Nutrient scavenging-fueled growth in pancreatic cancer depends on caveolae-mediated endocytosis under nutrient-deprived conditions

Pancreatic ductal adenocarcinoma (PDAC) is characterized by its nutrient-scavenging ability, crucial for tumor progression. Here, we investigated the roles of caveolae-mediated endocytosis (CME) in PDAC progression. Analysis of patient data across diverse datasets revealed a strong association of high caveolin-1 (Cav-1) expression with higher histologic grade, the most aggressive PDAC molecular subtypes, and worse clinical outcomes. Cav-1 loss markedly promoted longer overall and tumor-free survival in a genetically engineered mouse model. Cav-1-deficient tumor cell lines exhibited significantly reduced proliferation, particularly under low nutrient conditions. Supplementing cells with albumin rescued the growth of Cav-1-proficient PDAC cells, but not in Cav-1-deficient PDAC cells under low glutamine conditions. In addition, Cav-1 depletion led to significant metabolic defects, including decreased glycolytic and mitochondrial metabolism, and downstream protein translation signaling pathways. These findings highlight the crucial role of Cav-1 and CME in fueling pancreatic tumorigenesis, sustaining tumor growth, and promoting survival through nutrient scavenging.

A Bioinformatics Tool for Identifying Intratumoral Microbes from the ORIEN Dataset

Evidence supports significant interactions among microbes, immune cells, and tumor cells in at least 10%-20% of human cancers, emphasizing the importance of further investigating these complex relationships. However, the implications and significance of tumor-related microbes remain largely unknown. Studies have demonstrated the critical roles of host microbes in cancer prevention and treatment responses. Understanding interactions between host microbes and cancer can drive cancer diagnosis and microbial therapeutics (bugs as drugs). Computational identification of cancer-specific microbes and their associations is still challenging due to the high dimensionality and high sparsity of intratumoral microbiome data, which requires large datasets containing sufficient event observations to identify relationships, and the interactions within microbial communities, the heterogeneity in microbial composition, and other confounding effects that can lead to spurious associations. To solve these issues, we present a bioinformatics tool, microbial graph attention (MEGA), to identify the microbes most strongly associated with 12 cancer types. We demonstrate its utility on a dataset from a consortium of nine cancer centers in the Oncology Research Information Exchange Network. This package has three unique features: species-sample relations are represented in a heterogeneous graph and learned by a graph attention network; it incorporates metabolic and phylogenetic information to reflect intricate relationships within microbial communities; and it provides multiple functionalities for association interpretations and visualizations. We analyzed 2,704 tumor RNA sequencing samples and MEGA interpreted the tissue-resident microbial signatures of each of 12 cancer types. MEGA can effectively identify cancer-associated microbial signatures and refine their interactions with tumors.

SIGNIFICANCE

Studying the tumor microbiome in high-throughput sequencing data is challenging because of the extremely sparse data matrices, heterogeneity, and high likelihood of contamination. We present a new deep learning tool, MEGA, to refine the organisms that interact with tumors.

Comparative Analysis of Tumor Microbiome, Molecular Profile and Immune Cell Abundance by HPV Status in Head and Neck Cancers and Their Impact on Survival

PURPOSE/OBJECTIVE(S)

Traditional clinical and molecular prognostic factors offer valuable insight into the heterogeneous natural history and treatment response of head and neck squamous cell carcinoma (HNSCC) yet fail to explain the full spectrum of observed variability. The tumor microenvironment (TME), comprising microbiome and immune cells can impact treatment response and prognosis. We analyzed The Cancer Genome Atlas (TCGA) to evaluate the association of specific microbes and genes in TME with survival and their differential expression in HPV positive (+) and HPV negative (-) HNSCC.

MATERIALS/METHODS

HNSCC RNA sequencing (RNAseq) samples from TCGA were processed through the Exogenous sequencing in Tumors and Immune Cells (ExoTIC) pipeline to identify gene expression and microbial presence. HPV status was assessed by detection of papillomaviridae family of microbes. Clinical data from TCGA was extracted to compare overall survival (OS) and control for competing variables using Cox proportional hazards regression. Difference in immune cell abundance was evaluated by Kruskal-Wallis test. All statistical analysis was performed using R.

RESULTS

A total of 498 RNAseq samples from TCGA were analyzed. Oral cavity, oropharynx, hypopharynx, and larynx tumors comprised 21.6%, 15%, 1.8%, and 22.2% of specimens, respectively. HPV was detected in 111 patients (22%), most commonly Alpha papillomavirus 9 (90.1%). Of the 5838 enriched microbes, 330 were significantly associated with OS after controlling for tumor stage, smoking, and age. Specifically, the presence of Alpha papillomavirus 9 was associated with significantly improved OS [adjusted HR = 0.60 (95% CI 0.40 - 0.89, p = 0.01)]. Microbial species found in more abundance in HPV- tumors included Citrobacter farmeri, Thermoanaerobacter kivui and Yersinia pestis which are gram negative anaerobes. Genes related to cellular transport and DNA repair were enriched while genes related to proliferation (e.g., SAGE1) were depleted in HPV+ samples. HPV- tumors had a significantly higher number of M0 (p < 0.001) and M2 macrophages (p = 0.035) while HPV+ tumors had more T regulatory cells (p < 0.001) and CD8+ T-cells (p < 0.001).

CONCLUSION

Tumor microenvironment was significantly associated with survival for HNSCC patients, with particular microbes such as Alpha papillomavirus 9 correlating with improved OS. Greater abundance of certain anaerobic microbes was seen in HPV- tumors. These findings suggest TME can be used to predict patient outcomes and potentially guide personalized treatment approaches. We found an abundance of M0 and M2 macrophages in HPV- tumors, which are considered pro-tumorigenic, while anti-tumor M1 macrophages were similar in the two groups. This may help identify mechanism of resistance to immunotherapies and tailor novel immunotherapy combinations in specific patient subgroups. With further prospective research and external validation these findings have the potential to significantly impact the way we treat HNSCC in the future.

Prognostic Value of Hypoxia Gene Expression Signature in Early-Stage Non-Small Cell Lung Cancer Patients Treated with Stereotactic Body Radiation Therapy

PURPOSE/OBJECTIVE(S)

Stereotactic body radiation therapy (SBRT) is an effective alternative to surgery in the treatment of early-stage non-small cell lung cancer (NSCLC). However, disease recurrence occurs in approximately 20-30% of patients. Hypoxia is a well-known factor promoting solid tumor progression, radiation resistance, and immune evasion. In this study, we utilize a previously published hypoxia gene expression signature (Buffa) and measure its association with clinical outcomes in patients with NSCLC treated with SBRT.

MATERIALS/METHODS

Our study focused on patients with localized, node-negative NSCLC treated with SBRT, and we identified 92 patients treated at our institution between 2008 and 2018 with available gene expression data. Total RNA from formalin-fixed paraffin-embedded archival biopsy specimens (pre-therapy) was isolated and mRNA expression was analyzed using an assay for human samples. For each gene in the Buffa signature, the top 50% of mRNA abundance values were given a score of +1, and the bottom 50% were given a score of -1 to generate a tumor hypoxia score. High scores suggest a hypoxic tumor and low scores imply normoxia. Kaplan-Meier curves were used to assess overall survival, disease-free survival, local recurrence, regional nodal recurrence, and distant recurrence. Cox proportional hazards were performed to account for confounding due to age, T stage, ECOG performance status, biologically effective dose, patient sex, and histology (squamous vs non-squamous).

