Cheng et al.(5757 Cheng JQ, Jhanwar SC, Klein WM, Bell DW, Lee WC, Altomare DA, et al. p16 alterations and deletion mapping of 9p21-p22 in malignant mesothelioma. Cancer Res. 1994;54(21):5547-51. PMid:7923195.)
|
40 cell lines and 23 primary tumors |
Southern Blot and Targeted Seq of p16 |
Homozygous deletions on p16-INK in 85% both cell lines and 23% of tumors |
Xio et al.(5858 Xio S, Li D, Vijg J, Sugarbaker DJ, Corson JM, Fletcher JA. Codeletion of p15 and p16 in primary malignant mesothelioma. Oncogene. 1995;11(3):511-5. PMid:7630635.)
|
50 primary tumors |
FISH for p15 and p16. |
Co-deletion of p15 and p16 in 72% of cases. |
Sekido et al.(5959 Sekido Y, Pass HI, Bader S, Mew DJ, Christman MF, Gazdar AF, et al. Neurofibromatosis type 2 (NF2) gene is somatically mutated in mesothelioma but not in lung cancer. Cancer Res. 1995;55(6):1227-31. PMid:7882313.)
|
14 cell lines and 10 primary tumors |
SSCP and Southern Blot for NF2 |
NF2 mutations in 41% of cases. |
Bianchi et al.(6060 Bianchi AB, Mitsunaga SI, Cheng JQ, Klein WM, Jhanwar SC, Seizinger B, et al. High frequency of inactivating mutations in the neurofibromatosis type 2 gene (NF2) in primary malignant mesotheliomas. Proc Natl Acad Sci USA. 1995;92(24):10854-8. http://dx.doi.org/10.1073/pnas.92.24.10854. PMid:7479897. http://dx.doi.org/10.1073/pnas.92.24.108...
)
|
15 cell lines and 7 primary tumors |
SSCP; Targeted Seq for NF2 |
NF2 mutations in 53% of cases. |
Björkqvist et al.(6161 Björkqvist A-M, Wolf M, Nordling S, Tammilehto L, Knuuttila A, Kere J, et al. Deletions at 14q in malignant mesothelioma detected by microsatellite marker analysis. Br J Cancer. 1999;81(7):1111-5. PMid:10584869.)
|
34 primary tumors |
CGH array; Southern Blot. |
loss in 4q, 6q and 14q and gain in 15q and 7p |
Prins et al.(6262 Prins JB, Williamson KA, Kamp MM, Van Hezik EJ, Van der Kwast TH, Hagemeijer A, et al. The gene for the cyclin-dependent-kinase-4 inhibitor, CDKN2A, is preferentially deleted in malignant mesothelioma. Int J Cancer. 1997;95(4):649-53. PMid:9466670.)
|
12 cell lines |
PCR; FISH |
Chromosome 9 deletion including CDKN2A but not CDKN2B. |
Taniguchi et al.(6363 Taniguchi T, Karnan S, Fukui T, Yokoyama T, Tagawa H, Yokoi K, et al. Genomic profiling of malignant pleural mesothelioma with array-based comparative genomic hybridization shows frequent non-random chromosomal alteration regions including JUN amplification on 1p32. Cancer Sci. 2007;98(3):438-46. http://dx.doi.org/10.1111/j.1349-7006.2006.00386.x. PMid:17270034. http://dx.doi.org/10.1111/j.1349-7006.20...
)
|
17 primary tumors and 9 cell lines |
CGH array; Southern Blot; Targeted Seq of NF2; |
Gains in 1q, 5p, 7p, 8q24 and 20p; Loss in 1p36.33, 1p36.1, 1p21.3, 3p21.3, 4q22, 6q25, 9p21.3, 10p, 13q33.2, 14q32.13, 18q and 22q. |
Ivanov et al.(6464 Ivanov SV, Miller J, Lucito R, Tang C, Ivanova AV, Pei J, et al. Genomic events associated with progression of pleural malignant mesothelioma. Int J Cancer. 2009;124(3):589-99. http://dx.doi.org/10.1002/ijc.23949. PMid:18973227. http://dx.doi.org/10.1002/ijc.23949...
