One of our research fields is the biology of rhabdomyosarcoma (RMS), an aggressive and highly malignant form of childhood cancer. RMS is composed of skeletal myoblast-like cells that are poorly differentiated. Promoting differentiation in RMS can be considered a useful therapeutic endpoint because skeletal muscle differentiation is normally coupled to irreversible cell cycle arrest.
We study how the onset of mammalian skeletal muscle differentiation is normally controlled, especially how it is coupled to cell proliferation arrest. We also explore how those normal processes get derailed – and could be reprogrammed – in RMS.
Recent work in our laboratory has included a high content screen to identify protein kinases that block the initiation of differentiation in skeletal myoblasts. We identified 55 protein kinases including mTOR and SRC that negatively regulate the initial steps of differentiation in myoblasts (Wilson et al, Sci Rep. 2016). This study set a foundation to begin studies of how manipulating their activity might foster differentiation as a therapeutic approach in RMS.
We also recently developed a tandem computational and functional approach to identify oncogenic drivers and tumor suppressors in RMS. We identified 29 candidate genes and validated that more than half using a CRISPR/Cas9-based “mini-pool” screen (Xu et al, Cell Reports, 2018). Strikingly, the expression of more than half of the oncogenic driver genes is temporally regulated in a way implicates them as negative regulators of myogenic differentiation. They include EZH2 and D-types cyclins, both of which play oncogenic roles in other cancers.
We have already advanced studies of one of the aforementioned oncogenic drivers: PLAG1. This gene, not previously implicated in RMS, encodes a transcription factor that is known to induce the Insulin-like growth factor, IGF2. Because IGF2 is well-known to influence skeletal muscle growth, we studied it further. Our team showed that it, indeed, plays a critical role in regulating proliferation and survival of RMS cells, inspiring us to further study how it acts and whether its activity might be targeted (Zheng et al., Mol Cancer Res, 2020).
To carry forward all of these projects, we are using complementary computational biology and laboratory-based studies in cultured cells and model organism, employing a wide array of biochemical, molecular and cell biology, and histology approaches.
Developing better treatments for soft tissue sarcoma in children
An important part of Skapek laboratory research focuses on how to improve the outcomes for children with soft tissue sarcoma (STS), a large and heterogeneous collections of cancers that seem to arise from distinct mesenchymal tissues. Rhabdomyosarcoma (RMS) is the largest member of this class of cancers in children. Other relatively common types include malignant peripheral nerve sheath tumor (MPNST) and fibrosarcoma, but there are many others. Importantly, there are other types of childhood neoplasms that are difficult to treat but do not seem to meet the full definition of “cancer”. One relatively common form of tumor is known as infantile myofibromatosis, which is very similar to infantile fibromatosis but is not considered a malignancy.
In our laboratory, we are studying RMS in a more systematic way as outlined elsewhere, but we are tackling the other types of STS or STS-like processes when opportunities arise.
In one approach, members of our team help to drive a “Precision Medicine Program” housed in the Division of Hematology/Oncology in the Department of Pediatrics. Our PMP focuses on collecting and analyzing the molecular genetic derangements in cancers cared for by physicians in the Division of Hematology/Oncology at Children’s Medical Center Dallas. When interesting genetic mutations are identified in STS or STS-like tumors, our team often helps to carry out research to investigate how those mutant forms contribute to cancer. As one example, we recently reported how a complex chromosomal rearrangement creates super-activity in the Platelet-Derived Growth Factor Receptor beta (Hassan et al., Cold Spring Harb Mol Case Stud., 2019).
Through the years, we have collected molecular genetic information on close to 100 new specimens, many of which have “variants of unknown significance”, which are of interest to us.
We are also “reaching toward the clinic” by carrying out pre-clinical testing of new treatments for forms of STS. In some cases, those tests stem from our own research using commercially available drugs of interest, such as CDK4/6 or MEK inhibitors (Saab et al. 2006, Butler et al. 2020). In other cases, we collaborate with external partners to help carry out preclinical studies with emerging drugs, such as a new FGFR inhibitors we are testing. In most cases, these studies include in vitro testing as well as in vivo testing using Patient-Derived Xenograft (PDX) models in which specimens from a childhood STS biopsy are implanted and propagated in immunocompromised mouse. Often, these studies are coupled to molecular and histological analyses studying how the treatment influences cell behavior. And in a collaborative project with the Danuser lab, we are exploring how cells taken from a PDX behave when implanted into a zebrafish embryo, in which the cells’ journeys and shaped can be carefully tracked.
A third STS project focuses on understanding the best way to monitor how a molecularly targeted therapy is working. Such an “early response biomarker” could have tremendous value in the clinic because the sooner we know that a medication does NOT work, the sooner we can use something else.
In this case, we are focusing on STS’s that are frequently driven by RAS pathway activation, such as RMS and MPNST. In both cases, we are studying how radioactively labeled tracers, such as glucose or thymidine that can be measured by positron-emission tomography (PET) could give an early indication that a MEK1 inhibitor is working. We recently showed its value in a pilot study of MPNST (Butler et al., Pediatric Blood Cancer, 2020), and we are now considering other tracers that might be even better.