Sarcoma

Research Article

Molecular Analysis of a Recurrent Sarcoma Identifies a Mutation in FAF1

Table 2

RNA induced in the tumor. (a) Transcripts overexpressed in the tumor compared to muscle but not bone. (b) Transcripts overexpressed in the tumor compared to bone but not muscle. (c) Transcripts most abundantly overexpressed in the tumor compared to muscle and bone. (d) as (a) but limited to genes expressed at least at the level of 1 unit in the reference tissue (muscle or bone). (e) Altered expression of genes associated with NF-κB activity. Analysis of RNASeq for the transcription factor NF-κB and gene products that regulate its activity. RNA messages that are selectively associated with the TNF pathway to NF-κB activation are marked with bold font. log2-fold change indicates the alteration in the tumor compared to muscle or bone (the respective columns indicate the expression level for each organ).
(a)
  log2-fold change
 Muscle
Tumor over muscle  
NRG1Neuregulin 19.909
KSR2Kinase suppressor of ras 29.675
MMP13Matrix metallopeptidase 13 (collagenase 3)9.528
SPP1Secreted phosphoprotein 19.098
INHBAInhibin, beta A8.570
COL11A1Collagen, type XI, alpha 18.564
MMP9Matrix metallopeptidase 9 (gelatinase B, 92 kda gelatinase, 92 kda type IV collagenase)8.552
FBN2Fibrillin 28.495
LRRC15Leucine rich repeat containing 158.429
MMP11Matrix metallopeptidase 11 (stromelysin 3)8.336
E2F7E2F transcription factor 78.314
PRAMEPreferentially expressed antigen in melanoma8.179
PTK7PTK7 protein tyrosine kinase 77.996
DSCAMDown syndrome cell adhesion molecule7.761
RGS4Regulator of G-protein signaling 47.633
CNIH3Cornichon homolog 3 (Drosophila)7.632
OR10V1Olfactory receptor, family 10, subfamily V, member 17.610
CEP55Centrosomal protein 55 kda7.583
WNT5BWingless-type MMTV integration site family, member 5B7.569
CA12Carbonic anhydrase XII7.520
GALNT5UDP-N-acetyl-alpha-D-galactosamine:polypeptide N-acetylgalactosaminyltransferase 5 (GalNAc-T5)7.517
(b)
  log2-fold change
Bone
Tumor over bone  
ROS1c-ros oncogene 1, receptor tyrosine kinase10.987
GREM1Gremlin 110.604
NPTX1Neuronal pentraxin I8.813
GJB2Gap junction protein, beta 2, 26 kDa8.597
CREB3L1cAMP responsive element binding protein 3-like 18.506
KRT14Keratin 148.351
SERPINE1Serpin peptidase inhibitor, clade E (nexin, plasminogen activator inhibitor type 1), member 18.288
HOXD10Homeobox D108.105
ALPK2Alpha-Kinase 27.783
POU3F2POU class 3 homeobox 27.530
POSTNPeriostin, osteoblast specific factor7.497
NAA11N(alpha)-acetyltransferase 11, NatA catalytic subunit7.439
STC2Stanniocalcin 27.434
WNT5AWingless-type MMTV integration site family, member 5A7.412
IGFN1Immunoglobulin-like and fibronectin type III domain containing 17.387
STC1Stanniocalcin 17.385
FAM180AFamily with sequence similarity 180, member A7.315
KRT17Keratin 177.305
BBOX1Butyrobetaine (gamma), 2-oxoglutarate dioxygenase (gamma-butyrobetaine hydroxylase) 17.277
MAGEA1Melanoma antigen family A, 1 (directs expression of antigen MZ2-E)7.267
(c)
  log2-fold change
 MuscleBone
Tumor over bone/muscle   
ANO4Anoctamin 4 (TMEM16D), transmembrane calcium-activated chloride channel, facilitates smooth muscle contraction9.9378.542
SLCO1B3(OATP1B3) Solute carrier organic anion transporter family, member 1B39.5699.760
MARCH4Membrane-associated ring finger (C3HC4) 4, E3 ubiquitin ligase, located predominantly to the endoplasmic reticulum9.5387.406
IGF2BP1Insulin-like growth factor 2 mRNA binding protein 1 binds to and stabilizes mRNA9.4409.631
ADAMTS16ADAM metallopeptidase with thrombospondin type 1 motif, 16; zinc-dependent protease9.2608.450
SOX11SRY (sex determining region Y)-box 11, important in brain development9.1789.954
HAPLN1Hyaluronan and proteoglycan link protein 1 stabilizes aggregates of aggrecan and hyaluronan, giving cartilage its tensile strength and elasticity8.9518.142
MUC15Mucin 15, cell surface associated8.8017.992
HOXB9Homeobox B98.7737.378
MAGEC2Melanoma antigen family C, 28.6938.884
ST6GALNAC5ST6 (alpha-N-acetyl-neuraminyl-2,3-beta-galactosyl-1,3)-N-acetylgalactosaminide alpha-2,6-sialyltransferase 57.8488.038
