Enhancing standard of care chemotherapy efficacy using DNA-dependent protein kinase (DNA-PK) inhibition in preclinical models of Ewing sarcoma

Disruption of DNA damage repair via impaired homologous recombination is characteristic of Ewing sarcoma (EWS) cells. We hypothesize that this disruption results in increased reliance on non-homologous end joining (NHEJ) to repair DNA damage. In this study, we investigated if pharmacological inhibition of the enzyme responsible for NHEJ, the DNA-PK holoenzyme, alters the response of EWS cells to genotoxic standard of care chemotherapy. We used analyses of cell viability and proliferation to investigate the effects of clinical DNA-PK inhibitors (DNA-PKi) in combination with six therapeutic or experimental agents for EWS. We performed calculations of synergy using the Loewe Additivity Model. Immunoblotting evaluated treatment effects on DNA-PK, DNA damage, and apoptosis. Flow cytometric analyses evaluated effects on cell cycle and fate. We used orthotopic xenograft models to interrogate tolerability, drug mechanism, and efficacy in vivo. DNA-PKi demonstrated on-target activity, reducing phosphorylated DNA-PK levels in EWS cells. DNA-PKi sensitized EWS cell lines to agents that function as topoisomerase 2 (TOP2) poisons and enhanced the DNA damage induced by TOP2 poisons. Nanomolar concentrations of single agent TOP2 poisons induced G2M arrest and little apoptotic response, while adding DNA-PKi mediated apoptosis. In vivo, the combination of AZD-7648 and etoposide had limited tolerability but resulted in enhanced DNA damage, apoptosis, and EWS tumor shrinkage. The combination of DNA-PKi with standard of care TOP2 poisons in EWS models is synergistic, enhances DNA damage and cell death, and may form the basis of a promising future therapeutic strategy for EWS.

DNAJC9 prevents CENP-A mislocalization and chromosomal instability by maintaining the fidelity of histone supply chains

The centromeric histone H3 variant CENP-A is overexpressed in many cancers. The mislocalization of CENP-A to noncentromeric regions contributes to chromosomal instability (CIN), a hallmark of cancer. However, pathways that promote or prevent CENP-A mislocalization remain poorly defined. Here, we performed a genome-wide RNAi screen for regulators of CENP-A localization which identified DNAJC9, a J-domain protein implicated in histone H3-H4 protein folding, as a factor restricting CENP-A mislocalization. Cells lacking DNAJC9 exhibit mislocalization of CENP-A throughout the genome, and CIN phenotypes. Global interactome analysis showed that DNAJC9 depletion promotes the interaction of CENP-A with the DNA-replication-associated histone chaperone MCM2. CENP-A mislocalization upon DNAJC9 depletion was dependent on MCM2, defining MCM2 as a driver of CENP-A deposition at ectopic sites when H3-H4 supply chains are disrupted. Cells depleted for histone H3.3, also exhibit CENP-A mislocalization. In summary, we have defined novel factors that prevent mislocalization of CENP-A, and demonstrated that the integrity of H3-H4 supply chains regulated by histone chaperones such as DNAJC9 restrict CENP-A mislocalization and CIN.

ETS1, a target gene of the EWSR1::FLI1 fusion oncoprotein, regulates the expression of the focal adhesion protein TENSIN3

The mechanistic basis for the metastasis of Ewing sarcomas remains poorly understood, as these tumors harbor few mutations beyond the chromosomal translocation that initiates the disease. Instead, the epigenome of Ewing sarcoma (EWS) cells reflects the regulatory state of genes associated with the DNA binding activity of the fusion oncoproteins EWSR1::FLI1 or EWSR1::ERG. In this study, we examined the EWSR1::FLI1/ERG's repression of transcription factor genes, concentrating on those that exhibit a broader range of expression in tumors than in EWS cell lines. Focusing on one of these target genes, ETS1, we detected EWSR1::FLI1 binding and an H3K27me3 repressive mark at this locus. Depletion of EWSR1::FLI1 results in ETS1's binding of promoter regions, substantially altering the transcriptome of EWS cells, including the upregulation of the gene encoding TENSIN3 (TNS3), a focal adhesion protein. EWS cell lines expressing ETS1 (CRISPRa) exhibited increased TNS3 expression and enhanced movement compared to control cells. Visualization of control EWS cells showed a distributed vinculin signal and a network-like organization of F-actin; in contrast, ETS1-activated EWS cells showed an accumulation of vinculin and F-actin towards the plasma membrane. Interestingly, the phenotype of ETS1-activated EWS cell lines depleted of TNS3 resembled the phenotype of the control cells. Critically, these findings have clinical relevance as TNS3 expression in EWS tumors positively correlates with that of ETS1. Implications: ETS1's transcriptional regulation of the gene encoding the focal adhesion protein TENSIN3 in Ewing sarcoma cells promotes cell movement, a critical step in the evolution of metastasis.

Endogenous EWSR1 Exists in Two Visual Modalities That Reflect Its Associations with Nucleic Acids and Concentration at Sites of Active Transcription

EWSR1 is a member of the FET family of nucleic acid binding proteins that includes FUS and TAF15. Here, we report the systematic analysis of endogenous EWSR1's cellular organization in human cells. We demonstrate that EWSR1, which contains low complexity and nucleic acid binding domains, is present in cells in faster and slower-recovering fractions, indicative of a protein undergoing both rapid exchange and longer-term interactions. The employment of complementary high-resolution imaging approaches shows EWSR1 exists in two visual modalities, a distributed state which is present throughout the nucleoplasm, and a concentrated state consistent with the formation of foci. Both EWSR1 visual modalities localize with nascent RNA. EWSR1 foci concentrate in regions of euchromatin, adjacent to protein markers of transcriptional activation, and significantly colocalize with phosphorylated RNA polymerase II. Our results contribute to bridging the gap between our understanding of the biophysical and biochemical properties of FET proteins, including EWSR1, their functions as transcriptional regulators, and the participation of these proteins in tumorigenesis and neurodegenerative disease.

ETS1, a target gene of the EWSR1::FLI1 fusion oncoprotein, regulates the expression of the focal adhesion protein TENSIN3

The mechanistic basis for the metastasis of Ewing sarcomas remains poorly understood, as these tumors harbor few mutations beyond the chromosomal translocation that initiates the disease. Instead, the epigenome of Ewing sarcoma (EWS) cells reflects the regulatory state of genes associated with the DNA binding activity of the fusion oncoproteins EWSR1::FLI1 or EWSR1::ERG. In this study, we examined the EWSR1::FLI1/ERG's repression of transcription factor genes, concentrating on those that exhibit a broader range of expression in tumors than in EWS cell lines. Focusing on one of these target genes, ETS1, we detected EWSR1::FLI1 binding and an H3K27me3 repressive mark at this locus. Depletion of EWSR1::FLI1 results in ETS1's binding of promoter regions, substantially altering the transcriptome of EWS cells, including the upregulation of the gene encoding TENSIN3 (TNS3), a focal adhesion protein. EWS cell lines expressing ETS1 (CRISPRa) exhibited increased TNS3 expression and enhanced movement compared to control cells. The cytoskeleton of control cells and ETS1-activated EWS cell lines also differed. Specifically, control cells exhibited a distributed vinculin signal and a network-like organization of F-actin. In contrast, ETS1-activated EWS cells showed an accumulation of vinculin and F-actin towards the plasma membrane. Interestingly, the phenotype of ETS1-activated EWS cell lines depleted of TNS3 resembled the phenotype of the control cells. Critically, these findings have clinical relevance as TNS3 expression in EWS tumors positively correlates with that of ETS1.

The HNRNPF/H RNA binding proteins and disease

The members of the HNRNPF/H family of heterogeneous nuclear RNA proteins-HNRNPF, HNRNPH1, HNRNPH2, HNRNPH3, and GRSF1, are critical regulators of RNA maturation. Documented functions of these proteins include regulating splicing, particularly alternative splicing, 5' capping and 3' polyadenylation of RNAs, and RNA export. The assignment of these proteins to the HNRNPF/H protein family members relates to differences in the amino acid composition of their RNA recognition motifs, which differ from those of other RNA binding proteins (RBPs). HNRNPF/H proteins typically bind RNA sequences enriched with guanine (G) residues, including sequences that, in the presence of a cation, have the potential to form higher-order G-quadruplex structures. The need to further investigate members of the HNRNPF/H family of RBPs has intensified with the recent descriptions of their involvement in several disease states, including the pediatric tumor Ewing sarcoma and the hematological malignancy mantle cell lymphoma; newly described groups of developmental syndromes; and neuronal-related disorders, including addictive behavior. Here, to foster the study of the HNRNPF/H family of RBPs, we discuss features of the genes encoding these proteins, their structures and functions, and emerging contributions to disease. This article is categorized under: RNA in Disease and Development > RNA in Disease RNA Processing > Splicing Regulation/Alternative Splicing RNA Interactions with Proteins and Other Molecules > Protein-RNA Interactions: Functional Implications.

EWSR1's visual modalities are defined by its association with nucleic acids and RNA polymerase II

We report systematic analysis of endogenous EWSR1's cellular organization. We demonstrate that EWSR1, which contains low complexity and nucleic acid binding domains, is present in cells in faster and slower-recovering fractions, indicative of a protein undergoing both rapid exchange and longer-term interactions. The employment of complementary high-resolution imaging approaches shows EWSR1 exists in in two visual modalities, a distributed state which is present throughout the nucleoplasm, and a concentrated state consistent with the formation of foci. Both EWSR1 visual modalities localize with nascent RNA. EWSR1 foci concentrate in regions of euchromatin, adjacent to protein markers of transcriptional activation, and significantly colocalize with phosphorylated RNA polymerase II. Interestingly, EWSR1 and FUS, another FET protein, exhibit distinct spatial organizations. Our results contribute to bridging the gap between our understanding of the biophysical and biochemical properties of FET proteins, including EWSR1, their functions as transcriptional regulators, and the participation of these proteins in tumorigenesis and neurodegenerative disease.

Histone H3/H4 chaperone CHAF1B prevents the mislocalization of CENP-A for chromosomal stability

Restricting the localization of the evolutionarily conserved centromeric histone H3 variant CENP-A to centromeres prevents chromosomal instability (CIN). The mislocalization of CENP-A to non-centromeric regions contributes to CIN in yeasts, flies, and human cells. Even though overexpression and mislocalization of CENP-A have been reported in cancers the mechanisms responsible for its mislocalization remain poorly understood. Here, we used an imaging-based high-throughput RNAi screen to identify factors that prevent mislocalization of overexpressed YFP-tagged CENP-A (YFP-CENP-A) in HeLa cells. Amongst the top five lead candidates of the screen that showed increased nuclear YFP-CENP-A fluorescence were depletions of histone chaperones (CHAF1B/p60 and CHAF1A/p150). Follow-up validation and characterization experiments showed that CHAF1B-depleted cells exhibit CENP-A mislocalization, CIN phenotypes, and increased enrichment of CENP-A in the chromatin fraction. The depletion of DAXX, a histone H3.3 chaperone, suppressed CENP-A mislocalization and CIN in CHAF1B-depleted cells. We propose that in CHAF1B-depleted cells, DAXX promotes mislocalization of the overexpressed CENP-A to non-centromeric regions, resulting in CIN. In summary, we have identified regulators of CENP-A localization and defined a role for CHAF1B in preventing DAXX-dependent CENP-A mislocalization and CIN.

