EphA2- and HDAC-Targeted Combination Therapy in Endometrial Cancer

Endometrial cancer is the most frequent malignant tumor of the female reproductive tract but lacks effective therapy. EphA2, a receptor tyrosine kinase, is overexpressed by various cancers including endometrial cancer and is associated with poor clinical outcomes. In preclinical models, EphA2-targeted drugs had modest efficacy. To discover potential synergistic partners for EphA2-targeted drugs, we performed a high-throughput drug screen and identified panobinostat, a histone deacetylase inhibitor, as a candidate. We hypothesized that combination therapy with an EphA2 inhibitor and panobinostat leads to synergistic cell death. Indeed, we found that the combination enhanced DNA damage, increased apoptosis, and decreased clonogenic survival in Ishikawa and Hec1A endometrial cancer cells and significantly reduced tumor burden in mouse models of endometrial carcinoma. Upon RNA sequencing, the combination was associated with downregulation of cell survival pathways, including senescence, cyclins, and cell cycle regulators. The Axl-PI3K-Akt-mTOR pathway was also decreased by combination therapy. Together, our results highlight EphA2 and histone deacetylase as promising therapeutic targets for endometrial cancer.

Epichaperome inhibition targets TP53-mutant AML and AML stem/progenitor cells

TP 53-mutant acute myeloid leukemia (AML) remains the ultimate therapeutic challenge. Epichaperomes, formed in malignant cells, consist of heat shock protein 90 (HSP90) and associated proteins that support the maturation, activity, and stability of oncogenic kinases and transcription factors including mutant p53. High-throughput drug screening identified HSP90 inhibitors as top hits in isogenic TP53-wild-type (WT) and -mutant AML cells. We detected epichaperomes in AML cells and stem/progenitor cells with TP53 mutations but not in healthy bone marrow (BM) cells. Hence, we investigated the therapeutic potential of specifically targeting epichaperomes with PU-H71 in TP53-mutant AML based on its preferred binding to HSP90 within epichaperomes. PU-H71 effectively suppressed cell intrinsic stress responses and killed AML cells, primarily by inducing apoptosis; targeted TP53-mutant stem/progenitor cells; and prolonged survival of TP53-mutant AML xenograft and patient-derived xenograft models, but it had minimal effects on healthy human BM CD34+ cells or on murine hematopoiesis. PU-H71 decreased MCL-1 and multiple signal proteins, increased proapoptotic Bcl-2-like protein 11 levels, and synergized with BCL-2 inhibitor venetoclax in TP53-mutant AML. Notably, PU-H71 effectively killed TP53-WT and -mutant cells in isogenic TP53-WT/TP53-R248W Molm13 cell mixtures, whereas MDM2 or BCL-2 inhibition only reduced TP53-WT but favored the outgrowth of TP53-mutant cells. Venetoclax enhanced the killing of both TP53-WT and -mutant cells by PU-H71 in a xenograft model. Our data suggest that epichaperome function is essential for TP53-mutant AML growth and survival and that its inhibition targets mutant AML and stem/progenitor cells, enhances venetoclax activity, and prevents the outgrowth of venetoclax-resistant TP53-mutant AML clones. These concepts warrant clinical evaluation.

Vincristine Enhances the Efficacy of MEK Inhibitors in Preclinical Models of KRAS-mutant Colorectal Cancer

Mutations in KRAS are found in more than 50% of tumors from patients with metastatic colorectal cancer (mCRC). However, direct targeting of most KRAS mutations is difficult; even the recently developed KRASG12C inhibitors failed to show significant benefit in patients with mCRC. Single agents targeting mitogen-activated protein kinase kinase (MEK), a downstream mediator of RAS, have also been ineffective in colorectal cancer. To identify drugs that can enhance the efficacy of MEK inhibitors, we performed unbiased high-throughput screening using colorectal cancer spheroids. We used trametinib as the anchor drug and examined combinations of trametinib with the NCI-approved Oncology Library version 5. The initial screen, and following focused validation screens, identified vincristine as being strongly synergistic with trametinib. In vitro, the combination strongly inhibited cell growth, reduced clonogenic survival, and enhanced apoptosis compared with monotherapies in multiple KRAS-mutant colorectal cancer cell lines. Furthermore, this combination significantly inhibited tumor growth, reduced cell proliferation, and increased apoptosis in multiple KRAS-mutant patient-derived xenograft mouse models. In vivo studies using drug doses that reflect clinically achievable doses demonstrated that the combination was well tolerated by mice. We further determined that the mechanism underlying the synergistic effect of the combination was due to enhanced intracellular accumulation of vincristine associated with MEK inhibition. The combination also significantly decreased p-mTOR levels in vitro, indicating that it inhibits both RAS-RAF-MEK and PI3K-AKT-mTOR survival pathways. Our data thus provide strong evidence that the combination of trametinib and vincristine represents a novel therapeutic option to be studied in clinical trials for patients with KRAS-mutant mCRC.