RESULTS

The patient's gene expression data were dichotomized based on their median hypoxia score (Table 1). Median follow-up was 23.9 months (95% CI 20.6 - 26.6). A high hypoxia score was associated with squamous histology (p = 0.003). On univariate analysis, a high hypoxia score was significantly associated with local recurrence (hazard ratio [HR] = 5.63; 95% CI 1.03 - 30.78; p = 0.046) and distant recurrence (HR = 1.85; 95% CI 1.14 - 3.02; p = 0.013). There was no significant difference in overall survival (HR = 1.93; 95% CI 0.98 - 3.82; p = 0.058), disease-free survival (HR = 2.13; 95% CI 0.93 - 4.89; p = 0.074), or regional nodal recurrence (HR = 1.45; 95% CI 0.41 - 5.14; p = 0.57). On multivariate analysis, a high hypoxia score was associated with worse overall survival (HR = 2.73; 95% CI 1.23 - 6.07; p = 0.014), local recurrence (HR = 12.85; 95% CI 1.08 - 152.49; p = 0.043) and distant recurrence (HR = 1.91; 95% CI 1.13 - 3.22; p = 0.016).

CONCLUSION

Our findings demonstrate that a hypoxia gene signature is significantly associated with worse survival and increased local and distant recurrence after SBRT for localized NSCLC. This hypoxia signature may be useful in prognostication, selecting patients for surgery versus radiation, or selecting patients for treatment intensification with radiation or other systemic agents, and should be prospectively validated.

The tumor microbiome as a predictor of outcomes in patients with metastatic melanoma treated with immune checkpoint inhibitors

Emerging evidence supports the important role of the tumor microbiome in oncogenesis, cancer immune phenotype, cancer progression, and treatment outcomes in many malignancies. In this study, we investigated the metastatic melanoma tumor microbiome and potential roles in association with clinical outcomes, such as survival, in patients with metastatic disease treated with immune checkpoint inhibitors (ICIs). Baseline tumor samples were collected from 71 patients with metastatic melanoma before treatment with ICIs. Bulk RNA-seq was conducted on the formalin-fixed paraffin-embedded (FFPE) tumor samples. Durable clinical benefit (primary clinical endpoint) following ICIs was defined as overall survival ≥24 months and no change to the primary drug regimen (responders). We processed RNA-seq reads to carefully identify exogenous sequences using the {exotic} tool. The 71 patients with metastatic melanoma ranged in age from 24 to 83 years, 59% were male, and 55% survived >24 months following the initiation of ICI treatment. Exogenous taxa were identified in the tumor RNA-seq, including bacteria, fungi, and viruses. We found differences in gene expression and microbe abundances in immunotherapy responsive versus non-responsive tumors. Responders showed significant enrichment of several microbes including Fusobacterium nucleatum, and non-responders showed enrichment of fungi, as well as several bacteria. These microbes correlated with immune-related gene expression signatures. Finally, we found that models for predicting prolonged survival with immunotherapy using both microbe abundances and gene expression outperformed models using either dataset alone. Our findings warrant further investigation and potentially support therapeutic strategies to modify the tumor microbiome in order to improve treatment outcomes with ICIs.

A bioinformatics tool for identifying intratumoral microbes from the ORIEN dataset

Evidence supports significant interactions among microbes, immune cells, and tumor cells in at least 10-20% of human cancers, emphasizing the importance of further investigating these complex relationships. However, the implications and significance of tumor-related microbes remain largely unknown. Studies have demonstrated the critical roles of host microbes in cancer prevention and treatment responses. Understanding interactions between host microbes and cancer can drive cancer diagnosis and microbial therapeutics (bugs as drugs). Computational identification of cancer-specific microbes and their associations is still challenging due to the high dimensionality and high sparsity of intratumoral microbiome data, which requires large datasets containing sufficient event observations to identify relationships, and the interactions within microbial communities, the heterogeneity in microbial composition, and other confounding effects that can lead to spurious associations. To solve these issues, we present a bioinformatics tool, MEGA, to identify the microbes most strongly associated with 12 cancer types. We demonstrate its utility on a dataset from a consortium of 9 cancer centers in the Oncology Research Information Exchange Network (ORIEN). This package has 3 unique features: species-sample relations are represented in a heterogeneous graph and learned by a graph attention network; it incorporates metabolic and phylogenetic information to reflect intricate relationships within microbial communities; and it provides multiple functionalities for association interpretations and visualizations. We analyzed 2704 tumor RNA-seq samples and MEGA interpreted the tissue-resident microbial signatures of each of 12 cancer types. MEGA can effectively identify cancer-associated microbial signatures and refine their interactions with tumors.

Aldehyde dehydrogenase 3A1 deficiency leads to mitochondrial dysfunction and impacts salivary gland stem cell phenotype

Adult salivary stem/progenitor cells (SSPC) have an intrinsic property to self-renew in order to maintain tissue architecture and homeostasis. Adult salivary glands have been documented to harbor SSPC, which have been shown to play a vital role in the regeneration of the glandular structures postradiation damage. We have previously demonstrated that activation of aldehyde dehydrogenase 3A1 (ALDH3A1) after radiation reduced aldehyde accumulation in SSPC, leading to less apoptosis and improved salivary function. We subsequently found that sustained pharmacological ALDH3A1 activation is critical to enhance regeneration of murine submandibular gland after radiation damage. Further investigation shows that ALDH3A1 function is crucial for SSPC self-renewal and survival even in the absence of radiation stress. Salivary glands from Aldh3a1 -/- mice have fewer acinar structures than wildtype mice. ALDH3A1 deletion or pharmacological inhibition in SSPC leads to a decrease in mitochondrial DNA copy number, lower expression of mitochondrial specific genes and proteins, structural abnormalities, lower membrane potential, and reduced cellular respiration. Loss or inhibition of ALDH3A1 also elevates ROS levels, depletes glutathione pool, and accumulates ALDH3A1 substrate 4-hydroxynonenal (4-HNE, a lipid peroxidation product), leading to decreased survival of murine SSPC that can be rescued by treatment with 4-HNE specific carbonyl scavengers. Our data indicate that ALDH3A1 activity protects mitochondrial function and is important for the regeneration activity of SSPC. This knowledge will help to guide our translational strategy of applying ALDH3A1 activators in the clinic to prevent radiation-related hyposalivation in head and neck cancer patients.

Abstract P2-02-08: Slit2 induced anti-tumor activity may be mediated through metabolism driven immunomodulation

Metabolism of immune cells plays an important role in regulating tumor growth by modulating the anti-tumor M1 phenotype or pro-tumor M2 phenotype in macrophages. However, the role of bone marrow derived macrophages (BMDM) and their metabolic profile in promoting tumor growth is unknown. Slit2 is an anti-tumor molecule that is suppressed in breast cancer; however, the mechanism by which Slit2 mediates its function is not fully elucidated. We hypothesize that Slit2 mediated metabolic reprogramming of BMDMs favors anti-tumor M1 phenotype in these macrophages, which in turn reduces tumor growth.