)
|
22 primary tumors |
CNA array |
Deletions in 22q12.2, 19q13.32 and 17p13.1 in 55-74% and gain in 5p, 18q, 8q and 17q in 23-55% of cases. |
Cheung et al.(6565 Cheung M, Pei J, Pei Y, Jhanwar SC, Pass HI, Testa JR. The promyelocytic leukemia zinc-finger gene, PLZF, is frequently downregulated in malignant mesothelioma cells and contributes to cell survival. Oncogene. 2010;29(11):1633-40. http://dx.doi.org/10.1038/onc.2009.455. PMid:20010871. http://dx.doi.org/10.1038/onc.2009.455...
)
|
22 cell lines |
CNA array |
deletions of CDKN2A/ARF and CDKN2B, 1p36, 1p22, 3p21-22, 4q13-34, 11q23, 13q12-13, 14q32, 15q15, 18q12 and 22q12 in 55-90% |
Takeda et al.(6666 Takeda M, Kasai T, Enomoto Y, Takano M, Morita K, Kadota E, et al. Genomic gains and losses in malignant mesothelioma demonstrated by FISH analysis of paraffin-embedded tissues. J Clin Pathol. 2012;65(1):77-82. http://dx.doi.org/10.1136/jclinpath-2011-200208. PMid:22081786. http://dx.doi.org/10.1136/jclinpath-2011...
)
|
40 primary tumors |
9p21 FISH |
9p21 deletion in 35 of 40 cases (88%) |
Bott et al.(6767 Bott M, Brevet M, Taylor BS, Shimizu S, Ito T, Wang L, et al. The nuclear deubiquitinase BAP1 is commonly inactivated by somatic mutations and 3p21.1 losses in malignant pleural mesothelioma. Nat Genet. 2011;43(7):668-72. http://dx.doi.org/10.1038/ng.855. PMid:21642991. http://dx.doi.org/10.1038/ng.855...
)
|
53 primary tumors |
CGH array, FISH; Targeted Seq. |
Deletions at 9p21, 22q and 3p21. Mutations in BAP1, NF2, LATS1 |
Yoshikawa et al. (6868 Yoshikawa Y, Sato A, Tsujimura T, Emi M, Morinaga T, Fukuoka K, et al. Frequent inactivation of the BAP1 gene in epithelioid-type malignant mesothelioma. Cancer Sci. 2012;103(5):868-74. http://dx.doi.org/10.1111/j.1349-7006.2012.02223.x. PMid:22321046. http://dx.doi.org/10.1111/j.1349-7006.20...
)
|
23 primary tumors |
Targeted Seq of BAP1 |
biallelic BAP1 gene alterations in 14 of 23 MMs (61%) |
Guo et al.(6969 Guo G, Chmielecki J, Goparaju C, Heguy A, Dolgalev I, Carbone M, et al. Whole-exome sequencing reveals frequent genetic alterations in BAP1, NF2, CDKN2A, and CUL1 in malignant pleural mesothelioma. Cancer Res. 2015;75(2):264-9. http://dx.doi.org/10.1158/0008-5472.CAN-14-1008. PMid:25488749. http://dx.doi.org/10.1158/0008-5472.CAN-...
)
|
22 primary tumors |
Whole-exome Seq |
Major changes in copy numbers: BAP1, NF2, CDKN2A, CUL1.
|
Lo Iacono et al.(7070 Lo Iacono M, Monica V, Righi L, Grosso F, Libener R, Vatrano S, et al. Targeted next-generation sequencing of cancer genes in advanced stage malignant pleural mesothelioma: a retrospective study. J Thorac Oncol. 2015;10(3):492-9. http://dx.doi.org/10.1097/JTO.0000000000000436. PMid:25514803. http://dx.doi.org/10.1097/JTO.0000000000...
)
|
123 primary tumors |
Targeted NGS of 52 genes |
Alterations in p53/DNA repair (TP53, SMACB1, and BAP1) and PI3K–AKT pathways (PDGFRA, KIT, KDR, HRAS, PIK3CA, STK11, and NF2). |
Nasu et al.(7171 Nasu M, Emi M, Pastorino S, Tanji M, Powers A, Luk H, et al. High incidence of somatic BAP1 alterations in sporadic malignant mesothelioma. J Thorac Oncol. 2015;10(4):565-76. http://dx.doi.org/10.1097/JTO.0000000000000471. PMid:25658628. http://dx.doi.org/10.1097/JTO.0000000000...
