Skip to main content

Advertisement

Log in

Molecular profiling of sarcomas: new vistas for precision medicine

  • Invited Annual Review Issue
  • Published:
Virchows Archiv Aims and scope Submit manuscript

Abstract

Sarcoma is a large and heterogeneous group of malignant mesenchymal neoplasms with significant histological overlap. Accurate diagnosis can be challenging yet important for selecting the appropriate treatment approach and prognosis. The currently torrid pace of new genomic discoveries aids our classification and diagnosis of sarcomas, understanding of pathogenesis, development of new medications, and identification of alterations that predict prognosis and response to therapy. Unfortunately, demonstrating effective targets for precision oncology has been elusive in most sarcoma types. The list of potential targets greatly outnumbers the list of available inhibitors at the present time. This review will discuss the role of molecular profiling in sarcomas in general with emphasis on selected entities with particular clinical relevance.

This is a preview of subscription content, log in via an institution to check access.

Access this article

Price excludes VAT (USA)
Tax calculation will be finalised during checkout.

Instant access to the full article PDF.

Fig. 1
Fig. 2
Fig. 3
Fig. 4

Similar content being viewed by others

References

  1. Norberg SM, Movva S (2015) Role of genetic and molecular profiling in sarcomas. Curr Treat Options in Oncol 5:24

    Article  Google Scholar 

  2. Kallioniemi A, Kallioniemi OP, Sudar D et al (1992) Comparative genomic hybridization for molecular cytogenetic analysis of solid tumors. Science 5083:818–821

    Article  Google Scholar 

  3. Solinas-Toldo S, Lampel S, Stilgenbauer S et al (1997) Matrix-based comparative genomic hybridization: biochips to screen for genomic imbalances. Genes Chromosomes Cancer 4:399–407

    Article  Google Scholar 

  4. Weiss MM, Hermsen MA, Meijer GA et al (1999) Comparative genomic hybridisation. Mol Pathol 5:243–251

    Article  Google Scholar 

  5. Nielsen TO (2006) Microarray analysis of sarcomas. Adv Anat Pathol 4:166–173

    Article  Google Scholar 

  6. Zheng Z, Liebers M, Zhelyazkova B et al (2014) Anchored multiplex PCR for targeted next-generation sequencing. Nat Med 12:1479–1484

    Article  Google Scholar 

  7. Nielsen TO, West RB, Linn SC et al (2002) Molecular characterisation of soft tissue tumours: a gene expression study. Lancet 9314:1301–1307

    Article  Google Scholar 

  8. Subramanian S, West RB, Marinelli RJ et al (2005) The gene expression profile of extraskeletal myxoid chondrosarcoma. J Pathol 4:433–444

    Article  Google Scholar 

  9. Nagayama S, Katagiri T, Tsunoda T et al (2002) Genome-wide analysis of gene expression in synovial sarcomas using a cDNA microarray. Cancer Res 20:5859–5866

    Google Scholar 

  10. Segal NH, Pavlidis P, Antonescu CR et al (2003) Classification and subtype prediction of adult soft tissue sarcoma by functional genomics. Am J Pathol 2:691–700

    Article  Google Scholar 

  11. Baird K, Davis S, Antonescu CR et al (2005) Gene expression profiling of human sarcomas: insights into sarcoma biology. Cancer Res 20:9226–9235

    Article  Google Scholar 

  12. Konstantinopoulos PA, Fountzilas E, Goldsmith JD et al (2010) Analysis of multiple sarcoma expression datasets: implications for classification, oncogenic pathway activation and chemotherapy resistance. PLoS One 4:e9747

    Article  Google Scholar 

  13. Mills AM, Beck AH, Montgomery KD et al (2011) Expression of subtype-specific group 1 leiomyosarcoma markers in a wide variety of sarcomas by gene expression analysis and immunohistochemistry. Am J Surg Pathol 4:583–589

    Article  Google Scholar 

  14. Fletcher CD, Gustafson P, Rydholm A, Willen H, Akerman M (2001) Clinicopathologic re-evaluation of 100 malignant fibrous histiocytomas: prognostic relevance of subclassification. J Clin Oncol 12:3045–3050

    Article  Google Scholar 

  15. Italiano A, Lagarde P, Brulard C et al (2013) Genetic profiling identifies two classes of soft-tissue leiomyosarcomas with distinct clinical characteristics. Clin Cancer Res 5:1190–1196