SIGNIFICANCE

Our unbiased preclinical studies have identified vincristine as an effective combination partner for the MEK inhibitor trametinib and provide a novel therapeutic option to be studied in patients with KRAS-mutant colorectal cancer.

Evolution of cisplatin resistance through coordinated metabolic reprogramming of the cellular reductive state

BACKGROUND

Cisplatin (CDDP) is a mainstay treatment for advanced head and neck squamous cell carcinomas (HNSCC) despite a high frequency of innate and acquired resistance. We hypothesised that tumours acquire CDDP resistance through an enhanced reductive state dependent on metabolic rewiring.

METHODS

To validate this model and understand how an adaptive metabolic programme might be imprinted, we performed an integrated analysis of CDDP-resistant HNSCC clones from multiple genomic backgrounds by whole-exome sequencing, RNA-seq, mass spectrometry, steady state and flux metabolomics.

RESULTS

Inactivating KEAP1 mutations or reductions in KEAP1 RNA correlated with Nrf2 activation in CDDP-resistant cells, which functionally contributed to resistance. Proteomics identified elevation of downstream Nrf2 targets and the enrichment of enzymes involved in generation of biomass and reducing equivalents, metabolism of glucose, glutathione, NAD(P), and oxoacids. This was accompanied by biochemical and metabolic evidence of an enhanced reductive state dependent on coordinated glucose and glutamine catabolism, associated with reduced energy production and proliferation, despite normal mitochondrial structure and function.

CONCLUSIONS

Our analysis identified coordinated metabolic changes associated with CDDP resistance that may provide new therapeutic avenues through targeting of these convergent pathways.

Abstract 2847: Concurrent inactivation of PI3K and PLK1 is synergistic and overcomes acquired resistance to PI3K inhibitors in NOTCH1MUT HNSCC

Targeted therapies are limited for head and neck squamous cell carcinoma (HNSCC), as it is driven by mutations in tumor suppressors, including NOTCH1. We previously identified loss of function NOTCH1 mutations in HNSCC to be sensitive to phosphoinositide-3 kinase (PI3K) inhibitors through sustained Aurora kinase B levels. However, therapy resistance and modest responses are the leading causes of failure for targeted therapies. To address this pressing clinical need, we sought to identify drugs that would enhance the efficacy of PI3K inhibitors. We tested 5768 drugs (0-1µM) with diverse targets in NOTCH1 mutant (NOTCH1MUT - HN31, UMSCC22A, PCI-15B) HNSCC cell lines and copanlisib acquired resistant (CAR) HN31 clones. We determined drug efficacy using two metrics-area over the curve lethal dose (AOC_LD>0, cytotoxic) and area under the growth curve (AUC_GRI<0.9, cytostatic). These metrics are more robust than IC50 values as they use the normalized growth rate inhibition curve and avoid the confounding effect of the rate of cell division. Of 306 drug classes, 100 were effective with at least one drug being cytotoxic or cytostatic in at least one cell line. PLK inhibitors were the most effective class of drugs against NOTCH1MUT HNSCC cell lines (87% effective - 12 cytotoxic, 2 cytostatic, 2 ineffective). We further tested the PLK1-specific inhibitor onvansertib (0-100nM) combined with pan-PI3K inhibitor copanlisib (0-200nM) or dual inhibitor bimiralisib (0-1μM). We observed robust decreases in cell numbers at very low drug concentrations (50nM) with the combinations. We validated these results in vitro in NOTCH1MUT, NOTCH1WT, CAR NOTCH1MUT HNSCC models, and HEK293 by using independent approaches to test for apoptosis. A significant increase in cleaved PARP and cleaved caspase 3, and Annexin V/PI staining (>2x), was evident when PI3K and PLK1 were concurrently inactivated as compared to single agent treatment in HNSCC models. Furthermore, HEK293 cells were unaffected at these doses. We then investigated the role of PLK1 following PI3K inhibition in HNSCC models and found PLK1 protein levels to be downregulated. As PLK1 is downstream of Aurora kinases, we further determined the phospho-PLK1 (p-PLK1) levels in HNSCC models. Interestingly, p-PLK1 levels remained unaltered in NOTCH1WT and CAR NOTCH1MUT cells despite total protein level depletion. However, p-PLK1 levels drastically decreased in NOTCH1MUT HNSCC cells. This finding could explain the importance of PLK1 inactivation in addition to PI3K inhibition as a requirement for increased cell death in HNSCC models. We will further validate this combination in vivo to determine the effect of combined PI3K and PLK1 inhibition on tumor growth and survival. These novel findings may lead to the development of a better therapeutic approach for NOTCH1MUT HNSCC and for patients who develop acquired resistance to targeted therapies.

