Targeted exome sequencing profiles genetic alterations in leiomyosarcoma

Leiomyosarcoma (LMS) belongs to the class of genetically complex sarcomas and shows numerous, often non‐recurrent chromosomal imbalances and aberrations. We investigated a group of LMS using NGS platform to identify recurrent genetic abnormalities and possible therapeutic targets. Targeted exome sequencing of 230 cancer‐associated genes was performed on 35 primary soft tissue and visceral (extra‐uterine) LMS. Sequence data were analyzed to identify single nucleotide variants, small insertions/deletions (indels), and copy number alterations. Key alterations were further investigated using FISH assay. The study group included patients with median age of 64 years and median tumor size of 7 cm. The primary sites included retroperitoneal/intra‐abdominal, extremity, truncal, and visceral. Thirty‐one tumors were high grade LMS, while four were low grade. Losses of chromosomal regions involving key tumor suppressor genes PTEN (10q), RB1 (13q), CDH1 (16q), and TP53 (17p) were the most frequent genetic events. Gains mainly involved chromosome regions 17p11.2 (MYOCD) and 15q25‐26 (IGF1R). The most frequent mutations were identified in the TP53 gene in 13 of 35 (37%) cases. FISH analysis showed amplification of the myocardin (MYOCD) gene in 5 of 25 (20%) cases analyzed. None of the four low grade LMS showed losses or mutations of PTEN or TP53 genes. Genetic complexity is the hallmark of LMS with losses of important tumor suppressor genes being a common feature. MYOCD, a key gene associated with smooth muscle differentiation, is amplified in a subset of both retroperitoneal and extremity LMS. Further studies are necessary to investigate the significance of gains/amplifications in the development of these tumors. © 2015 Wiley Periodicals, Inc.

[1]  Donavan T. Cheng,et al.  Memorial Sloan Kettering-Integrated Mutation Profiling of Actionable Cancer Targets (MSK-IMPACT): A Hybridization Capture-Based Next-Generation Sequencing Clinical Assay for Solid Tumor Molecular Oncology. , 2015, The Journal of molecular diagnostics : JMD.

[2]  T. Soussi,et al.  TP53 Mutations in Human Cancer: Database Reassessment and Prospects for the Next Decade , 2014, Human mutation.

[3]  M. Berger,et al.  Detecting somatic genetic alterations in tumor specimens by exon capture and massively parallel sequencing. , 2013, Journal of visualized experiments : JoVE.

[4]  A. Sivachenko,et al.  Sensitive detection of somatic point mutations in impure and heterogeneous cancer samples , 2013, Nature Biotechnology.

[5]  Narasimhan P. Agaram,et al.  Predictors of Survival and Recurrence in Primary Leiomyosarcoma , 2013, Annals of Surgical Oncology.

[6]  Nikhil Wagle,et al.  High-throughput detection of actionable genomic alterations in clinical tumor samples by targeted, massively parallel sequencing. , 2012, Cancer discovery.

[7]  M. DePristo,et al.  A framework for variation discovery and genotyping using next-generation DNA sequencing data , 2011, Nature Genetics.

[8]  David M. Thomas,et al.  Comprehensive Mapping of p53 Pathway Alterations Reveals an Apparent Role for Both SNP309 and MDM2 Amplification in Sarcomagenesis , 2010, Clinical Cancer Research.

[9]  C. Antonescu,et al.  EWSR1‐POU5F1 fusion in soft tissue myoepithelial tumors. A molecular analysis of sixty‐six cases, including soft tissue, bone, and visceral lesions, showing common involvement of the EWSR1 gene , 2010, Genes, chromosomes & cancer.

[10]  Derek Y. Chiang,et al.  Subtype-specific genomic alterations define new targets for soft tissue sarcoma therapy , 2010, Nature Genetics.

[11]  T. Miki,et al.  Myocardin functions as an effective inducer of growth arrest and differentiation in human uterine leiomyosarcoma cells. , 2010, Cancer research.

[12]  David M. Thomas,et al.  Comprehensive Mapping of p 53 Pathway Alterations Reveals an Apparent Role for Both SNP 309 and MDM 2 Amplification in Sarcomagenesis , 2010 .

[13]  L. Guillou,et al.  Soft tissue sarcomas with complex genomic profiles , 2010, Virchows Archiv.

[14]  Richard Durbin,et al.  Sequence analysis Fast and accurate short read alignment with Burrows – Wheeler transform , 2009 .

[15]  O. Mariani,et al.  Strong smooth muscle differentiation is dependent on myocardin gene amplification in most human retroperitoneal leiomyosarcomas. , 2009, Cancer research.

[16]  K. Hunt,et al.  Genetic aberrations in soft tissue leiomyosarcoma. , 2009, Cancer letters.

[17]  P. Pandolfi,et al.  The AKT-mTOR pathway plays a critical role in the development of leiomyosarcomas , 2007, Nature Medicine.

[18]  C. Blomqvist,et al.  Clinical course of nonvisceral soft tissue leiomyosarcoma in 225 patients from the Scandinavian Sarcoma Group , 2007, Cancer.

[19]  S. Devesa,et al.  Incidence patterns of soft tissue sarcomas, regardless of primary site, in the surveillance, epidemiology and end results program, 1978–2001: An analysis of 26,758 cases , 2006, International journal of cancer.

[20]  S. Knuutila,et al.  Gene copy number profiling of soft-tissue leiomyosarcomas by array-comparative genomic hybridization. , 2006, Cancer genetics and cytogenetics.

[21]  E. Creemers,et al.  The myocardin family of transcriptional coactivators: versatile regulators of cell growth, migration, and myogenesis. , 2006, Genes & development.

[22]  M. Miettinen,et al.  Evaluation of biological potential of smooth muscle tumours , 2006, Histopathology.

[23]  U. Surti,et al.  Loss of DNA copy number of 10q is associated with aggressive behavior of leiomyosarcomas: a comparative genomic hybridization study. , 2005, Cancer genetics and cytogenetics.

[24]  Da-Zhi Wang,et al.  Myocardin is a master regulator of smooth muscle gene expression , 2003, Proceedings of the National Academy of Sciences of the United States of America.

[25]  M. Lu,et al.  Myocardin Is a Critical Serum Response Factor Cofactor in the Transcriptional Program Regulating Smooth Muscle Cell Differentiation , 2003, Molecular and Cellular Biology.

[26]  Tsuyoshi Saito,et al.  PTEN/MMAC1 gene mutation is a rare event in soft tissue sarcomas without specific balanced translocations , 2003, International journal of cancer.

[27]  S. Weiss.  Smooth Muscle Tumors of Soft Tissue , 2002, Advances in anatomic pathology.

[28]  U. Surti,et al.  Genomic alterations in uterine leiomyosarcomas: Potential markers for clinical diagnosis and prognosis , 2001, Genes, chromosomes & cancer.