Here we assessed cellular metabolism in BMDMs from the MMTV-PyMT mouse, a model showing spontaneous tumor development. Shortly, age matched female mice with palpable tumors and control mice without tumors were treated with recombinant Slit2 (Slit2) or PBS intraperitoneally every third for 2 weeks (n=4 mice per group). Tumor volume was measured in each mouse before and at the end of treatment. Next, mice were euthanized and bone marrow was flushed from both the tibia and femor for culturing in vitro in the presence of macrophage chemotactic factor rich conditioned media. Rate of glycolysis was described based on extracellular acidification rate (ECAR) as measured by the Seahorse Bioanalyzer® under glycostress conditions. Lactate dehydrogenase (LDH) activity, which is linked with breast cancer progression and pro-tumor macrophage phenotype in experimental models, was also assayed using a commercially available kit. Finally, to elucidate potential pathways involved in Slit2 induced metabolic change, we assessed the expression of several proteins and factors involved in cellular metabolism.

Firstly, we observed that PyMT mice treated with Slit2 showed lower tumor volume compared to mice treated with PBS confirming Slit2 anti-tumor activity. Hematoxylin & Eosin staining of tumor sections from these mice also showed better tissue structure, with a higher cytoplasm to nuclear ratio in Slit2 treated PyMT mice compared to PBS treated mice. Furthermore, BMDMs from PyMT mice show lower aerobic glycolysis with higher lactate dehydrogenase activity (LDH) compared to control mice. Moreover, treatment with Slit2 appeared to lower LDH activity and trended to increase glycolysis in the BMDMs isolated from Slit2 treated PyMT compared to PBS treated PyMT.

Expression analyses using quantitative PCR showed a 2-4 fold decrease in PGC-1α and CPT-2 in Slit2 treated BMDMs, indicating a reduction in fatty acid oxidation in these cells. This coupled with a 3 fold increase in IL-6 expression, and 2-3 fold decrease in arginase and IL-10 expression in tumor tissue suggest a potential shift from pro-tumor M2 to anti-tumor M1 phenotype. In spite of these preliminary trends, changes in metabolism and associated signals may be clearer in isolated, enriched populations of macrophages alone. Nevertheless, our findings suggest that Slit2 reduces tumor growth by affecting immune cell metabolism. Furthermore, these studies provide novel evidence of the potential immunomodulatory effects of Slit2 on macrophages. This may lead to development of Slit2 as a novel non-invasive therapeutic strategy against highly aggressive and metastatic cancers associated with high mortality and low quality of life.

Citation Format: Kaul K, Ahirwar DK, Benej M, Denko N, Ganju R. Slit2 induced anti-tumor activity may be mediated through metabolism driven immunomodulation [abstract]. In: Proceedings of the 2018 San Antonio Breast Cancer Symposium; 2018 Dec 4-8; San Antonio, TX. Philadelphia (PA): AACR; Cancer Res 2019;79(4 Suppl):Abstract nr P2-02-08.

Abstract 983: Metabolic radiosensitization: Overcoming the radioresistance of hypoxic tumors by targeting OXPHOS

It has been recognized decades ago that lower oxygen tension decreases the efficiency of radiation therapy (RT). Strategies to clinically overcome hypoxia have been disappointing. We have addressed this issue by targeting the tumor metabolism. “Metabolic radiosensitization” is a concept of achieving a temporary decrease in the oxygen consumption (OCR) of tumor cells and therefore reduce hypoxia prior to RT. Inhibiting mitochondrial respiration will cause a decrease in the demand for oxygen that will in turn lead to a decrease of tumor hypoxia providing a therapeutic window to deliver RT. A number of FDA-approved drugs have been shown to inhibit mitochondrial OCR as an off-target effect. Repurposing one of these drugs with well-established safety profiles for radiosensitization would thus provide an exciting opportunity for clinical translation. We found that papaverine (PPV) showed the most promising results by rapidly achieving up to 40% inhibition of OCR within minutes in clinically achievable doses in the low micromolar range. Using near infra-red optical spectroscopy (NIRS) with a mouse flank xenotransplantation model we confirmed that a single dose of the drug caused a 1.3-1.4x increase of tumor oxygenation in vivo in the first 30 minutes, while the normal tissue oxygenation remained unaffected. We then determined that combination of papaverine followed by RT after 30 minutes enhanced the tumor radiation growth delay significantly by 2.1-3.9x compared to RT alone. Papaverine has been traditionally used as a vasodilator and anti-spasmodic and is thought to act through its ability to inhibit phosphodiesterase 10A (PDE10A). However, we found that increased cAMP did not inhibit OCR in vitro, suggesting that PPV has dual functions as PDE10A and OCR inhibitor. To mechanistically establish that PPV is radiosensitizing through inhibition of mitochondrial complex I, we generated tumor cells with PPV-resistant mitochondria. We used CRISPR/Cas9 to knock out a gene essential for complex I core activity. We then rescued partial mitochondrial function in these cells by introducing papaverine-resistant yeast complex I encoded by the NDI1 gene. Analysis of these cells by Seahorse confirmed that they were resistant to the effects of PPV on OCR. These PPV-resistant tumor cells were used to grow tumors, and in radiation growth delay experiments, NDI1-expressing tumors were resistant to PPV radiosensitization. These findings confirm that PPV radiosensitizes hypoxic tumors though inhibition of complex I. In conclusion, our data indicate that repurposing FDA approved papaverine for metabolic radiosensitization has a strong potential for translation into the clinics.

Citation Format: Martin Benej, Xiangqian Hong, Bing Yu, Ioanna Papandreou, Nicholas Denko. Metabolic radiosensitization: Overcoming the radioresistance of hypoxic tumors by targeting OXPHOS [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 983.

Abstract 5467: Phosphoproteomic analysis of pyruvate dehydrogenase in response to environmental stress

Pyruvate dehydrogenase is a mitochondrial enzyme that regulates the flux of carbohydrates into oxidative phosphorylation. The activity of PDH is largely regulated by reversible phosphorylation. The pyruvate dehydrogenase kinases add inhibitory phosphorylations to PDH on the E1α subunit at positions 232, 293, and 300. Interestingly, there is a family of 4 related PDHK genes with overlapping affinity for the 3 phosphorylation sites. PDHK1 and PDHK3 have been identified as hypoxia-inducible at the transcriptional level, and PDHK1 has been shown to be important for the growth of model tumors. This work attempts to more carefully define the functions of PDHK1 and 3 using CRISPR technology in colorectal cancer lines in vitro and genetically engineered mice in vivo.

Using antibodies specific for the phosphorylated sites on E1α, we find that PDHK1 is essential for the phosphorylation of the 232 site in response to hypoxia and partially responsible for the hyperphosphorylation of 293 and 300. The level of phosphorylation in response to hypoxia is also sensitive to nutrients in the environment, with high levels of glucose enhancing E1α phosphorylation in hypoxia. Analysis of the number of phosporylations on individual E1α molecules using isoelectric focusing shows a range of events, with some molecules having 2 or 3 phosphorylations, while a large fraction of the E1α remains unphosphorylated in hypoxia. This type of pattern suggests a non-random phosphorylation of the multiple sites.

