Comparative gene expression profiling of benign and malignant lesions reveals candidate therapeutic compounds for leiomyosarcoma

Establishment and characterization of NCC-LMS3-C1: a novel patient-derived cell line of leiomyosarcoma

Leiomyosarcoma (LMS) is an aggressive mesenchymal malignancy, which originates from the smooth muscle cells or from the precursor mesenchymal stem cells that potentially differentiate into smooth muscle cells. LMS is one of the most common sarcomas. LMS has genomic instability, reflecting complex and unbalanced karyotypes, and the cytogenetic and molecular changes in LMS are not consistent. The standard treatment of the primary LMS is complete resection, and the metastasis is often observed even after curative surgery. Patient-derived cancer models are a key bioresource to develop a novel therapy, and we aimed to establish and characterize a novel cell line for LMS. We established a cell line from tumor tissues of the patient with LMS and named it NCC-LMS3-C1. We maintained NCC-LMS3-C1 cells for 12 months and passed them more than 30 times. Genome-wide copy number analysis demonstrated that NCC-LMS3-C1 cells harbored genetic abnormalities. NCC-LMS3-C1 cells exhibited aggressive phenotypes such as continuous growth, spheroid formation, and invasion in the tissue culture condition, which may reflect the clinical behaviors of LMS. We performed a drug screening using NCC-LMS3-C1 cells and found that four anti-cancer agents, such as bortezomib, dasatinib, mitoxantrone, and romidepsin, had remarkable anti-proliferative effects on NCC-LMS3-C1 cells. We conclude that NCC-LMS3-C1 cells will be a useful resource for the study of LMS.

Estimating intraclonal heterogeneity and subpopulation changes from bulk expression profiles in CMap

Premnas is a computational framework that provides a new perspective to interpret perturbational data in LINC L1000 CMap by learning an ad hoc subpopulation representation from scRNA-seq and performing the digital cytometry to estimate the abundance of undetermined subpopulations.

The connectivity among signatures upon perturbations curated in the CMap library provides a valuable resource for understanding therapeutic pathways and biological processes associated with the drugs and diseases. However, because of the nature of bulk-level expression profiling by the L1000 assay, intraclonal heterogeneity and subpopulation compositional change that could contribute to the responses to perturbations are largely neglected, hampering the interpretability and reproducibility of the connections. In this work, we proposed a computational framework, Premnas, to estimate the abundance of undetermined subpopulations from L1000 profiles in CMap directly according to an ad hoc subpopulation representation learned from a well-normalized batch of single-cell RNA-seq datasets by the archetypal analysis. By recovering the information of subpopulation changes upon perturbation, the potentials of drug-resistant/susceptible subpopulations with CMap L1000 were further explored and examined. The proposed framework enables a new perspective to understand the connectivity among cellular signatures and expands the scope of the CMAP and other similar perturbation datasets limited by the bulk profiling technology.

Turning 'Cold' tumors 'Hot': immunotherapies in sarcoma

Immunotherapies have an established role in the management of several advanced malignancies. Their responses are largely dependent on the presence of PD-L1, microsatellite instability (MSI), and high tumor mutation burden. Sarcomas are heterogenous tumors which comprise over 100 subtypes. They are broadly considered immunologically inert or “cold”. Immunotherapy as monotherapy has shown interesting responses in a certain handful of subtypes, such as undifferentiated pleomorphic sarcoma, dedifferentiated and pleomorphic liposarcoma, and alveolar soft part sarcoma. However, the mechanisms of action of immunotherapy agents in several sarcoma subtypes remains unknown. Several sarcoma types such as leiomyosarcoma have been shown to have an immunosuppressive microenvironment. Early clinical studies suggest the emergence of B cell infiltration in sarcoma tumor tissues as well as the role of PD-1 and PD-L1 as biomarkers of response. Immunotherapy combinations with conventional chemotherapies, radiation therapies, tyrosine kinase inhibitors and oncolytic viruses are showing promise in turning these “cold” tumors “hot”. Several novel agents as well as repurposing therapies with the potential to enhance immunotherapy responses are undergoing pre-clinical and clinical studies in other tumor types. Herein we review current clinical studies which have explored the use of immunotherapeutic agents in the management of sarcomas and discuss the challenges and future directions.

