A Single-Arm Phase II Trial of Sitravatinib in Advanced Well-Differentiated/Dedifferentiated Liposarcoma.

PURPOSE: To evaluate sitravatinib, an inhibitor of multiple receptor tyrosine kinases (RTK), for the treatment of well-differentiated/dedifferentiated liposarcoma (WD/DD LPS). PATIENTS AND METHODS: This multicenter, open-label, Phase II trial enrolled patients with advanced WD/DD LPS who had received at least one prior systemic regimen and had progression within 12 weeks of enrollment. Patients received sitravatinib 150 mg (later amended to 120 mg) orally daily. A Simon two-stage design was used to evaluate for an improvement in the primary endpoint, progression-free rate at 12 weeks (PFR12), from 20% to 40%. Secondary endpoints included antitumor activity and safety. A subset of patients underwent paired biopsies analyzed using reverse-phase protein array. RESULTS: Twenty-nine patients enrolled. Median age was 62 years and 31% had received 3 or more prior lines. Most patients (93%) had DDLPS or mixed WD/DD LPS. Overall, 12 of 29 patients (41%) were alive and progression-free at 12 weeks and the study met the primary endpoint. There were no confirmed responses. Median progression-free survival was 11.7 weeks [95% confidence interval (CI): 5.9-35.9] and median overall survival was 31.7 weeks (95% CI: 18.1-90.1). The most common treatment-related adverse events were diarrhea (59%), hypertension (52%), hoarseness (41%), mucositis (31%), and nausea (31%). Baseline expression of phospho-RTKs was not significantly different between patients with and without clinical benefit from sitravatinib, but the number of samples was small. CONCLUSIONS: Sitravatinib provided a PFR12 of 41% and meaningful disease control in a subset of patients with advanced, progressive WD/DD LPS.

Homologous recombination repair deficiency as a therapeutic target in sarcoma.

Sarcoma is a rare cancer arising from soft tissue and bone and consists of more than 50 distinct subtypes. There is an increasing emphasis on understanding the cancer biology of individual sarcoma subtypes to inform the development of targeted and immunotherapy-based treatment approaches. While some advances have recently been made in this respect, most sarcomas are still treated with chemotherapy. The homologous recombination DNA repair pathway plays an important role in repairing highly cytotoxic double-stranded DNA breaks and restarting stalled replication forks. A subset of human cancers, notably ovarian, breast, prostate, and pancreatic cancers, harbor defects in components of the homologous recombination repair pathway, such as mutation or loss of BRCA1/2, and are sensitive to treatments which induce double stranded DNA breaks or replication fork arrest, including oral small molecule poly-ADP-ribose polymerase (PARP) inhibitors. Our understanding of DNA repair defects in sarcoma remains at an early stage. Recently, uterine leiomyosarcoma was identified as a sarcoma subtype with characteristic defects in the homologous recombination repair pathway and frequent BRCA2 loss. Preclinical data, presented here, demonstrates marked activity for the PARP inhibitor olaparib in combination with the alkylating agent temozolomide in leiomyosarcoma models. Ongoing research promises to identify other sarcomas with DNA repair defects and may offer a new opportunity for the targeted treatment of this rare, aggressive cancer.

A Novel Role of Chromodomain Protein CBX8 in DNA Damage Response.

Induction of DNA damage induces a dynamic repair process involving DNA repair factors and epigenetic regulators. Chromatin alterations must occur for DNA repair factors to gain access to DNA lesions and restore original chromatin configuration to preserve the gene expression profile. We characterize the novel role of CBX8, a chromodomain-containing protein with established roles in epigenetic regulation in DNA damage response. CBX8 protein rapidly accumulates at the sites of DNA damage within 30 s and progresses to accumulate until 4 min before gradually dispersing back to its predamage distribution by 15 min. CBX8 recruitment to the sites of DNA damage is dependent upon PARP1 activation and not dependent on ATM activation. CBX8 biochemically interacts with TRIM33, and its recruitment to DNA damage is also dependent on the presence of TRIM33. Knockdown of CBX8 using siRNA significantly reduces the efficiency of both homologous and the other non-homologous recombination, as well as increases sensitivity of cells to ionizing radiation. These findings demonstrate that CBX8 functions in the PARP-dependent DNA damage response partly through interaction with TRIM33 and is required for efficient DNA repair.