    Article  Google Scholar 

  16. Segal NH, Pavlidis P, Noble WS et al (2003) Classification of clear-cell sarcoma as a subtype of melanoma by genomic profiling. J Clin Oncol 9:1775–1781

    Article  Google Scholar 

  17. Chibon F, Lagarde P, Salas S et al (2010) Validated prediction of clinical outcome in sarcomas and multiple types of cancer on the basis of a gene expression signature related to genome complexity. Nat Med 7:781–787

    Article  Google Scholar 

  18. Francis P, Namlos HM, Muller C, et al. (2007) Diagnostic and prognostic gene expression signatures in 177 soft tissue sarcomas: hypoxia-induced transcription profile signifies metastatic potential. BMC Genomics:73.

  19. Ferreira BI, Alonso J, Carrillo J et al (2008) Array CGH and gene-expression profiling reveals distinct genomic instability patterns associated with DNA repair and cell-cycle checkpoint pathways in Ewing’s sarcoma. Oncogene 14:2084–2090

    Article  Google Scholar 

  20. Przybyl J, Sciot R, Wozniak A, et al. (2014) Metastatic potential is determined early in synovial sarcoma development and reflected by tumor molecular features. Int J Biochem Cell Biol:505–513.

  21. Lagarde P, Przybyl J, Brulard C et al (2013) Chromosome instability accounts for reverse metastatic outcomes of pediatric and adult synovial sarcomas. J Clin Oncol 5:608–615

    Article  Google Scholar 

  22. Movva S, Wen W, Chen W et al (2015) Multi-platform profiling of over 2000 sarcomas: identification of biomarkers and novel therapeutic targets. Oncotarget 14:12234–12247

    Article  Google Scholar 

  23. Jour G, Scarborough JD, Jones RL et al (2014) Molecular profiling of soft tissue sarcomas using next-generation sequencing: a pilot study toward precision therapeutics. Hum Pathol 8:1563–1571

    Article  Google Scholar 

  24. Egas-Bejar D, Anderson PM, Agarwal R et al (2014) Theranostic profiling for actionable aberrations in advanced high risk osteosarcoma with aggressive biology reveals high molecular diversity: the human fingerprint hypothesis. Oncoscience 2:167–179

    Article  Google Scholar 

  25. Cancer Genome Atlas Research N (2013) Comprehensive molecular characterization of clear cell renal cell carcinoma. Nature 7456:43–49

    Google Scholar 

  26. Rutkowski P, Hompes D (2016) Combined therapy of gastrointestinal stromal tumors. Surg Oncol Clin N Am 4:735–759

    Article  Google Scholar 

  27. Al-Zaid T, Somaiah N, Lazar AJ (2014) Targeted therapies for sarcomas: new roles for the pathologist. Histopathology 1:119–133

    Article  Google Scholar 

  28. Tiwari A, Gupta VG, Bakhshi S (2017) Newer medical therapies for metastatic soft tissue sarcoma. Expert Rev Anticancer Ther

  29. Singer S, Socci ND, Ambrosini G et al (2007) Gene expression profiling of liposarcoma identifies distinct biological types/subtypes and potential therapeutic targets in well-differentiated and dedifferentiated liposarcoma. Cancer Res 14:6626–6636

    Article  Google Scholar 

  30. Gobble RM, Qin LX, Brill ER et al (2011) Expression profiling of liposarcoma yields a multigene predictor of patient outcome and identifies genes that contribute to liposarcomagenesis. Cancer Res 7:2697–2705

    Article  Google Scholar 

  31. Dickson MA, Tap WD, Keohan ML et al (2013) Phase II trial of the CDK4 inhibitor PD0332991 in patients with advanced CDK4-amplified well-differentiated or dedifferentiated liposarcoma. J Clin Oncol 16:2024–2028

    Article  Google Scholar 

  32. Muller CR, Paulsen EB, Noordhuis P, Pedeutour F, Saeter G, Myklebost O (2007) Potential for treatment of liposarcomas with the MDM2 antagonist Nutlin-3A. Int J Cancer 1:199–205

    Article  Google Scholar 

  33. Ray-Coquard I, Blay JY, Italiano A et al (2012) Effect of the MDM2 antagonist RG7112 on the P53 pathway in patients with MDM2-amplified, well-differentiated or dedifferentiated liposarcoma: an exploratory proof-of-mechanism study. Lancet Oncol 11:1133–1140

