 MRPL45 MRPL30 MRPS27 AURKAIP1 MRPL18 MRPL3 MRPS6 MRPS18B MRPL41 MRPS2 MRPL34 GADD45GIP1 ERAL1 MRPL37 MRPS10 MRPL42 MRPL19 MRPS35 MRPL9 MRPL24 MRPS5 MRPL44 MRPS23 MRPS25 ITB ITB ITB ITB ICa ICr original ICr ITL ICa ITL ICa ITL original ICr ITL ICr ICa translational elongation DIO2 MRPS18B MRPL41 6 MRPS2 MRPL34 GADD45GIP1 4 ERAL1 MRPL37 2 MRPS10 MRPL42 MRPL19 0 MRPL30 MRPS27 AURKAIP1 −2 MRPL18 MRPL3 MRPS6 MRPS35 MRPL9 EEF2K MRPL50 MRPS5 MRPL44 MRPS23 MRPS25 MRPL24 MRPS33 MRPL52 EIF5A2 MRPL17 SECISBP2 MRPS15 MRPL45 MRPS18A MRPS17 MRPL20 MRPL28 MRPS26 MRPS21 PTCD3 ITB ITB ITB ITB ICa ICr ICr ITL original ITL ICa ICa ITL ICr ICr ICa original
  • C6orf203 Controls OXPHOS Function Through Modulation of Mitochondrial Protein Biosynthesis

    C6orf203 Controls OXPHOS Function Through Modulation of Mitochondrial Protein Biosynthesis

    bioRxiv preprint doi: https://doi.org/10.1101/704403; this version posted July 17, 2019. The copyright holder for this preprint (which was not certified by peer review) is the author/funder. All rights reserved. No reuse allowed without permission. C6orf203 controls OXPHOS function through modulation of mitochondrial protein biosynthesis number of characters excluding Materials and Methods: 40,651 Sara Palacios-Zambrano1,2, Luis Vázquez-Fonseca1,2, Cristina González-Páramos1,2, Laura Mamblona1,2, Laura Sánchez-Caballero3, Leo Nijtmans3, Rafael Garesse1,2 and Miguel Angel Fernández-Moreno1,2,* 1 Departamento de Bioquímica, Instituto de Investigaciones Biomédicas “Alberto Sols” UAM CSIC and Centro de Investigación Biomédica en Red en Enfermedades Raras (CIBERER). Facultad de Medicina, Universidad Autónoma de Madrid. Madrid 28029, Spain. 2 Instituto de Investigación Sanitaria Hospital 12 de Octubre (imas12), Madrid 28041, Spain. 3 Department of Pediatrics, Radboud Center for Mitochondrial Medicine, Radboud University Medical Center, Nijmegen, The Netherlands. * To whom correspondence should be addressed. Tel:+34 91 497 31 29; Email: [email protected] Running title “C6orf203 controls mt-proteins synthesis” bioRxiv preprint doi: https://doi.org/10.1101/704403; this version posted July 17, 2019. The copyright holder for this preprint (which was not certified by peer review) is the author/funder. All rights reserved. No reuse allowed without permission. ABSTRACT Mitochondria are essential organelles present in the vast majority of eukaryotic cells. Their central function is to produce cellular energy through the OXPHOS system, and functional alterations provoke so-called mitochondrial OXPHOS diseases. It is estimated that several hundred mitochondrial proteins have unknown functions. Very recently, C6orf203 was described to participate in mitochondrial transcription under induced mitochondrial DNA depletion stress conditions.