Tripartite Motif-containing 33 (TRIM33) protein functions in the poly(ADP-ribose) polymerase (PARP)-dependent DNA damage response through interaction with Amplified in Liver Cancer 1 (ALC1) protein.

Activation of poly(ADP-ribose) polymerase (PARP) near sites of DNA breaks facilitates recruitment of DNA repair proteins and promotes chromatin relaxation in part through the action of chromatin-remodeling enzyme Amplified in Liver Cancer 1 (ALC1). Through proteomic analysis we find that ALC1 interacts after DNA damage with Tripartite Motif-containing 33 (TRIM33), a multifunctional protein implicated in transcriptional regulation, TGF-ß signaling, and tumorigenesis. We demonstrate that TRIM33 is dynamically recruited to DNA damage sites in a PARP1- and ALC1-dependent manner. TRIM33-deficient cells show enhanced sensitivity to DNA damage and prolonged retention of ALC1 at sites of DNA breaks. Conversely, overexpression of TRIM33 alleviates the DNA repair defects conferred by ALC1 overexpression. Thus, TRIM33 plays a role in PARP-dependent DNA damage response and regulates ALC1 activity by promoting its timely removal from sites of DNA damage.

BMI1 is recruited to DNA breaks and contributes to DNA damage-induced H2A ubiquitination and repair.

DNA damage activates signaling pathways that lead to modification of local chromatin and recruitment of DNA repair proteins. Multiple DNA repair proteins having ubiquitin ligase activity are recruited to sites of DNA damage, where they ubiquitinate histones and other substrates. This DNA damage-induced histone ubiquitination is thought to play a critical role in mediating the DNA damage response. We now report that the polycomb protein BMI1 is rapidly recruited to sites of DNA damage, where it persists for more than 8 h. The sustained localization of BMI1 to damage sites is dependent on intact ATM and ATR and requires H2AX phosphorylation and recruitment of RNF8. BMI1 is required for DNA damage-induced ubiquitination of histone H2A at lysine 119. Loss of BMI1 leads to impaired repair of DNA double-strand breaks by homologous recombination and the accumulation of cells in G(2)/M. These data support a crucial role for BMI1 in the cellular response to DNA damage.

Identifying mRNA targets of microRNA dysregulated in cancer: with application to clear cell Renal Cell Carcinoma.

BACKGROUND: MicroRNA regulate mRNA levels in a tissue specific way, either by inducing degradation of the transcript or by inhibiting translation or transcription. Putative mRNA targets of microRNA identified from seed sequence matches are available in many databases. However, such matches have a high false positive rate and cannot identify tissue specificity of regulation. RESULTS: We describe a simple method to identify direct mRNA targets of microRNA dysregulated in cancers from expression level measurements in patient matched tumor/normal samples. The word "direct" is used here in a strict sense to: a) represent mRNA which have an exact seed sequence match to the microRNA in their 3'UTR, b) the seed sequence match is strictly conserved across mouse, human, rat and dog genomes, c) the mRNA and microRNA expression levels can distinguish tumor from normal with high significance and d) the microRNA/mRNA expression levels are strongly and significantly anti-correlated in tumor and/or normal samples. We apply and validate the method using clear cell Renal Cell Carcinoma (ccRCC) and matched normal kidney samples, limiting our analysis to mRNA targets which undergo degradation of the mRNA transcript because of a perfect seed sequence match. Dysregulated microRNA and mRNA are first identified by comparing their expression levels in tumor vs normal samples. Putative dysregulated microRNA/mRNA pairs are identified from these using seed sequence matches, requiring that the seed sequence be conserved in human/dog/rat/mouse genomes. These are further pruned by requiring a strong anti-correlation signature in tumor and/or normal samples. The method revealed many new regulations in ccRCC. For instance, loss of miR-149, miR-200c and mir-141 causes gain of function of oncogenes (KCNMA1, LOX), VEGFA and SEMA6A respectively and increased levels of miR-142-3p, miR-185, mir-34a, miR-224, miR-21 cause loss of function of tumor suppressors LRRC2, PTPN13, SFRP1, ERBB4, and (SLC12A1, TCF21) respectively. We also found strong anti-correlation between VEGFA and the miR-200 family of microRNA: miR-200a*, 200b, 200c and miR-141. Several identified microRNA/mRNA pairs were validated on an independent set of matched ccRCC/normal samples. The regulation of SEMA6A by miR-141 was verified by a transfection assay. CONCLUSIONS: We describe a simple and reliable method to identify direct gene targets of microRNA in any cancer. The constraints we impose (strong dysregulation signature for microRNA and mRNA levels between tumor/normal samples, evolutionary conservation of seed sequence and strong anti-correlation of expression levels) remove spurious matches and identify a subset of robust, tissue specific, functional mRNA targets of dysregulated microRNA.