Abstract B012: Visualization of EWSR1’s colocalization with phosphorylated RNA-Polymerase II reveals its concentration at a subset of active regions of transcription in ewing sarcoma cells

EWSR1, a member of the FET protein family, contains low complexity and nucleic acid binding domains and functions in transcription regulation and RNA metabolism. Recent biochemical and EWSR1-depletion studies demonstrated that EWSR1 regulates critical phosphorylation events that control basal transcription. In Ewing sarcoma (EWS) cells, the interaction of EWSR1 and the fusion oncoprotein EWS-FLI1 results in EWSR1 no longer functioning as an effective regulator of transcription, which following DNA damage, enhances R-loop formation. To further elucidate EWSR1’s function in EWS and its contribution to EWS-FLI1’s deregulation of gene expression, we have generated reporter systems to visualize and quantify its endogenous expression within EWS cells. We used CRISPR-Cas9 and sgRNAs targeting sequences at the 5’ end of the first exon of EWSR1 to insert a fluorescent mNeonGreen (mNG) reporter gene into the EWSR1 loci of A673 or TC-32 EWS cell lines. We employed sequencing and RNAi-based analysis to identify and validate successfully modified clones. All modified clones harbored insertions into the unrearranged EWSR1 allele. We then employed super-resolution confocal microscopy to assess EWSR1’s localization in EWS cells. Analysis of modified EWS-cells showed mNG-EWSR1 forms puncta, restricted to the nucleoplasm, consistent with a nuclear protein in an active state. A subset of puncta exhibits a high density (HD) mNG-EWSR1 signal, defined by fluorescence at least twice the background signal. Our results show minimal colocalization of mNG-EWSR1 (total or HD) and a marker of chromatin accessibility, H3K27Ac. A small percentage (~5%) of total Ser5-phosphorylated RNA-pol II (pS5-RP-II), a marker of transcription initiation, colocalizes with total mNG-EWSR1, but critically the HD mNG-EWSR1 puncta all colocalize with pS5-RP-II. About 20% of total Ser2-phosphorylated RNA-pol II (pS2-RP-II), a marker of transcription elongation colocalizes with total mNG-EWSR1. As observed for pS5-RP-II, 100% of HD-mNG-EWSR1 puncta colocalize with pS2-RP-II. Finally, when we examined nuclear speckle structures (SC35/SRSF2 >200 µm), we observed a 20% overlap in their signals. We have seen comparable results using the mNG-EWSR1 expressing A673 cells. These findings demonstrate image-based quantification of endogenous EWSR1’s colocalization with RNA-polymerase II within EWS cells. Overall, EWSR1 colocalizes with about 20% of RNA-pol II in a state consistent with active transcription, and over 90% of high-density EWSR1 colocalizes with phosphorylated RNA pol II. Ongoing studies will assess changes in the distribution of EWSR1’s interactions with different proteins following inhibition of RNA-pol II phosphorylation, alterations in EWS-FLI1 expression, or the disruption of low complexity domain interactions. We anticipate findings from these studies will offer critical insights into the functional interactions that EWSR1 contributes to regulating gene expression in EWS cells.

Citation Format: Natasha J. Caplen, Soumya Sundara Rajan, Vernon Ebegboni, Tamara L. Jones, Michael J. Kruhlak, Jan Wisniewski, Patricio Pichling, Katelyn R. Ludwig, Javed Khan, Raj Chari. Visualization of EWSR1’s colocalization with phosphorylated RNA-Polymerase II reveals its concentration at a subset of active regions of transcription in ewing sarcoma cells [abstract]. In: Proceedings of the AACR Special Conference: Sarcomas; 2022 May 9-12; Montreal, QC, Canada. Philadelphia (PA): AACR; Clin Cancer Res 2022;28(18_Suppl):Abstract nr B012.

HNRNPH1 destabilizes the G-quadruplex structures formed by G-rich RNA sequences that regulate the alternative splicing of an oncogenic fusion transcript

In the presence of physiological monovalent cations, thousands of RNA G-rich sequences can form parallel G-quadruplexes (G4s) unless RNA-binding proteins inhibit, destabilize, or resolve the formation of such secondary RNA structures. Here, we have used a disease-relevant model system to investigate the biophysical properties of the RNA-binding protein HNRNPH1's interaction with G-rich sequences. We demonstrate the importance of two EWSR1-exon 8 G-rich regions in mediating the exclusion of this exon from the oncogenic EWS-FLI1 transcripts expressed in a subset of Ewing sarcomas, using complementary analysis of tumor data, long-read sequencing, and minigene studies. We determined that HNRNPH1 binds the EWSR1-exon 8 G-rich sequences with low nM affinities irrespective of whether in a non-G4 or G4 state but exhibits different kinetics depending on RNA structure. Specifically, HNRNPH1 associates and dissociates from G4-folded RNA faster than the identical sequences in a non-G4 state. Importantly, we demonstrate using gel shift and spectroscopic assays that HNRNPH1, particularly the qRRM1-qRRM2 domains, destabilizes the G4s formed by the EWSR1-exon 8 G-rich sequences in a non-catalytic fashion. Our results indicate that HNRNPH1's binding of G-rich sequences favors the accumulation of RNA in a non-G4 state and that this contributes to its regulation of RNA processing.

Cancer biology functional genomics: From small RNAs to big dreams

The year 2021 marks the 20th anniversary of the first publications reporting the discovery of the gene silencing mechanism, RNA interference (RNAi) in mammalian cells. Along with the many studies that delineated the proteins and substrates that form the RNAi pathway, this finding changed our understanding of the posttranscriptional regulation of mammalian gene expression. Furthermore, the development of methods that exploited the RNAi pathway began the technological revolution that eventually enabled the interrogation of mammalian gene function-from a single gene to the whole genome-in only a few days. The needs of the cancer research community have driven much of this progress. In this perspective, we highlight milestones in the development and application of RNAi-based methods to study carcinogenesis. We discuss how RNAi-based functional genetic analysis of exemplar tumor suppressors and oncogenes furthered our understanding of cancer initiation and progression and explore how such studies formed the basis of genome-wide scale efforts to identify cancer or cancer-type specific vulnerabilities, including studies conducted in vivo. Furthermore, we examine how RNAi technologies have revealed new cancer-relevant molecular targets and the implications for cancer of the first RNAi-based drugs. Finally, we discuss the future of functional genetic analysis, highlighting the increasing availability of complementary approaches to analyze cancer gene function.

Abstract B25: HNRNPH1-dependent splicing of the fusion oncogene EWS-FLI1 reveals a targetable RNA G-quadruplex interaction

The primary oncogenic event in ~85% of Ewing sarcomas is a chromosomal translocation that generates a fusion gene encoding an aberrant transcription factor EWS-FLI1. In a third of EWS-FLI1 driven tumors, translocations that retain exon 8 of EWSR1 must exclude this exon to synthesize a protein-encoding mRNA. We have previously demonstrated that the heterogeneous nuclear ribonucleoprotein H1 (HNRNPH1) binds to G-rich sequences within EWSR1 exon 8 and that this binding event is required to express an in-frame EWS-FLI1 mature mRNA. G-rich nucleic acids may fold into stable tertiary structures, such as RNA guanine quadruplexes (rG4s). Our current studies are focused on the tertiary RNA structure of the G-rich regions within EWSR1 exon 8 and its role in HNRNPH1-dependent RNA processing. Here, we show that the processing of distinct EWS-FLI1 pre-mRNAs by HNRNPH1, but not other homologous family members, resembles alternative splicing of rare transcript variants of wild-type EWSR1. We demonstrate that guanine-rich sequences within EWSR1 exon 8 can fold into RNA G-quadruplex structures and that HNRNPH1 preferentially binds these RNAs when in a folded state. Critically, we also demonstrate that transfection of a single-stranded RNA oligomer corresponding to one of these G-rich sequences (rG1) reduces the expression of EWS-FLI1 mRNA and EWS-FLI1 protein and decreases its transcriptional activity. Small molecules that can displace HNRNPH1 binding may provide a therapeutic vulnerability in a subset of Ewing sarcoma. To evaluate if this protein-RNA interaction is amenable to small molecules, we performed displacement assays with HNRNPH1 protein and an EWSR1 exon 8 RNA oligomer (rG1) at varying concentrations of a G4-binding molecule, pyridostatin (PDS). We found that PDS disrupts the formation of the HNRNPH1-rG1 complex (IC50 of 7 micromolar). Furthermore, treatment with PDS selectivity inhibits the growth of Ewing sarcoma cell lines harboring EWSR1 exon 8 fusions, decreases EWS-FLI1 activity in cell-based reporter assays, and restores mRNA expression of EWS-FLI1 deregulated transcriptional targets. Our findings illustrate that modulation of the alternative splicing of EWS-FLI1 pre-mRNA is a promising strategy for future therapeutics against this fusion oncogene expressed in a third of Ewing sarcoma.

Citation Format: Carla Neckles, Robert E. Boer, Nicholas Aboreden, Allison M. Cross, Robert L. Walker, Bong-Hyun Kim, Suntae Kim, John S. Schneekloth, Natasha J. Caplen. HNRNPH1-dependent splicing of the fusion oncogene EWS-FLI1 reveals a targetable RNA G-quadruplex interaction [abstract]. In: Proceedings of the AACR Special Conference on the Advances in Pediatric Cancer Research; 2019 Sep 17-20; Montreal, QC, Canada. Philadelphia (PA): AACR; Cancer Res 2020;80(14 Suppl):Abstract nr B25.

CDK9 Blockade Exploits Context-dependent Transcriptional Changes to Improve Activity and Limit Toxicity of Mithramycin for Ewing Sarcoma

There is a need to develop novel approaches to improve the balance between efficacy and toxicity for transcription factor-targeted therapies. In this study, we exploit context-dependent differences in RNA polymerase II processivity as an approach to improve the activity and limit the toxicity of the EWS-FLI1-targeted small molecule, mithramycin, for Ewing sarcoma. The clinical activity of mithramycin for Ewing sarcoma is limited by off-target liver toxicity that restricts the serum concentration to levels insufficient to inhibit EWS-FLI1. In this study, we perform an siRNA screen of the druggable genome followed by a matrix drug screen to identify mithramycin potentiators and a synergistic "class" effect with cyclin-dependent kinase 9 (CDK9) inhibitors. These CDK9 inhibitors enhanced the mithramycin-mediated suppression of the EWS-FLI1 transcriptional program leading to a shift in the IC₅₀ and striking regressions of Ewing sarcoma xenografts. To determine whether these compounds may also be liver protective, we performed a qPCR screen of all known liver toxicity genes in HepG2 cells to identify mithramycin-driven transcriptional changes that contribute to the liver toxicity. Mithramycin induces expression of the BTG2 gene in HepG2 but not Ewing sarcoma cells, which leads to a liver-specific accumulation of reactive oxygen species (ROS). siRNA silencing of BTG2 rescues the induction of ROS and the cytotoxicity of mithramycin in these cells. Furthermore, CDK9 inhibition blocked the induction of BTG2 to limit cytotoxicity in HepG2, but not Ewing sarcoma cells. These studies provide the basis for a synergistic and less toxic EWS-FLI1-targeted combination therapy for Ewing sarcoma.

HNRNPH1-dependent splicing of a fusion oncogene reveals a targetable RNA G-quadruplex interaction

The primary oncogenic event in ∼85% of Ewing sarcomas is a chromosomal translocation that generates a fusion oncogene encoding an aberrant transcription factor. The exact genomic breakpoints within the translocated genes, EWSR1 and FLI1, vary; however, in EWSR1, breakpoints typically occur within introns 7 or 8. We previously found that in Ewing sarcoma cells harboring EWSR1 intron 8 breakpoints, the RNA-binding protein HNRNPH1 facilitates a splicing event that excludes EWSR1 exon 8 from the EWS-FLI1 pre-mRNA to generate an in-frame mRNA. Here, we show that the processing of distinct EWS-FLI1 pre-mRNAs by HNRNPH1, but not other homologous family members, resembles alternative splicing of transcript variants of EWSR1 We demonstrate that HNRNPH1 recruitment is driven by guanine-rich sequences within EWSR1 exon 8 that have the potential to fold into RNA G-quadruplex structures. Critically, we demonstrate that an RNA mimetic of one of these G-quadruplexes modulates HNRNPH1 binding and induces a decrease in the growth of an EWSR1 exon 8 fusion-positive Ewing sarcoma cell line. Finally, we show that EWSR1 exon 8 fusion-positive cell lines are more sensitive to treatment with the pan-quadruplex binding molecule, pyridostatin (PDS), than EWSR1 exon 8 fusion-negative lines. Also, the treatment of EWSR1 exon 8 fusion-positive cells with PDS decreases EWS-FLI1 transcriptional activity, reversing the transcriptional deregulation driven by EWS-FLI1. Our findings illustrate that modulation of the alternative splicing of EWS-FLI1 pre-mRNA is a novel strategy for future therapeutics against the EWSR1 exon 8 containing fusion oncogenes present in a third of Ewing sarcoma.

Fusion transcripts: Unexploited vulnerabilities in cancer?

Gene fusions are an important class of mutations in several cancer types and include genomic rearrangements that fuse regulatory or coding elements from two different genes. Analysis of the genetics of cancers harboring fusion oncogenes and the proteins they encode have enhanced cancer diagnosis and in some cases patient treatment. However, the effect of the complex structure of fusion genes on the biogenesis of the resulting chimeric transcripts they express is not well studied. There are two potential RNA‐related vulnerabilities inherent to fusion‐driven cancers: (a) the processing of the fusion precursor messenger RNA (pre‐mRNA) to the mature mRNA and (b) the mature mRNA. In this study, we discuss the effects that the genetic organization of fusion oncogenes has on the generation of translatable mature RNAs and the diversity of fusion transcripts expressed in different cancer subtypes, which can fundamentally influence both tumorigenesis and treatment. We also discuss functional genomic approaches that can be utilized to identify proteins that mediate the processing of fusion pre‐mRNAs. Furthermore, we assert that an enhanced understanding of fusion transcript biogenesis and the diversity of the chimeric RNAs present in fusion‐driven cancers will increase the likelihood of successful application of RNA‐based therapies in this class of tumors.