    Article  Google Scholar 

  34. Wagner AJ, U. Benerji, Amit Mahipal, Somaiah N, et al. (2015) A phase I trial of the human double minute 2 (HDM2) inhibitor MK-8242 in patients (pts) with advanced solid tumors. J Clin Oncol 33:suppl; abstr 10564

  35. Barretina J, Taylor BS, Banerji S et al (2010) Subtype-specific genomic alterations define new targets for soft-tissue sarcoma therapy. Nat Genet 8:715–721

    Article  Google Scholar 

  36. Antonescu CR, Yoshida A, Guo T et al (2009) KDR activating mutations in human angiosarcomas are sensitive to specific kinase inhibitors. Cancer Res 18:7175–7179

    Article  Google Scholar 

  37. Behjati S, Tarpey PS, Sheldon H et al (2014) Recurrent PTPRB and PLCG1 mutations in angiosarcoma. Nat Genet 4:376–379

    Article  Google Scholar 

  38. Guo T, Zhang L, Chang NE, Singer S, Maki RG, Antonescu CR (2011) Consistent MYC and FLT4 gene amplification in radiation-induced angiosarcoma but not in other radiation-associated atypical vascular lesions. Genes Chromosomes Cancer 1:25–33

    Article  Google Scholar 

  39. Maki RG, D'Adamo DR, Keohan ML et al (2009) Phase II study of sorafenib in patients with metastatic or recurrent sarcomas. J Clin Oncol 19:3133–3140

    Article  Google Scholar 

  40. Park MS, Ravi V, Araujo DM (2010) Inhibiting the VEGF-VEGFR pathway in angiosarcoma, epithelioid hemangioendothelioma, and hemangiopericytoma/solitary fibrous tumor. Curr Opin Oncol 4:351–355

    Article  Google Scholar 

  41. Kollar A, Jones RL, Stacchiotti S et al (2017) Pazopanib in advanced vascular sarcomas: an EORTC Soft Tissue and Bone Sarcoma Group (STBSG) retrospective analysis. Acta Oncol 1:88–92

    Article  Google Scholar 

  42. Ray-Coquard I, Italiano A, Bompas E et al (2012) Sorafenib for patients with advanced angiosarcoma: a phase II trial from the French Sarcoma Group (GSF/GETO). Oncologist 2:260–266

    Article  Google Scholar 

  43. Namlos HM, Kresse SH, Muller CR, et al. (2012) Global gene expression profiling of human osteosarcomas reveals metastasis-associated chemokine pattern. Sarcoma:639038

  44. Salas S, Jezequel P, Campion L et al (2009) Molecular characterization of the response to chemotherapy in conventional osteosarcomas: predictive value of HSD17B10 and IFITM2. Int J Cancer 4:851–860

    Article  Google Scholar 

  45. Choy E, Hornicek F, MacConaill L et al (2012) High-throughput genotyping in osteosarcoma identifies multiple mutations in phosphoinositide-3-kinase and other oncogenes. Cancer 11:2905–2914

    Article  Google Scholar 

  46. Barr FG (1999) The role of chimeric paired box transcription factors in the pathogenesis of pediatric rhabdomysarcoma. Cancer Res 7 Suppl:1711s-1715s

  47. Davicioni E, Finckenstein FG, Shahbazian V, Buckley JD, Triche TJ, Anderson MJ (2006) Identification of a PAX-FKHR gene expression signature that defines molecular classes and determines the prognosis of alveolar rhabdomyosarcomas. Cancer Res 14:6936–6946

    Article  Google Scholar 

  48. Missiaglia E, Williamson D, Chisholm J et al (2012) PAX3/FOXO1 fusion gene status is the key prognostic molecular marker in rhabdomyosarcoma and significantly improves current risk stratification. J Clin Oncol 14:1670–1677

    Article  Google Scholar 

  49. Kohsaka S, Shukla N, Ameur N et al (2014) A recurrent neomorphic mutation in MYOD1 defines a clinically aggressive subset of embryonal rhabdomyosarcoma associated with PI3K-AKT pathway mutations. Nat Genet 6:595–600

    Article  Google Scholar 

  50. Amary MF, Bacsi K, Maggiani F et al (2011) IDH1 and IDH2 mutations are frequent events in central chondrosarcoma and central and periosteal chondromas but not in other mesenchymal tumours. J Pathol 3:334–343

    Article  Google Scholar 

  51. Au KS, Hebert AA, Roach ES, Northrup H (1999) Complete inactivation of the TSC2 gene leads to formation of hamartomas. Am J Hum Genet 6:1790–1795