Citation Format: Pooja A. Shah, Tuhina Mazumdar, Reid T. Powell, Li Shen, Jing Wang, Clifford C. Stephen, Mitchell J. Frederick, Faye M. Johnson. Concurrent inactivation of PI3K and PLK1 is synergistic and overcomes acquired resistance to PI3K inhibitors in NOTCH1MUT HNSCC [abstract]. In: Proceedings of the American Association for Cancer Research Annual Meeting 2023; Part 1 (Regular and Invited Abstracts); 2023 Apr 14-19; Orlando, FL. Philadelphia (PA): AACR; Cancer Res 2023;83(7_Suppl):Abstract nr 2847.

Abstract 453: Targeting FOXL2C402Gvulnerabilities in adult type ovarian granulosa cell tumors

Background: Nearly all adult-type granulosa cell tumors of the ovary (aGCTs) carry the same oncogenic mutation affecting the second winged helix domain of the Forkhead family transcription factor FOXL2 (c.C402G; p.C134W). There are no currently available therapies that exploit the high prevalence of FOXL2 mutations in this disease.

Objectives: Exploit FOXL2-C402G oncogenic addiction in order to identify FDA-approved compounds with differential potency in KGN-FOXL2WT/C402G cells and isogenic KGN-FOXL2—/— cells.

Methods: CRISPR/Cas9 was used to generate isogenic derivatives of KGN, a cell line derived from a recurrent aGCT. Parental cells (KGN-FOXL2WT/C402G) or isogenic cells lacking both FOXL2 alleles (KGN-FOXL2—/—) were functionally characterized and loss of Foxl2 protein was confirmed by immunoblot. Two drug libraries comprising a total of 2,416 compounds (majority FDA approved) were screened for effectiveness in KGN-FOXL2WT/C402G cells and KGN-FOXL2—/— cells. Our assay included staining with DAPI, followed by automated image analysis of each well to enumerate nuclei/cell numbers. Based on Fraction Affected (FA) statistics, compounds were ranked according to effectiveness in KGN-FOXL2WT/C402G cells. FA-area under the curve (FA-AUC) cutoff >0.1 yielded 152 drug candidates, categorized into 13 drug classes. 40 drug candidates, including the top 1-4 hits in each drug class were chosen for further validation. Validation rate in the confirmatory screen was at 95%. A novel primary tumor organoid culture system for aGCT was developed and validated using whole exome sequencing and immunophenotype. Selected candidate compounds were further investigated in aGCT organoid cultures from two relapsed tumors.