Analysis of PDH activity supports the in vitro findings that any single phosphorylation event is sufficient to inhibit PDH complex activity. Preliminary mitochondrial oxygen consumption experiments show that colorectal cancer cells are less dependent on PDHK1 for regulating mitochondrial function compared to published data in pancreatic and head and neck cancer. Finally, analysis of PDH phosphorylation in mice supports a role for PDHK1 in the regulation of PDH activity in response to fasting and blood glucose levels.

In conclusion, regulation of PDH in normal and cancerous colonocytes appears to be sensitive to environmental oxygen and nutrients. PDHK1 is the PDHK family member with the greatest influence on the addition of non-random inhibitory phosphorylation events. These in vitro findings will be analyzed with respect to the findings obtained using the new PDHK1 fl/fl villin Cre mouse.

Citation Format: Wendi O'Neill, Tereza Golias, Martin Benej, Nicholas Denko. Phosphoproteomic analysis of pyruvate dehydrogenase in response to environmental stress [abstract]. In: Proceedings of the American Association for Cancer Research Annual Meeting 2017; 2017 Apr 1-5; Washington, DC. Philadelphia (PA): AACR; Cancer Res 2017;77(13 Suppl):Abstract nr 5467. doi:10.1158/1538-7445.AM2017-5467

Abstract 5841: Hypoxic tumors can be sensitized to radiation therapy by repurposing papaverine as an inhibitor of mitochondrial respiration

Tumor hypoxia is a characteristic feature of solid tumors. Low oxygen tension represents a barrier to effective radiation therapy because oxygen is required to fix the DNA damage induced by ionizing radiation. Many strategies have been proposed as a means to increase the radiosensitivity of hypoxic tumors but the clinical benefits have been disappointing. Finding an effective way to radiosensitize hypoxic tumors thus represents a major challenge for improving the current protocols for clinical radiation therapy.

Decreasing the demand for oxygen within the tumor has been proposed as a way to reduce hypoxia, as reduced demand could lead to increased tumor oxygenation prior to delivery of radiation. Although several compounds have been proposed based on this approach, the toxicity and/or required dose have proven to be a limitation of their potential clinical benefit. Papaverine is an opiate alkaloid that has been used in clinical practice for over 70 years as a smooth muscle relaxant. The drug has a long established safety profile, short biological half-life and most importantly, high potency in its off-target effect limiting mitochondrial oxygen consumption. We therefore hypothesized that papaverine could effectively radiosensitize hypoxic tumors by decreasing tumor hypoxia.

At clinically achievable concentrations in the low micromolar range, papaverine efficiently reduced the rate of oxygen consumption (OCR) in all tested cell lines in vitro. Within the first 30 minutes, 10 uM of the drug reduced the OCR by 30-40%. We identified the mechanism of OCR reduction as direct binding and inhibition of mitochondrial complex I, independent of the drug’s activity as a phosphodiesterase inhibitor. More importantly, a single dose of 2 mg/kg papaverine injected I.V. significantly increased tumor oxygenation in vivo by 1.2-1.3 fold in nude mice harboring EO771 and A549 xenografts. Because normal tissue is fully oxygenated, we found muscle oxygenation remained unchanged after drug delivery. Finally, 2 mg/kg papaverine injected 35 minutes prior to a single dose of irradiation resulted in a 2.0 fold relative growth delay in E0771 tumors compared to irradiation alone. In addition, in the more hypoxic A549 xenografts, the benefit provided by papaverine was a 3.0 fold relative growth delay. In conclusion, according to our data a single, clinically relevant dose of papaverine administered shortly before irradiation reduces tumor hypoxia and thus provides significant benefit over irradiation alone, strongly highlighting its potential to improve current strategies to enhance response to radiation therapy.

Citation Format: Martin Benej, Ioanna Papandreou, Xiangqian Hong, Bing Yu, Nicholas Denko. Hypoxic tumors can be sensitized to radiation therapy by repurposing papaverine as an inhibitor of mitochondrial respiration [abstract]. In: Proceedings of the American Association for Cancer Research Annual Meeting 2017; 2017 Apr 1-5; Washington, DC. Philadelphia (PA): AACR; Cancer Res 2017;77(13 Suppl):Abstract nr 5841. doi:10.1158/1538-7445.AM2017-5841

The PI3K/Akt Pathway Regulates Oxygen Metabolism via Pyruvate Dehydrogenase (PDH)-E1α Phosphorylation

Inhibition of the PI3K/Akt pathway decreases hypoxia within SQ20B human head and neck cancer xenografts. We set out to understand the molecular mechanism underlying this observation. We measured oxygen consumption using both a Clark electrode and an extracellular flux analyzer. We made these measurements after various pharmacologic and genetic manipulations. Pharmacologic inhibition of the PI3K/mTOR pathway or genetic inhibition of Akt/PI3K decreased the oxygen consumption rate (OCR) in vitro in SQ20B and other cell lines by 30% to 40%. Pharmacologic inhibition of this pathway increased phosphorylation of the E1α subunit of the pyruvate dehydrogenase (PDH) complex on Ser293, which inhibits activity of this critical gatekeeper of mitochondrial respiration. Expressing wild-type PTEN in a doxycycline-inducible manner in a cell line with mutant PTEN led to an increase in PDH-E1α phosphorylation and a decrease in OCR. Pretreatment of SQ20B cells with dichloroacetate (DCA), which inhibits PDH-E1α phosphorylation by inhibiting dehydrogenase kinases (PDK), reversed the decrease in OCR in response to PI3K/Akt/mTOR inhibition. Likewise, introduction of exogenous PDH-E1α that contains serine to alanine mutations, which can no longer be regulated by phosphorylation, also blunted the decrease in OCR seen with PI3K/mTOR inhibition. Our findings highlight an association between the PI3K/mTOR pathway and tumor cell oxygen consumption that is regulated in part by PDH phosphorylation. These results have important implications for understanding the effects of PI3K pathway activation in tumor metabolism and also in designing cancer therapy trials that use inhibitors of this pathway.

Abstract 854: Inhibition of PRMT5 results in radiosensitization in lung cancer cell lines

Background: Protein arginine methylation is a post translational modification that influences signal transduction, mRNA splicing, gene transcription and DNA repair. Among the PRMT family members, PRMT5 is a type II enzyme that symmetrically methylates histone H4 at Arginine 3 and histone H3 at Arginine 8. Studies have recently linked this modification to carcinogenesis and metastasis. The function of PRMT5 in carcinogenesis is related to cell proliferation through modulation of E2F1, p53, EGFR, and CRAF. It is known to accelerate progression through the G1 phase of cell cycle by influencing proteins like CDK4 and CDK6. Previous work on human lung cancer specimens has demonstrated an overexpression of PRMT5 in cancerous tissue when compared to normal lung parenchyma. Suppression of PRMT5 significantly inhibits cell proliferation in lung cancer cell lines A549 and H1299. We hypothesized inhibition of PRMT5 can lead to increased radiosensitivity in lung cancer cells.

Method: Several lung cancer cell lines were used in the experiments, including A549, H1299 and H23. SiRNA (Dharmacon) and lentiviral shRNA (Sigma) were used to knock down (KD) PRMT5 levels transiently or stably in A549 cell line in which p53 is present in its wild type form. Forty eight hours after transient transfection, cells were plated for clonogenic survival assay and subsequently exposed to ionizing radiation at 0, 2, and 8 Gy. Cellular PRMT5 protein levels were estimated by western blotting analysis for PRMT5 KD and scramble control cell lines. The scramble control and siRNA knockdown cells were subjected to cell cycle analysis by flow cytometry. We also tested specific PRMT5 inhibitors with and without radiation therapy in the lung cancer cell lines to see if PRMT5 inhibitors could lead to increased radiosensitivity.

