Genomic Landscape of Pheochromocytoma and Paraganglioma

A) Mutations in PHEO/PGL susceptibility genes belonging to the pseudohypoxic signaling cluster result in direct or indirect activation of the hypoxia signaling (HIF) pathway even in the presence of sufficient amount of oxygen (pseudohypoxia). Inactivating mutations in SDHx, SDHAF2, FH, or MDH2 lead to accumulation of Krebs cycle metabolites, such as succinate, fumarate, pyruvate, or glutamine, which is followed by activation of pseudohypoxic signaling and transcription of HIF target genes. VHL, EGLN1/2, and HIF2A genes are directly involved in hypoxic signaling. Mutations in these genes are associated with activation of the HIF signaling pathway. Pseudohypoxic signaling drives cell proliferation, deregulation of cellular energy and metabolism, angiogenesis, invasion and metastasis. B) Kinase signaling cluster includes mutations in genes involved in abnormal activation of kinase signaling, particularly PI3K/AKT, mTOR, and RAS/MAPK pathways. Activation of these pathways is associated with cell proliferation and survival, evasion from apoptosis, and chromatin remodeling. Kinase signaling pathways in PHEO and PGL can be disrupted by mutations in NF1, KIF1B, MAX, RET, TMEM127, H-RAS, and ATRX genes. Rarely, mutations in K-RAS, FGFR genes and fusion genes involving NGFR, BRAF, or NF1 can be found in PHEOs/PGLs. C) Recently, the Wnt signaling pathway has been implied to play role in PHEO/PGL pathogenesis based on the identification of CSDE1 mutations and MAML3 fusion genes []. D) Mutations in SDHx and FH genes result in an accumulation of succinate and fumarate and mutated IDH1 activity that results in conversion of α-ketoglutarate to the oncometabolite D2HG. Succinate, fumarate, D2HG, and L2HG function as competitive inhibitors of α-ketoglutarate–dependent dioxygenases. Inhibition of reactions mediated by α-ketoglutarate-dependent dioxygenases leads to DNA and histone hypermethylation, activation of hypoxic responses, and inhibition of collagen maturation and folding.Abbreviations: 4EBP1, eukaryotic translation initiation factor 4E binding protein 1; α-KGDH, alpha-ketoglutarate dehydrogenase; Acetyl-CoA, acetyl-coenzyme A; ACO, aconitase; AKT, AKT serine/threonine kinase; ATRX, ATRX, chromatin remodeler; BRAF, B-Raf proto-oncogene; CS, citrate synthase; CSDE1, cold shock domain containing E1; D2HG, D-2-hydroxyglutarate; Dvl, Dishevelled segment polarity protein; EGLN1/2/3, egl-9 prolyl hydroxylase 1, 2, 3; ERK, mitogen-activated protein kinase 1; FGFR, fibrablast growth factor receptor; FH, fumarate hydratase; Gli1/2, GLI family zinc finger 1, 2; GLUT, glucose transporter; GSK3, glycogen synthase kinase 3; HIF, hypoxia-inducible factor; HIF2A, hypoxia-inducible factor 2 alpha; H-RAS, HRas proto-oncogene, GTPase; IDH1/2, isocitrate dehydrogenase 1, 2; JMJD, Jumoni C domain-containing histone lysine demethylases; KIF1B, kinesin family member 1B; K-RAS, KRAS proto-oncogene, GTPase; L2HG, L-2-hydroxyglutarate; MAPK, mitogen activated kinase; MAML3, mastermind like transcriptional coactivator 3; MAX, MYC associated factor X; MDH2, malate dehydrogenase 2; MDM2, MDM2 proto-oncogene; mTOR, mechanistic target of rapamycin; MYC, MYC proto-oncogene; NF1, neurofibromin 1; NGFR, nerve growth factor receptor; PDH, pyruvate dehydrogenase; PHD1/2, egl-9 family hypoxia inducible factor 2, 1; PHEO/PGL, pheochromocytoma/paraganglioma; PI3K, phosphatidylinositol-3-kinase; RAC, Rho guanine nucleotide exchange factors; RAS, RAS type GTPase family; RET, RET proto-oncogene; Rheb, Ras homolog enriched in brain; ROS, reactive oxygen species; SDHx, succinate dehydrogenase subunits A, B, C, D, SDHAF2, succinate dehydrogenase complex assembly factor 2; SMO, Smoothened, frizzled class receptor; SUCLG, succinyl-coenzyme A ligase; TETs, tet methylcytosine dioxygenases; TMEM127, transmembrane protein 127; TP53, tumor protein 53; TSC1/2, TSC complex subunit 1, 2; VHL, von Hippel-Lindau tumor suppressor,
Genomic Landscape of Pheochromocytoma and Paraganglioma

Publication

Genomic Landscape of Pheochromocytoma and Paraganglioma. () Ivana Jochmanova, et al. Trends Cancer. ;4(1):6-9. Figure: F1.