Results: We identified classes of drugs such as the inhibitors of Bromodomain family proteins and Hydroxy-Camptothecin analogs, with enhanced activity in KGN-FOXL2WT/C402G cells relative to KGN-FOXL2—/— cells. Unexpectedly glucocorticoids as a class were found to stimulate proliferation of KGN-FOXL2WT/C402G cells whereas they lacked this activity in KGN-FOXL2—/— cells. For 36 glucocorticoids present in the screen, FA-AUC ranged from -0.3191 to -0.1342 (highest proliferation index among all test compounds) in KGN-FOXL2WT/C402G cells compared to -0.0353 to +0.1667 in KGN-FOXL2—/— cells. In recurrent aGCT organoids, the high-potency glucocorticoid dexamethasone induced cell proliferation and co-treatment with glucocorticoids increased the IC50 of paclitaxel in KGN-FOXL2WT/C402G cells from 1.43 nM to 4.04 nM.

Conclusion: Mutant FOXL2 mediates a proliferative response to glucocorticoids in cultured cells and primary aGCT organoids. Paclitaxel is a standard of care chemotherapy in the treatment of aGCTs and is often administered with glucocorticoid pre-medication. The adverse effect of glucocorticoids on paclitaxel efficiency shown here should thus be taken into consideration in the clinic.

Citation Format: Thomas Welte, Veena Vuttaradhi, Eleonora Khlebus, Barrett Lawson, Robert T. Hillman, Nghi Nguyen, Mary Sobieski, Reid T. Powell, Clifford Stephan. Targeting FOXL2C402Gvulnerabilities in adult type ovarian granulosa cell tumors [abstract]. In: Proceedings of the American Association for Cancer Research Annual Meeting 2023; Part 1 (Regular and Invited Abstracts); 2023 Apr 14-19; Orlando, FL. Philadelphia (PA): AACR; Cancer Res 2023;83(7_Suppl):Abstract nr 453.

Combination of EphA2- and Wee1-Targeted Therapies in Endometrial Cancer

EphA2 tyrosine kinase is upregulated in many cancers and correlated with poor survival of patients, including those with endometrial cancer. EphA2-targeted drugs have shown modest clinical benefit. To improve the therapeutic response to such drugs, we performed a high-throughput chemical screen to discover novel synergistic partners for EphA2-targeted therapeutics. Our screen identified the Wee1 kinase inhibitor, MK1775, as a synergistic partner to EphA2, and this finding was confirmed using both in vitro and in vivo experiments. We hypothesized that Wee1 inhibition would sensitize cells to EphA2-targeted therapy. Combination treatment decreased cell viability, induced apoptosis, and reduced clonogenic potential in endometrial cancer cell lines. In vivo Hec1A and Ishikawa-Luc orthotopic mouse models of endometrial cancer showed greater anti-tumor responses to combination treatment than to either monotherapy. RNASeq analysis highlighted reduced cell proliferation and defective DNA damage response pathways as potential mediators of the combination's effects. In conclusion, our preclinical findings indicate that Wee1 inhibition can enhance the response to EphA2-targeted therapeutics in endometrial cancer; this strategy thus warrants further development.

Screening of GPCR drugs for repurposing in breast cancer

Drug repurposing can overcome both substantial costs and the lengthy process of new drug discovery and development in cancer treatment. Some Food and Drug Administration (FDA)-approved drugs have been found to have the potential to be repurposed as anti-cancer drugs. However, the progress is slow due to only a handful of strategies employed to identify drugs with repurposing potential. In this study, we evaluated GPCR-targeting drugs by high throughput screening (HTS) for their repurposing potential in triple-negative breast cancer (TNBC) and drug-resistant human epidermal growth factor receptor-2-positive (HER2+) breast cancer (BC), due to the dire need to discover novel targets and drugs in these subtypes. We assessed the efficacy and potency of drugs/compounds targeting different GPCRs for the growth rate inhibition in the following models: two TNBC cell lines (MDA-MB-231 and MDA-MB-468) and two HER2+ BC cell lines (BT474 and SKBR3), sensitive or resistant to lapatinib + trastuzumab, an effective combination of HER2-targeting therapies. We identified six drugs/compounds as potential hits, of which 4 were FDA-approved drugs. We focused on β-adrenergic receptor-targeting nebivolol as a candidate, primarily because of the potential role of these receptors in BC and its excellent long-term safety profile. The effects of nebivolol were validated in an independent assay in all the cell line models. The effects of nebivolol were independent of its activation of β3 receptors and nitric oxide production. Nebivolol reduced invasion and migration potentials which also suggests its inhibitory role in metastasis. Analysis of the Surveillance, Epidemiology and End Results (SEER)-Medicare dataset found numerically but not statistically significant reduced risk of all-cause mortality in the nebivolol group. In-depth future analyses, including detailed in vivo studies and real-world data analysis with more patients, are needed to further investigate the potential of nebivolol as a repurposed therapy for BC.

