S1: A) Agarose gels showing PCR amplification of a region within HIF-2α exon 2 from genomic DNA from 786-0 HIF-2α deletion mutants, EPAS1-/- #4 and EPAS1-/-#11 compared to 786-0 cells transfected with Nickase control (NicCon). Clone #4 and #11 were generated using separate pairs of guide strands targeting different regions within exon 2. B) PCR primers used for amplification. C) Western blot showing HIF-2α protein levels in 786-0 Crispr clones compared to Nickase Control. D) Luciferase assay showing luciferase activity of a transiently transfected hypoxia-responsive element (HRE) - luciferase reporter normalized to a co-transfected beta-actin Renilla luciferase reporter in 786-0 Crispr clones compared to parental 786-0 cells. E) Genetic characterization of EPAS1-/-#4 aligned to EPAS1 NCBI RefSeq NG_016000.1. Clone #4 is a clonal population of cells with a 70bp deletion within one EPAS1 (HIF-2α) allele, and multiple indels within the corresponding region of the second allele: 5 insertions (underlined), 8 mutations (caps). F) Genetic characterization of EPAS-/- #11 aligned to EPAS1 NCBI RefSeq NG_016000.1. Clone #11 is a polyclonal cell population containing at least three variants of EPAS1 (HIF-2α), each with multiple mutations/indels within the targeted region. No wild-type allele was detected. S2: A) Growth curves of 786-0 Vec and HAF overexpressing CCRCC cells in normoxia. B) Normalized densitometry values of Western blots shown in Fig. 5A S3: Western blot showing expression levels of total PDGFR in ACHN, 786-0 and Caki-1 cells. S4: Western blot showing dose-dependent effect of SCH772984 on levels of phosphorylated and total p42/p44 ERK, and their downstream targets, the p90 ribosomal S6 kinases (RSK1/2/3) in 786-0 cells in normoxia. S5: Quantitation of HAF nuclear positivity in CCRCC tumor microarray comprising tumor cores of patients treated with sorafenib. Representative tumor cores image with low and high HAF levels with Aperio quantitation of HAF staining (given by % positivity) are shown. S6: HAF (SART1) expression data from TCGA-KIRC with associated survival data and HAF expression level group stratification. To show survival in months (in Figure 7), survival in days was divided by an average of 30 days per month. S7: A) Western blot showing levels of phosphorylated and total p70 ribosomal S6 protein (S6 ribosomal protein) in 786-0 cells stably expressing HAF or HAF DM after 24 hours' exposure to normoxia or hypoxia. B) Impact of 24 hours' rapamycin treatment on levels of phospho- and total mTOR, S6RP and ERK in 786-0 cells stably expressing empty vector or HAF.

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Clear cell renal cell carcinoma (ccRCC), the most common form of kidney cancer, is typically initiated by inactivation of the von Hippel Lindau (VHL) gene, which results in the constitutive activation of the hypoxia inducible factors, HIF-1α and HIF-2α. Using a high throughput screen, we identify novel compounds that decrease HIF-1/2α levels and induce ferroptosis by targeting Iron Sulfur Cluster Assembly 2 (ISCA2), a component of the late mitochondrial Iron Sulfur Cluster (L-ISC) assembly complex. ISCA2 inhibition either pharmacologically or using siRNA decreases HIF-2α protein levels by blocking iron-responsive element (IRE)-dependent translation, and at higher concentrations, also decreases HIF-1α translation through unknown mechanisms. Additionally, ISCA2 inhibition triggers the iron starvation response, resulting in iron/metals overload and death via ferroptosis. ISCA2 levels are decreased in ccRCC compared to normal kidney, and decreased ISCA2 levels are associated with pVHL loss and with sensitivity to ferroptosis induced by ISCA2 inhibition. Strikingly, pharmacological inhibition of ISCA2 using an orally available ISCA2 inhibitor significantly reduced ccRCC xenograft growth in vivo, decreased HIF-α levels and increased lipid peroxidation, suggesting increased ferroptosis in vivo. Thus, the targeting of ISCA2 may be a promising therapeutic strategy to inhibit HIF-1/2α and to induce ferroptosis in pVHL deficient cells.