    Article  Google Scholar 

  52. Carbonara C, Longa L, Grosso E et al (1996) Apparent preferential loss of heterozygosity at TSC2 over TSC1 chromosomal region in tuberous sclerosis hamartomas. Genes Chromosomes Cancer 1:18–25

    Article  Google Scholar 

  53. Al-Saleem T, Wessner LL, Scheithauer BW et al (1998) Malignant tumors of the kidney, brain, and soft tissues in children and young adults with the tuberous sclerosis complex. Cancer 10:2208–2216

    Article  Google Scholar 

  54. Carsillo T, Astrinidis A, Henske EP (2000) Mutations in the tuberous sclerosis complex gene TSC2 are a cause of sporadic pulmonary lymphangioleiomyomatosis. Proc Natl Acad Sci U S A 11:6085–6090

    Article  Google Scholar 

  55. Huang J, Manning BD (2008) The TSC1-TSC2 complex: a molecular switchboard controlling cell growth. Biochem J 2:179–190

    Article  Google Scholar 

  56. Huang J, Dibble CC, Matsuzaki M, Manning BD (2008) The TSC1-TSC2 complex is required for proper activation of mTOR complex 2. Mol Cell Biol 12:4104–4115

    Article  Google Scholar 

  57. Benvenuto G, Li S, Brown SJ et al (2000) The tuberous sclerosis-1 (TSC1) gene product hamartin suppresses cell growth and augments the expression of the TSC2 product tuberin by inhibiting its ubiquitination. Oncogene 54:6306–6316

    Article  Google Scholar 

  58. Fadare O, Parkash V, Yilmaz Y, et al. (2004) Perivascular epithelioid cell tumor (PEComa) of the uterine cervix associated with intraabdominal “PEComatosis”: a clinicopathological study with comparative genomic hybridization analysis. World J Surg Oncol:35.

  59. Subbiah V, Trent JC, Kurzrock R (2010) Resistance to mammalian target of rapamycin inhibitor therapy in perivascular epithelioid cell tumors. J Clin Oncol 24:e415

    Article  Google Scholar 

  60. Agaram NP, Sung YS, Zhang L et al (2015) Dichotomy of genetic abnormalities in PEComas with therapeutic implications. Am J Surg Pathol 6:813–825

    Article  Google Scholar 

  61. Ladanyi M, Lui MY, Antonescu CR et al (2001) The der(17)t(X;17)(p11;q25) of human alveolar soft part sarcoma fuses the TFE3 transcription factor gene to ASPL, a novel gene at 17q25. Oncogene 1:48–57

    Article  Google Scholar 

  62. Tsuda M, Davis IJ, Argani P et al (2007) TFE3 fusions activate MET signaling by transcriptional up-regulation, defining another class of tumors as candidates for therapeutic MET inhibition. Cancer Res 3:919–929

    Article  Google Scholar 

  63. Stockwin LH, Vistica DT, Kenney S, et al. (2009) Gene expression profiling of alveolar soft-part sarcoma (ASPS). BMC Cancer:22

  64. Lazar AJ, Das P, Tuvin D et al (2007) Angiogenesis-promoting gene patterns in alveolar soft part sarcoma. Clin Cancer Res 24:7314–7321

    Article  Google Scholar 

  65. Selvarajah S, Pyne S, Chen E et al (2014) High-resolution array CGH and gene expression profiling of alveolar soft part sarcoma. Clin Cancer Res 6:1521–1530

    Article  Google Scholar 

  66. Conley AP, Trinh VA, Zobniw CM, Posey K, Martinez JD, Arrieta OG, Wang WL, Lazar AJ, Somaiah N, Roszik J, Patel SR (2017) Positive Tumor Response to Combined Checkpoint Inhibitors in a Patient with Refractory Alveolar Soft Part Sarcoma: A Case Report. J Global Oncol, in press

  67. Doyle LA, Vivero M, Fletcher CD, Mertens F, Hornick JL (2014) Nuclear expression of STAT6 distinguishes solitary fibrous tumor from histologic mimics. Mod Pathol 3:390–395

    Google Scholar 

  68. Demicco EG, Harms PW, Patel RM et al (2015) Extensive survey of STAT6 expression in a large series of mesenchymal tumors. Am J Clin Pathol 5:672–682

    Article  Google Scholar 

  69. Bertucci F, Bouvier-Labit C, Finetti P et al (2013) Gene expression profiling of solitary fibrous tumors. PLoS One 5:e64497