Gene mentions


Organism Group Word Match Source NCBI Symbol NCBI ID
Drosophila melanogaster Invertebrates GLUT GLUT ncbigene_synonym Eaat1 34251
Drosophila melanogaster Invertebrates GLUT GLUT ncbigene_synonym Glut1 38109
Drosophila melanogaster Invertebrates GLUT GLUT ncbigene_synonym Glut4EF 41217
Drosophila melanogaster Invertebrates GLUT GLUT ncbigene_synonym Glut3 42036
Drosophila melanogaster Invertebrates FH FH ncbigene_symbol fh 31845
Drosophila melanogaster Invertebrates MDH2 MDH2 ncbigene_symbol Mdh2 42185
Drosophila melanogaster Invertebrates MDH2 MDH2 ncbigene_synonym Mdh1 34414
Drosophila melanogaster Invertebrates SDH SDH ncbigene_synonym LKRSDH 34064
Drosophila melanogaster Invertebrates SDH SDH ncbigene_synonym SdhB 35590
Drosophila melanogaster Invertebrates SDH SDH ncbigene_synonym SdhA 37228
Drosophila melanogaster Invertebrates SDH SDH ncbigene_synonym Sodh-2 41313
Drosophila melanogaster Invertebrates SDH SDH ncbigene_synonym SdhC 41340
Drosophila melanogaster Invertebrates VHL VHL ncbigene_symbol Vhl 53433
Drosophila melanogaster Invertebrates HIFa HIFA ncbigene_synonym sima 43580
Drosophila melanogaster Invertebrates cycle CYCLE ncbigene_synonym CycE 34924
Drosophila melanogaster Invertebrates cycle CYCLE ncbigene_synonym cyc 40162
Drosophila melanogaster Invertebrates ACO ACO ncbigene_symbol Aco 5657836
Drosophila melanogaster Invertebrates ACO ACO ncbigene_synonym Acox57D-d 37446
Drosophila melanogaster Invertebrates Wnt WNT ncbigene_synonym Wnt5 32838
Drosophila melanogaster Invertebrates Wnt WNT ncbigene_synonym Wnt4 34007
Drosophila melanogaster Invertebrates Wnt WNT ncbigene_synonym wg 34009
Drosophila melanogaster Invertebrates Wnt WNT ncbigene_synonym Wnt2 35975
Drosophila melanogaster Invertebrates Bcatenin BCATENIN ncbigene_synonym arm 31151
Drosophila melanogaster Invertebrates Dvl DVL ncbigene_synonym dsh 32078
Drosophila melanogaster Invertebrates Dv DV ncbigene_symbol dv 45286
Drosophila melanogaster Invertebrates IDH IDH ncbigene_symbol Idh 44291
Drosophila melanogaster Invertebrates IDH IDH ncbigene_synonym Idh3b 42586
Drosophila melanogaster Invertebrates RAC RAC ncbigene_synonym Rac1 38146
Drosophila melanogaster Invertebrates RAC RAC ncbigene_synonym Rac2 38831
Drosophila melanogaster Invertebrates RAC RAC ncbigene_synonym Akt 41957
Drosophila melanogaster Invertebrates RAC RAC ncbigene_synonym Mtl 43319
Drosophila melanogaster Invertebrates MYC MYC ncbigene_symbol Myc 31310
Drosophila melanogaster Invertebrates GSK3 GSK3 ncbigene_synonym sgg 31248
Drosophila melanogaster Invertebrates and AND ncbigene_synonym CkIIbeta 32132
Drosophila melanogaster Invertebrates and AND ncbigene_synonym Andorra 32798
Drosophila melanogaster Invertebrates and AND ncbigene_synonym Anp 43595
Drosophila melanogaster Invertebrates and AND ncbigene_synonym Acam 44913
Drosophila melanogaster Invertebrates SMO SMO ncbigene_symbol smo 33196
Drosophila melanogaster Invertebrates SMO SMO ncbigene_synonym sm 37254