This article is categorized under:

RNA Processing > RNA Editing and Modification

RNA Processing > Splicing Regulation/Alternative Splicing

RNA in Disease and Development > RNA in Disease

Abstract 4494: HNRNPH1-dependent splicing of a fusion oncogene reveals a targetable RNA G-quadruplex interaction

Ewing sarcoma (EWS) is the second most common bone tumor in children and adolescents. The primary oncogenic event in ~85% of EWS is a chromosomal translocation that generates a fusion gene encoding the aberrant transcription factor EWS-FLI1. A third of EWS-FLI1 driven tumors harbor translocations that retain exon 8 of the EWSR1 gene, and in these tumors, skipping of this exon is vital to express an in-frame EWS-FLI1 mRNA. We have shown previously that the heterogeneous nuclear ribonucleoprotein H1 (HNRNPH1) binds to G-rich sequences within EWSR1 exon 8 and facilitates the exclusion of this exon from distinct EWS-FLI1 pre-mRNAs. Guanine-rich nucleic acids may fold into stable tertiary structures, such as RNA guanine quadruplexes (rG4s). Our current studies are focused on the tertiary RNA structure of the G-rich regions within EWSR1 exon 8 and its role in HNRNPH1-dependent RNA processing. Here, we show that the processing of distinct EWS-FLI1 pre-mRNAs by HNRNPH1, but not other homologous family members, resembles alternative splicing of transcript variants of wild-type EWSR1. We demonstrate that guanine-rich sequences within EWSR1 exon 8 can fold into RNA G-quadruplex structures and that this structure favors the recruitment of HNRNPH1. Bioinformatic analysis of transcriptome-wide profiles for RNA G-quadruplexes and RNA targets of HNRNPH1 revealed sequences containing two-quartet G-quadruplex configurations are central for HNRNPH1 binding to exonic elements. Critically, we also demonstrate that the glycine-tyrosine-arginine-rich domain of HNRNPH1 is the minimal domain required for G-quadruplex recognition. Small molecules that can displace HNRNPH1 binding may provide a therapeutic vulnerability in a subset of Ewing sarcoma. To evaluate if this protein-RNA interaction is amenable to small molecules, we performed displacement assays with HNRNPH1 protein and an EWSR1 exon 8 RNA oligomer at varying concentrations of the pan-quadruplex binding molecule, pyridostatin (PDS). PDS disrupts the HNRNPH1-RNA complex with an IC50 of 7 micromolar. Furthermore, treatment with PDS selectivity inhibits the growth of EWS cells harboring EWSR1 exon 8 fusions, decreases EWS-FLI1 activity in cell-based reporter assays, and restores mRNA expression of EWS-FLI1 deregulated transcriptional targets. Our findings illustrate that splicing modulation of EWS-FLI1 pre-mRNA is a promising strategy for future therapeutics against this fusion oncogene expressed in a third of Ewing sarcoma.

Citation Format: Carla Neckles, Robert Boer, Nicholas Aboreden, Robert L. Walker, Bong-Hyun Kim, Suntae Kim, John S. Schneekloth, Natasha J. Caplen. HNRNPH1-dependent splicing of a fusion oncogene reveals a targetable RNA G-quadruplex interaction [abstract]. In: Proceedings of the American Association for Cancer Research Annual Meeting 2019; 2019 Mar 29-Apr 3; Atlanta, GA. Philadelphia (PA): AACR; Cancer Res 2019;79(13 Suppl):Abstract nr 4494.

EWS-FLI1 reprograms the metabolism of Ewing sarcoma cells via positive regulation of glutamine import and serine-glycine biosynthesis

Ewing sarcoma (EWS) is a soft tissue and bone tumor that occurs primarily in adolescents and young adults. In most cases of EWS, the chimeric transcription factor, EWS-FLI1 is the primary oncogenic driver. The epigenome of EWS cells reflects EWS-FLI1 binding and activation or repression of transcription. Here, we demonstrate that EWS-FLI1 positively regulates the expression of proteins required for serine-glycine biosynthesis and uptake of the alternative nutrient source glutamine. Specifically, we show that EWS-FLI1 activates expression of PHGDH, PSAT1, PSPH, and SHMT2. Using cell-based studies, we also establish that EWS cells are dependent on glutamine for cell survival and that EWS-FLI1 positively regulates expression of the glutamine transporter, SLC1A5 and two enzymes involved in the one-carbon cycle, MTHFD2 and MTHFD1L. Inhibition of serine-glycine biosynthesis in EWS cells impacts their redox state leading to an accumulation of reactive oxygen species, DNA damage, and apoptosis. Importantly, analysis of EWS primary tumor transcriptome data confirmed that the aforementioned genes we identified as regulated by EWS-FLI1 exhibit increased expression compared with normal tissues. Furthermore, retrospective analysis of an independent data set generated a significant stratification of the overall survival of EWS patients into low- and high-risk groups based on the expression of PHGDH, PSAT1, PSPH, SHMT2, SLC1A5, MTHFD2, and MTHFD1L. In summary, our study demonstrates that EWS-FLI1 reprograms the metabolism of EWS cells and that serine-glycine metabolism or glutamine uptake are potential targetable vulnerabilities in this tumor type.

Abstract 5471: EWS-FLI1 reprograms the metabolism of Ewing sarcoma cells via positive regulation of glutamine import and serine-glycine biosynthesis

Ewing sarcoma (EWS) is a soft tissue and bone tumor found primarily in adolescents and young adults. In most cases of EWS, the chimeric transcription factor, EWS-FLI1 is the primary oncogenic driver. The expression profile of EWS cells reflects EWS-FLI1 binding and activation or repression of transcription. Recent studies have shown EWS-FLI1 deregulates proteins that function in tryptophan metabolism (Mutz et al., 2016, FEBS Lett. 590, 2063) or serine-glycine biosynthesis (Tanner et al., 2017, Mol. Cancer Res., 11, 1517). In our study, we extend these findings by establishing that EWS-FLI1 transcriptionally regulates the expression of enzymes required for serine-glycine biosynthesis and the mitochondrial one-carbon cycle, and the uptake of the alternative nutrient source glutamine, directly. To identify metabolic pathways regulated by EWS-FLI1, we interrogated the expression profiles of EWS-FLI1-silenced TC32 EWS cells. We observed that silencing of EWS-FLI1 results in the decreased expression of genes required for serine-glycine biosynthesis specifically, PHGDH, PSAT1, PSPH, and SHMT2. Using ChIP analysis, we demonstrated that EWS-FLI1 binds specific regulatory regions within these four serine-glycine biosynthesis genes. Also, ectopic expression in 293T cells results in increased expression of PHGDH, PSAT1, PSPH, and SHMT2. Consistent with the ability of EWS cells to synthesize serine and glycine de novo, EWS cells grown in medium depleted of these amino acids exhibit no change in viability. However, EWS cells were sensitive to the depletion of glutamine. Analysis of the expression profiles of EWS-FLI1-silenced TC32 EWS cells showed EWS-FLI1 positively regulates expression of the glutamine transporter, SLC1A5 and that EWS cells require glutamine for glycine synthesis. Next, we examined metabolic processes downstream of serine-glycine biosynthesis and showed that enzymes associated with the mitochondrial one-carbon cycle, MTHFD2 and MTHD1L, are transcriptional targets of EWS-FLI1, but not their cytosolic counterpart MTHFD1. Our data suggests EWS-FLI1 favors activation of enzymes associated with the mitochondrial one-carbon cycle, which provides the reducing equivalents GSH and NADPH. Depletion of EWS-FLI1 or the inhibition of PHGDH reduced the GSH/GSSG and NADPH/NADP ratios in EWS cells resulting in increased production of reactive oxygen species, inducing DNA damage and apoptosis. Importantly, analysis of EWS primary tumor transcriptome data confirmed that the aforementioned metabolism genes we identified as regulated by EWS-FLI1 exhibit increased expression compared with normal tissues. In summary, our study demonstrates that EWS-FLI1 reprograms the metabolism of EWS cells and that serine-glycine metabolism and glutamine uptake are potential vulnerabilities in this tumor type.

Citation Format: Nirmalya Sen, Allison M. Cross, Philip L. Lorenzi, Javed Khan, Berkley E. Gryder, Suntae Kim, Natasha J. Caplen. EWS-FLI1 reprograms the metabolism of Ewing sarcoma cells via positive regulation of glutamine import and serine-glycine biosynthesis [abstract]. In: Proceedings of the American Association for Cancer Research Annual Meeting 2018; 2018 Apr 14-18; Chicago, IL. Philadelphia (PA): AACR; Cancer Res 2018;78(13 Suppl):Abstract nr 5471.

Abstract IA04: Targeting the expression of EWS-FLI1

Post-translational modifications (PTMs) of transcription factors represent potential therapeutic targets for a variety of diseases, including cancer. In the majority of cases of the bone and soft tissue tumor Ewing sarcoma (ES), a chromosomal translocation, t(11:22), results in expression of the fusion transcription factor EWS-FLI1. Few PTMs of EWS-FLI1 have been identified. Using functional genetic methods and mass spectrometry analysis, we have identified a phosphorylated serine residue in the FLI1 domain of EWS-FLI1 that regulates the stability of the EWS-FLI1 oncoprotein. Loss of phosphorylation of this serine residue triggers ubiquitination and proteasomal degradation of EWS-FLI1, and apoptotic cell death. Xenograft studies suggest this post-translational modification of EWS-FLI1 can be targeted in vivo and that this inhibits ES tumor growth.

Citation Format: Nirmalya Sen, Katelyn Ludwig, Guillermo O. Rangel-Rivera, Suntae Kim, Konrad Huppi, Lisa Jenkins, Jennifer E. Dwyer, Shelley Hoover, Lee Helman, Mark Simpson, Arnulfo Mendoza, Amanda B. Hummon, Natasha J. Caplen. Targeting the expression of EWS-FLI1 [abstract]. In: Proceedings of the AACR Conference on Advances in Sarcomas: From Basic Science to Clinical Translation; May 16-19, 2017; Philadelphia, PA. Philadelphia (PA): AACR; Clin Cancer Res 2018;24(2_Suppl):Abstract nr IA04.

Abstract 2008: Ewing sarcoma cells harboring a translocation that retains EWSR1 exon 8 require HNRNPH1 to express the in-frame oncogenic fusion transcript EWS-FLI1

The primary oncogenic event in ∼85% of Ewing sarcomas is a t(11:22)(q24:q12) translocation. This translocation generates a fusion gene containing the 5’ end of the EWSR1 gene and the 3’ end of the FLI1 gene referred to as EWS-FLI1. The exact genomic breakpoints within the EWSR1 and FLI1 genes vary, but typically occur within introns and require the splicing machinery to generate an in-frame EWS-FLI1 transcript. In an estimated 40% of EWS-FLI1 driven tumors, the generation of an in-frame EWS-FLI1 fusion transcript requires alternative splicing. In particular, translocations that retain exon 8 of EWSR1 generate an out-of-frame transcript unless this exon is removed. In this study, we demonstrate that Ewing sarcoma cells harboring a genomic breakpoint that retains exon 8 of EWSR1 require HNRNPH1 to express an in-frame EWS-FLI1 mature mRNA.

Using a genome-wide RNAi screen, we identified several proteins involved in RNA processing as required for the activity of EWS-FLI1, including the heterogeneous nuclear ribonucleoprotein H1 (HNRNPH1). The role of HNRNPH1 in alternative splicing led us to hypothesize that ES cells are dependent on HNRNPH1 for the expression of the EWS-FLI1 transcript. Analysis of the expression of EWS-FLI1 following HNRNPH1 silencing in Ewing sarcoma cell lines representing different translocation breakpoints and transcript isoforms showed that only Ewing sarcoma cell lines retaining EWSR1 exon 8 at a genomic level (TC32 and SKNMC cells) are dependent on HNRNPH1 expression. Silencing of HNRNPH1 in TC32 or SKNMC cells, results in the expression of an out-of-frame EWS-FLI1 transcript that cannot express the EWS-FLI1 oncogenic transcription factor. This leads to the reversal of expression of EWS-FLI1 gene targets and cell death. Ewing sarcoma cell lines that harbor a translocation upstream of EWSR1 exon 8 (TC71 and RD-ES) exhibit none of these molecular or phenotypic changes upon HNRNPH1 silencing.