AbstractPurpose: Clear cell renal cell carcinoma (ccRCC) is frequently associated with inactivation of the von Hippel–Lindau tumor suppressor, resulting in activation of HIF-1α and HIF-2α. The current paradigm, established using mechanistic cell-based studies, supports a tumor promoting role for HIF-2α, and a tumor suppressor role for HIF-1α. However, few studies have comprehensively examined the clinical relevance of this paradigm. Furthermore, the hypoxia-associated factor (HAF), which regulates the HIFs, has not been comprehensively evaluated in ccRCC. Experimental Design: To assess the involvement of HAF/HIFs in ccRCC, we analyzed their relationship to tumor grade/stage/outcome using tissue from 380 patients, and validated these associations using tissue from 72 additional patients and a further 57 patients treated with antiangiogenic therapy for associations with response. Further characterization was performed using single-cell mRNA sequencing (scRNA-seq), RNA-in situ hybridization (RNA-ISH), and IHC. Results: HIF-1α was primarily expressed in tumor-associated macrophages (TAMs), whereas HIF-2α and HAF were expressed primarily in tumor cells. TAM-associated HIF-1α was significantly associated with high tumor grade and increased metastasis and was independently associated with decreased overall survival. Furthermore, elevated TAM HIF-1α was significantly associated with resistance to antiangiogenic therapy. In contrast, high HAF or HIF-2α were associated with low grade, decreased metastasis, and increased overall survival. scRNA-seq, RNA-ISH, and Western blotting confirmed the expression of HIF-1α in M2-polarized CD163-expressing TAMs. Conclusions: These findings highlight a potential role of TAM HIF-1α in ccRCC progression and support the reevaluation of HIF-1α as a therapeutic target and marker of disease progression.

AbstractLow oxygen or hypoxia is a feature of all solid tumors and has been associated with aggressive disease. Here, we describe a novel mechanism for the hypoxia-dependent degradation of the Ras-GTPase–activating protein neurofibromin, by hypoxia-associated factor (HAF). We have previously characterized HAF as an oxygen-independent ubiquitin ligase for HIF-1α. Here, we show that HAF promotes neurofibromin ubiquitination and degradation independently of oxygen and pVHL, resulting in Ras–ERK pathway activation. Hypoxia enhanced HAF:neurofibromin binding independently of HAF-SUMOylation, whereas HAF knockdown increased neurofibromin levels primarily in hypoxia, supporting the role of HAF as a hypoxia-specific neurofibromin regulator. HAF overexpression increased p-ERK levels and promoted resistance of clear cell kidney cancer (ccRCC) cells to sorafenib and sunitinib in both normoxia and hypoxia. However, a greater-fold increase in sorafenib/sunitinib resistance was observed during hypoxia, particularly in pVHL-deficient cells. Intriguingly, HAF-mediated resistance was HIF-2α–dependent in normoxia, but HIF-2α–independent in hypoxia indicating two potential mechanisms of HAF-mediated resistance: a HIF-2α–dependent pathway dominant in normoxia, and the direct activation of the Ras–ERK pathway through neurofibromin degradation dominant in hypoxia. Patients with ccRCC with high HAF transcript or protein levels showed significantly decreased overall survival compared with those with low HAF. Thus, we establish a novel, nonmutational pathway of neurofibromin inactivation through hypoxia-induced HAF-mediated degradation, leading to Ras–ERK activation and poor prognosis in ccRCC.Implications:We describe a novel mechanism of neurofibromin degradation induced by hypoxia that leads to activation of the prooncogenic Ras–ERK pathway and resistance to therapy.

Osteosarcoma (OS) is a highly aggressive mesenchymal malignancy and the most common primary bone tumor in the pediatric population. OS frequently presents with or develops distal metastases. Patients with metastatic disease have extremely poor survival rates, thus necessitating improved molecular insights into OS metastatic biology. Utilizing our previously characterized genetically engineered mouse model (GEMM) of metastatic OS, we identified enhanced differential expression of Transglutaminase-2 (TGM2) in metastatic OS. However, the role of TGM2 in sarcoma development and metastatic progression remains largely undefined. To further investigate the role of TGM2 in OS metastasis, we performed both gain- and loss-of-function studies for TGM2 in human and mouse OS cell lines. Our data provide evidence that enhanced expression of TGM2 in metastatic OS contributes to migratory and invasive phenotypes. Besides the effects on metastatic phenotypes, we also observed that TGM2 contributes to OS stem-like properties. In addition, treatment with transglutaminase inhibitors had analogous effects on proliferation and migration to TGM2 knockdown. Finally, in vivo xenograft studies demonstrated that TGM2 functionally alters metastatic potential and survival outcome. Together, these data highlight TGM2 as a pro-metastatic factor in OS and a potential avenue for future therapeutic intervention to inhibit metastatic disease.