)
|
22 primary tumors |
Targeted BAP1 Sanger Seq.; MLPA |
alteration of BAP1 in 63.6% of cases |
Borczuk et al.(7272 Borczuk AC, Pei J, Taub RN, Levy B, Nahum O, Chen J, et al. Genome-wide analysis of abdominal and pleural malignant mesothelioma with DNA arrays reveals both common and distinct regions of copy number alteration. Cancer Biol Ther. 2016;17(3):328-35. http://dx.doi.org/10.1080/15384047.2016.1145850. PMid:26853494. http://dx.doi.org/10.1080/15384047.2016....
)
|
48 peritoneal and 41 pleural tumors |
CNA array |
Loss in BAP1, CDKN2A and NF2 in both tumor sites. Copy number gain were more common in peritoneum, loss were more common in pleura |
Kato et al.(7373 Kato S, Tomson BN, Buys TPH, Elkin SK, Carter JL, Kurzrock R. Genomic landscape of malignant mesotheliomas. Mol Cancer Ther. 2016;15(10):2498-507. http://dx.doi.org/10.1158/1535-7163.MCT-16-0229. PMid:27507853. http://dx.doi.org/10.1158/1535-7163.MCT-...
)
|
42 primary tumors |
Targeted NGS of 236 genes |
Alterations in BAP1 (47,6%), NF2 (38,1%) and CDKN2A/B (35,7%). |
Kang et al.(7474 Kang HC, Kim HK, Lee S, Mendez P, Kim W, Woodard G, et al. Whole exome and targeted deep sequencing identify genome- wide allelic loss and frequent SETDB1 mutations in malignant pleural mesotheliomas. Oncotarget. 2016;7(7):8321-31. http://dx.doi.org/10.18632/oncotarget.7032. PMid:26824986. http://dx.doi.org/10.18632/oncotarget.70...
)
|
78 primary tumors |
Targeted Seq of SETDB1 |
Mutations in 7 patients |
Ugurluer et al.(7575 Ugurluer G, Chang K, Gamez ME, Arnett AL, Jayakrishnan R, Miller RC, et al. Genome-based mutational analysis by next generation sequencing in patients with malignant pleural and peritoneal mesothelioma. Anticancer Res. 2016;36(5):2331-8. PMid:27127140.)
|
11 primary tumors |
Targeted NGS of 236 mutations |
Mutations in 86% of pleural and 50% of peritoneal cases. Most mutated genes were BAP1 (36%), CDKNA2A/B (27%) and NF2 (27%). |
Chirac et al.(7676 Chirac P, Maillet D, Leprêtre F, Isaac S, Glehen O, Figeac M, et al. Genomic copy number alterations in 33 malignant peritoneal mesothelioma analyzed by comparative genomic hybridization array. Hum Pathol. 2016;55:72-82. http://dx.doi.org/10.1016/j.humpath.2016.04.015. PMid:27184482. http://dx.doi.org/10.1016/j.humpath.2016...
)
|
33 peritoneal primary tumors |
CGH array |
Genomic pattern similar to pleural mesothelioma: loss of 3p21, 9p21, and 22q12. novel CNA included 15q26.2 and 8p11.22 |
Bueno et al.(7777 Bueno R, Stawiski EW, Goldstein LD, Durinck S, De Rienzo A, Modrusan Z, et al. Comprehensive genomic analysis of malignant pleural mesothelioma identifies recurrent mutations, gene fusions and splicing alterations. Nat Genet. 2016;48(4):407-16. http://dx.doi.org/10.1038/ng.3520. PMid:26928227. http://dx.doi.org/10.1038/ng.3520...
)
|
216 primary tumors |
Whole Exome Seq, Targeted NGS |
BAP1, NF2, TP53, SETD2, DDX3X, ULK2, RYR2, CFAP45, SETDB1 and DDX51 significantly mutated genes. Gene fusion and splice alterations in NF2, BAP1 and SETD2. Alterations in Hippo, mTOR, histone methylation, RNA helicase and p53 signaling pathways. |
Yoshikawa et al.(7878 Yoshikawa Y, Emi M, Hashimoto-Tamaoki T, Ohmuraya M, Sato A, Tsujimura T, et al. High-density array-CGH with targeted NGS unmask multiple noncontiguous minute deletions on chromosome 3p21 in mesothelioma. Proc Natl Acad Sci USA. 2016;113(47):13432-7. http://dx.doi.org/10.1073/pnas.1612074113. PMid:27834213. http://dx.doi.org/10.1073/pnas.161207411...