We next employed an RNA pull-down and PCR strategy to identify putative binding sites for HNRNPH1 on the EWS-FLI1 pre-mRNA. This analysis showed enrichment for the binding of EWSR1 exon 8 by HNRNPH1. Towards the 3’ end of EWSR1 exon 8 we identified two G-rich sequences, a motif typically bound by HNRNPH1. To determine if HNRNPH1 binds one or both of these sites, we developed an in vitro protein-RNA-oligomer binding assay. This assay confirmed the binding of HNRNPH1 to both G-rich sites in EWSR1 exon 8. Current studies are focused on using the protein-RNA-oligomer binding assay to fully map the interaction of HNRNPH1 with sequences within EWSR1 exon 8 and understand the molecular mechanism to target it. These results demonstrate a sequence-specific, breakpoint-dependent vulnerability in Ewing sarcoma that has the potential to be exploited as a therapeutic target and suggests a novel strategy to target fusion oncogenes.

Citation Format: Suntae Kim, Christiane Olivero, Guillermo O. Rangel Rivera, Nirmalya Sen, Sara Haddock, Konrad Huppi, Lee J. Helman, Patrick J. Grohar, Natasha J. Caplen. Ewing sarcoma cells harboring a translocation that retains EWSR1 exon 8 require HNRNPH1 to express the in-frame oncogenic fusion transcript EWS-FLI1. [abstract]. In: Proceedings of the 107th Annual Meeting of the American Association for Cancer Research; 2016 Apr 16-20; New Orleans, LA. Philadelphia (PA): AACR; Cancer Res 2016;76(14 Suppl):Abstract nr 2008.

Functional Genomic Screening Reveals Splicing of the EWS-FLI1 Fusion Transcript as a Vulnerability in Ewing Sarcoma

Ewing sarcoma cells depend on the EWS-FLI1 fusion transcription factor for cell survival. Using an assay of EWS-FLI1 activity and genome-wide RNAi screening, we have identified proteins required for the processing of the EWS-FLI1 pre-mRNA. We show that Ewing sarcoma cells harboring a genomic breakpoint that retains exon 8 of EWSR1 require the RNA-binding protein HNRNPH1 to express in-frame EWS-FLI1. We also demonstrate the sensitivity of EWS-FLI1 fusion transcripts to the loss of function of the U2 snRNP component, SF3B1. Disrupted splicing of the EWS-FLI1 transcript alters EWS-FLI1 protein expression and EWS-FLI1-driven expression. Our results show that the processing of the EWS-FLI1 fusion RNA is a potentially targetable vulnerability in Ewing sarcoma cells.

Abstract 479: Inhibition of the splicing of the EWS-FLI1 fusion transcript reverses EWS-FLI1 driven oncogenic expression in Ewing sarcoma

Ewing sarcoma (ES) is a highly aggressive cancer of the bone and soft tissue. In ∼85% of ES tumors the primary oncogenic event is a t(11:22)(q24:q12) translocation that generates a fusion of the 5′ end of EWSR1 and the 3′ end of FLI1 referred to as EWS-FLI1. The exact genomic breakpoints within the EWSR1 and FLI1 genes vary, but typically occur within introns and require the splicing machinery to generate an in-frame EWS-FLI1 transcript. The most common EWS-FLI1 transcripts fuse either exon 7 of EWSR1 to exon 6 of FLI1 (a type I or a 7/6 fusion), or fuse exon 7 of EWSR1 to exon 5 of FLI1 (a type II or 7/5 fusion). In an estimated 40% of EWS-FLI1 driven tumors the generation of an in-frame EWS-FLI1 fusion transcript requires alternative splicing. In particular, translocations that retain exon 8 of EWSR1 generate an out-of-frame transcript unless this exon is removed. Using an assay of EWS-FLI1 activity and genome-wide siRNA screening we have identified RNA processing as a therapeutic vulnerability in ES.

Parallel genome-wide siRNA-mediated RNAi screens were conducted in ES TC32 cell lines expressing a luciferase (luc) reporter protein driven by either the promoter of the EWS-FLI1 target gene NR0B1 (TC32-NR0B1-luc) or the CMV promoter (TC32-CMV-luc). The top gene ontology terms associated with the 28 priority candidate genes that when silenced induced a differential decrease in the TC32-NR0B1-luc signal versus the TC32-CMV-luc signal were mRNA splicing (p-value = 1.42E-08) and mRNA processing (p-value = 2.32E-07). To investigate the mechanistic basis for the identification of specific RNA processing proteins as required for the activity of EWS-FLI1 we focused on two lead candidate genes, the heterogeneous nuclear ribonucleoprotein H1, HNRNPH1, and the core splicing factor, SF3B1. Using PCR analysis we determined that HNRNPH1 is required for the splicing of EWS-FLI1 fusion transcripts expressed in ES cells in which the chromosome 22 breakpoint retains EWSR1 exon 8, specifically in TC32 and SKNMC ES cells. We also show ES cell lines harboring 7/ 6 (TC32, SKNMC, and TC71) or 7/ 5 (RD-ES) EWS-FLI1 fusions are all sensitive to the loss-of-function of SF3B1. Quantitative RT-PCR, immunoblot, and whole transcriptome analysis show that disrupted splicing of the EWS-FLI1 transcript alters its expression and reverses the expression of a significant proportion of genes that are targets of EWS-FLI1. These observations were confirmed in four ES cell lines using the splicing inhibitor Pladienolide B.

Our results provide the basis for a novel strategy to target fusion oncogenes by interfering with RNA processing. This study has implications for the treatment of ES through inhibition of proteins required for expression of the EWS-FLI1 transcript and identifies a candidate lead compound for further clinical development. Our findings may also open up strategies for treatment of other cancers driven by fusion oncogenes.

Citation Format: Patrick J. Grohar, Suntae Kim, Sara Haddock, Guillermo Rangel Rivera, Matt Harlow, Nichole K. Maloney, Konrad Huppi, Kristen Gehlhaus, Magdalena Grandin, Carleen Klumpp-Thomas, Eugen Buehler, Lee J. Helman, Scott E. Martin, Natasha J. Caplen. Inhibition of the splicing of the EWS-FLI1 fusion transcript reverses EWS-FLI1 driven oncogenic expression in Ewing sarcoma. [abstract]. In: Proceedings of the 106th Annual Meeting of the American Association for Cancer Research; 2015 Apr 18-22; Philadelphia, PA. Philadelphia (PA): AACR; Cancer Res 2015;75(15 Suppl):Abstract nr 479. doi:10.1158/1538-7445.AM2015-479

Targeting MPS1 Enhances Radiosensitization of Human Glioblastoma by Modulating DNA Repair Proteins

To ensure faithful chromosome segregation, cells use the spindle assembly checkpoint (SAC), which can be activated in aneuploid cancer cells. Targeting the components of SAC machinery required for the growth of aneuploid cells may offer a cancer cell-specific therapeutic approach. In this study, the effects of inhibiting Monopolar spindle 1, MPS1 (TTK), an essential SAC kinase, on the radiosensitization of glioblastoma (GBM) cells were analyzed. Clonogenic survival was used to determine the effects of the MPS1 inhibitor NMS-P715 on radiosensitivity in multiple model systems, including GBM cell lines, a normal astrocyte, and a normal fibroblast cell line. DNA double-strand breaks (DSB) were evaluated using γH2AX foci, and cell death was measured by mitotic catastrophe evaluation. Transcriptome analysis was performed via unbiased microarray expression profiling. Tumor xenografts grown from GBM cells were used in tumor growth delay studies. Inhibition of MPS1 activity resulted in reduced GBM cell proliferation. Furthermore, NMS-P715 enhanced the radiosensitivity of GBM cells by decreased repair of DSBs and induction of postradiation mitotic catastrophe. NMS-P715 in combination with fractionated doses of radiation significantly enhanced the tumor growth delay. Molecular profiling of MPS1-silenced GBM cells showed an altered expression of transcripts associated with DNA damage, repair, and replication, including the DNA-dependent protein kinase (PRKDC/DNAPK). Next, inhibition of MPS1 blocked two important DNA repair pathways. In conclusion, these results not only highlight a role for MPS1 kinase in DNA repair and as prognostic marker but also indicate it as a viable option in glioblastoma therapy.

IMPLICATIONS

Inhibition of MPS1 kinase in combination with radiation represents a promising new approach for glioblastoma and for other cancer therapies.

Loss-of-function RNAi screens in breast cancer cells identify AURKB, PLK1, PIK3R1, MAPK12, PRKD2, and PTK6 as sensitizing targets of rapamycin activity

The use of molecularly targeted drugs as single agents has shown limited utility in many tumor types, largely due to the complex and redundant nature of oncogenic signaling networks. Targeting of the PI3K/AKT/mTOR pathway through inhibition of mTOR in combination with aromatase inhibitors has seen success in particular sub-types of breast cancer and there is a need to identify additional synergistic combinations to maximize the clinical potential of mTOR inhibitors. We have used loss-of-function RNAi screens of the mTOR inhibitor rapamycin to identify sensitizers of mTOR inhibition. RNAi screens conducted in combination with rapamycin in multiple breast cancer cell lines identified six genes, AURKB, PLK1, PIK3R1, MAPK12, PRKD2, and PTK6 that when silenced, each enhanced the sensitivity of multiple breast cancer lines to rapamycin. Using selective pharmacological agents we confirmed that inhibition of AURKB or PLK1 synergizes with rapamycin. Compound-associated gene expression data suggested histone deacetylation (HDAC) inhibition as a strategy for reducing the expression of several of the rapamycin-sensitizing genes, and we tested and validated this using the HDAC inhibitor entinostat in vitro and in vivo. Our findings indicate new approaches for enhancing the efficacy of rapamycin including the use of combining its application with HDAC inhibition.

Abstract 520: Functional genomic screens identify microRNA regulators of the oncogenic fusion transcription factor EWS-FLI1

Ewing sarcoma (ES) is a highly aggressive malignant pediatric cancer of the bone and soft tissue with a poor prognosis. The genetic hallmark of ES is the t(11:22)(q24:q12) translocation that generates a fusion transcript containing the 5’ end of EWSR1 and the 3’ end of FLI1 referred to as EWS-FLI1. This fusion generates an oncogenic transcription factor, EWS-FLI1 that is responsible for malignant transformation and is necessary for ES cell survival. To enhance our understanding of the molecular mechanisms underlying ES, with the long-term aim of enhanced treatment for this cancer, we are applying RNAi functional genomic approaches. MicroRNAs (miRNAs) are critical regulators of gene expression. There is evidence that many transcription factors and miRNAs act in concert to regulate gene expression. To identify miRNAs that directly or indirectly modulate EWS-FLI1 activity we conducted parallel screens of mimics or inhibitors of the human miRome using a cell-based reporter assay. The reporter assay consists of two isogenic reporter cell lines generated in the EWS-FLI1 expressing TC32 cell line. One line harbors a luciferase reporter driven by the promoter of an established EWS-FLI1 target NR0B1, while the second line expresses luciferase from a constitutive CMV promoter. A comparison of the effects of a miRNA on these two reporter constructs can identify proteins that specifically modulate EWS-FLI1 activity. We first identified those miRNAs for which a differential effect was seen when the NR0B1- and CMV-luciferase signals were compared and prioritized those where the mimic and inhibitor corresponding to a specific miRNA exhibited opposite effects. Twenty-eight miRNAs were identified, including miR-145, an established regulator of EWS-FLI1. The screen also identified miRNAs that have not been linked to EWS biology. One such candidate is miR-200b, a known regulator of epithelial-mesenchymal transition and tumor progression. We have confirmed that biotinylated-miR-200b captures the EWS-FLI1 mRNA when transfected into TC32 and ∼300 other mRNAs that includes EWS-FLI1 target genes. This functional genomic approach gives us an opportunity to investigate the co-regulatory activity of an oncogenic transcription factor and miRNAs in a systematic fashion that could be extended to investigate the co-regulation of other transcription factors and miRNAs.