BACKGROUND:Osteosarcoma (OS) is the most common bone malignancy in the paediatric population, principally affecting adolescents and young adults. Minimal advancements in patient prognosis have been made over the past two decades because of the poor understanding of disease biology. Runx2, a critical transcription factor in bone development, is frequently amplified and overexpressed in OS. However, the molecular and biological consequences of Runx2 overexpression remain unclear. METHODS:si/shRNA and overexpression technology to alter Runx2 levels in OS cells. In vitro assessment of doxorubicin (doxo)-induced apoptosis and in vivo chemosensitivity studies. Small-molecule inhibitor of c-Myc transcriptional activity was used to assess its role. RESULTS:Loss of Runx2 sensitises cells to doxo-induced apoptosis both in vitro and in vivo. Furthermore, in conjunction with chemotherapy, decreasing Runx2 protein levels activates both the intrinsic and extrinsic apoptotic pathways. Transplanted tumour studies demonstrated that loss of endogenous Runx2 protein expression enhances caspase-3 cleavage and tumour necrosis in response to chemotherapy. Finally, upon doxo-treated Runx2 knockdown OS cells there was evidence of enhanced c-Myc expression and transcriptional activity. Inhibition of c-Myc under these conditions resulted in decreased activation of apoptosis, therefore insinuating a role for c-Myc in dox-induced activation of apoptotic pathways. CONCLUSIONS:Therefore, we have established a novel molecular mechanism by which Runx2 provides a chemoprotective role in OS, indicating that in conjunction to standard chemotherapy, targeting Runx2 may be a new therapeutic strategy for patients with OS.

Osteosarcomas (OSs) are characterized by high levels of genomic instability (GI). To gain insights into the GI and its contribution toward understanding the genetic basis of OS, we characterized 19 primary and 13 metastatic mouse tumors in a genetically engineered novel mouse model of OS by a combination of genomic techniques. Through the bone‐specific deletion of the wild‐type Trp53 locus or activation of a metastatic‐promoting missense R172Hp53 allele, C57BL/6 mice developed either localized or metastatic OS. Subsequent tumors were isolated and primary cultures created from primary bone and/or distal metastatic lesions, for example, lung and liver. These tumors exhibited high levels of GI with complex chromosomal rearrangements, amplifications, and deletions comparable to human OS. The combined genomic approaches identified frequent amplification of chromosome 15D1 and loss of 11B4 by CGH and/or SKY. Both 15D1 and 11B4 have homology with frequently altered chromosomal bands 8q24 and 17p13 in human OS, respectively. Subsequent array CGH, FISH, and qRT‐PCR analysis identified coamplification and overexpression of Myc/Pvt1 transcripts from the 15D1 amplicon and loss and decreased expression of the Nlrp1b from 11B4. The Nlrp1 gene is the key mediator of apoptosis and interacts strongly with caspase 2. © 2015 Wiley Periodicals, Inc.

Background: Recent clinical trials of VEGF inhibitors have shown promise in the treatment of recurrent glioblastomas (GBM). However, the survival benefit is usually short-lived as tumors escape anti-VEGF therapies. Here we tested the hypothesis that Platelet Derived Growth Factor-C (PDGF-C), an isoform of the PDGF family, affects GBM progression independent of VEGF pathway and hinders anti-VEGF therapy.Principal Findings: We first showed that PDGF-C is present in human GBMs. Then, we overexpressed or downregulated PDGF-C in a human GBM cell line, U87MG, and grew them in cranial windows in nude mice to assess vessel structure and function using intravital microscopy. PDGF-C overexpressing tumors had smaller vessel diameters and lower vascular permeability compared to the parental or siRNA-transfected tumors. Furthermore, vessels in PDGF-C overexpressing tumors had more extensive coverage with NG2 positive perivascular cells and a thicker collagen IV basement membrane than the controls. Treatment with DC101, an anti-VEGFR-2 antibody, induced decreases in vessel density in the parental tumors, but had no effect on the PDGF-C overexpressing tumors.Conclusion: These results suggest that PDGF-C plays an important role in glioma vessel maturation and stabilization, and that it can attenuate the response to anti-VEGF therapy, potentially contributing to escape from vascular normalization.

This paper presents methods to model complex vasculature in three-dimensional (3-D) images using cylindroidal superellipsoids, along with robust estimation and detection algorithms for automated image analysis. This model offers an explicit, low-order parameterization, enabling joint estimation of boundary, centerlines, and local pose. It provides a geometric framework for directed vessel traversal, and extraction of topological information like branch point locations and connectivity. M-estimators provide robust region-based statistics that are used to drive the superellipsoid toward a vessel boundary. A robust likelihood ratio test is used to differentiate between noise, artifacts, and other complex unmodeled structures, thereby verifying the model estimate. The proposed methodology behaves well across scale-space, shows a high degree of insensitivity to adjacent structures and implicitly handles branching. When evaluated on synthetic imagery mimicking specific structural complexities in tumor microvasculature, it consistently produces ubvoxel accuracy estimates of centerlines and widths in the presence of closely-adjacent vessels, branch points, and noise. An edit-based validation demonstrated a precision level of 96.6% at a recall level of 95.4%. Overall, it is robust enough for large-scale application.