    Article  Google Scholar 

  70. Park MS, Patel SR, Ludwig JA et al (2011) Activity of temozolomide and bevacizumab in the treatment of locally advanced, recurrent, and metastatic hemangiopericytoma and malignant solitary fibrous tumor. Cancer 21:4939–4947

    Article  Google Scholar 

  71. Park MS, Ravi V, Conley A et al (2013) The role of chemotherapy in advanced solitary fibrous tumors: a retrospective analysis. Clin Sarcoma Res 1:7

    Article  Google Scholar 

  72. Guillou L, Aurias A (2010) Soft tissue sarcomas with complex genomic profiles. Virchows Arch 2:201–217

    Article  Google Scholar 

  73. Lee W, Teckie S, Wiesner T et al (2014) PRC2 is recurrently inactivated through EED or SUZ12 loss in malignant peripheral nerve sheath tumors. Nat Genet 11:1227–1232

    Article  Google Scholar 

  74. Zhang M, Wang Y, Jones S et al (2014) Somatic mutations of SUZ12 in malignant peripheral nerve sheath tumors. Nat Genet 11:1170–1172

    Article  Google Scholar 

  75. Schaefer IM, Fletcher CD, Hornick JL (2016) Loss of H3K27 trimethylation distinguishes malignant peripheral nerve sheath tumors from histologic mimics. Mod Pathol 1:4–13

    Article  Google Scholar 

  76. Cleven AH, Sannaa GA, Briaire-de Bruijn I et al (2016) Loss of H3K27 tri-methylation is a diagnostic marker for malignant peripheral nerve sheath tumors and an indicator for an inferior survival. Mod Pathol 6:582–590

    Article  Google Scholar 

  77. Prieto-Granada CN, Wiesner T, Messina JL, Jungbluth AA, Chi P, Antonescu CR (2016) Loss of H3K27me3 expression is a highly sensitive marker for sporadic and radiation-induced MPNST. Am J Surg Pathol 4:479–489

    Article  Google Scholar 

  78. Hashizume R, Andor N, Ihara Y et al (2014) Pharmacologic inhibition of histone demethylation as a therapy for pediatric brainstem glioma. Nat Med 12:1394–1396

    Article  Google Scholar 

  79. Tawbi HA-H, Burgess MA, Crowley J, et al. (2016) Safety and efficacy of PD-1 blockade using pembrolizumab in patients with advanced soft tissue (STS) and bone sarcomas (BS): results of SARC028—a multicenter phase II study. J Clin Oncol 34:suppl; abstr 10564

  80. Doebele RC, Davis LE, Vaishnavi A et al (2015) An oncogenic NTRK fusion in a patient with soft-tissue sarcoma with response to the tropomyosin-related kinase inhibitor LOXO-101. Cancer Discov 10:1049–1057

    Article  Google Scholar 

  81. Haller F, Knopf J, Ackermann A et al (2016) Paediatric and adult soft tissue sarcomas with NTRK1 gene fusions: a subset of spindle cell sarcomas unified by a prominent myopericytic/haemangiopericytic pattern. J Pathol 5:700–710

    Article  Google Scholar 

  82. Pavlick D, Schrock AB, Malicki D, et al. (2017) Identification of NTRK fusions in pediatric mesenchymal tumors. Pediatr Blood Cancer

Download references

Author information

Authors and Affiliations

Authors

Corresponding author

Correspondence to Alexander J. Lazar.

Ethics declarations

Funding

This study was supported by Amschwand Sarcoma Cancer Foundation (WLW, AJL).

Conflict of interest

Potentially relevant to the content of this manuscript, Dr. Lazar is a Consultant to, on Advisory Boards for, or receives research support from BMS, Novartis, ArcherDX, Genentech/Roche, Medimmune/AstraZeneca, GSK, and Merck. The remaining authors report no potential conflicts.

Rights and permissions

Reprints and permissions

About this article

Check for updates. Verify currency and authenticity via CrossMark

Cite this article

Al-Zaid, T., Wang, WL., Somaiah, N. et al. Molecular profiling of sarcomas: new vistas for precision medicine. Virchows Arch 471, 243–255 (2017). https://doi.org/10.1007/s00428-017-2174-3

Download citation

  • Received:

  • Revised:

  • Accepted:

  • Published:

  • Issue Date:

  • DOI: https://doi.org/10.1007/s00428-017-2174-3

Keywords

Navigation