Triple-negative breast cancers and the human mammary epithelial cell hierarchy.

Triple-negative breast cancers (TNBCs) are a diverse set of aggressive breast cancers that lack expression of estrogen and progesterone receptors, and lack HER2 amplification. Gene expression profiling has revealed distinct subsets of TNBCs, each characterized by unique patterns of gene expression and genomic changes. Comparative analysis of gene expression profiles also suggests that the different subclasses of TNBCs may arise from specific sets of mammary progenitor cell populations. In this article, recent data regarding characterization of a human mammary stem cell hierarchy and its relationship to the pathogenesis of subsets of triple-negative breast cancers will be reviewed.

Changes in the regulation of heat shock gene expression in neuronal cell differentiation.

Neuronal differentiation of the NG108-15 neuroblastoma-glioma hybrid cells is accompanied by a marked attenuation in the heat shock induction of the Hsp70-firefly luciferase reporter gene activity. Analysis of the amount and activation of heat shock factor 1, induction of mRNA(hsp), and the synthesis and accumulation of heat shock proteins (HSPs) in the undifferentiated and differentiated cells suggest a transcriptional mechanism for this attenuation. Concomitant with a decreased induction of the 72-kDa Hsp70 protein in the differentiated cells, there is an increased abundance of the constitutive 73-kDa Hsc70, a protein known to function in vesicle trafficking. Assessment of sensitivity of the undifferentiated and differentiated cells against stress-induced cell death reveals a significantly greater vulnerability of the differentiated cells toward the cytotoxic effects of arsenite and glutamate/glycine. This study shows that changes in regulation of the HSP and HSC proteins are components of the neuronal cell differentiation program and that the attenuated induction of HSPs likely contributes to neuronal vulnerability whereas the increased expression of Hsc70 likely has a role in neural-specific functions.

Neural differentiation and the attenuated heat shock response.

Differentiation of neural progenitor cells of neuroblastoma, pheochromocytoma, and surrogate stem cell lineages from a state resembling stem cells to a state resembling neurons is accompanied by a marked attenuation in induction of the heat shock protein 70 promoter driven-luciferase reporter gene, and induction of the reporter gene in primary embryonic neurons from hippocampus, cortex, and spinal cord is lower still when compared to the differentiated cells. Neural specificity of this phenotype is demonstrated by a negative correlation of hsp70-reporter gene expression and neurite extension under various experimental conditions. Analysis of biochemical events involved in induction of the heat shock response (HSR) reveal a blunted activation of HSF1 DNA-binding activity, and decreased induction of the mRNA(hsp70) and the 72 kDa HSP70 protein. Immunocytochemical staining for HSP70 demonstrates a cytoplasmic staining pattern; heat shock greatly increased the HSP70 staining intensity in the undifferentiated cells and less so in the differentiated cells. Vulnerability of the differentiated cells towards the oxidizer, arsenite, and the excitotoxic glutamate/glycine is demonstrated by the dose-dependent cytotoxic effects of these agents on cell viability and activation of caspase 3/7. Importantly, conditioning heat shock as well as increased expression of HSP70 by gene transfer conferred protection against such cytotoxicity. Together, our results show that neural differentiation is associated with a decreased induction of the heat shock response and an increased vulnerability to stress induced pathologies and death.