Discovery of novel candidates for anti- liposarcoma therapies by medium-scale high- throughput drug screening

Discovery of novel candidates for anti-liposarcoma therapies by medium-scale high-throughput drug screening

Abstract

Sarcomas are a heterogeneous group of mesenchymal orphan cancers and new treatment alternatives beyond traditional chemotherapeutic regimes are much needed. So far, tumor mutation analysis has not led to significant treatment advances, and we have attempted to bypass this limitation by performing direct drug testing of a library of three hundred fifty-three anti-cancer compounds that are either FDA-approved, in clinical trial, or in advanced stages of preclinical development on a panel of thirteen liposarcoma cell lines. We identified and validated six drugs, targeting different mechanisms and with good efficiency across the cell lines: MLN two two three eight - a proteasome inhibitor, GSK two one two six four five eight - a PI three K/mTOR inhibitor, JNJ two six four eight one five eight five - a histone deacetylase inhibitor, triptolide - a multi-target drug, YM one fifty-five - a survivin inhibitor, and APO eight sixty-six (FK eight sixty-six) - a nicotinamide phosphoribosyl transferase inhibitor. GR fifty's for those drugs were mostly in the nanomolar range, and in many cases below ten nanomolars. These drugs had long-lasting effect upon drug withdrawal, limited toxicity to normal cells and good efficacy also against tumor explants. Finally, we identified potential genomic biomarkers of their efficacy. Being approved or in clinical trials, these drugs are promising candidates for liposarcoma treatment.

One. Introduction

Sarcomas make up about one percent of all cancers and are divided into bone and soft tissue sarcomas. The latter group, accounting for eighty-seven percent of all sarcomas, comprises more than fifty histological subtypes, and this diversity represents a significant diagnostic and therapeutic challenge. According to statistics from the National Cancer Institute about fifty percent of patients with soft tissue sarcoma die within five years of diagnosis. Prognosis depends on the tumor subtype, but also tumor location - those in the abdomen are more difficult to completely eradicate. Due to their rarity, diversity and the limited biological mechanistic understanding, there is only moderate commercial interest to develop sarcoma-specific therapies.

Liposarcomas are the largest subtype of soft tissue sarcoma, accounting for approximately twenty percent of the cases. They resemble adipose tissue, with four principal histological subtypes comprising well-differentiated/dedifferentiated, myxoid/round celled, and pleomorphic liposarcomas. Though liposarcomas may have characteristic karyotypic aberrations which help in diagnosis, those cannot yet be therapeutically exploited.

Current first-line treatment for liposarcoma is surgery, alone or in combination with radiotherapy, while chemotherapy is the option for patients with high risk of recurrence or with widespread disease. Chemotherapy for soft tissue sarcoma generally uses a combination of several conventional chemotherapeutic agents, often ifosfamide, dacarbazine and doxorubicin. Doxorubicin monotherapy is the main first-line treatment, while second-line standards are not set. Two novel drugs have been approved by FDA for the treatment of liposarcomas, although with moderate efficacy, the microtubule inhibitor eribulin and the DNA alkylating drug trabectedin.

Personalized medicine focuses on the correlation of drug responses with molecular features which could be used as biomarkers for patient stratification. In case of liposarcomas, several studies on their genome landscapes have been done, but mainly two characteristic molecular markers are known, amplification of the twelve q thirteen to fifteen region (including MDM two, FRS two and usually also CDK four), which is detected in almost all well-differentiated/dedifferentiated liposarcoma or dedifferentiated liposarcoma, and the fusion oncogenes FUS-DDIT three or EWSR one-DDIT three in myxoid and round cell liposarcoma. Those markers are used mainly for diagnosis, although trials on targeting MDM two and CDK four have been performed with limited success, and further clinical trials with such inhibitors are underway. A systematic effort to find molecular drivers of soft tissue sarcoma was done by Barretina and colleagues, who tried to identify novel subtype-specific genomic alterations in, among others, ninety-five liposarcoma patient samples. They identified mutations in PIK three C A in myxoid/round cell liposarcoma and T P fifty-three and N F one in pleomorphic liposarcoma. Although those mutations might help to identify tumors that might be responsive to PI three K or mTOR inhibitors, they were only present in some patients. Moreover, a clinical trial with a dual PI three K/mTOR inhibitor has shown no association of responses with PIK three C A mutations. More recently, The Cancer Genome Atlas soft tissue sarcoma study confirmed low mutation burden in dedifferentiated liposarcoma and identified JUN amplification as a potential marker of poor survival in a subset of samples. They also showed recurrent deletions of ATRX and CDKN two A in a minority of samples but pointed out the importance of overall methylation status as a biomarker in dedifferentiated liposarcoma.

Drug sensitivity screens provide a different, phenotype-based approach to identification of new anti-cancer therapies. The National Cancer Institute sixty, Cancer Cell Line Encyclopedia and Genomics of Drug Sensitivity in Cancer projects have made collections of data from approximately one thousand cell lines. Those huge, collaborative efforts report not only sensitivities of those cell lines to multiple drugs, but also correlate drug sensitivity to genomic features. Unfortunately, none of those databases comprise liposarcomas. Even a sarcoma-specific drug screen of sixty-three sarcoma cell lines contained just two liposarcoma cell lines. Just recently, the first multidrug screening of three myxoid liposarcoma cell lines was published, showing the survivin inhibitor YM one fifty-five to limit tumor growth.

In this work we have used medium-scale high-throughput drug sensitivity screening on a panel of liposarcoma cell lines to identify compounds that broadly target liposarcoma. This approach identified several candidate drugs that are presently not used for sarcoma treatment, but which in vitro were generally more efficient than the currently used anti-sarcoma chemotherapeutics in the tested concentration ranges.