Drosophila melanogaster Invertebrates G1 G1 ncbigene_synonym LanB2 39118
Drosophila melanogaster Invertebrates G1 G1 ncbigene_synonym anon-70Db 5657481
Drosophila melanogaster Invertebrates G1/2 G2 ncbigene_synonym anon-70Dc 5657482
Drosophila melanogaster Invertebrates D&E DE ncbigene_symbol de 248301
Drosophila melanogaster Invertebrates low LOW ncbigene_symbol Low 44325
Drosophila melanogaster Invertebrates Rheb RHEB ncbigene_symbol Rheb 117332
Drosophila melanogaster Invertebrates ATRX ATRX ncbigene_synonym XNP 43080
Drosophila melanogaster Invertebrates RET RET ncbigene_symbol Ret 43875
Drosophila melanogaster Invertebrates RET RET ncbigene_synonym reticulated 44319
Drosophila melanogaster Invertebrates RET RET ncbigene_synonym reti 252522
Drosophila melanogaster Invertebrates RET RET ncbigene_synonym rets 252556
Drosophila melanogaster Invertebrates PI3K PI3K ncbigene_synonym Pi3K21B 33203
Drosophila melanogaster Invertebrates PI3K PI3K ncbigene_synonym Pi3K59F 37733
Drosophila melanogaster Invertebrates PI3K PI3K ncbigene_synonym Pi3K68D 39329
Drosophila melanogaster Invertebrates PI3K PI3K ncbigene_synonym Pi3K92E 42446
Drosophila melanogaster Invertebrates FGFR FGFR ncbigene_synonym btl 39564
Drosophila melanogaster Invertebrates FGFR FGFR ncbigene_synonym htl 42160
Drosophila melanogaster Invertebrates CyclinD CYCLIND ncbigene_synonym CycD 32551
Drosophila melanogaster Invertebrates MAX MAX ncbigene_symbol Max 40095
Drosophila melanogaster Invertebrates MAX MAX ncbigene_synonym mof 31518
Drosophila melanogaster Invertebrates RAS RAS ncbigene_symbol ras 43873
Drosophila melanogaster Invertebrates RAS RAS ncbigene_synonym Ras64B 38494
Drosophila melanogaster Invertebrates RAS RAS ncbigene_synonym Ras85D 41140
Drosophila melanogaster Invertebrates ERK ERK ncbigene_synonym Erk7 31877
Drosophila melanogaster Invertebrates ERK ERK ncbigene_synonym rl 3354888
Drosophila melanogaster Invertebrates NF1 NF1 ncbigene_symbol Nf1 43149
Drosophila melanogaster Invertebrates Кey: EY ncbigene_symbol ey 43812
Drosophila melanogaster Invertebrates Кey: KEY ncbigene_symbol key 37967
Drosophila melanogaster Invertebrates TSC1/2 TSC2 ncbigene_synonym gig 40201
Drosophila melanogaster Invertebrates TSC1/2 TSC1 ncbigene_symbol Tsc1 42862
Homo sapiens Primates GLUT GLUT ncbigene_synonym SLC2A1 6513
Homo sapiens Primates |POH POH ncbigene_synonym GNAS 2778
Homo sapiens Primates FH FH ncbigene_symbol FH 2271
Homo sapiens Primates MDH2 MDH2 ncbigene_symbol MDH2 4191
Homo sapiens Primates SDH SDH ncbigene_synonym SARDH 1757
Homo sapiens Primates SDH SDH ncbigene_synonym SDHB 6390
Homo sapiens Primates SDH SDH ncbigene_synonym SORD 6652
Homo sapiens Primates SDH SDH ncbigene_synonym SDS 10993
Homo sapiens Primates VHL VHL ncbigene_symbol VHL 7428
Homo sapiens Primates HIFa HIFA famplex_relations HIF1A 3091
Homo sapiens Primates HIFa HIFA famplex_relations EPAS1 2034
Homo sapiens Primates HIFa HIFA famplex_relations HIF3A 64344
Homo sapiens Primates CSDE1 CSDE1 ncbigene_symbol CSDE1 7812