Combined TRIP13 and Aurora Kinase Inhibition Induces Apoptosis in Human Papillomavirus-Driven Cancers

PURPOSE

Human papillomavirus (HPV) causes >5% of cancers, but no therapies uniquely target HPV-driven cancers.

EXPERIMENTAL DESIGN

We tested the cytotoxic effect of 864 drugs in 16 HPV-positive and 17 HPV-negative human squamous cancer cell lines. We confirmed apoptosis in vitro and in vivo using patient-derived xenografts. Mitotic pathway components were manipulated with drugs, knockdown, and overexpression.

RESULTS

Aurora kinase inhibitors were more effective in vitro and in vivo in HPV-positive than in HPV-negative models. We hypothesized that the mechanism of sensitivity involves retinoblastoma (Rb) expression because the viral oncoprotein E7 leads to Rb protein degradation, and basal Rb protein expression correlates with Aurora inhibition-induced apoptosis. Manipulating Rb directly, or by inducing E7 expression, altered cells' sensitivity to Aurora kinase inhibitors. Rb affects expression of the mitotic checkpoint genes MAD2L1 and BUB1B, which we found to be highly expressed in HPV-positive patient tumors. Knockdown of MAD2L1 or BUB1B reduced Aurora kinase inhibition-induced apoptosis, whereas depletion of the MAD2L1 regulator TRIP13 enhanced it. TRIP13 is a potentially druggable AAA-ATPase. Combining Aurora kinase inhibition with TRIP13 depletion led to extensive apoptosis in HPV-positive cancer cells but not in HPV-negative cancer cells.

CONCLUSIONS

Our data support a model in which HPV-positive cancer cells maintain a balance of MAD2L1 and TRIP13 to allow mitotic exit and survival in the absence of Rb. Because it does not affect cells with intact Rb function, this novel combination may have a wide therapeutic window, enabling the effective treatment of Rb-deficient cancers.

Molecular pathways enhance drug response prediction using transfer learning from cell lines to tumors and patient-derived xenografts

Computational models have been successful in predicting drug sensitivity in cancer cell line data, creating an opportunity to guide precision medicine. However, translating these models to tumors remains challenging. We propose a new transfer learning workflow that transfers drug sensitivity predicting models from large-scale cancer cell lines to both tumors and patient derived xenografts based on molecular pathways derived from genomic features. We further compute feature importance to identify pathways most important to drug response prediction. We obtained good performance on tumors (AUROC = 0.77) and patient derived xenografts from triple negative breast cancers (RMSE = 0.11). Using feature importance, we highlight the association between ER-Golgi trafficking pathway in everolimus sensitivity within breast cancer patients and the role of class II histone deacetylases and interlukine-12 in response to drugs for triple-negative breast cancer. Pathway information support transfer of drug response prediction models from cell lines to tumors and can provide biological interpretation underlying the predictions, serving as a steppingstone towards usage in clinical setting.

Abstract 1858: Rb deficient HPV+ HNSCC experienced enhanced sensitivity to aurora kinase inhibitors by altering the balance of MAD2 and TRIP13 levels