Citation Format: Suntae Kim, Patrick J. Grohar, Carleen Klumpp, Ashish Lal, Scott E. Martin, Lee J. Helman, Natasha J. Caplen. Functional genomic screens identify microRNA regulators of the oncogenic fusion transcription factor EWS-FLI1. [abstract]. In: Proceedings of the 105th Annual Meeting of the American Association for Cancer Research; 2014 Apr 5-9; San Diego, CA. Philadelphia (PA): AACR; Cancer Res 2014;74(19 Suppl):Abstract nr 520. doi:10.1158/1538-7445.AM2014-520

Identification and validation of genes with expression patterns inverse to multiple metastasis suppressor genes in breast cancer cell lines

Metastasis suppressor genes (MSGs) have contributed to an understanding of regulatory pathways unique to the lethal metastatic process. When re-expressed in experimental models, MSGs block cancer spread to, and colonization of distant sites without affecting primary tumor formation. Genes have been identified with expression patterns inverse to a single MSG, and found to encode functional, druggable signaling pathways. We now hypothesize that common signaling pathways mediate the effects of multiple MSGs. By gene expression profiling of human MCF7 breast carcinoma cells expressing a scrambled siRNA, or siRNAs to each of 19 validated MSGs (NME1, BRMS1, CD82, CDH1, CDH2, CDH11, CASP8, MAP2K4, MAP2K6, MAP2K7, MAPK14, GSN, ARHGDIB, AKAP12, DRG1, CD44, PEBP1, RRM1, KISS1), we identified genes whose expression was significantly opposite to at least five MSGs. Five genes were selected for further analysis: PDE5A, UGT1A, IL11RA, DNM3 and OAS1. After stable downregulation of each candidate gene in the aggressive human breast cancer cell line MDA-MB-231T, in vitro motility was significantly inhibited. Two stable clones downregulating PDE5A (phosphodiesterase 5A), an enzyme involved in the regulation of cGMP-specific signaling, exhibited no difference in cell proliferation, but reduced motility by 47 and 66 % compared to the empty vector-expressing cells (p = 0.01 and p = 0.005). In an experimental metastasis assay, two shPDE5A-MDA-MB-231T clones produced 47-62 % fewer lung metastases than shRNA-scramble expressing cells (p = 0.045 and p = 0.009 respectively). This study demonstrates that previously unrecognized genes are inversely related to the expression of multiple MSGs, contribute to aspects of metastasis, and may stand as novel therapeutic targets.

Identification of novel molecular regulators of tumor necrosis factor-related apoptosis-inducing ligand (TRAIL)-induced apoptosis in breast cancer cells by RNAi screening

INTRODUCTION

Tumor necrosis factor-related apoptosis-inducing ligand (TRAIL) binds to its receptors, TRAIL-receptor 1 (TRAIL-R1) and TRAIL-receptor 2 (TRAIL-R2), leading to apoptosis by activation of caspase-8 and the downstream executioner caspases, caspase-3 and caspase-7 (caspase-3/7). Triple-negative breast cancer (TNBC) cell lines with a mesenchymal phenotype are sensitive to TRAIL, whereas other breast cancer cell lines are resistant. The underlying mechanisms that control TRAIL sensitivity in breast cancer cells are not well understood. Here, we performed small interfering RNA (siRNA) screens to identify molecular regulators of the TRAIL pathway in breast cancer cells.

METHODS

We conducted siRNA screens of the human kinome (691 genes), phosphatome (320 genes), and about 300 additional genes in the mesenchymal TNBC cell line MB231. Forty-eight hours after transfection of siRNA, parallel screens measuring caspase-8 activity, caspase-3/7 activity, or cell viability were conducted in the absence or presence of TRAIL for each siRNA, relative to a negative control siRNA (siNeg). A subset of genes was screened in cell lines representing epithelial TNBC (MB468), HER2-amplified breast cancer (SKBR3), and estrogen receptor-positive breast cancer (T47D). Selected putative negative regulators of the TRAIL pathway were studied by using small-molecule inhibitors.

RESULTS

The primary screens in MB231 identified 150 genes, including 83 kinases, 4 phosphatases, and 63 nonkinases, as potential negative regulators of TRAIL. The identified genes are involved in many critical cell processes, including apoptosis, growth factor-receptor signaling, cell-cycle regulation, transcriptional regulation, and DNA repair. Gene-network analysis identified four genes (PDPK1, IKBKB, SRC, and BCL2L1) that formed key nodes within the interaction network of negative regulators. A secondary screen of a subset of the genes identified in additional cell lines representing different breast cancer subtypes and sensitivities to TRAIL validated and extended these findings. Further, we confirmed that small-molecule inhibition of SRC or BCL2L1, in combination with TRAIL, sensitizes breast cancer cells to TRAIL-induced apoptosis, including cell lines resistant to TRAIL-induced cytotoxicity.

CONCLUSIONS

These data identify novel molecular regulators of TRAIL-induced apoptosis in breast cancer cells and suggest strategies for the enhanced application of TRAIL as a therapy for breast cancer.

Inhibition of polo-like kinase 1 in glioblastoma multiforme induces mitotic catastrophe and enhances radiosensitisation

Glioblastoma multiforme (GBM) is the most common primary brain tumour in the United States of America (USA) with a median survival of approximately 14 months. Low survival rates are attributable to the aggressiveness of GBM and a lack of understanding of the molecular mechanisms underlying GBM. The disruption of signalling pathways regulated either directly or indirectly by protein kinases is frequently observed in cancer cells and thus the development of inhibitors of specific kinases has become a major focus of drug discovery in oncology. To identify protein kinases required for the survival of GBM we performed a siRNA-based RNAi screen focused on the human kinome in GBM. Inhibition of the polo-like kinase 1 (PLK1) induced a reduction in the viability in two different GBM cell lines. To assess the potential of inhibiting PLK1 as a treatment strategy for GBM we examined the effects of a small molecule inhibitor of PLK1, GSK461364A, on the growth of GBM cells. PLK1 inhibition arrested cells in the mitotic phase of the cell cycle and induced cell kill by mitotic catastrophe. GBM engrafts treated with GSK461364A showed statistically significant inhibition of tumour growth. Further, exposure of different GBM cells to RNAi or GSK461364A prior to radiation resulted in an increase in their radiosensitivity with dose enhancement factor ranging from 1.40 to 1.53 with no effect on normal cells. As a measure of DNA double strand breaks, γH2AX levels were significantly higher in the combined modality as compared to the individual treatments. This study suggests that PLK1 is an important therapeutic target for GBM and can enhance radiosensitivity in GBM.

Abstract 1584: Targeting the mitotic checkpoint with inhibition of MPS1 kinase enhances radiosensitivity of glioblastoma cancer cells

During the cell cycle, genomic stability requires accurate chromosome segregation. Errors in this process can cause aneuploidy and lead to tumorigenesis. To ensure faithful chromosome segregation, cells develop a mechanism called the spindle assembly checkpoint (SAC). Cancer cells are addicted to the components of SAC machinery for a faithful entry of the cell into anaphase. Thus, targeting the molecular mechanisms required for the growth of aneuploid cells may be a more cancer cell specific therapeutic approach applicable to broader tumor histologies. Previously, using a siRNA based RNAi screen we identified MPS1 kinase, (also known as TTK) as an important kinase for GBM cell survival. MPS1 is an essential SAC enzyme aberrantly overexpressed in a wide range of tumors and necessary for tumor cell proliferation.

We observed inhibition of GBM cell growth when MPS1 was downregulated by number of MPS1 specific siRNAs. This was further validated using a selective and orally bioavailable MPS1 inhibitor NMS-P715 in various in-vitro cell assays. The inhibition of cell death was induced partly by apoptosis; however, the major mechanism was mitotic catastrophe. Cells treated with NMS-P715 showed an increase in cells in G2-M phase of cell cycle compared to control cells followed by mitotic catastrophe. Moreover, inhibition of MPS1 resulted in radiosensitization of GBM cells. We observed decrease in DNA damage repair and significant retention of γH2AX foci after combination of radiation (RT) with NMS-P715 compared to individual treatments. Next, radiation in combination with NMS-P715 inhibited cell survival ability of GBM cells in a colony formation assay. Further, NMS-P715 could inhibit GBM tumor growth in an orthotopic brain tumor model. Finally, in order to determine MPS1 associated molecular pathways, we compared gene expression profile in MPS1 knockdown cells compared to the control by microarray analysis. Ingenuity pathway and Gene Set Enrichment Analysis were used to investigate the biological relevance of the MPS1 modulated genes. We identified genes important in cell assembly, cell organization, DNA repair and cell death pathways. Thus, inhibiting MPS1 kinase in combination with radiation could represent a promising new approach to GBM therapy.

Citation Format: Anita T. Tandle, Ryan Hanson, Uday B. Maachani, Tamalee Meushaw, Shuping Zhao, Uma Shankavaram, Philip Tofilon, Natasha J. Caplen, Kevin Camphausen. Targeting the mitotic checkpoint with inhibition of MPS1 kinase enhances radiosensitivity of glioblastoma cancer cells. [abstract]. In: Proceedings of the 104th Annual Meeting of the American Association for Cancer Research; 2013 Apr 6-10; Washington, DC. Philadelphia (PA): AACR; Cancer Res 2013;73(8 Suppl):Abstract nr 1584. doi:10.1158/1538-7445.AM2013-1584

Abstract 1834: Noncoding RNAs of the 8q24 locus: Consequences of the over-expression or suppression of miR-1204 and PVT1 in developing B cells

Immortalized models of the mouse B lymphocyte lineage have proven to be valuable resources for a wide variety of B cell neoplasms and for the study of normal B cell differentiation. Whether these models have been engineered in mice (in vivo) or in cell culture (in vitro), there are distinct advantages and disadvantages to both. Homogeneity and ease of accessibility can be considered a benefit of working with cultured cells, whereas the contribution from accessory or stromal cells can be an important element not readily available in the in vitro model system. We originally used immortalized Burkitt's Lymphoma (BL) cells to discover a cluster of microRNAs, miR-1204∼1208, that map within the noncoding PVT1 locus in the region of human 8q24 region down-stream of MYC. The BL cell lines allowed us to isolate a large amount of RNA from a homogeneous resource that enhanced discovery of low-level transcripts. Using probes for mouse miR-1204∼1208 to examine expression in a panel of mouse cell lines representing different stages of B cell development, we were able to show that expression of miR-1204∼1208 appeared to arise at the small B cell stage and that these higher levels of expression continued through to the mature plasma cell. This suggested that the pre-B cell or naïve small B cell stages may be most illuminating in assigning targets and function to miR-1204∼1208 or PVT1.

To determine if over-expression of one of these miRNAs, miR-1204, influences the latency and/or type of B cell malignancy we used two mouse transgenic (TG) models of B cell malignancy, H2-Ld-hu-IL6 and iMyc, lentiviral expression of miR-1204 reduced the latency of tumor development in both models and in the case of iMyc-TG, there was also a shift in tumor type from late stage plasmacytoma to the earlier stage of large B cell lymphoma. However, further interpretation of these results was confounded by heterogeneity of lentiviral integration and expression among tumors. Thus, we turned to several human and mouse in vitro models of B cell development, representing pro-B, pre-B, small B, mature B and plasma cell stages to address the effects of modulating the expression of miR-1204 and its host noncoding transcript, PVT1. Over-expression of miR-1204 has been achieved through the use of lentiviruses or synthetic mimics and suppressed expression has been achieved through application of synthetic inhibitors. We also over-expressed PVT1 using a lentiviral vector and suppressed PVT1 expression through the use of siRNA corresponding to various exons of PVT1. Resultant changes in growth and morphology of these cell lines hint that microarray expression analyses will reveal functional targets of miR-1204 in normal and malignant lymphoid development. It will also be of interest to examine whether over-expression or inhibition of miR-1204 plays an additional role in maturation of the normal B cell.

Citation Format: Konrad Huppi, Oliver L. Ou, Jason J. Pitt, Brady Wahlberg, Tamara L. Jones, Vishala Neppalli, Siegfried Janz, Natasha J. Caplen. Noncoding RNAs of the 8q24 locus: Consequences of the over-expression or suppression of miR-1204 and PVT1 in developing B cells. [abstract]. In: Proceedings of the 104th Annual Meeting of the American Association for Cancer Research; 2013 Apr 6-10; Washington, DC. Philadelphia (PA): AACR; Cancer Res 2013;73(8 Suppl):Abstract nr 1834. doi:10.1158/1538-7445.AM2013-1834

Genetic amplification of the NOTCH modulator LNX2 upregulates the WNT/β-catenin pathway in colorectal cancer

Chromosomal copy number alterations (aneuploidy) define the genomic landscape of most cancer cells, but identification of the oncogenic drivers behind these imbalances remains an unfinished task. In this study, we conducted a systematic analysis of colorectal carcinomas that integrated genomic copy number changes and gene expression profiles. This analysis revealed 44 highly overexpressed genes mapping to localized amplicons on chromosome 13, gains of which occur often in colorectal cancers (CRC). RNA interference (RNAi)-mediated silencing identified eight candidates whose loss-of-function reduced cell viability 20% or more in CRC cell lines. The functional space of the genes NUPL1, LNX2, POLR1D, POMP, SLC7A1, DIS3, KLF5, and GPR180 was established by global expression profiling after RNAi exposure. One candidate, LNX2, not previously known as an oncogene, was involved in regulating NOTCH signaling. Silencing LNX2 reduced NOTCH levels but also downregulated the transcription factor TCF7L2 and markedly reduced WNT signaling. LNX2 overexpression and chromosome 13 amplification therefore constitutively activates the WNT pathway, offering evidence of an aberrant NOTCH-WNT axis in CRC.