C11orf41Chromosome 11 open reading frame 417.7818.141
MMP1Matrix metallopeptidase 1 (interstitial collagenase)7.4557.646
(d)
SymbolNamelog2-fold changelog2-fold change
MuscleBone
Tumor over bone/muscle     
FN1Fibronectin 17.3286.2936.45719.860
COL1A1Collagen, type I, alpha 16.7683.7065.86811.934
CCND1Cyclin D15.5953.9585.0989.637
RGS1Regulator of G-protein signaling 15.1181.0564.6532.533
ITGBL1Integrin, beta-like 1 (with EGF-like repeat domains)5.0713.1773.89512.415
COL1A2Collagen, type I, alpha 24.8528.7564.91014.503
MXRA5Matrix-remodelling associated 54.8341.3524.6312.685
POSTNPeriostin, osteoblast specific factor4.5135.8707.4971.267
PLOD2Procollagen-lysine, 2-oxoglutarate 5-dioxygenase 24.2851.8014.0233.730
COL5A2Collagen, type V, alpha 24.2751.2974.8331.517
COL3A1Collagen, type III, alpha 14.00313.1185.8016.500
SEMA3CSema domain, immunoglobulin domain (Ig), short basic domain, secreted3.9541.1644.2151.675
FBN1Fibrillin 13.9126.9574.01811.148
AEBP1AE binding protein 13.8083.2124.0024.843
SIK1Salt-inducible kinase 13.8051.2193.5662.484
SERPINH1Serpin peptidase inhibitor, clade H (heat shock protein 47), member 13.7061.6524.1452.098
ANTXR1Anthrax toxin receptor 13.6703.7893.6906.445
(e)
SymbolNamelog2-fold changelog2-fold change
MuscleBone
HELLSHelicase, lymphoid-specific5.3156020.155898−0.8271320.2489
TNFRSF11ATumor necrosis factor receptor superfamily, member 11a, and NFKB activator3.0179220.030911.4009930.202453
NFKBIDNuclear factor of kappa light polypeptide gene enhancer in B-cells inhibitor, delta2.6553520−1.476150.504341
TNFRSF25Tumor necrosis factor receptor superfamily, member 252.4329590.0463880.1639540.490795
NFKBIENuclear factor of kappa light polypeptide gene enhancer in B-cells inhibitor, epsilon2.1210150.0623950.3114410.43382
TNFTumor necrosis factor1.8479970−1.421010.03733
TNFRSF10DTumor necrosis factor receptor superfamily, member 10d, decoy with truncated death domain1.7548880.172968−0.17571.183343
TNFRSF1BTumor necrosis factor receptor superfamily, member 1B1.4734380.709902−0.970116.729401
TNFRSF10ATumor necrosis factor receptor superfamily, member 10a1.4118980.8282190.3577013.004386
NFKBIBNuclear factor of kappa light polypeptide gene enhancer in B-cells inhibitor, beta1.1939931.2098160.460553.484692
TNFRSF10BTumor necrosis factor receptor superfamily, member 10b1.0941571.9085970.4254465.242006
TNFRSF21Tumor necrosis factor receptor superfamily, member 211.0557623.8820380.7458158.305711
TNFRSF1ATumor necrosis factor receptor superfamily, member 1A0.8751673.790938−0.1170713.0344
NFKBIZNuclear factor of kappa light polypeptide gene enhancer in B-cells inhibitor, zeta0.5759743.6989510.3446577.493136
RIPK1Receptor (TNFRSF)-interacting serine-threonine kinase 10.4944673.11749−1.0885416.1392
NKRFNFKB repressing factor0.4757222.156087−0.863979.434166
NFKB1Nuclear factor of kappa light polypeptide gene enhancer in B-cells 10.4329592.054532−0.658657.568586
CHUKConserved helix-loop-helix ubiquitous kinase0.1761262.961281−1.2020413.30333
RELAV-rel reticuloendotheliosis viral oncogene homolog A (avian)0.0138481.2638370.2871671.803044
NFKB2Nuclear factor of kappa light polypeptide gene enhancer in B-cells 2 (p49/p100)−0.086410.3129930.4858820.360442
NKAPP1NFKB activating protein pseudogene 1−0.106920.825177−0.994492.655392
TNFRSF10CTumor necrosis factor receptor superfamily, member 10c, decoy without an intracellular domain−0.1520.064676−5.568916.321515
NKIRAS2NFKB inhibitor interacting Ras-like 2−0.607681.095135−0.887582.299946
NFKBIL1Nuclear factor of kappa light polypeptide gene enhancer in B-cells inhibitor-like 1−0.87190.141933−0.083570.140418
NKIRAS1NFKB inhibitor interacting Ras-like 1−0.874286.2963991.4677352.122983
TANKTRAF family member-associated NFKB activator−0.9836.777124−1.5190816.95872
NKAPNFKB activating protein−1.3573514.22458−0.7824316.46287
NFKBIANuclear factor of kappa light polypeptide gene enhancer in B-cells inhibitor, alpha−1.8548340.32743−0.3180223.95275
NKAPLNFKB activating protein-like−5.573475.875743−1.402150.534643