Human papilloma virus (HPV)-driven head and neck squamous cell carcinoma (HNSCC) is common in young patients (<60 years). All patients experience either permanent toxicity from standard therapy or death from recurrent disease. To address this unmet need for more effective and less toxic therapy, we performed a high throughput drug screen comparing drug efficacy in HPV+ and HPV- cell lines. We tested the drug sensitivity of 864 unique drugs (0-3.1 µM) divided into 51 classes based on their targets in 33 squamous cancer cell lines using a parameter that is independent of cell division. Only one class of drugs, Aurora kinase inhibitors, was more effective in HPV+ than HPV- cell lines. To validate our screening results, we tested two Aurora kinase inhibitors (Alisertib, Barasertib) and observed significant cell death in HPV+ cells, but not in HPV- cells. Alisertib reduced tumor volume in HPV+ PDX mouse models without toxicity. To investigate the underlying mechanism, we compared the expression of ~300 proteins, using RPPA, to drug efficacy and validated the results using immunoblotting. The expression of Rb, pRb(S807/811), and p16 correlated with drug sensitivity. To establish role for Rb, we used a bidirectional approach to manipulate RB1. Reduction in RB1 levels using either shRNA or stable E7 overexpression in HPV- cells resulted in increased Alisertib-induced apoptosis. We also used siRNA to knock down E7 expression in two HPV+ cell lines which resulted in elevated levels of Rb, thereby rescuing the cells from Alisertib-induced apoptosis. Studies have shown Rb-deficient cells have elevated levels of the mitotic-checkpoint protein MAD2, that may impact cell fitness. To test the role of MAD2, we depleted the levels of MAD2 and observed diminishing levels of cyclin B1 accumulation and reduced Alisertib-induced apoptosis. Additionally, we altered the activated levels of MAD2 protein by overexpression of TRIP13 that resulted in partially rescuing cells from undergoing Alisertib-induced apoptosis. These results indicate that Rb- deficient MAD2 overexpressing cells require a finely tuned balance of MAD2 and TRIP13 levels for their mitotic exit. Furthermore, we observed combined inhibition of TRIP13 with Aurora A led to more apoptosis in Rb-deficient cells than the single agents. Our results demonstrate that Rb-deficient cancers are sensitive to Aurora A inhibition due to an imbalance between MAD2 and TRIP13. Based on the above finding, our present study shows that TRIP13 inhibition in combination with Aurora kinase inhibitors leads to more apoptosis and can pave a path for novel therapies in the management of HPV+ tumors.

Citation Format: Soma Ghosh, Tuhina Mazumdar, Wei Xu, Reid T. Powell, Clifford Stephan, Li Shen, Curtis R. Pickering, Jing Wang, Faye M. Johnson. Rb deficient HPV+ HNSCC experienced enhanced sensitivity to aurora kinase inhibitors by altering the balance of MAD2 and TRIP13 levels [abstract]. In: Proceedings of the American Association for Cancer Research Annual Meeting 2022; 2022 Apr 8-13. Philadelphia (PA): AACR; Cancer Res 2022;82(12_Suppl):Abstract nr 1858.

MODL-29. Molecular Landscape of a comprehensive panel of pediatric brain cancer Patient-derived orthotopic xenograft (PDOX) models inform unique targets for drug responsiveness

Brain tumor is a leading cause of cancer related death in children. In addition to replicating histopathology, animal models faithfully replicating genetic/epigenetic abnormalities, molecular subtypes and broad inter-tumoral heterogeneities are needed. Through direct implantation of patient surgical or autopsied tumor tissues into matching locations in the brains of SCID mice, we developed a panel of 150 PDOX mouse models. Here, we report the analysis of 74 of the 150 PDOX models, 45 matching patient tissues and 60 non-tumorigenic samples to a well-annotated reference cohort of 2,801 methylation profiles of primary brain tumors. Our data showed that the lack of tumorigenicity was neither correlated with molecular subtypes nor predicted by low cell viabilities of the patient samples. Methylation profiling identified PDOX models representing nearly a full spectrum of molecular subtypes of pediatric brain tumors including GBM, medulloblastoma, ependymoma and ATRT. Direct comparison with the original patient tumors confirmed the replication of molecular subtypes. ONCOplot [FB1] analysis of PDOX models derived from matching pairs of primary and recurrent tumors (n=8) revealed close clustering with the patient tumors. Investigation of metastatic properties was performed in 13 MB models by harvesting and sub-transplanting matching PDOX primary tumors in the cerebella and metastatic tumors in the spinal cords. To confirm the potential and power of PDOX models in preclinical drug testing, we applied fractionated radiation (2 Gy/day x 5 days) and optimized multi-agent combinatory chemotherapies in MB models of the four major subgroups. High-throughput combination drug screening with ~ 8,000 drugs in PDOX-derived GBM cell lines and primary cultures of MB PDOX cells identified a library of ~ 3,500 drugs that were active in pediatric brain tumors. In summary, this study provides detailed information on molecular subclassification of a uniquely large cohort of PDOX models to serve as essential tools for brain tumor research.