Establishment and characterization of NCC-LMS2-C1-a novel patient-derived cancer cell line of leiomyosarcoma

Leiomyosarcoma (LMS) is a rare and aggressive mesenchymal malignancy, derived from smooth muscle cells or precursor mesenchymal stem cells for this tissue type. LMS has highly complex and unstable karyotypes, and the clinical outcomes in patients with LMS remain dismal as evidenced by the 5-year-survival of 64%. Novel therapeutic approaches are required to improve its clinical outcomes. Patient-derived cancer cell lines are indispensable as a tool to study the molecular mechanisms underlying clinical behaviors of tumor cells such as resistance to treatments, metastasis, and recurrence. However, only a limited number of LMS cell lines are publicly available, probably because of the rarity of patients with LMS, and a paucity of cell lines hinders the research on LMS. This study aimed to develop a patient-derived LMS cell line. We successfully established a cell line from the primary tumor tissue of a 90-year-old female patient with pleomorphic LMS, which we named NCC-LMS2-C1. NCC-LMS2-C1 cells were maintained as a monolayer culture for over 29 passages spanning 10 months. NCC-LMS2-C1 cells exhibited continuous growth, the ability to form spheroid, and invasion capability. We screened 213 anti-cancer drugs to find those that have anti-proliferation effects on NCC-LMS2-C1 cells, and identified a histone deacetylase inhibitor, romidepsin. In conclusion, we have established a novel LMS cell line, NCC-LMS2-C1, which will be a useful resource to study the mechanisms of LMS progression and perform high-throughput screening for anti-cancer drug discovery.

Recurrent broad ligament leiomyosarcoma with pancreatic and thigh metastasis: a case report

BACKGROUND

Leiomyosarcoma (LMS) is an uncommon mesenchymal neoplasm, which infrequently metastasizes to pancreas and thigh. Clinical presentation and imaging findings of metastatic broad ligament LMS are often nonspecific. Complete excision plays an important role in treatment of patients with localized LMS.

CASE PRESENTATION

Here, we report a case of a 33-year-old woman with recurrent broad ligament LMS metastasizing to pancreas and thigh. Previously, she was diagnosed with broad ligament LMS and underwent hysterectomy, bilateral salpingo-oophorectomy. The disease-free interval was 2.5 years until metastases were found. Computerized tomography (CT) of abdomen and thighs, magnetic resonance imaging (MRI) of thighs and whole-body 18-fluorodeoxyglucose positron emission tomography - computed tomography (PET-CT) performed, revealed pancreatic and thigh metastasis. Ultrasonography-guided biopsy and histological examinations confirmed LMS at both the sites. Pancreatic metastasis was completely resected first. Then the patient underwent surgical resection of thigh metastasis when both chemotherapy and radiotherapy failed. She recovered well and remained free of disease recurrence in the 2 years follow-up.

CONCLUSIONS

Though imaging lacks specificity, it is a valuable asset in assessing the burden of disease and characterizing lesions while histological examination with immunohistochemistry is helpful for the diagnosis of LMS. Complete surgical resection of all metastatic sites where-ever feasible should be strongly considered in a treated case of broad ligament LMS with a durable disease-free interval.

Genetic variants and copy number changes in soft tissue leiomyosarcoma detected by targeted amplicon sequencing

Aims

Leiomyosarcomas (LMSs) occur in various tissues and harbour potential for metastases. The genomic landscape of LMS is poorly understood. In an effort to improve understanding of the LMS genome, we analysed 11 LMSs of somatic soft tissue including matching tissue of normal phenotype.

Methods

DNA derived from microdissected tumour domains and matching normal tissue underwent amplicon sequencing of 409 tumour suppressors and oncogenes using the Ion Torrent Comprehensive Cancer Panel.

Results

Genomic changes were heterogeneous with few recurrent abnormalities detected. Coding variants were identified in genes involved in signal transduction, transcriptional regulation and DNA repair. There were variants in several genes related to angiogenesis and GPR124 variants (TEM5) were confirmed by immunohistochemical analysis of a LMS tissue microarray. Surprisingly, there were shared coding variants in tumour and corresponding normal tissue.

Conclusions

LMSs are a very heterogeneous population lacking recurrent somatic abnormalities. The presence of damaging mutations in normal tissue may reflect either a germline predisposition or field effect rather than tissue contamination. Hopeful therapeutic targets appear to be those related to AKT/MTOR pathway.

