A Genomic Strategy for Each Patient? Sarcomas Are That Complex

Although chemotherapy options for patients with sarcoma have expanded in recent months, efforts to advance treatment beyond a therapeutic plateau have long been hindered by a paucity of targetable genomic alterations and the rarity of these tumor types.

A Therapeutic Challenge

In the hopes of identifying new targets, researchers are focusing genomic sequencing studies on many different types of sarcomas. The insights gained have served to emphasize the significant heterogeneity and the unique molecular mechanisms underlying the development of these cancers. Moving forward may require the realization of truly individualized cancer therapy.Encompassing more than 50 distinct histological subtypes, sarcomas are a rare group of cancers that arise in cells of mesenchymal origin. This type of cancer disproportionately affects children and adolescents; sarcomas account for an estimated 1% of adult cancers and 15% of childhood cancers, although the exact incidence remains unknown in part because of inexact classification and subtyping.

Broadly, they are classed as bone sarcomas and soft tissue sarcomas, depending upon the location of the primary tumor. More specifically, each subtype is named for the type of cell or tissue from which it develops. For example, rhabdomyosarcomas occur in the skeletal muscle, liposarcomas in the fat tissue, leiomyosarcomas in smooth muscle tissue. Among the bone sarcomas, osteosarcoma arises in the osteoid tissue and chondrosarcoma in the cartilaginous tissue. Ewing sarcoma forms in both the bone and the soft tissue, though the former is more common.

Despite their biological and histological differences, sarcomas are generally treated in the same manner, with a combination of surgery, chemotherapy, and radiation therapy. Unfortunately, many patients, particularly those diagnosed at advanced stages of disease, are not surgically treatable.

Approved Agents

Although chemotherapy has vastly improved outcomes in some subtypes such as osteosarcoma, it has generated poor responses among patients with other subtypes and, even among those who do respond, recurrence often occurs.In recent months, the FDA has approved two new chemotherapy agents expected to help improve outcomes among subsets of patients.

In January, eribulin mesylate (Halaven) became the first FDA-approved drug for patients with advanced or unresectable liposarcoma to demonstrate an improvement in overall survival (OS); the median OS was 15.6 months with the microtubule inhibitor versus 8.4 months with dacarbazine.

In October 2015, the FDA approved trabectedin (Yondelis), an alkylating agent, for patients with unresectable or metastatic liposarcoma or leiomyosarcoma who have received a prior anthracycline- containing regimen. The approval was based on a statistically significant improvement in median progression-free survival (PFS): 4.2 months with trabectedin versus 1.5 months with dacarbazine.

Nevertheless, response rates for both drugs were relatively low. The objective response rate was 4.0% (95% CI, 1.8-7.5) with eribulin and 7% (95% CI, 4.4-9.8) with trabectedin.

Although many molecularly targeted therapies have been tested, success has been limited. Imatinib (Gleevec), which the FDA approved for the treatment of KIT-positive gastrointestinal stromal tumors (GISTs), has proved particularly successful. Approximately half of the patients in one pivotal study responded to the TKI dosed at 400 mg and median OS was 49 months. In another study, the objective response rate hit 68.5%. Two other drugs, regorafenib (Stivarga) and sunitinib (Sutent), have been approved as GIST therapy on the basis of PFS and time to progression, respectively.

Many Sides of the Genomic Coin

Pazopanib (Votrient) was approved in soft tissue sarcoma after demonstrating a median PFS of 4.6 months compared with 1.6 months for placebo in a clinical trial that had enrolled patients with leiomyosarcoma, synovial sarcoma, and other soft tissue subtypes not including GISTs.Thus far, large-scale genomic characterization of cancers has focused on epithelial and hematologic malignancies, and relatively few studies of sarcomas have been performed. That is slowly beginning to change as researchers are undertaking collaborative efforts to overcome the scarcity of samples. The Cancer Genome Atlas (TCGA) has also turned its attention to sarcoma and has included the study of these types of cancers in its Rare Tumor Characterization Project, although only a few types of sarcoma are being studied. The picture that is emerging from the limited studies that have been done is of at least two genomically distinct types of sarcoma. Some sarcomas have a very stable genome, with very few molecular alterations—in some cases, only a single defining abnormality that is maintained throughout the tumor’s evolution.

Most commonly, the alterations involve chromosomal translocations, which occur when part of one chromosome breaks off and then reattaches to another. This can result in the formation of gene fusions, when part of one gene joins onto part of a completely different gene; if the coding sequence of the genes is undisturbed, a fusion protein is generated.

In sarcomas, these chromosomal translocations predominantly seem to involve genes encoding transcription factors. The resulting gene fusions thereby aberrantly activate the expression of the target genes of these transcription factors. This may partly explain the relatively stable genomes of these tumor types since the same goal—driving certain hallmark cellular processes—is achieved by activating the transcriptional programs that orchestrate them.