Results: We observed a &gt;90% PRMT5 KD in transiently transfected cells at 48 h and 72 h post transfection as verified by western blot analysis. This transient KD lead to a small but significant decrease in colony survival after radiation. This radiosensitization was not observed in cells selected for stable KD of PRMT5 protein by lentiviral RNA transfection. There is an increase of cell population in G1 arrest in PRMT5 transient KD cells but not in stable KD cells. Additionally, cells treated with PRMT5 specific inhibitors (“cpd5” or “cpd65”) demonstrated increased radiosensitivity in A549 cells but not in H1299 suggesting that this effect may be p53-dependent.

Conclusion: PRMT5 inhibition by siRNA or its specific inhibitors lead to radiosensitivity in A549 lung cancer cell line. This effect may be partially dependent on p53-dependent cell cycle arrest. Further work to inhibit PRMT5 in other lung cancer cell lines with different p53 activities will be investigated.

Citation Format: Smitha Sharma, X Wu, P Smith, N Denko, C Li, H Lai, F Yan, K Shilo, A Chakravarti, S Sif, R Baiocchi, G Otterson, Meng Xu-Welliver. Inhibition of PRMT5 results in radiosensitization in lung cancer cell lines. [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 854. doi:10.1158/1538-7445.AM2014-854

5'-AMP-activated protein kinase (AMPK) supports the growth of aggressive experimental human breast cancer tumors

Rapid tumor growth can establish metabolically stressed microenvironments that activate 5'-AMP-activated protein kinase (AMPK), a ubiquitous regulator of ATP homeostasis. Previously, we investigated the importance of AMPK for the growth of experimental tumors prepared from HRAS-transformed mouse embryo fibroblasts and for primary brain tumor development in a rat model of neurocarcinogenesis. Here, we used triple-negative human breast cancer cells in which AMPK activity had been knocked down to investigate the contribution of AMPK to experimental tumor growth and core glucose metabolism. We found that AMPK supports the growth of fast-growing orthotopic tumors prepared from MDA-MB-231 and DU4475 breast cancer cells but had no effect on the proliferation or survival of these cells in culture. We used in vitro and in vivo metabolic profiling with [(13)C]glucose tracers to investigate the contribution of AMPK to core glucose metabolism in MDA-MB-231 cells, which have a Warburg metabolic phenotype; these experiments indicated that AMPK supports tumor glucose metabolism in part through positive regulation of glycolysis and the nonoxidative pentose phosphate cycle. We also found that AMPK activity in the MDA-MB-231 tumors could systemically perturb glucose homeostasis in sensitive normal tissues (liver and pancreas). Overall, our findings suggest that the contribution of AMPK to the growth of aggressive experimental tumors has a critical microenvironmental component that involves specific regulation of core glucose metabolism.

Abstract 1000: Oncogenic Kras inhibits mitochondrial metabolism by regulating the pyruvate dehydrogenase complex under conditions of nutrient stress

Kras is one of the most frequently mutated oncogenes in human cancer. Previous studies have suggested a role for oncogenic Kras in regulating glucose metabolism, although the exact mechanism is unclear. By analyzing the transcriptional consequences of Kras mutation under conditions of nutrient stress, a direct role for oncogenic Kras in regulating oxidative phosphorylation was observed. Signaling downstream of Kras via the MEK/ERK pathway inhibits expression of PDP1, a mitochondrial phosphatase that regulates the pyruvate dehydrogenase complex (PDC). PDC is a key enzyme in the conversion of pyruvate into acetyl-CoA. Decreased expression of PDP1 induced by oncogenic Kras leads to increased phosphorylation and thereby inactivation of PDC. Therefore, oncogenic Kras represses mitochondrial function and oxygen consumption by maintaining PDC in an inactive state. This effect is not apparent under the high-glucose conditions in which cells are typically cultured. However, at glucose concentrations more closely reflective of what cells experience in vivo, the effect of oncogenic Kras signaling on PDP1 expression becomes readily apparent. This study demonstrates a novel role for oncogenic Kras in the regulation of mitochondrial metabolism. Further studies underway may clarify a role for this pathway as a target for therapeutic intervention in Kras-mutant tumors.

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 1000. doi:1538-7445.AM2012-1000

Hypoxia induces a novel signature of chromatin modifications and global repression of transcription

Tumor cells respond to the harsh hypoxic microenvironment, in part, by transcriptional regulation of specific target genes. We found that hypoxia-mediated activation of selected genes occurs amidst widespread repression of transcription that is neither cell type-specific nor HIF-1-dependent. Despite overall repression, hypoxia induces a pool of histone modifications typically associated with transcriptional activation or repression. Chromatin immunoprecipitation analyses showed that this global mixture of hypoxia-modified histones is sorted in a gene-specific manner to correlate with transcriptional response to hypoxia. Exceptions to this were unexpected increases in H3K4me3 levels, typically associated with transcriptional activation, and decreased H3K27me3 levels, generally a marker of transcriptional silencing, at core promoters of both hypoxia-activated and -repressed genes. These data suggest that a novel signature of chromatin modifications is induced under hypoxic stress, which may play a role in gene regulatory switches active in proliferating tumor cells undergoing cycles of hypoxia and reoxygenation.

Induction of activating transcription factor 3 by anoxia is independent of p53 and the hypoxic HIF signalling pathway

Solid tumors often have an inadequate blood supply, which results in large regions that are subjected to hypoxic or anoxic stress. Hypoxia-inducible factor-1 (HIF-1) is a transcription factor that regulates much of the transcriptional response of cells to hypoxia. Activating transcription factor 3 (ATF3) is another transcription factor that responds to a variety of stresses and is often upregulated in cancer. We investigated the regulation of ATF3 by oxygen deprivation. ATF3 induction occurred most robustly under anoxia, is common, and it is not dependent on presence of HIF-1 or p53, but is sensitive to the inhibition of c-Jun NH2-terminal kinase activation and the antioxidant N-acetylcystein. ATF3 could also be induced by desferrioxamine but not by the mitochondrial poison cyanide or the nonspecific 2-oxoglutarate dioxygenase inhibitor dimethyloxalylglycine. We also show that anoxic ATF3 mRNA is more stable than normoxic mRNA providing a mechanism for this induction. Thus, this study demonstrates that the regulation of ATF3 under anoxia is independent of 2-oxoglutarate dioxygenase, HIF-1 and p53, presumably involving multiple regulatory pathways.

Overcoming physiologic barriers to cancer treatment by molecularly targeting the tumor microenvironment

It is widely recognized that the vasculature of the tumor is inadequate to meet the demands of the growing mass. The malformed vasculature is at least in part responsible for regions of the tumor that are hypoxic, acidotic, and exposed to increased interstitial fluid pressure. These unique aspects of the tumor microenvironment have been shown to act as barriers to conventional chemotherapy or radiation-based therapies. It now seems that while the vasculature initiates these tumor-specific conditions, the cells within the tumor respond to these stresses and add to the unique solid tumor physiology. Gene expression changes have been reported in the tumor for vascular endothelial growth factor, carbonic anhydrase IX, and pyruvate dehydrogenase kinase 1. The activity of these gene products then influences the tumor physiology through alterations in vascular permeability and interstitial fluid pressure, extracellular acidosis, and mitochondrial oxygen consumption and hypoxia, respectively. Novel molecular strategies designed to interfere with the activities of these gene products are being devised as ways to overcome the physiologic barriers in the tumor to standard anticancer therapies.

