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Supplement Table S4 Entrez Gene ID Symbol Gene name Down-regulated fold 1 53405 CLIC5 chloride intracellular channel 5 20.15 2 79625 C4orf31 chromosome 4 open reading frame 31 19.26 3 650 BMP2 bone morphogenetic protein 2 18.27 4 23109 DDN dendrin 17.68 5 259217 HSPA12A heat shock 70kDa protein 12A 17.54 6 51196 PLCE1 phospholipase C, epsilon 1 15.57 7 5800 PTPRO protein tyrosine phosphatase, receptor type, O 14.68 8 5730 PTGDS prostaglandin D2 synthase 21kDa (brain) 14.33 9 4311 MME membrane metallo-endopeptidase (neutral endopeptidase, enkep 14.01 10 2028 ENPEP glutamyl aminopeptidase (aminopeptidase A) 13.54 11 199 AIF1 allograft inflammatory factor 1 12.50 12 1286 COL4A4 collagen, type IV, alpha 4 11.21 13 23213 SULF1 sulfatase 1 10.48 14 22925 PLA2R1 phospholipase A2 receptor 1, 180kDa 10.40 15 5058 PAK1 p21/Cdc42/Rac1-activated kinase 1 (STE20 homolog, yeast) 9.14 16 55752 SEPT11 septin 11 8.94 17 6943 TCF21 transcription factor 21 8.45 18 9863 MAGI2 membrane associated guanylate kinase, WW and PDZ domain c 8.22 19 7139 TNNT2 troponin T type 2 (cardiac) 8.19 20 2152 F3 coagulation factor III (thromboplastin, tissue factor) 7.83 21 5734 PTGER4 prostaglandin E receptor 4 (subtype EP4) 7.64 22 7422 VEGFA vascular endothelial growth factor A 7.52 23 10402 ST3GAL6 ST3 beta-galactoside alpha-2,3-sialyltransferase 6 7.19 24 7301 TYRO3 TYRO3 protein tyrosine kinase 6.98 25 2149 F2R coagulation factor II (thrombin) receptor 6.93 26 347 APOD apolipoprotein D 6.69 27 1490 CTGF connective tissue growth factor 6.58 28 23022 PALLD palladin, cytoskeletal associated protein 6.51 29 4189 DNAJB9 DnaJ (Hsp40) homolog, subfamily B, member 9 6.49 30 7490 WT1 Wilms tumor 1 6.42 31 7739 ZNF185 zinc finger protein 185 (LIM domain) 6.39 32 51232 CRIM1 cysteine rich transmembrane BMP regulator 1 (chordin-like) 6.23 33 1545 CYP1B1 cytochrome P450, family 1, subfamily B, polypeptide 1 6.14 34 10602 CDC42EP3 CDC42 effector protein (Rho GTPase binding) 3 6.08 35 9636 ISG15 ISG15 ubiquitin-like modifier 6.01 36 221981 THSD7A thrombospondin, type I, domain containing 7A 6.00 37 4868 NPHS1 nephrosis 1, congenital, Finnish type (nephrin) 5.94 38 1285 COL4A3 collagen, type IV, alpha 3 (Goodpasture antigen) 5.85 39 2195 FAT FAT tumor suppressor homolog 1 (Drosophila) 5.82 40 9806 SPOCK2 sparc/osteonectin, cwcv and kazal-like domains proteoglycan (te 5.76 41 9037 SEMA5A sema domain, seven thrombospondin repeats (type 1 and type 1 5.48 42 3485 IGFBP2 insulin-like growth factor binding protein 2, 36kDa 5.36 43 5654 HTRA1 HtrA serine peptidase 1 5.30 44 3621 ING1 inhibitor of growth family, member 1 5.29 45 1028 CDKN1C cyclin-dependent kinase inhibitor 1C (p57, Kip2) 4.94 46 7049 TGFBR3 transforming growth factor, beta receptor III 4.81 47 4023 LPL lipoprotein lipase 4.77 48 10391 CORO2B coronin, actin binding protein, 2B 4.66 49 715 C1R complement component 1, r subcomponent 4.63 50 2697 GJA1 gap junction protein, alpha 1, 43kDa 4.47 51 716 C1S complement component 1, s subcomponent 4.36 52 25999 CLIP3 CAP-GLY domain containing linker protein 3 4.08 53 23114 NFASC neurofascin homolog (chicken) 4.05 54 23380 SRGAP2 SLIT-ROBO Rho GTPase activating protein 2 