Homo sapiens Primates ACO ACO ncbigene_synonym KLK15 55554
Homo sapiens Primates Wnt WNT famplex_relations WNT1 7471
Homo sapiens Primates Wnt WNT famplex_relations WNT2 7472
Homo sapiens Primates Wnt WNT famplex_relations WNT2B 7482
Homo sapiens Primates Wnt WNT famplex_relations WNT3 7473
Homo sapiens Primates Wnt WNT famplex_relations WNT3A 89780
Homo sapiens Primates Wnt WNT famplex_relations WNT4 54361
Homo sapiens Primates Wnt WNT famplex_relations WNT6 7475
Homo sapiens Primates Wnt WNT famplex_relations WNT7A 7476
Homo sapiens Primates Wnt WNT famplex_relations WNT7B 7477
Homo sapiens Primates Wnt WNT famplex_relations WNT8A 7478
Homo sapiens Primates Wnt WNT famplex_relations WNT8B 7479
Homo sapiens Primates Wnt WNT famplex_relations WNT9A 7483
Homo sapiens Primates Wnt WNT famplex_relations WNT9B 7484
Homo sapiens Primates Wnt WNT famplex_relations WNT10A 80326
Homo sapiens Primates Wnt WNT famplex_relations WNT10B 7480
Homo sapiens Primates Wnt WNT famplex_relations WNT11 7481
Homo sapiens Primates Wnt WNT famplex_relations WNT16 51384
Homo sapiens Primates Wnt WNT famplex_relations WNT5A 7474
Homo sapiens Primates Wnt WNT famplex_relations WNT5B 81029
Homo sapiens Primates Bcatenin CTNNB1 ncbigene_symbol CTNNB1 1499
Homo sapiens Primates cis CIS ncbigene_synonym CISH 1154
Homo sapiens Primates Dvl DVL ncbigene_synonym DVL1 1855
Homo sapiens Primates Dvl DVL ncbigene_synonym DVL1P1 8215
Homo sapiens Primates Dvl DVL famplex_relations DVL2 1856
Homo sapiens Primates Dvl DVL famplex_relations DVL3 1857
Homo sapiens Primates Dvl DV1 ncbigene_synonym IFT81 28981
Homo sapiens Primates IDH IDH ncbigene_synonym IDH1 3417
Homo sapiens Primates IDH IDH ncbigene_synonym IDH2 3418
Homo sapiens Primates RAC RAC ncbigene_synonym AKT1 207
Homo sapiens Primates RAC RAC famplex_relations RAC1 5879
Homo sapiens Primates RAC RAC famplex_relations RAC2 5880
Homo sapiens Primates RAC RAC famplex_relations RAC3 5881
Homo sapiens Primates RAC RAC famplex_relations RHOG 391
Homo sapiens Primates MYC MYC ncbigene_symbol MYC 4609
Homo sapiens Primates GSK3 GSK3 famplex_relations GSK3A 2931
Homo sapiens Primates GSK3 GSK3 famplex_relations GSK3B 2932
Homo sapiens Primates Hedgehog HEDGEHOG famplex_relations DHH 50846
Homo sapiens Primates Hedgehog HEDGEHOG famplex_relations IHH 3549
Homo sapiens Primates Hedgehog HEDGEHOG famplex_relations SHH 6469
Homo sapiens Primates HIF HIF famplex_relations ARNT 405
Homo sapiens Primates HIF HIF famplex_relations ARNT2 9915
Homo sapiens Primates HIF HIF famplex_relations BMAL1 406
Homo sapiens Primates SMO SMO ncbigene_symbol SMO 6608
Homo sapiens Primates SMO SMO ncbigene_synonym SMOX 54498
Homo sapiens Primates G1/2 G2 ncbigene_synonym WARS1 7453
Homo sapiens Primates Rheb RHEB ncbigene_symbol RHEB 6009
Homo sapiens Primates Rheb RHEB ncbigene_synonym RHEBP1 6008
Homo sapiens Primates ATRX ATRX ncbigene_symbol ATRX 546
Homo sapiens Primates MOM2 MOM2 ncbigene_synonym ATP5F1A 498