Cross-species genomic and functional analyses identify a combination therapy using a CHK1 inhibitor and a ribonucleotide reductase inhibitor to treat triple-negative breast cancer

Introduction

Triple-negative breast cancer (TNBC) is an aggressive subtype of breast cancer that is diagnosed in approximately 15% of all human breast cancer (BrCa) patients. Currently, no targeted therapies exist for this subtype of BrCa and prognosis remains poor. Our laboratory has previously identified a proliferation/DNA repair/cell cycle gene signature (Tag signature) that is characteristic of human TNBC. We hypothesize that targeting the dysregulated biological networks in the Tag gene signature will lead to the identification of improved combination therapies for TNBC.

Methods

Cross-species genomic analysis was used to identify human breast cancer cell lines that express the Tag signature. Knock-down of the up-regulated genes in the Tag signature by siRNA identified several genes that are critical for TNBC cell growth. Small molecule inhibitors to two of these genes were analyzed, alone and in combination, for their effects on cell proliferation, cell cycle, and apoptosis in vitro and tumor growth in vivo. Synergy between the two drugs was analyzed by the Chou-Talalay method.

Results

A custom siRNA screen was used to identify targets within the Tag signature that are critical for growth of TNBC cells. Ribonucleotide reductase 1 and 2 (RRM1 and 2) and checkpoint kinase 1 (CHK1) were found to be critical targets for TNBC cell survival. Combination therapy, to simultaneously attenuate cell cycle checkpoint control through inhibition of CHK1 while inducing DNA damage with gemcitabine, improved therapeutic efficacy in vitro and in xenograft models of TNBC.

Conclusions

This combination therapy may have translational value for patients with TNBC and improve therapeutic response for this aggressive form of breast cancer.

RNAi screening identifies TAK1 as a potential target for the enhanced efficacy of topoisomerase inhibitors

In an effort to develop strategies that improve the efficacy of existing anticancer agents, we have conducted a siRNA-based RNAi screen to identify genes that, when targeted by siRNA, improve the activity of the topoisomerase I (Top1) poison camptothecin (CPT). Screening was conducted using a set of siRNAs corresponding to over 400 apoptosisrelated genes in MDA-MB-231 breast cancer cells. During the course of these studies, we identified the silencing of MAP3K7 as a significant enhancer of CPT activity. Follow-up analysis of caspase activity and caspase-dependent phosphorylation of histone H2AX demonstrated that the silencing of MAP3K7 enhanced CPT-associated apoptosis. Silencing MAP3K7 also sensitized cells to additional compounds, including CPT clinical analogs. This activity was not restricted to MDA-MB-231 cells, as the silencing of MAP3K7 also sensitized the breast cancer cell line MDA-MB-468 and HCT-116 colon cancer cells. However, MAP3K7 silencing did not affect compound activity in the comparatively normal mammary epithelial cell line MCF10A, as well as some additional tumorigenic lines. MAP3K7 encodes the TAK1 kinase, an enzyme that is central to the regulation of many processes associated with the growth of cancer cells (e.g. NF- κB, JNK, and p38 signaling). An analysis of TAK1 signaling pathway members revealed that the silencing of TAB2 also sensitizes MDA-MB-231 and HCT-116 cells towards CPT. These findings may offer avenues towards lowering the effective doses of Top1 inhibitors in cancer cells and, in doing so, broaden their application.

The 8q24 gene desert: an oasis of non-coding transcriptional activity

Understanding the functional effects of the wide-range of aberrant genetic characteristics associated with the human chromosome 8q24 region in cancer remains daunting due to the complexity of the locus. The most logical target for study remains the MYC proto-oncogene, a prominent resident of 8q24 that was first identified more than a quarter of a century ago. However, many of the amplifications, translocation breakpoints, and viral integration sites associated with 8q24 are often found throughout regions surrounding large expanses of the MYC locus that include other transcripts. In addition, chr.8q24 is host to a number of single nucleotide polymorphisms associated with cancer risk. Yet, the lack of a direct correlation between cancer risk alleles and MYC expression has also raised the possibility that MYC is not always the target of these genetic associations. The 8q24 region has been described as a "gene desert" because of the paucity of functionally annotated genes located within this region. Here we review the evidence for the role of other loci within the 8q24 region, most of which are non-coding transcripts, either in concert with MYC or independent of MYC, as possible candidate gene targets in malignancy.

Abstract 199: Noncoding RNAs of the 8q24 locus

The 8q24 locus has been found to be involved in many types of cancers as a consequence of somatic changes associated with chromosome instability including amplification, translocation or deletion or frequent viral integration (HPV). A number of SNPs in Genome Wide Association (GWA) studies have also implicated the 8q24 locus as a region of susceptibility for many types of cancer. The most likely 8q24 candidate target may be the MYC proto-oncogene that is a well characterized transcription factor. However, the assumed correlation between MYC expression and disease is lacking suggesting a connection between 8q24 involvement and disease is much more complicated than simply targeting MYC. While other transcription units also reside within the 8q24 locus (PRNCR1, POU5F1P1, PVT1 and the miRNA cluster miR-1204∼1208), they are remarkable in that no coding potential has been readily associated with any of these genes. Thus, the region has been referred to as the “8q24 Gene Desert”. With the renewed realization that many noncoding RNAs do have a functional role, the location of the miR-1204∼1208 cluster of miRNAs within the PVT1 lincRNA transcriptional unit actually suggests an “Oasis of transcription” that could be the additional or alternative target to MYC. We have now compared expression of transcripts of the miR-1204∼1208 cluster with MYC and PVT1 in multiple cancer cell lines and we have found them to be uniformly up-regulated in expression, particularly in those cell lines with amplified or translocated 8q24. These results confirm a pilot study of microdissected primary prostate tumors that also show correlated high expression in MYC, miR-1204∼1208 and PVT1. To further analyze the functional role of the 8q24 transcripts, we have now introduced mimics or inhibitors of each miRNA and siRNAs corresponding to MYC and PVT1 into prostate or colon cell lines (with and without amplified 8q24). In amplified prostate cell lines, mimics of miR-1204, miR-1206 and miR-1208 appear to be as effective as MYC or PVT1 siRNAs in arresting cell growth and inducing apoptosis. This result is not seen in normal prostate cells. Predictably, inhibitors of the miR-1204, miR-1206 and miR-1208 seem to have no effect or seem to enhance cellular proliferation. In colon cell lines with amplified 8q24, miR-1204, miR-1206, miR-1207 and miR-1208 mimics all appear to be as effective in arresting growth as silencing MYC or PVT1. What is particularly striking is that down-regulation or silencing of PVT1 produces the same effect as over-expression (mimic) of the embedded cluster of miRNAs suggesting opposing actions of miRNAs and host transcript. Experiments to determine whether synergy or promoter competition of the PVT1/miR-1204∼1208 cluster is specifically active in amplified 8q24 will be presented. Nevertheless, we can already assign viable functional roles to transcripts besides MYC that could represent alternative molecular targets within the 8q24 locus for cancer susceptibility.

Citation Format: {Authors}. {Abstract title} [abstract]. In: Proceedings of the 103rd Annual Meeting of the American Association for Cancer Research; 2012 Mar 31-Apr 4; Chicago, IL. Philadelphia (PA): AACR; Cancer Res 2012;72(8 Suppl):Abstract nr 199. doi:1538-7445.AM2012-199

Abstract 96: From genome-wide association studies (GWAS) to functional genomics of prostate cancer: exploring the role of candidate transcripts through RNAi-based analysis

Recent genome-wide association studies (GWAS) have identified multiple genomic regions that harbor single nucleotide polymorphisms (SNPs) associated with human prostate cancer. Determining the biological basis of association data requires the identification of molecular phenotypes that correlate to these sequence variants. However, many of these variants are located in intergenic regions or gene deserts, making it difficult to identify the underlying biological mechanisms these association studies suggest. Two SNPS identified by prostate cancer GWAS include rs10486567 located within intron 2 of JAZF1 gene on chromosome 7p15.2, and rs4430796 located on chromosome 17 near the HNF1B gene. JAZF1 (JAZF zinc finger 1) is a putative transcriptional repressor. SNPs in JAZF1 have also been associated with height body stature, and risk of type-2 diabetes and systemic lupus erythematosus. HNF1B (HNF1 homeobox B) is a homeodomain containing transcription factor; SNPs at this locus show an inverse association with risk of type-2 diabetes and this locus has also been identified as associated with endometrial cancer susceptibility. As the function of JAZF1 and HFNB1 is poorly characterized we are using RNAi based loss-of-function analysis, initially in a prostate cancer cell line, to assess the molecular consequences of silencing these genes. First the transfection conditions for the prostate cancer cell line LNCAP were optimized for synthetic siRNA transfection and multiple siRNAs (from two different vendors) corresponding to JAZF1 and HFN1B were assessed for efficiency of gene specific silencing. To assess the functional consequence of silencing in an unbiased manner we have generated gene specific expression profiles for JAZF1 and HFN1B in LNCAP cells. Briefly, gene expression microarray analysis was conducted on RNA prepared 72 hours post siRNA transfection and expression profiles were generated from data using three different siRNAs corresponding to each gene transfected in triplicate compared to negative control transfected cells. Following silencing of JAZF1 approximately 150 genes were identified as showing significant changes in gene expression, with over 500 other genes showing evidence of altered expression but not at significant level. Following silencing of HFN1B, over 250 genes were identified as showing significant changes in gene expression, with over 400 other genes showing evidence of altered expression but not at significant level. Further analysis and validation of these expression profiles is ongoing.

Citation Format: {Authors}. {Abstract title} [abstract]. In: Proceedings of the 103rd Annual Meeting of the American Association for Cancer Research; 2012 Mar 31-Apr 4; Chicago, IL. Philadelphia (PA): AACR; Cancer Res 2012;72(8 Suppl):Abstract nr 96. doi:1538-7445.AM2012-96

Systems-wide RNAi analysis of CASP8AP2/FLASH shows transcriptional deregulation of the replication-dependent histone genes and extensive effects on the transcriptome of colorectal cancer cells

Background

Colorectal carcinomas (CRC) carry massive genetic and transcriptional alterations that influence multiple cellular pathways. The study of proteins whose loss-of-function (LOF) alters the growth of CRC cells can be used to further understand the cellular processes cancer cells depend upon for survival.

Results

A small-scale RNAi screen of ~400 genes conducted in SW480 CRC cells identified several candidate genes as required for the viability of CRC cells, most prominently CASP8AP2/FLASH. To understand the function of this gene in maintaining the viability of CRC cells in an unbiased manner, we generated gene specific expression profiles following RNAi. Silencing of CASP8AP2/FLASH resulted in altered expression of over 2500 genes enriched for genes associated with cellular growth and proliferation. Loss of CASP8AP2/FLASH function was significantly associated with altered transcription of the genes encoding the replication-dependent histone proteins as a result of the expression of the non-canonical polyA variants of these transcripts. Silencing of CASP8AP2/FLASH also mediated enrichment of changes in the expression of targets of the NFκB and MYC transcription factors. These findings were confirmed by whole transcriptome analysis of CASP8AP2/FLASH silenced cells at multiple time points. Finally, we identified and validated that CASP8AP2/FLASH LOF increases the expression of neurofilament heavy polypeptide (NEFH), a protein recently linked to regulation of the AKT1/ß-catenin pathway.