)
|
33 primary tumors |
CGH array for the 3p21 region; Targeted NGS of 4 genes |
biallelic gene inactivation in SETD2 (9 of 33, 27%), BAP1 (16 of 33, 48%), PBRM1 (5 of 33, 15%), and SMARCC1 (2 of 33, 6%) |
Desmeules et al.(7979 Desmeules P, Joubert P, Zhang L, Al-Ahmadie HA, Fletcher CD, Vakiani E, et al. A subset of malignant mesotheliomas in young adults are associated with recurrent EWSR1/FUS-ATF1 fusions. Am J Surg Pathol. 2017;41(7):980-8. http://dx.doi.org/10.1097/PAS.0000000000000864. PMid:28505004. http://dx.doi.org/10.1097/PAS.0000000000...
)
|
25 primary tumors |
FISH |
Identification of a EWSR1/FUS-ATF1 gene fusion in 4 cases |
Hung et al.(8080 Hung YP, Dong F, Watkins JC, Nardi V, Bueno R, Dal Cin P, et al. Identification of ALK rearrangements in malignant peritoneal mesothelioma. JAMA Oncol. 2018;4(2):235-8. http://dx.doi.org/10.1001/jamaoncol.2017.2918. PMid:28910456. http://dx.doi.org/10.1001/jamaoncol.2017...
)
|
88 peritoneal primary tumors |
FISH; Targeted NGS for ALK |
ALK rearrangements in 3 cases with ATG16L1, STRN, and TPM1 |
Kim et al.(99 Kim J, Bhagwandin S, Labow DM. Malignant peritoneal mesothelioma: a review. Ann Transl Med. 2017;5(11):236. http://dx.doi.org/10.21037/atm.2017.03.96. PMid:28706904. http://dx.doi.org/10.21037/atm.2017.03.9...
)
|
13 peritoneal primary tumors |
Targeted NGS of 510 genes; |
Bi-allelic inactivation of BAP1 (9/13 cases), mutation in NF2 (3/13); SETD2 (2/13) e DDX3X (2/13).
|
Hmeljak et al.(8181 Hmeljak J, Sanchez-Vega F, Hoadley KA, Shih J, Stewart C, Heiman D, et al. Integrative molecular characterization of malignant pleural mesothelioma. Cancer Discov. 2018;8(12):1548-65. http://dx.doi.org/10.1158/2159-8290.CD-18-0804. PMid:30322867. http://dx.doi.org/10.1158/2159-8290.CD-1...
)
|
74 primary tumors |
Whole Exome Seq.; CNA array |
Inactivating alterations by mutation and CNA in: BAP1, CDKN2A, NF2, TP53, LATS2, and SETD2. Novel molecular subtype (3% of cases) genomic near-haploidization and TP53 and SETDB1 mutations |
Hassan et al.(8282 Hassan R, Morrow B, Thomas A, Walsh T, Lee MK, Gulsuner S, et al. Inherited predisposition to malignant mesothelioma and overall survival following platinum chemotherapy. Proc Natl Acad Sci USA. 2019;116(18):9008-13. http://dx.doi.org/10.1073/pnas.1821510116. PMid:30975761. http://dx.doi.org/10.1073/pnas.182151011...
)
|
239 genomic DNA from MM patients |
Targeted NGS of 73 genes |
12% of cases had germline mutations: 16 in BAP1 and 12 distributed among CHEK2, PALB2, BRCA2, MLH1, POT1, TP53, and MRE11A |
Nastase et al.(8383 Nastase A, Mandal A, Lu SK, Anbunathan H, Morris-Rosendahl D, Zhang YZ, et al. Multiple therapeutic pathways in malignant mesothelioma identified by genomic mapping. medRxiv. 2020. In press.)
|
121 primary tumors |
CNA array, Whole Exome Seq.; |
CDKN2A deletion in 60% of tumours; BAP1 mutated or deleted in 54%; RASSF7 amplification in 33%; RB1 deleted or mutated in 26%; NF2 mutated in 20%; TP53 mutated in 8%; SETD2 in 6%; DDX3X in 5% and LATS2 in 5%. |
Quetel et al.(8484 Quetel L, Meiller C, Assié JB, Blum Y, Imbeaud S, Montagne F, et al. Genetic alterations of malignant pleural mesothelioma: association with tumor heterogeneity and overall survival. Mol Oncol. 2020;14(6):1207-23. http://dx.doi.org/10.1002/1878-0261.12651. PMid:32083805. http://dx.doi.org/10.1002/1878-0261.1265...
)
|
266 primary tumors |
Targeted NGS 21 genes |
TERT promoter, NF2, and TP53 mutations associated w/ worse survival. |