Homo sapiens Primates RET RET ncbigene_symbol RET 5979
Homo sapiens Primates PI3K PI3K ncbigene_synonym PIK3CA 5290
Homo sapiens Primates PI3K PI3K ncbigene_synonym PIK3CB 5291
Homo sapiens Primates PI3K PI3K ncbigene_synonym PIK3CD 5293
Homo sapiens Primates PI3K PI3K ncbigene_synonym PIK3CG 5294
Homo sapiens Primates PI3K PI3K famplex_relations PIK3R3 8503
Homo sapiens Primates PI3K PI3K famplex_relations PIK3R4 30849
Homo sapiens Primates PI3K PI3K famplex_relations PIK3R5 23533
Homo sapiens Primates PI3K PI3K famplex_relations PIK3R6 146850
Homo sapiens Primates PI3K PI3K famplex_relations PIK3R1 5295
Homo sapiens Primates PI3K PI3K famplex_relations PIK3R2 5296
Homo sapiens Primates AKT AKT famplex_relations AKT2 208
Homo sapiens Primates AKT AKT famplex_relations AKT3 10000
Homo sapiens Primates FGFR FGFR famplex_relations FGFR1 2260
Homo sapiens Primates FGFR FGFR famplex_relations FGFR2 2263
Homo sapiens Primates FGFR FGFR famplex_relations FGFR3 2261
Homo sapiens Primates FGFR FGFR famplex_relations FGFR4 2264
Homo sapiens Primates FGFR FGFR famplex_relations FGFRL1 53834
Homo sapiens Primates NGFR NGFR ncbigene_symbol NGFR 4804
Homo sapiens Primates CyclinD CYCLIND famplex_relations CCND1 595
Homo sapiens Primates CyclinD CYCLIND famplex_relations CCND2 894
Homo sapiens Primates CyclinD CYCLIND famplex_relations CCND3 896
Homo sapiens Primates MAX MAX ncbigene_symbol MAX 4149
Homo sapiens Primates RAS RAS famplex_relations KRAS 3845
Homo sapiens Primates RAS RAS famplex_relations HRAS 3265
Homo sapiens Primates RAS RAS famplex_relations NRAS 4893
Homo sapiens Primates ERK ERK ncbigene_synonym EPHB2 2048
Homo sapiens Primates ERK ERK ncbigene_synonym MAPK1 5594
Homo sapiens Primates ERK ERK famplex_relations MAPK3 5595
Homo sapiens Primates NF1 NF1 ncbigene_symbol NF1 4763
Homo sapiens Primates Histone HISTONE famplex_relations H1-0 3005
Homo sapiens Primates Histone HISTONE famplex_relations H1-1 3024
Homo sapiens Primates Histone HISTONE famplex_relations H1-2 3006
Homo sapiens Primates Histone HISTONE famplex_relations H1-3 3007
Homo sapiens Primates Histone HISTONE famplex_relations H1-4 3008
Homo sapiens Primates Histone HISTONE famplex_relations H1-5 3009
Homo sapiens Primates Histone HISTONE famplex_relations H1-6 3010
Homo sapiens Primates Histone HISTONE famplex_relations H1-7 341567
Homo sapiens Primates Histone HISTONE famplex_relations H1-8 132243
Homo sapiens Primates Histone HISTONE famplex_relations H1-10 8971
Homo sapiens Primates Histone HISTONE famplex_relations NA NaN
Homo sapiens Primates Histone HISTONE famplex_relations H2AB1 474382
Homo sapiens Primates Histone HISTONE famplex_relations H2AJ 55766
Homo sapiens Primates Histone HISTONE famplex_relations H2AZ2 94239
Homo sapiens Primates Histone HISTONE famplex_relations H2AX 3014
Homo sapiens Primates Histone HISTONE famplex_relations MACROH2A1 9555
Homo sapiens Primates Histone HISTONE famplex_relations MACROH2A2 55506
Homo sapiens Primates Histone HISTONE famplex_relations H2AZ1 3015