Cellular reaction to hypoxia: sensing and responding to an adverse environment

Multicellular organisms have developed sophisticated physiologic mechanisms by which they maintain their tissues at the optimal oxygen concentration. This level is important so that the benefits of free oxygen can be realized, while limiting the potential harms. Despite these efforts, there exist physiologic and pathophysiologic conditions where oxygen delivery drops below what is necessary for the tissue. Under these circumstances, the cell then goes through a series of coordinated responses in a time and oxygen concentration-dependent manner. The gene expression changes are designed to maintain cellular and tissue viability, and are comprised of transcriptional as well as post-transcriptional events. As we understand more about the hypoxic response, we realize how it can impact normal development, wound healing, and the malignant progression of a solid tumor.

Functional characterization of human proapoptotic molecules in yeastS. cerevisiae

The presence of a complete (BH1-3) proapoptotic molecule is necessary for the induction of the intrinsic apoptotic cascade in mammalian cells. It is unclear, however, what distinct roles the members of the large family of BH3-only proapoptotic molecules play in apoptosis. Although biochemical analysis of these molecules can characterize binding efficiencies of BH3 family members, the biologic consequences of these interactions are difficult to predict. We have, therefore, established three functional categories of BH3-only human proapoptotic proteins based on their toxicity after expression in budding yeast: directly killing (tBid), sensitizing in Bax/Bcl-2 expressing cells (Bad or Puma), and non-toxic (BNip3, BNip3L, and Noxa). The mechanism of killing by the proapoptotic molecules in yeast, however, is not due to activation of the recently described yeast metacaspase MCA1.

Hypoxia actively represses transcription by inducing negative cofactor 2 (Dr1/DrAP1) and blocking preinitiation complex assembly

Hypoxia is a growth inhibitory stress associated with multiple disease states. We find that hypoxic stress actively regulates transcription not only by activation of specific genes but also by selective repression. We reconstituted this bimodal response to hypoxia in vitro and determined a mechanism for hypoxia-mediated repression of transcription. Hypoxic cell extracts are competent for transcript elongation, but cannot assemble a functional preinitiation complex (PIC) at a subset of promoters. PIC assembly and RNA polymerase II C-terminal domain (CTD) phosphorylation were blocked by hypoxic induction and core promoter binding of negative cofactor 2 protein (NC2 alpha/beta, Dr1/DrAP1). Immunodepletion of NC2 beta/Dr1 protein complexes rescued hypoxic-repressed transcription without alteration of normoxic transcription. Physiological regulation of NC2 activity may represent an active means of conserving energy in response to hypoxic stress.

Epigenetic regulation of gene expression in cervical cancer cells by the tumor microenvironment

Evidence is accumulating that the adverse tumor microenvironment both modifies the malignant progression of tumor cells and contributes to chemotherapy and radiation resistance. We hypothesized that some of the effects on malignant progression are mediated through the transcriptional regulation of genes responsive to the stresses of the microenvironment, such as low oxygen or low glucose conditions. To determine epigenetic changes in gene expression that were consistent with that hypothesis, we used an in vitro subtractive hybridization method, representational difference analysis, to identify hypoxia-induced cDNAs from cultured human cervical epithelial cells. We identified 12 induced genes: two novel genes (HIG1 and HIG2), three genes known to be hypoxia-inducible (tissue factor, GAPDH, thioredoxin), and seven genes not previously identified as hypoxia-inducible [HNRNP(a1), ribosomal L7, annexin V, lipocortin 2, Ku(70), PRPP synthase, and acetoacetyl-CoA thiolase]. In cultured cells, HIG1 and HIG2 expression is induced by hypoxia and by glucose deprivation, but their expression is not induced by serum deprivation, UV, or ionizing radiation. The putative HIG1 and HIG2 open reading frames are expressed in cells, as confirmed by epitope tagging. In addition, tumor xenografts derived from human cervical cancer cells display increased expression of HIG1 and HIG2 when they are deprived of oxygen. Taken together, these data suggest a coordinated transcriptional response of eukaryotic cells to microenvironmental stresses found in the solid tumor.

Uncoupling of S-phase and mitosis by recombinant cytotoxic necrotizing factor 2 (CNF2)

Cytotoxic necrotizing factor 2 (CNF2) is an exotoxin identified from virulent clinical isolates of Escherichia coli. It has been characterized in adherent cell lines as an inducer of cellular death, hyperploidy (multinucleation), and cytoskeletal reorganization. The molecular mechanism of these actions is unclear. Two cellular mechanisms can be hypothesized to explain the DNA content increase (hyperploidy) induced by the toxin. The first is that the toxin interferes with cytoplasmic division without interfering with normal nuclear cycling, such that DNA is replicated in the absence of cell division. The second is that the toxin drives the nuclear machinery to replicate the DNA multiple times within one cell cycle, without interfering with cytoplasmic division. In order to investigate these phenomena, we have constructed a recombinant CNF2 gene that expresses a toxin with both an epitope tag and a polyhistidine tag. Extracts made from E. coli that express this gene have a high multinucleating activity that colocalizes with the recombinant 115-kDa protein. To distinguish between these hypotheses, we used recombinant CNF2 and several growth conditions (time, partial differentiation, and stage of growth) to establish a relationship between cellular divisions and generation of hyperploidy. It was also determined that the toxin had no effect upon in vitro DNA replication using a Xenopus egg extract system. In aggregate, these data are consistent with the hypothesis that CNF2 is affecting cytoplasmic division and thereby removing the requirement for a completed mitosis before the initiation of another S-phase. These data are discussed in relation to the generation of polyploid cells during megakaryopoeisis and the generation of aneuploid cells during tumorigenesis.

Protease inhibitor TPCK represses Ha-ras (Val12) transformation and nuclear factor-kappa B activation

Certain chymotrypsin-like protease inhibitors such as TPCK exhibit a well described anti-tumorigenic activity by an as yet undescribed mechanism. One potential cellular target for TPCK in transformed cells is the ms-inducible NF-kappa B family of transcription factors. We therefore used TPCK to examine the physiologic role of NF-kappa B during Ha-ras induced transformation, independent of another major downstream effector of Ha-ras, AP-1. Using a conditionally transformed NIH3T3 cell line, we found that TPCK (but not the control inhibitor TLME) inhibited the anchorage-independent growth of Ha-ras transformed cells, but not their anchorage-dependent growth on plastic tissue culture dishes. Likewise, TPCK reduced the ability of Ha-ras to stimulate DNA synthesis in growth factor depleted cells, but not the ability of serum to stimulate DNA synthesis in the same growth factor depleted cells. Gel shift analysis and reporter gene expression indicated that TPCK blocked Ha-ras-induced NF-kappa B activity, while only having minimal effects on Ha-ras-induced AP-1 activity. TPCK is therefore able to Inhibit the Ha-ras transformed phenotype of cells by inhibiting the transcriptional activity of NF-kappa B, while having little effect upon transcriptional activity of AP-1.