3.92 55 1605 DAG1 dystroglycan 1 (dystrophin-associated glycoprotein 1) 3.92 56 5653 KLK6 kallikrein-related peptidase 6 3.91 57 8556 CDC14A CDC14 cell division cycle 14 homolog A (S. cerevisiae) 3.91 58 10398 MYL9 myosin, light chain 9, regulatory 3.85 59 961 CD47 CD47 molecule 3.73 60 56941 C3orf37 chromosome 3 open reading frame 37 3.72 61 9435 CHST2 carbohydrate (N-acetylglucosamine-6-O) sulfotransferase 2 3.71 62 3693 ITGB5 integrin, beta 5 3.68 63 7357 UGCG UDP-glucose ceramide glucosyltransferase 3.68 64 5352 PLOD2 procollagen-lysine, 2-oxoglutarate 5-dioxygenase 2 3.64 65 1604 CD55 CD55 molecule, decay accelerating factor for complement (Crom 3.58 66 4638 MYLK myosin, light chain kinase 3.57 67 10217 CTDSPL CTD (carboxy-terminal domain, RNA polymerase II, polypeptide 3.54 68 868 CBLB Cas-Br-M (murine) ecotropic retroviral transforming sequence b 3.53 69 9748 SLK STE20-like kinase (yeast) 3.51 70 10521 DDX17 DEAD (Asp-Glu-Ala-Asp) box polypeptide 17 3.40 71 805 CALM2 calmodulin 2 (phosphorylase kinase, delta) 3.37 72 2920 CXCL2 chemokine (C-X-C motif) ligand 2 3.29 73 4170 MCL1 myeloid cell leukemia sequence 1 (BCL2-related) 3.17 74 29970 SCHIP1 schwannomin interacting protein 1 3.16 75 3675 ITGA3 integrin, alpha 3 (antigen CD49C, alpha 3 subunit of VLA-3 recep 3.01 76 1843 DUSP1 dual specificity phosphatase 1 2.89 77 4204 MECP2 methyl CpG binding protein 2 (Rett syndrome) 2.83 78 5420 PODXL podocalyxin-like 2.81 79 133 ADM adrenomedullin 2.79 80 2869 GRK5 G protein-coupled receptor kinase 5 2.79 81 10140 TOB1 transducer of ERBB2, 1 2.78 82 5054 SERPINE1 serpin peptidase inhibitor, clade E (nexin, plasminogen activator 2.76 83 8519 IFITM1 interferon induced transmembrane protein 1 (9-27) 2.71 84 8412 BCAR3 breast cancer anti-estrogen resistance 3 2.68 85 120 ADD3 adducin 3 (gamma) 2.65 86 23370 ARHGEF18 rho/rac guanine nucleotide exchange factor (GEF) 18 2.64 87 9788 MTSS1 metastasis suppressor 1 2.61 88 301 ANXA1 annexin A1 2.60 89 7091 TLE4 transducin-like enhancer of split 4 (E(sp1) homolog, Drosophila) 2.56 90 26471 NUPR1 nuclear protein 1 2.54 91 54587 MXRA8 matrix-remodelling associated 8 2.54 92 1647 GADD45A growth arrest and DNA-damage-inducible, alpha 2.52 93 7453 WARS tryptophanyl-tRNA synthetase 2.52 94 558 AXL AXL receptor tyrosine kinase 2.51 95 7073 TIAL1 TIA1 cytotoxic granule-associated RNA binding protein-like 1 2.51 96 11346 SYNPO synaptopodin 2.48 97 1595 CYP51A1 cytochrome P450, family 51, subfamily A, polypeptide 1 2.48 98 2534 FYN FYN oncogene related to SRC, FGR, YES 2.47 99 3320 HSP90AA1 heat shock protein 90kDa alpha (cytosolic), class A member 1 2.46 100 2316 FLNA filamin A, alpha (actin binding protein 280) 2.45 101 7431 VIM vimentin 2.45 102 10370 CITED2 Cbp/p300-interacting transactivator, with Glu/Asp-rich carboxy-te 2.42 103 10631 POSTN periostin, osteoblast specific factor 2.41 104 56288 PARD3 par-3 partitioning defective 3 homolog (C. elegans) 2.40 105 9846 GAB2 GRB2-associated binding protein 2 2.39 106 23741 EID1 EP300 interacting inhibitor of differentiation 1 2.37 107 330 BIRC3 baculoviral IAP repeat-containing 3 2.36 108 4643 MYO1E myosin IE 2.33 109 1859 DYRK1A dual-specificity tyrosine-(Y)-phosphorylation regulated kinase 1A 2.32 