FGFR2 is overexpressed in myxoid liposarcoma and inhibition of FGFR signaling impairs tumor growth in vitro

Myxoid liposarcomas account for more than one third of liposarcomas and about 10% of all adult soft tissue sarcomas. The tumors are characterized by specific chromosomal translocations leading to the chimeric oncogenes FUS-DDIT3 or EWS1R-DDIT3. The encoded fusion proteins act as aberrant transcription factors. Therefore, we implemented comparative expression analyses using whole-genome microarrays in tumor and fat tissue samples. We aimed at identifying differentially expressed genes which may serve as diagnostic or prognostic biomarkers or as therapeutic targets. Microarray analyses revealed overexpression of FGFR2 and other members of the FGF/FGFR family. Overexpression of FGFR2 was validated by qPCR, immunohistochemistry and western blot analysis in primary tumor samples. Treatment of the myxoid liposarcoma cell lines MLS 402 and MLS 1765 with the FGFR inhibitors PD173074, TKI258 (dovitinib) and BGJ398 as well as specific siRNAs reduced cell proliferation, induced apoptosis and delayed cell migration. Combination of FGFR inhibitors with trabectedin further increased the effect. Our study demonstrates overexpression of FGFR2 and a functional role of FGFR signaling in myxoid liposarcoma. As FGFR inhibition showed effects on proliferation and cell migration and induced apoptosis in vitro, our data indicate the potential use of FGFR inhibitors as a targeted therapy for these tumors.

Increased Nicotinamide Phosphoribosyltransferase in Rhabdomyosarcomas and Leiomyosarcomas Compared to Skeletal and Smooth Muscle Tissue

Nicotinamide phosphoribosyltransferase (NAMPT) catalyzes the rate-limiting step in NAD synthesis and is up-regulated in several human malignancies, including breast, colon, prostate, thyroid, gastric, and several hematopoietic malignancies. In some malignancies, such as gastric, thyroid, and prostate carcinomas, higher NAMPT expression correlates with deeper tumor invasion, increased metastatic potential and chemotherapy resistance. We employed tissue microarray immunohistochemistry to examine NAMPT expression in benign skeletal and smooth muscle, leiomyomas, leiomyosarcomas (graded low-, intermediate-, and high-grade), and spindle, embryonal, pleomorphic, and alveolar rhabdomyosarcomas. We found low to intermediate NAMPT expression in benign tissue, leiomyomas, leiomyosarcomas (low- and intermediate-grades), and spindle cell rhabdomyosarcomas. In contrast, high-grade leiomyosarcomas and embryonal, alveolar, and pleomorphic rhabdomyosarcomas showed high NAMPT expression. Herein we show for the first time that NAMPT is overexpressed in certain sarcoma types and the level of NAMPT expression correlates with tumor behavior.

Recent advances in understanding and managing leiomyosarcomas

Leiomyosarcomas are malignant mesenchymal tumours that derive from the smooth muscle lineage. They are studied and frequently treated as if they are the same as other soft tissue sarcomas. Recent developments suggest that a different approach may be more appropriate. Their underlying genetic mechanisms remain unclear, and complex. Unbalanced karyotypic defects are the only shared features observed across different leiomyosarcoma subtypes. Unlike other soft tissue sarcomas, leiomyosarcomas are particularly sensitive to the combination of gemcitabine and docetaxel. Furthermore, treatment with trabectedin has shown a good efficacy in leiomyosarcomas, mainly in the form of chronic disease stabilisation.

Molecular diagnostics in soft tissue sarcomas and gastrointestinal stromal tumors

Soft tissue sarcomas are rare malignant heterogenous tumors of mesenchymal origin with over fifty subtypes. The use of hematoxylin and eosin stained sections (and immunohistochemistry) in the morphologic assessment of these tumors has been the bane of clinical diagnosis until recently. The last decade has witnessed considerable progress in the understanding and application of molecular techniques in refining the current understanding of soft tissue sarcomas and gastrointestinal stromal tumors beyond the limits of traditional approaches. Indeed, the identification of reciprocal chromosomal translocations and fusion genes in some subsets of sarcomas with potential implications in the pathogenesis, diagnosis and treatment has been revolutionary. The era of molecular targeted therapy presents a platform that continues to drive biomarker discovery and personalized medicine in soft tissue sarcomas and gastrointestinal stromal tumors. In this review, we highlight how the different molecular techniques have enhanced the diagnosis of these tumors with prognostic and therapeutic implications.