Homo sapiens Primates Histone HISTONE famplex_relations H2AC1 221613
Homo sapiens Primates Histone HISTONE famplex_relations H2AC6 8334
Homo sapiens Primates Histone HISTONE famplex_relations H2AC7 3013
Homo sapiens Primates Histone HISTONE famplex_relations H2AC12 85235
Homo sapiens Primates Histone HISTONE famplex_relations H2AC14 8331
Homo sapiens Primates Histone HISTONE famplex_relations H2AC21 317772
Homo sapiens Primates Histone HISTONE famplex_relations H2AC20 8338
Homo sapiens Primates Histone HISTONE famplex_relations H2AC25 92815
Homo sapiens Primates Histone HISTONE famplex_relations H2BC1 255626
Homo sapiens Primates Histone HISTONE famplex_relations H2BC3 3018
Homo sapiens Primates Histone HISTONE famplex_relations H2BC5 3017
Homo sapiens Primates Histone HISTONE famplex_relations H2BC9 8345
Homo sapiens Primates Histone HISTONE famplex_relations H2BC11 8970
Homo sapiens Primates Histone HISTONE famplex_relations H2BC12 85236
Homo sapiens Primates Histone HISTONE famplex_relations H2BC13 8340
Homo sapiens Primates Histone HISTONE famplex_relations H2BC14 8342
Homo sapiens Primates Histone HISTONE famplex_relations H2BC15 8341
Homo sapiens Primates Histone HISTONE famplex_relations H2BC17 8348
Homo sapiens Primates Histone HISTONE famplex_relations H2BC18 440689
Homo sapiens Primates Histone HISTONE famplex_relations H2BC19P 337874
Homo sapiens Primates Histone HISTONE famplex_relations H2BC20P 337873
Homo sapiens Primates Histone HISTONE famplex_relations H2BC21 8349
Homo sapiens Primates Histone HISTONE famplex_relations H2BC26 128312
Homo sapiens Primates Histone HISTONE famplex_relations H2BC12L 54145
Homo sapiens Primates Histone HISTONE famplex_relations H2BW2 286436
Homo sapiens Primates Histone HISTONE famplex_relations H2BW1 158983
Homo sapiens Primates Histone HISTONE famplex_relations H3-4 8290
Homo sapiens Primates Histone HISTONE famplex_relations H3-5 440093
Homo sapiens Primates Histone HISTONE famplex_relations H4C7 8369
Homo sapiens Primates TSC1/2 TSC2 ncbigene_symbol TSC2 7249
Homo sapiens Primates TSC1/2 TSC1 ncbigene_symbol TSC1 7248
Homo sapiens Primates TSC1/2 TSC1 ncbigene_synonym CCL26 10344
Homo sapiens Primates TMEM127 TMEM127 ncbigene_symbol TMEM127 55654

Chemical mentions

Word Match MeSH Name ChEBI
Glucose Glucose mesh:D005947 D-glucopyranose chebi:4167
Lactate NA mesh:D019344
Pyruvate NA mesh:D011773
Acetyl-CoA Acetyl Coenzyme A mesh:D000105 acetyl-CoA chebi:15351
Fumarate NA mesh:D005650
Oxaloacetate NA mesh:D010071
Succinate Succinates mesh:D013386 succinate chebi:26806
Citrate NA mesh:C102006
Succinyl-CoA NA mesh:C012046
KGOH NA
Aconitate Aconitic Acid mesh:D000156 aconitic acid chebi:22211
Isocitrate NA mesh:D007523
Glutamine Arg-Gln mesh:C578860 arginyl-glutamine chebi:73813
Fatty acid Fatty Acids mesh:D005227 fatty acid chebi:35366
fatty acid Fatty Acids mesh:D005227 fatty acid chebi:35366

Disease mentions

Word Match MeSH Name DOID
VHL NA mesh:D006623
Hypoxia NA mesh:D000860