Conclusions

We have used unbiased RNAi based approaches to identify and characterize the function of CASP8AP2/FLASH, a protein not previously reported as required for cell survival. This study further defines the role CASP8AP2/FLASH plays in the regulating expression of the replication-dependent histones and shows that its LOF results in broad and reproducible effects on the transcriptome of colorectal cancer cells including the induction of expression of the recently described tumor suppressor gene NEFH.

p53-Dependent induction of PVT1 and miR-1204

p53 is a tumor suppressor protein that acts as a transcription factor to regulate (either positively or negatively) a plethora of downstream target genes. Although its ability to induce protein coding genes is well documented, recent studies have implicated p53 in the regulation of non-coding RNAs, including both microRNAs (e.g. miR-34a) and long non-coding RNAs (e.g. lincRNA-p21). We have identified the non-protein coding locus PVT1 as a p53-inducible target gene. PVT1, a very large (>300 kb) locus located downstream of c-myc on chromosome 8q24, produces a wide variety of spliced non-coding RNAs as well as a cluster of six annotated microRNAs: miR-1204, miR-1205, miR-1206, miR-1207-5p, miR-1207-3p, and miR-1208. Chromatin immunoprecipitation (ChIP), electrophoretic mobility shift assay (EMSA), and luciferase assays reveal that p53 binds and activates a canonical response element within the vicinity of miR-1204. Consistently, we demonstrate the p53-dependent induction of endogenous PVT1 transcripts and consequent up-regulation of mature miR-1204. Finally, we have shown that ectopic expression of miR-1204 leads to increased p53 levels and causes cell death in a partially p53-dependent manner.

Abstract C111: Genes cooperatively targeted by combined mTOR/histone deactylase (HDAC) inhibition are predictive of increased multiple myeloma patient survival

The molecular pathogenesis of many cancer types, including multiple myeloma (MM), involves alterations in the PI3K/Akt/mTOR and cyclin/CDK/CDKI/Rb (Rb) pathways. Targeting these pathways individually has shown limited efficacy. Here, however, we show the combination of an HDAC inhibitor with rapamycin synergistically inhibits proliferation in 88% of human myeloma cell lines tested (p<0.01), as well as effectively controlling tumor growth in long-term preclinical studies. To understand the synergistic molecular mechanism of this combination, candidate pathway analysis and a systems-level approach were taken. We found the combination antagonized the oncogenic activation of the AKT pathway associated with single-agent rapamycin treatment, along with inhibiting the ERK/MAPK pathway to a much greater extent than either single agent alone. For a more unbiased approach, gene expression profiling (GEP) was coupled with a systems-level gene co-expression network analysis. This analysis delineated the contribution of each inhibitor to the overall gene expression change of the combination by considering not only measures of fold-change and significance testing, but also the degree of gene expression inter-connectedness. With these findings, a network of five gene modules was constructed, where each module represents a particular gene expression effect of the combination. Each module of genes was then individually tested for functional and clinical enrichment. Of particular interest, the module containing genes cooperatively affected by both compounds was highly enriched (p<0.001) for genes involved in cell cycle (especially mitotic processes), immune recognition, and DNA damage/repair, which we have investigated further. Specifically, we confirmed the down-regulation of RRM2, a gene involved in DNA synthesis and repair, by western blot and validated an increase in DNA damage markers with combination treatment. Additionally, we determined that specific RRM2 inhibition decreased MM cell viability, which decreased further when combined with rapamycin. Gene Set Enrichment Analysis of drug-induced gene expression profiles demonstrated that all gene expression modules associated with the drug combination were significantly enriched (p<0.01) when comparing healthy donors to MM patients in a large, publicly available GEP dataset. Finally, interrogation of the cooperative drug signature in publicly available patient GEP datasets with survival annotation found it predictive of increased survival (p<0.01), thus linking the drug combination-induced transcriptional changes to predictions for enhanced survival.

Citation Format: {Authors}. {Abstract title} [abstract]. In: Proceedings of the AACR-NCI-EORTC International Conference: Molecular Targets and Cancer Therapeutics; 2011 Nov 12-16; San Francisco, CA. Philadelphia (PA): AACR; Mol Cancer Ther 2011;10(11 Suppl):Abstract nr C111.

Genomic instability and mouse microRNAs

Tumor progression is the continual selection of variant subpopulations of malignant cells that have acquired increasing levels of genetic instability (Nowell Science 1976, 194, 23-28). This instability is manifested as chromosomal aneuploidy or translocations, viral integration or somatic mutations that typically affect the expression of a gene (oncogene) that is especially damaging to the proper function of a cell. With the recent discovery of non-coding RNAs such as microRNAs (miRNAs), the concept that a target of genetic instability must be a protein-encoding gene is no longer tenable. Over the years, we have conducted several studies comparing the location of miRNA genes to positions of genetic instability, principally retroviral integration sites and chromosomal translocations in the mouse as a means of identifying miRNAs of importance in carcinogenesis. In this current study, we have used the most recent annotation of the mouse miRome (miRBase, release 16.0), and several datasets reporting the sites of integration of different retroviral vectors in a variety of mouse strains and mouse models of cancer, including for the first time a model that shows a propensity to form solid tumors, as a means to further identify or define, candidate oncogenic miRNAs. Several miRNA genes and miRNA gene clusters stand out as interesting new candidate oncogenes due to their close proximity to common retroviral integration sites including miR-29a/b/c and miR106a~363. We also discussed some recently identified miRNAs including miR-1965, miR-1900, miR-1945, miR-1931, miR-1894, and miR-1936 that are close to common retroviral integration sites and are therefore likely to have some role in cell homeostasis.

Abstract 1181: Expression studies from the PVT1 region of 8q24

Several SNPs in the area surrounding the PVT1 noncoding gene region on human chromosome 8q24 have recently been found by Genome Wide Association (GWA) to be associated with susceptibility to a number of malignancies including Hodgkin's Lymphoma and other diseases including Type II Diabetes and End Stage Renal Disease in Type I Diabetes. This genetically unstable region is one of the most frequent targets of retroviral integration of the Human Papilloma Virus Type 18 (HPV18 in Cervical Carcinoma) and is the frequent target of chromosomal translocation in lymphoid malignancies such as Non-Hodgkin's Lymphoma [incl. Burkitt's Lymphoma (BL) and Diffuse Large B Cell Lymphoma (DLBL)]. Gene amplification in carcinomas such as breast, prostate, ovarian, colon, pancreatic, esophageal, as well as osteogenic sarcoma usually encompasses the proximal region of PVT1 along with its well-known neighboring transcript, MYC, whereas chromosomal deletion (in hematodermic NK lymphoma) affects the distal segment of PVT1. In a search for functionality to PVT1, many laboratories (including our own) have cloned and sequenced transcripts from the PVT1 region from many species in addition to human, with the conclusion that PVT1 is a noncoding or lincRNA with many alternatively spliced isoforms. We have systematically documented these isoforms with a particular focus on promoter and regulatory elements that are found in the region. Our laboratory has also identified a cluster of at least 6 miRNAs (miR-1204∼1208) that span the PVT1 region adding yet another level of complexity to the locus. To begin to assign some function to PVT1 based transcripts in these disease phenotypes, we have made 4th generation (CMV promoter with WPE enhancer) over-expressing lentiviral constructs containing either a large segment of PVT1 (Exons 1b-10) or the most proximal and abundant miRNA, miR-1204. These constructs follow earlier studies with a 3rd generation lentivirus (CMV promoter) containing miR-1204 that rapidly generated DLBL in cooperation with MYC or IL6 transgenes (∼16 days or 82 days respectively). While these results pointed to over-expression of miR-1204 playing a specific role in the development of B cell malignancy, additional studies with the LentiCMV-miR-1204 construct in other tumor cell lines (prostate and breast) also revealed potential phenotypic changes in cell proliferation and migration. With the new 4th generation constructs, experiments are now underway in cell lines and mouse models to determine if over-expression of miR-1204 or PVT1 alone is sufficient to induce phenotypic changes.

Citation Format: {Authors}. {Abstract title} [abstract]. In: Proceedings of the 102nd Annual Meeting of the American Association for Cancer Research; 2011 Apr 2-6; Orlando, FL. Philadelphia (PA): AACR; Cancer Res 2011;71(8 Suppl):Abstract nr 1181. doi:10.1158/1538-7445.AM2011-1181

A genomic strategy for the functional validation of colorectal cancer genes identifies potential therapeutic targets

Genes that are highly overexpressed in tumor cells can be required for tumor cell survival and have the potential to be selective therapeutic targets. In an attempt to identify such targets, we combined a functional genomics and a systems biology approach to assess the consequences of RNAi-mediated silencing of overexpressed genes that were selected from 140 gene expression profiles from colorectal cancers (CRCs) and matched normal mucosa. In order to identify credible models for in-depth functional analysis, we first confirmed the overexpression of these genes in 25 different CRC cell lines. We then identified five candidate genes that profoundly reduced the viability of CRC cell lines when silenced with either siRNAs or short-hairpin RNAs (shRNAs), i.e., HMGA1, TACSTD2, RRM2, RPS2 and NOL5A. These genes were further studied by systematic analysis of comprehensive gene expression profiles generated following siRNA-mediated silencing. Exploration of these RNAi-specific gene expression signatures allowed the identification of the functional space in which the five genes operate and showed enrichment for cancer-specific signaling pathways, some known to be involved in CRC. By comparing the expression of the RNAi signature genes with their respective expression levels in an independent set of primary rectal carcinomas, we could recapitulate these defined RNAi signatures, therefore, establishing the biological relevance of our observations. This strategy identified the signaling pathways that are affected by the prominent oncogenes HMGA1 and TACSTD2, established a yet unknown link between RRM2 and PLK1 and identified RPS2 and NOL5A as promising potential therapeutic targets in CRC.

A genomic strategy for the functional validation of colorectal cancer genes identifies potential therapeutic targets

Genes that are highly overexpressed in tumor cells can be required for tumor cell survival and have the potential to be selective therapeutic targets. In an attempt to identify such targets, we combined a functional genomics and a systems biology approach to assess the consequences of RNAi-mediated silencing of overexpressed genes that were selected from 140 gene expression profiles from colorectal cancers (CRCs) and matched normal mucosa. In order to identify credible models for in-depth functional analysis, we first confirmed the overexpression of these genes in 25 different CRC cell lines. We then identified five candidate genes that profoundly reduced the viability of CRC cell lines when silenced with either siRNAs or short-hairpin RNAs (shRNAs), i.e., HMGA1, TACSTD2, RRM2, RPS2 and NOL5A. These genes were further studied by systematic analysis of comprehensive gene expression profiles generated following siRNA-mediated silencing. Exploration of these RNAi-specific gene expression signatures allowed the identification of the functional space in which the five genes operate and showed enrichment for cancer-specific signaling pathways, some known to be involved in CRC. By comparing the expression of the RNAi signature genes with their respective expression levels in an independent set of primary rectal carcinomas, we could recapitulate these defined RNAi signatures, therefore, establishing the biological relevance of our observations. This strategy identified the signaling pathways that are affected by the prominent oncogenes HMGA1 and TACSTD2, established a yet unknown link between RRM2 and PLK1 and identified RPS2 and NOL5A as promising potential therapeutic targets in CRC.

Abstract 247: A functional genomics and a systems biology approach identify POMP as a potential therapeutic target for colorectal cancer

Colorectal cancer (CRC) is one of the most frequent malignancies in many parts of the world and a leading cause of cancer deaths in both men and women. The identification of rationale therapeutic targets is one possibility to provide personalized medicine to cancer patients. Our approach consisted of identifying overexpressed genes located at sites of recurrent chromosomal amplifications, as these regions are likely to harbor genes required for cancer cell survival. Thirty-one colon cancers and 15 CRC cell lines were analyzed by high-resolution array CGH and microarray gene expression profiling. RNA interference (RNAi)-based analysis identified a subset of genes whose loss-of-function (LOF) reduced the cellular viability of CRC cell lines. Consistent with previous reports, the vast majority of CRC assayed exhibited amplification of the chromosome band 13q12.13-q12.3. Among the genes residing within the 13q12.13-q12.3 amplified region showing an overexpression level of at least two-fold higher in the tumor compared to normal mucosa and whose gene silencing impaired cellular survival, we identified NUPL1, LNX2, POLR1D, CDX2, POMP, and SLC7A1. As little is know of the function of these proteins, we decided to use an unbiased systems biology approach to identify genes, pathways and networks altered following RNAi-mediated LOF of each of these candidate genes. To do this we perturbed the expression of each candidate gene through application of two or more siRNAs corresponding to each gene, followed by whole genome expression profiling to monitor cellular transcriptional responses to gene specific LOF. Concordant gene expression signatures generated using three different RNAi effectors targeting POMP, over a time-course (10, 24, 48, and 72 hours), showed that a decrease in POMP expression of more than 80% at 24 hours initially resulted in only minor downstream changes in gene expression. However, by 48 hours approximately 100 genes exhibited altered expression and by 72 hours nearly 2000 genes. At this last time point a statistically significant enrichment (p<0.05) for the altered expression of genes linked to the gene ontologies of cancer, cell death, and cellular growth was observed. POMP, a proteasome maturation protein, is an essential factor for mammalian proteasome biogenesis. This dynamic loss-of-function approach revealed a regulatory network that controls the transcriptional response of colorectal cancer cells after impairing the function of the proteasome. We are also investigating whether the gene expression profiles observed following silencing of POMP resemble the transcriptomic changes that undergo cells treated with proteasome inhibitors as this may shed further light on the mechanism of action of this new class of anti-cancer drugs particularly in CRC.