A genomic signature approach to rescue ΔF508-cystic fibrosis transmembrane conductance regulator biosynthesis and function

The most common cystic fibrosis (CF) mutation, ΔF508, causes protein misfolding, leading to proteosomal degradation. We recently showed that expression of miR-138 enhances CF transmembrane conductance regulator (CFTR) biogenesis and partially rescues ΔF508-CFTR function in CF airway epithelia. We hypothesized that a genomic signature approach can be used to identify new bioactive small molecules affecting ΔF508-CFTR rescue. The Connectivity Map was used to identify 27 small molecules with potential to restore ΔF508-CFTR function in airway epithelia. The molecules were screened in vitro for efficacy in improving ΔF508-CFTR trafficking, maturation, and chloride current. We identified four small molecules that partially restore ΔF508-CFTR function in primary CF airway epithelia. Of these, pyridostigmine showed cooperativity with corrector compound 18 in improving ΔF508-CFTR function. There are few CF therapies based on new molecular insights. Querying the Connectivity Map with relevant genomic signatures offers a method to identify new candidates for rescuing ΔF508-CFTR function.

Unbiased compound screening identifies unexpected drug sensitivities and novel treatment options for gastrointestinal stromal tumors

Most gastrointestinal stromal tumors (GIST) are caused by oncogenic KIT or platelet-derived growth factor receptor activation, and the small molecule kinase inhibitor imatinib mesylate is an effective first-line therapy for metastatic or unresectable GIST. However, complete remissions are rare and most patients ultimately develop resistance, mostly because of secondary mutations in the driver oncogenic kinase. Hence, there is a need for novel treatment options to delay failure of primary treatment and restore tumor control in patients who progress under therapy with targeted agents. Historic data suggest that GISTs do not respond to classical chemotherapy, but systematic unbiased screening has not been performed. In screening a compound library enriched for U.S. Food and Drug Administration (FDA)-approved chemotherapeutic agents (NCI Approved Oncology Drugs Set II), we discovered that GIST cells display high sensitivity to transcriptional inhibitors and topoisomerase II inhibitors. Mechanistically, these compounds exploited the cells' dependency on continuous KIT expression and/or intrinsic DNA damage response defects, explaining their activity in GIST. Mithramycin A, an indirect inhibitor of the SP1 transcription factor, and mitoxantrone, a topoisomerase II inhibitor, exerted significant antitumor effects in mouse xenograft models of human GIST. Moreover, these compounds were active in patient-derived imatinib-resistant primary GIST cells, achieving efficacy at clinically relevant concentrations. Taken together, our findings reveal that GIST cells have an unexpectedly high and specific sensitivity to certain types of FDA-approved chemotherapeutic agents, with immediate implications for encouraging their clinical exploration.

BRCA-Monet: a breast cancer specific drug treatment mode-of-action network for treatment effective prediction using large scale microarray database

BACKGROUND

Connectivity map (cMap) is a recent developed dataset and algorithm for uncovering and understanding the treatment effect of small molecules on different cancer cell lines. It is widely used but there are still remaining challenges for accurate predictions.

METHOD

Here, we propose BRCA-MoNet, a network of drug mode of action (MoA) specific to breast cancer, which is constructed based on the cMap dataset. A drug signature selection algorithm fitting the characteristic of cMap data, a quality control scheme as well as a novel query algorithm based on BRCA-MoNet are developed for more effective prediction of drug effects.

RESULT

BRCA-MoNet was applied to three independent data sets obtained from the GEO database: Estrodial treated MCF7 cell line, BMS-754807 treated MCF7 cell line, and a breast cancer patient microarray dataset. In the first case, BRCA-MoNet could identify drug MoAs likely to share same and reverse treatment effect. In the second case, the result demonstrated the potential of BRCA-MoNet to reposition drugs and predict treatment effects for drugs not in cMap data. In the third case, a possible procedure of personalized drug selection is showcased.

CONCLUSIONS

The results clearly demonstrated that the proposed BRCA-MoNet approach can provide increased prediction power to cMap and thus will be useful for identification of new therapeutic candidates.

Leiomyosarcoma: Principles of management

The term soft-tissue sarcomas (STS) embraces more than 50 different sub-types that are often associated with poor prognosis. Only a very limited number of agents are active against STS. Doxorubicin and ifosfamide are widely accepted as the most effective compounds. However, their low response rates and poor impact on the overall survival of the patients illustrate the need for new treatment options. Among them, leiomyosarcomas are one of the most frequently occurring subtypes. In spite of the relatively high incidence of leiomyosarcomas, the overall effectiveness of the currently available systemic treatments is still poor. The heterogeneity of its biological origin, clinical behavior and responsiveness to chemotherapy, together with the scarcity of successful clinical trials, makes the treatment of leiomyosarcoma especially challenging. In addition, the evidence-based treatment for leiomyosarcoma comes from trials in which, in the majority of cases, no distinctions have been made among the different STS sub-types. As a result, every therapeutic decision should be made on an individual basis in collaboration with the patient. The results of new specific histology-designed clinical trials should aid decision making in this complex field.