Mitotic and post mitotic consequences of genomic instability induced by oncogenic Ha-ras

Induced expression of a mutant human Ha-ras oncogene in NIH3T3 cells leads to the rapid production of multicentric chromosomes, acentric chromosome fragments, double minute chromosomes, increased heteroploidy, and increased capacity to undergo gene amplification. In this study we have used fluorescent-in-situ hybridization (FISH) to demonstrate that induction of the Ha-ras oncogene also leads to disruption of the mitotic machinery, resulting in aberrant mitoses and abnormal daughter cells. Cells induced to express an oncogenic Ha-ras transgene accumulate chromosomes that lag outside of the rest of the chromosomal architecture, chromosomes that form bridges between daughter nuclei at anaphase, and that form micronuclei. Many of these mitotic aberrations contain structurally abnormal chromosomes. These ras-induced changes were suppressed by the introduction of a gene encoding the dominant negative effector of ras, raf 301. Expression of raf301 in cells induced to express Ha-ras reduced the level of growth in soft agar, chromosome aberrations, mitotic aberrations, and frequency of gene amplification. These data provide evidence for an association between Ha-ras induced transformation, chromosome aberrations and gene amplification. Furthermore they offer insight into how the cell responds to the formation of aberrant chromosomes, and how disrupting chromosomal architecture could lead to further imbalances in the distribution of genetic material between daughter cells.

A 55 kDa antigen of Pneumocystis carinii: analysis of the cellular immune response and characterization of the gene

Rat-derived Pneumocystis carinii contains a major antigen complex of 45-55 kDa. The fusion protein of a cDNA encoding the 3' portion of the 55kDa antigen, which had previously been shown to be recognized by serum antibodies of exposed subjects, was investigated for its ability to stimulate a cellular immune response. Rats exposed to P. carinii via the environment exhibited a vigorous proliferative response to the antigen whereas unexposed rats did not. The full-length cDNA for a 55kDa antigen was cloned and found to contain a 1245bp open reading frame capable of encoding a 414-amino-acid peptide. The gene encoding this protein contained a single 39bp intron and transcribed a 1.45kb RNA message. The cloning and characterization of the 55kDa antigen gene will allow production of the specific immunological reagents necessary to characterize this molecule and study its role in the biology and pathogenesis of P. carinii.

Expression of the lacZ gene targeted to the HPRT locus in embryonic stem cells and their derivatives

Transgenes in mice often exhibit different expression patterns in different transgenic lines. While the basis for this phenomenon is not understood, it is widely believed that the site at which the transgene becomes integrated into the mouse genome is a major factor in determining the pattern of expression. Most transgenic mice have been produced by microinjection of DNA into the male pronucleus, which results in integration of tandem arrays of the transgene at random chromosomal sites. In the experiments described in this report, electroporation of embryonic stem (ES) cells was used to place single copies of a lacZ transgene into either random sites or into the HPRT (hypoxanthine phosphoribosyl transferase) locus of the mouse genome. Expression of lacZ was assayed by histochemical staining for Escherichia coli beta-galactosidase activity in ES cells and in differentiated derivatives obtained by teratocarcinoma formation. Several of the randomly integrated cell lines expressed lacZ at high levels in a variety of cell types present in the tumours, but most notably in epithelial cells. Targeted cell lines with lacZ in opposite orientation to the direction of HPRT gene transcription also expressed well in epithelial cells, but the targeted cell lines did not express in a wider variety of cell types than some of the nontargeted cell lines. Targeted cell lines transcribing lacZ in the same orientation as HPRT transcription did not express high levels of lacZ in any differentiated cell type. Analysis of transcripts suggested that this orientation effect may have been the result of transcriptional interference perpetrated by the HPRT gene promoter.

Two methods for assaying DNA double-strand break repair in mammalian cells by asymmetric field inversion gel electrophoresis

The rejoining of gamma-ray-induced DNA double-strand breaks (DSBs) in mammalian cells was measured after various doses of gamma rays by using a version of pulsed-field gel electrophoresis to elute fragments of DNA from an agarose plug into the lane of an agarose gel. Two approaches for measuring the kinetics of DNA repair were compared. In the first method, cells are irradiated and incubated at 37 degrees C in monolayers, after which the cells are suspended in agarose and DNA is isolated and subjected to electrophoresis. In the second approach, cells are suspended in agarose first, then irradiated and incubated for repair, and the DNA is isolated for electrophoresis. In both methods the kinetics of repair appears to be biphasic, with an initial fast phase and a second slow phase. At equal doses the t1/2 for fast repair is two-fold less in cells incubated in monolayers than in cells suspended in agarose (11 min compared to 20-23 min) and threefold less after subtracting the slow repair component. In the agarose method the t1/2 values for fast repair increase with increasing radiation dose, while in the monolayer method they are constant. In both methods t1/2 values for slow repair are approximately constant with radiation dose. At a given radiation dose, the level of initial damage is two- to threefold higher as assessed by the agarose method than by the monolayer method in which DNA repair can occur during the preparation of samples. The detection of higher levels of initial damage by the agarose method permits DNA repair to be assayed at doses as low as 8 Gy and enables fast repair processes to be assayed more readily. However, in the monolayer approach, repair occurs under normal growth conditions and is not subjected to the effects of prior manipulations and/or the rates of nutrient diffusion. Thus this approach might be more representative of normal intracellular repair kinetics.

Detection of DNA double-strand breaks in synchronous cultures of CHO cells by means of asymmetric field inversion gel electrophoresis

A pulsed field gel electrophoresis technique, asymmetric field inversion gel electrophoresis (AFIGE), was used to evaluate induction by X-rays of DNA damage in CHO cells. The fraction of DNA activity released from the plug (FAR) was used as a measure for the amount of radiation-induced DNA damage, predominantly DNA double-strand breaks (dsb) (Stamato and Denko 1990), and was determined at various stages of growth and phases of the cell cycle in a range of doses between zero and 70 Gy. The FAR per unit dose fluctuated throughout the cell cycle and was high for cells irradiated in G1; it decreased as cells entered S and reached a minimum in the middle of this phase. The FAR per unit dose increased again as cells progressed towards the end of S, and reached values in G2 similar to those measured in G1. When damage was introduced into DNA by means of 125I decay similar fluctuations in the FAR per decay were observed throughout the cell cycle, suggesting that the variations in the FAR per unit of radiation dose observed throughout the cell cycle do not derive from alterations in the induction of dsb. The fluctuations in the FAR per unit dose throughout the cell cycle were quantitatively similar to the fluctuations in the fraction of activity eluted in irradiated cells assayed by the non-unwinding filter elution assay throughout the cycle (Okayasu et al. 1988), and suggest that both techniques respond to similar DNA replication-associated alterations of the biophysical and/or biochemical properties of the DNA molecule. It is concluded that caution needs to be exercised before differences observed in the FAR between different cell lines or between various phases of the cell cycle after exposure to a given dose of radiation are interpreted as suggesting differences in the induction of DNA dsb.