110 6595 SMARCA2 SWI/SNF related, matrix associated, actin dependent regulator o 2.32 111 84159 ARID5B AT rich interactive domain 5B (MRF1-like) 2.30 112 5516 PPP2CB protein phosphatase 2 (formerly 2A), catalytic subunit, beta isofo 2.28 113 3301 DNAJA1 DnaJ (Hsp40) homolog, subfamily A, member 1 2.27 114 9180 OSMR oncostatin M receptor 2.23 115 7290 HIRA HIR histone cell cycle regulation defective homolog A (S. cerevis 2.23 116 10096 ACTR3 ARP3 actin-related protein 3 homolog (yeast) 2.21 117 10627 MRCL3 myosin regulatory light chain MRCL3 2.21 118 10133 OPTN optineurin 2.20 119 5928 RBBP4 retinoblastoma binding protein 4 2.18 120 4059 BCAM basal cell adhesion molecule (Lutheran blood group) 2.15 121 28951 TRIB2 tribbles homolog 2 (Drosophila) 2.15 122 4664 NAB1 NGFI-A binding protein 1 (EGR1 binding protein 1) 2.14 123 3490 IGFBP7 insulin-like growth factor binding protein 7 2.08 124 71 ACTG1 actin, gamma 1 2.07 125 9231 DLG5 discs, large homolog 5 (Drosophila) 2.06 126 23048 FNBP1 formin binding protein 1 2.04 127 7534 YWHAZ tyrosine 3-monooxygenase/tryptophan 5-monooxygenase activat 2.03 128 9778 KIAA0232 KIAA0232 gene product 1.80 129 7322 UBE2D2 ubiquitin-conjugating enzyme E2D 2 (UBC4/5 homolog, yeast) 1.78.
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  • Mutational Landscape Differences Between Young-Onset and Older-Onset Breast Cancer Patients Nicole E

    Mutational Landscape Differences Between Young-Onset and Older-Onset Breast Cancer Patients Nicole E

    Mealey et al. BMC Cancer (2020) 20:212 https://doi.org/10.1186/s12885-020-6684-z RESEARCH ARTICLE Open Access Mutational landscape differences between young-onset and older-onset breast cancer patients Nicole E. Mealey1 , Dylan E. O’Sullivan2 , Joy Pader3 , Yibing Ruan3 , Edwin Wang4 , May Lynn Quan1,5,6 and Darren R. Brenner1,3,5* Abstract Background: The incidence of breast cancer among young women (aged ≤40 years) has increased in North America and Europe. Fewer than 10% of cases among young women are attributable to inherited BRCA1 or BRCA2 mutations, suggesting an important role for somatic mutations. This study investigated genomic differences between young- and older-onset breast tumours. Methods: In this study we characterized the mutational landscape of 89 young-onset breast tumours (≤40 years) and examined differences with 949 older-onset tumours (> 40 years) using data from The Cancer Genome Atlas. We examined mutated genes, mutational load, and types of mutations. We used complementary R packages “deconstructSigs” and “SomaticSignatures” to extract mutational signatures. A recursively partitioned mixture model was used to identify whether combinations of mutational signatures were related to age of onset. Results: Older patients had a higher proportion of mutations in PIK3CA, CDH1, and MAP3K1 genes, while young- onset patients had a higher proportion of mutations in GATA3 and CTNNB1. Mutational load was lower for young- onset tumours, and a higher proportion of these mutations were C > A mutations, but a lower proportion were C > T mutations compared to older-onset tumours. The most common mutational signatures identified in both age groups were signatures 1 and 3 from the COSMIC database.