Other types of sarcomas are genomically complex. Characterized by mutations in the “guardian of the genome,” the TP53 gene, they display frequent somatic mutations that are not necessarily consistent from patient to patient. These sarcomas also tend to be associated with alterative lengthening of telomeres (ALT); by contrast, telomerase activation (TA) is more frequently observed in those with stable genomes.

ALT and TA represent two mechanisms of maintaining the telomeres, which are the protective caps on the end of the DNA. Steady erosion of the telomeres limits the number of times a cell can divide before it dies; thus, by maintaining the telomeres, cancer cells can achieve immortality. A recent analysis has also identified a third group of sarcomas of intermediate complexity; these are characterized by chromosome 12 amplifications involving genes such as CDK4 and MDM2. Included in this group are well-differentiated and dedifferentiated liposarcomas.

These differences in the genomic background of sarcoma subtypes have therapeutic implications as they are likely to require very different treatment strategies. Although genomically complex tumors offer up many potential targets, the fact that few of the many underlying alterations are recurrent makes picking an effective one challenging. Their genomic instability might make these types of sarcoma more amenable to immunotherapy and early-stage trials of immune- targeting drugs are underway.

Soft Tissue Sarcoma Mutations

Translocation-defined sarcomas are also difficult to treat because this type of abnormality is not yet readily druggable. The most promising strategy is to identify the targets of these transcription factors and block their activation. The insulin-like growth factor 1 receptor (IGF1R) pathway emerged as such in Ewing sarcoma, which served in part as the rationale for the clinical investigation of IGF1R inhibitors in this tumor type. It has also been suggested that these chromosomal translocations might arise as a result of epigenetic alterations, and the potential of small molecules targeting epigenetic mechanisms is also being investigated.The broadest portrait of genomic activity in sarcomas comes from TCGA, which sequenced the tumors of 242 patients with eight different types of soft tissue sarcomas including leiomyosarcomas (38%), dedifferentiated liposarcoma (21%), and undifferentiated pleomorphic sarcomas (18%).

Gastrointestinal stromal tumors

Statistically significant recurrent mutations included inactivating mutations in the tumor suppressors TP53, ATRX, and RB1, with overall frequencies of 27.3%, 8.7%, and 6.2%, respectively, although this differed between subtypes.In general, very few highly recurrent driver genes have been identified in soft tissue sarcomas. One significant exception is GIST, which display oncogenic mutations in several targetable kinases.

Most notably, the KIT gene is mutated in around 85% of cases. There are also less frequent mutations in the platelet-derived growth factor receptor alpha gene (PDGFRA) and rare mutations in the BRAF gene. The dependence of GIST on activated KIT and PDGFRα prompted the development of the kinase inhibitor imatinib, which was approved by the FDA in 2002 for this tumor type and prolongs survival in a substantial proportion of patients with certain types of activating KIT mutations.

Leiomyosarcoma

Indeed, the GIST field has evolved into a robust area of exploration since the early 1990s, when the tumor type became increasingly recognized as a distinct pathological entity. Before that, GISTs frequently were classified as leiomyoma, leiomyosarcoma, or leiomyoblastoma.Leiomyosarcoma is the prototypical example of a genomically complex sarcoma and, unsurprisingly, one study of the subtype found the most common recurrent somatic mutations were in the TP53 gene, present in 35% of cases. Recurrent mutations in a second gene, ATRX, were also observed (17%); ATRX-mutated tumors were poorly differentiated with worse overall survival than those without these mutations.

Liposarcoma

The ATRX protein is an ATP-dependent helicase. Together with a second protein, DAXX, it acts as a histone chaperone and deposits histone proteins at various regions of the genome, including the telomeres, where it plays a role in telomere stability. Mutations in ATRX are closely linked to ALT, which could explain why this phenomenon is more common in genomically complex sarcomas.Liposarcomas are composed of five different subtypes; well-differentiated, dedifferentiated, myxoid, pleomorphic, and mixed-type. Depending on the specific type, they display both complex and simple karyotypes. Myxoid liposarcoma, for example, is characterized by a recurrent chromosomal translocation that results in the FUS-CHOP gene fusion in more than 95% of cases.

Ewing Sarcoma

A next-generation sequencing study in liposarcoma found numerous amplified genes, most notably the carboxypeptidase M gene (CPM) in well-differentiated and dedifferentiated liposarcoma, in addition to a number of recurrently mutated genes. The study authors characterized the functional role of CPM and discovered that it may be oncogenic in liposarcoma through activation of the epidermal growth factor receptor (EGFR) pathway, thus offering a potential therapeutic target. Exceptional Responders in Bone SarcomasIf leiomyosarcomas are the prototypical genomically complex sarcomas, sarcomas with simpler genomes are exemplified by Ewing sarcoma, with a mutational load of 0.15 mutations/Mb. These tumors very often express one of several translocations that result in gene fusions between members of the TET family of RNA-binding proteins and of the ETS family of transcription factors; in 85% to 90% of cases, the EWSR1-FLI1 fusion is the result. Although these gene fusions were discovered many years ago, they have yet to translate into any novel targeted therapies. There have been attempts to target this alteration using inhibitors of the IGF1R pathway, which is thought to be dysregulated downstream.