Human chromosome 5 complements the DNA double-strand break-repair deficiency and gamma-ray sensitivity of the XR-1 hamster variant

XR-1 is a Chinese hamster ovary (CHO) cell mutant which is unusually sensitive to killing by gamma rays in the G1 portion of the cell cycle but has nearly normal resistance to gamma-ray damage in late S phase. The cell-cycle sensitivity correlates with the mutant's inability to repair DNA double-strand breaks (DSBs) produced by ionizing radiation and restriction enzymes. We have previously shown in somatic cell hybrids of XR-1 cells and human fibroblasts that the XR-1 mutation is a recessive mutation. In this study, using somatic cell hybrids formed between XR-1 and human fibroblasts, we map the human complementing gene to chromosome 5 by chromosome-segregation analysis. This gene biochemically restores the hamster defect to wild-type levels of gamma-ray and bleomycin resistance as well as restoring its proficiency to repair DNA DSBs, suggesting that a single gene is responsible for the XR-1 phenotype. We have tentatively assigned the name XRCC4 (X-ray-complementing Chinese hamster gene 4) to this human gene until its biochemical function in repair is discovered.

Increased sensitivity to killing by restriction enzymes in the XR-1 DNA double-strand break repair-deficient mutant

Repair or misrepair of DNA double-strand breaks (DSBs) is critical in determining cellular survival after gamma-irradiation. In this report, we focus on the cellular and biochemical consequences of restriction enzyme induced DSBs in wild-type Chinese hamster ovary (CHO) cells and the DNA DSB repair-defective mutant XR-1. We find that XR-1 possesses reduced cellular survival after the introduction of restriction enzymes that produce either cohesive or blunt ends. XR-1's sensitivity to killing by restriction enzymes strongly mimics its response to gamma-rays. Using pulsed field electrophoresis, we find that for each enzyme, similar numbers of DNA DSBs are being introduced in both cell lines. The simplest explanation for the increased sensitivity to restriction enzymes in the mutant is that the biochemical defect in XR-1 is not confined to the repair of ionizing radiation induced ends, but extends to DSBs that possess ligatable 3'-hydroxyl and 5'-phosphate ends as well.

Asymmetric field inversion gel electrophoresis: a new method for detecting DNA double-strand breaks in mammalian cells

A new method is described for detecting DNA double-strand breaks (DSBs) that utilizes asymmetric field inversion gel electrophoresis (AFIGE). DNA purified from cells in agarose plugs is subjected to AFIGE and DNA breakage quantitated by the fraction of DNA released from the plug. To test the specificity of the method for DNA DSBs, purified DNA in agarose plugs was treated for increasing times with restriction endonuclease, XhoI. After an initial time period, the fraction of DNA released increased in direct proportion to time. This correlates with the expected response for a randomly broken DNA molecule. In contrast, treatment with the single-strand breaking agent, hydrogen peroxide, over a 1000-fold range produced no release of DNA from the plug. Thus the assay appears to be specific for DNA DSBs and was used to measure DNA breaks induced by gamma radiation. Purified DNA, irradiated in agarose plugs, exhibited a log-linear dose response up to doses that release greater than 90% DNA from the plug. When live cells were irradiated in agarose, a similar linear dose response was observed up to 40 Gy and a significant signal as low as 2.5 Gy. Also in live cells, a threefold lower percentage of DNA was released from the plug over the same dose range. However, less DNA per gray is released at doses above 40 Gy and may reflect a crosslinking effect produced by the irradiation of DNA in live cells. DNA which was "pulse-labeled" was used to test the effect of DNA replication on the ability of AFIGE to detect DNA DSBs. Replicating DNA irradiated in the cell or after purification exhibited a reduced rate of release from the plug per dose of irradiation. Overall, the above results indicate that AFIGE is a sensitive method for detecting DSBs in DNA.

Isolation and characterization of glucose-6-phosphate dehydrogenase-deficient Chinese hamster cells derived from pure mutant colonies

Ten pure glucose-6-phosphate dehydrogenase (G6PD)-deficient mutants were isolated from colonies composed entirely of cells which lacked G6PD staining activity. These mutants were analyzed for G6PD enzyme activity and the presence of immunologically cross-reactive proteins using immunoblotting techniques and antiserum directed against bovine G6PD. Four mutants had no detectable enzyme activity and did not contain protein which produces a detectable cross-reaction with G6PD antibody. One mutant had residual enzyme activity and altered electrophoretic mobility but did not have detectable immunological cross-reactivity. These results could be explained by either a DNA deletion or point mutational mechanism. On the other hand, five of the 10 mutants analyzed had characteristics consistent with a point mutation in the G6PD gene. All contain a protein which cross-reacts with the G6PD antibody and have the same subunit molecular weight as the parent cell's G6PD enzyme. Four of the five mutants had residual G6PD enzyme activity. Thus, the mechanism for the formation of pure mutants is not simply DNA deletion but is probably a more complex process involving the transfer of altered genetic information from one DNA strand to the other.

An asymmetric field inversion gel electrophoresis method for the separation of large DNA molecules

An electrophoretic method for separating large DNA molecules which uses periodically inverted electric fields of different magnitude in the two directions is described. Net DNA migration is either in the high field direction or in the low field direction, depending on the relative duration of the pulses. With this approach, molecules of up to 1.6 million base pairs can be separated in parallel lanes after a single run under fixed timing conditions. An inexpensive switching unit is the only device needed in addition to the conventional gel box.

Genetic analysis of XR-1 mutation in hamster and human hybrids

We investigated the dominant/recessive nature of the XR-1 mutant locus in intraspecies Chinese hamster ovary (CHO) hybrids and interspecies hybrids with human cell lines that possess different radioresistances. The XR-1 cell is abnormally sensitive to killing by gamma rays in the G1 phase of the cell cycle, while late-S-phase cells have wild-type resistance. [3H]Thymidine selection was used to eliminate the resistant S-phase population. In both intraspecies and interspecies hybrids, the XR-1 mutation is recessive to the wild-type cell and is not influenced by differences in chromosome ploidy. Analysis of hybrids between human ataxia telangiectasia fibroblasts AT5BI and XR-1 cells revealed that they possess different genetic defects as they complemented each other in three of four hybrids tested. These data suggest that the XR-1 locus is evolutionarily conserved between hamster and human cells.

Isolation and characterization of bleomycin-sensitive Chinese hamster ovary cells

Nineteen bleomycin-sensitive Chinese hamster ovary cell mutants have been isolated using a replica plating and photography approach. As judged by the dose which reduces cell survival to 37% of the untreated control, these mutants are from 2.5- to 32-fold more sensitive to a 16-h bleomycin treatment than the parental cell, while for chronic bleomycin exposure, the increase in sensitivity was 5 to 58 times that of the parental cell. Four bleomycin-sensitive mutants had increased sensitivities to killing by gamma-rays (2- to 3-fold), mitomycin C (2-fold), and ethyl methane sulfonate (4- to 5-fold), while six other mutants were resistant to these agents. Nine other bleomycin-sensitive mutants displayed a variable pattern of cross-sensitivities to these agents. Using the technique of alkaline elution, the relative frequency of single-strand DNA breaks introduced by varying concentrations of bleomycin was examined in one mutant and its parent cell. The elution profiles of both cells were similar, suggesting that the bleomycin sensitivity of this mutant is not due to a greater frequency of single-strand breaks introduced by bleomycin.