Citation Format: {Authors}. {Abstract title} [abstract]. In: Proceedings of the 101st Annual Meeting of the American Association for Cancer Research; 2010 Apr 17-21; Washington, DC. Philadelphia (PA): AACR; Cancer Res 2010;70(8 Suppl):Abstract nr 247.

Abstract 1683: ATF4 down-regulation potentiates L-asparaginase activity in ovarian cancer cell lines

The enzyme-drug L-asparaginase (L-ASP) has been used for four decades to treat acute lymphoblastic leukemia. However, its unique mechanism of action is still poorly understood, and its clinical efficacy has proven unpredictable. Those problems have prompted a continuing search for biomarkers that predict L-ASP response. We previously found that the expression of asparagine synthetase (ASNS) is strongly correlated with L-ASP activity in leukemia cell lines of the NCI-60 cell line panel. Unexpectedly, however, the correlation was also apparent in ovarian cancer lines, suggesting that L-ASP might be effective against a low-ASNS subset of ovarian cancers if salient characteristics of the cell lines reflect clinical ovarian tumors. Using siRNA to down-regulate ASNS by 5-fold produced a proportional ∼5-fold potentiation of L-ASP activity in some ovarian cancer lines (OVCAR-3 and OVCAR-4). Surprisingly, ASNS siRNAs yielded a striking >500-fold potentiation in other ovarian lines (OVCAR-8 and OVCAR-8/ADR). Taken together, those findings suggest that the L-ASP/ASNS correlation is causal but also support the hypothesis that L-ASP activity is modulated by additional molecules or pathways. To address that hypothesis and to further elucidate the L-ASP mechanism of action, we have initiated genome-wide siRNA library screening. Preliminary screens in the OVCAR-8 cell line using a 418-gene apoptosis library, a custom 392-gene metabolic library, and the MTS assay as an endpoint yielded Z′ factors >0.90, indicating a robust screen. RNAi-mediated down-regulation of apoptosis genes had little or no effect on L-ASP's anticancer activity. That was surprising because L-ASP has been reported to cause apoptosis through glutamine depletion. Knock-down of ATF4, a transcription factor involved in cell metabolism, did markedly potentiate L-ASP activity (>500-fold). Furthermore, ATF4 knock-down markedly enhanced L-ASP anticancer activity toward the highly resistant cell line, OVCAR-4. These findings suggest that ATF4 is an important mediator of L-ASP resistance and provide rationale for investigation of ATF4 as a predictive biomarker of L-ASP effect.

Note: This abstract was not presented at the AACR 101st Annual Meeting 2010 because the presenter was unable to attend.

Citation Format: {Authors}. {Abstract title} [abstract]. In: Proceedings of the 101st Annual Meeting of the American Association for Cancer Research; 2010 Apr 17-21; Washington, DC. Philadelphia (PA): AACR; Cancer Res 2010;70(8 Suppl):Abstract nr 1683.

Abstract 1952: The rapid generation of mouse B cell lymphomas by lentiviral mediated overexpression of miR-1204 from a genetically unstable region of human 8q24

SNPs in the area surrounding MYC on human 8q24 have recently been found by Genome Wide Association (GWA) to be associated with susceptibility to a number of malignancies including prostate, breast, colorectal and bladder carcinomas (CA). This genetically unstable region is also a frequent target of chromosomal translocation (Tx), amplification or retroviral integration in a number of CAs such as breast, prostate, ovarian, colon, pancreatic, and cervical. In one example, essentially 100% of patients with Burkitt's lymphoma exhibit one of three characteristic non-random chromosomal Txs that places MYC or the immediate surrounding region in close proximity to enhancers of the immunoglobulin (Ig) heavy chain or light chain loci. Although de-regulated MYC expression could be assumed to be the target of the genomic instability or GWA-based susceptibility, no clear correlation between MYC expression and disease has been established. A possible alternative target has been identified in a series of transcripts cloned from the PVT1 region downstream of MYC. However, the extent of alternative splicing coupled with the lack of a coding region has made it difficult to assign a specific role for any PVT1-derived transcripts. Recently, we have identified a cluster of small RNAs exhibiting the hairpin formation, sequence conservation and expression characteristics of miRNAs (miR-1204∼1208) within the transcriptional domain of PVT1. Increased expression of several of these miRNAs in tumors harboring amplified MYC/PVT1 or Burkitt lymphomas with the 8q24 Tx suggests a possible role for these miRNAs in tumorigenesis, especially for miR-1204 which is found 60 kb downstream of MYC, flanking exon 1b of PVT1. An increased expression of miR-1204 in pre-B cells compared to pro-B cells also suggested a lymphoid specific developmental pattern of expression. Lentiviral constructs of miR-1204 under control of a CMV promoter (LentiCMV-miR-1204) revealed a possible effect on MYC, but in a pre-B (not pro-B) specific environment. Introduction of LentiCMV-miR-1204 into mice harboring either a MYC (C.iMYC) or IL6 (C.IL6) transgene resulted in high frequency and rapid onset of large B cell lymphomas (∼16 or 82 days vs. 91 or 117 days for controls, respectively). While these results point to over-expression of miR-1204 playing a specific role in the development of B cell malignancy, additional studies with the LentiCMV-miR-1204 construct in other tumor cell lines (prostate and breast) also reveal phenotypic changes in cell proliferation and migration. Further studies using lentiviruses with alternative promoters for miR-1204 and the other 8q24 associated miRNAs are underway to identify downstream targets and pathways not only in lymphoid malignancy but also in the wide range of malignancies associated with GWA-susceptibility and genomic instability.

Citation Format: {Authors}. {Abstract title} [abstract]. In: Proceedings of the 101st Annual Meeting of the American Association for Cancer Research; 2010 Apr 17-21; Washington, DC. Philadelphia (PA): AACR; Cancer Res 2010;70(8 Suppl):Abstract nr 1952.

Abstract 2098: The receptor tyrosine kinase AXL is a target for the human miR-34a microRNA

Determining the protein targets of microRNAs (miRNAs) will be critical to understanding the role these non-coding RNAs play in regulating gene function and what impact they have in cancer biology. In this study, we show by a combination of microarray, Northern, and PCR-based analyses that the human miR-34a miRNA is significantly under-expressed in basal-like breast cancer cell lines exhibiting triple receptor negative characteristics, as compared to a non-tumorigenic mammary epithelial cell line control. Introduction of a synthetic mimic of hsa-miR-34a into MDA-MB-231 cells resulted in a substantial alteration in both the mRNA and protein levels of the receptor tyrosine kinase AXL, 48 hours post-transfection. Furthermore, the transfection of the hsa-miR-34a mimic decreased the migratory potential of these cells in a manner consistent with the function of AXL as a promoter of cell proliferation, invasion, and metastasis in a number of cancer cell types including breast cancer. This observed phenotypic effect supports the hypothesis that miR-34a functions as a tumor suppressor, with the direct translational repression of AXL representing just one of many possible targets that this miRNA regulates.

Citation Format: {Authors}. {Abstract title} [abstract]. In: Proceedings of the 101st Annual Meeting of the American Association for Cancer Research; 2010 Apr 17-21; Washington, DC. Philadelphia (PA): AACR; Cancer Res 2010;70(8 Suppl):Abstract nr 2098.

Abstract A120: Cellular inhibition of Chk2 kinase and potentiation of camptothecins and radiation by the novel Chk2 inhibitor PV1019

Chk2 is a checkpoint kinase involved in the ATM pathway, which is activated by genomic instability and DNA damage, leading to either cell death (apoptosis) or cell cycle arrest. Chk2 provides an unexplored therapeutic target against cancer cells. We recently reported NSC 109555 as a novel chemotype Chk2 inhibitor. We have now synthesized a derivative of NSC 109555, PV1019 (NSC 744039), which is a selective sub-micromolar inhibitor of Chk2 in vitro. The co-crystal structure of PV1019 bound in the ATP binding pocket of Chk2 confirmed enzymatic/biochemical observations that PV1019 acts as a competitive inhibitor of Chk2 with respect to ATP. PV1019 was found to inhibit Chk2 in cells. It inhibits Chk2 autophosphorylation (which represents the cellular kinase activation of Chk2), Cdc25C phosphorylation, and HDMX degradation in response to DNA damage. PV1019 also protects normal mouse thymocytes against IR-induced apoptosis, and it shows synergistic antiproliferative activity with topotecan, camptothecin, and radiation in human tumor cell lines. We also show that PV1019 as well as Chk2 siRNA can exert antiproliferative activity themselves in the cancer cells with high Chk2 expression in the NCI60 screen. These data indicate that PV1019 is a potent and selective inhibitor of Chk2 with chemotherapeutic and radiosensitization potential.

Citation Information: Mol Cancer Ther 2009;8(12 Suppl):A120.

Identification of WEE1 as a potential molecular target in cancer cells by RNAi screening of the human tyrosine kinome

Breast cancers can be classified into those that express the estrogen (ER) and progesterone (PR) receptors, those with ERBB2 (HER-2/Neu) amplification, and those without expression of ER, PR, or amplification of ERBB2 (referred to as triple-negative or basal-like breast cancer). In order to identify potential molecular targets in breast cancer, we performed a synthetic siRNA-mediated RNAi screen of the human tyrosine kinome. A primary RNAi screen conducted in the triple-negative/basal-like breast cancer cell line MDA-MB231 followed by secondary RNAi screens and further studies in this cell line and two additional triple-negative/basal-like breast cancer cell lines, BT20 and HCC1937, identified the G2/M checkpoint protein, WEE1, as a potential therapeutic target. Similar sensitivity to WEE1 inhibition was observed in cell lines from all subtypes of breast cancer. RNAi-mediated silencing or small compound inhibition of WEE1 in breast cancer cell lines resulted in an increase in gammaH2AX levels, arrest in the S-phase of the cell cycle, and a significant decrease in cell proliferation. WEE1-inhibited cells underwent apoptosis as demonstrated by positive Annexin V staining, increased sub-G1 DNA content, apoptotic morphology, caspase activation, and rescue by the pan-caspase inhibitor, Z-VAD-FMK. In contrast, the non-transformed mammary epithelial cell line, MCF10A, did not exhibit any of these downstream effects following WEE1 silencing or inhibition. These results identify WEE1 as a potential molecular target in breast cancer.

Cellular inhibition of checkpoint kinase 2 (Chk2) and potentiation of camptothecins and radiation by the novel Chk2 inhibitor PV1019 [7-nitro-1H-indole-2-carboxylic acid {4-[1-(guanidinohydrazone)-ethyl]-phenyl}-amide]

Chk2 is a checkpoint kinase involved in the ataxia telangiectasia mutated pathway, which is activated by genomic instability and DNA damage, leading to either cell death (apoptosis) or cell cycle arrest. Chk2 provides an unexplored therapeutic target against cancer cells. We recently reported 4,4'-diacetyldiphenylurea-bis(guanylhydrazone) (NSC 109555) as a novel chemotype Chk2 inhibitor. We have now synthesized a derivative of NSC 109555, PV1019 (NSC 744039) [7-nitro-1H-indole-2-carboxylic acid {4-[1-(guanidinohydrazone)-ethyl]-phenyl}-amide], which is a selective submicromolar inhibitor of Chk2 in vitro. The cocrystal structure of PV1019 bound in the ATP binding pocket of Chk2 confirmed enzymatic/biochemical observations that PV1019 acts as a competitive inhibitor of Chk2 with respect to ATP. PV1019 was found to inhibit Chk2 in cells. It inhibits Chk2 autophosphorylation (which represents the cellular kinase activation of Chk2), Cdc25C phosphorylation, and HDMX degradation in response to DNA damage. PV1019 also protects normal mouse thymocytes against ionizing radiation-induced apoptosis, and it shows synergistic antiproliferative activity with topotecan, camptothecin, and radiation in human tumor cell lines. We also show that PV1019 and Chk2 small interfering RNAs can exert antiproliferative activity themselves in the cancer cells with high Chk2 expression in the NCI-60 screen. These data indicate that PV1019 is a potent and selective inhibitor of Chk2 with chemotherapeutic and radiosensitization potential.