IGF1R inhibitors showed notable responses in a small number of patients in clinical trials, but these responses were short-lived and insufficient to advocate monotherapy. One potential explanation for these limited responses is the development of resistance through activation of downstream pathways including the mammalian target of rapamycin (mTOR) pathway. Clinical trials of a combination of mTOR and IGF1R inhibitors were notable only for one or two patients who experienced a dramatic response.

Osteosarcoma

Although development of these drugs stalled, researchers are now focusing on unraveling the molecular mechanisms of these exceptional responders to gain additional clues as to how to treat these tumors in so-called N-of-1 studies.Unlike Ewing sarcoma, the other major type of bone sarcoma is much more genomically complex, with a mutational load of 1.2 mutations/Mb. Several sequencing studies have been performed in this type of sarcoma and, as with other genomically complex sarcomas, the TP53 gene was frequently mutated (22%). In addition to frequent mutations of the gene, other molecular alterations that lead to the inactivation of p53 were also observed.

Although no other genes were recurrently mutated, among the chaos of frequent somatic mutations, those involved in the phosphatidylinositol 3-kinase (PI3K) pathway were altered in around a quarter of all tumors. PI3K pathway alterations included mutations in PTEN, AKT, TSC2, NF1, and PIK3CA, among others.

Jane de Lartigue, PhD, is a freelance medical writer and editor based in New Haven, Connecticut.

KEY RESEARCH

• Brohl AS, Solomon DA, Chang W, et al. The genomic landscape of the Ewing sarcoma family of tumors reveals recurrent STAG2 mutation. PLoS Genet. 2014;10(7):e1004475. doi: 10.1371/journal.pgen.1004475. eCollection 2014.
• Brohl AS, Shah HR, Wang YC, et al. The somatic mutational landscape in soft tissue sarcoma: early results from TCGA data. J Clin Oncol. 2015;33(suppl; abstr 10508). Corless CL, Fletcher JA, Heinrich MC. Biology of gastrointestinal stromal tumors. J Clin Oncol. 2004;22(18):3813-3825.
• Crompton BD, Stewart C, Taylor-Weiner A, et al. The genomic landscape of pediatric Ewing sarcoma. Cancer Discov. 2014;4(11):1326-1341.
• Ducimetière F, Lurkin A, Ranchère-Vince D, et al. Incidence of sarcoma histotypes and molecular subtypes in a prospective epidemiological study with central pathology review and molecular testing. PLoS One. 2011;6(8):e20294. doi:10.1371/journal.pone.0020294.
• Jour G, Scarborough JD, Jones RL, et al. Molecular profiling of soft tissue sarcomas using next-generation sequencing: a pilot study toward precision therapeutics. Hum Pathol. 2014;45(8):1563-1571.
• Kanojia D, Nagata Y, Garg M, et al. Genomic landscape of liposarcoma. Oncotarget 2015;6(40):42429-42444.
• Lorenz S, Barøy T, Sun J, et al. Unscrambling the genomic chaos of osteosarcoma reveals extensive transcript fusion, recurrent rearrangements and frequent novel TP53 aberrations. Oncotarget 2015;7(5):5273-5288.
• Mäkinen N, Aavikko M, Heikkinen T, et al. Exome sequencing of uterine leiomyosarcomas identifies frequent mutations in TP53, ATRX, and MED12. PLoS Genet. 2016;12(2):e1005850. Doi;10.1371/journal. pgen.1005850.
• Perry JA, Kiezun A, Tonzi P, et al. Complementary genomic approaches highlight the PI3K/mTOR pathway as a common vulnerability in osteosarcoma. Proc Natl Acad Sci USA 2014;111(51):E5564-5573.
• Sand LG, Szuhai K, Hogendoorn PCW. Sequencing overview of Ewing sarcoma: a journey across genomic, epigenomic and transcriptomic landscapes. Int J Mol Sci. 2015;16(7):16176-16215.
• Seki M, Nishimura R, Yoshida K, et al. Integrated genetic and epigenetic analysis defines novel molecular subgroups in rhabdomyosarcoma. Nat Commun. 2015;6:7557-7565. Tirode F, Surdez D, Ma X, et al. Genomic landscape of Ewing sarcoma defines an aggressive subtype with co-association of STAG2 and TP53 mutations. Cancer Discov. 2014;4(11):1342-1353.
• Yang JL. Investigation of sarcoma genomics and its impact on targeted therapy: an international collaboration to conquer human osteosarcoma. Chin J Cancer 2014;33(12):575-580.
• Yang CY, Liau J-Y, Huang W-J, et al. Targeted next-generation sequencing of cancer genes identified frequent TP53 and ATRX mutations in leiomyosarcoma. Am J Transl Res. 2015;7(10):2072-2081. eCollection 2015.