deepOrganoid: A brightfield cell viability model for screening matrix-embedded organoids

High-throughput viability screens are commonly used in the identification and development of chemotherapeutic drugs. These systems rely on the fidelity of the cellular model systems to recapitulate the drug response that occurs in vivo. In recent years, there has been an expansion in the utilization of patient-derived materials as well as advanced cell culture techniques, such as multi-cellular tumor organoids, to further enhance the translational relevance of cellular model systems. Simple quantitative analysis remains a challenge, primarily due to the difficulties of robust image segmentation in heterogenous 3D cultures. However, explicit segmentation is not required with the advancement of deep learning, and it can be used for both continuous (regression) or categorical classification problems. Deep learning approaches are additionally benefited by being fully data-driven and highly automatable, thus they can be established and run with minimal to no user-defined parameters. In this article, we describe the development and implementation of a regressive deep learning model trained on brightfield images of patient-derived organoids and use the terminal viability readout (CellTiter-Glo) as training labels. Ultimately, this has led to the generation of a non-invasive and label-free tool to evaluate changes in organoid viability.

Endocrine disrupting chemicals differentially alter intranuclear dynamics and transcriptional activation of estrogen receptor-α

Transcription is a highly regulated sequence of stochastic processes utilizing many regulators, including nuclear receptors (NR) that respond to stimuli. Endocrine disrupting chemicals (EDCs) in the environment can compete with natural ligands for nuclear receptors to alter transcription. As nuclear dynamics can be tightly linked to transcription, it is important to determine how EDCs affect NR mobility. We use an EPA-assembled set of 45 estrogen receptor-α (ERα) ligands and EDCs in our engineered PRL-Array model to characterize their effect upon transcription using fluorescence in situ hybridization and fluorescence recovery after photobleaching (FRAP). We identified 36 compounds that target ERα-GFP to a transcriptionally active, visible locus. Using a novel method for multi-region FRAP analysis we find a strong negative correlation between ERα mobility and inverse agonists. Our findings indicate that ERα mobility is not solely tied to transcription but affected highly by the chemical class binding the receptor.

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Development of a new algorithm for multi-foci FRAP analysis

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ERα agonists can be segregated into fast-moving and slow-moving receptor groups

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ERα inverse agonists receptor mobility inversely correlates with transcription

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Steroidal compounds result in a slower moving receptor than other classes

Rational Combination of CRM1 Inhibitor Selinexor and Olaparib Shows Synergy in Ovarian Cancer Cell Lines and Mouse Models

CRM1 inhibitors have demonstrated antitumor effects in ovarian and other cancers; however, rational combinations are largely unexplored. We performed a high-throughput drug library screen to identify drugs that might combine well with selinexor in ovarian cancer. Next, we tested the combination of selinexor with the top hit from the drug screen in vitro and in vivo Finally, we assessed for mechanisms underlying the identified synergy using reverse phase protein arrays (RPPA). The drug library screen assessing 688 drugs identified olaparib (a PARP inhibitor) as the most synergistic combination with selinexor. Synergy was further demonstrated by MTT assays. In the A2780luc ip1 mouse model, the combination of selinexor and olaparib yielded significantly lower tumor weight and fewer tumor nodules compared with the control group (P < 0.04 and P < 0.03). In the OVCAR5 mouse model, the combination yielded significantly fewer nodules (P = 0.006) and markedly lower tumor weight compared with the control group (P = 0.059). RPPA analysis indicated decreased expression of DNA damage repair proteins and increased expression of tumor suppressor proteins in the combination treatment group. Collectively, our preclinical findings indicate that combination with selinexor to expand the utility and efficacy of PARP inhibitors in ovarian cancer warrants further exploration.

A High-throughput Approach to Identify Effective Systemic Agents for the Treatment of Anaplastic Thyroid Carcinoma

BACKGROUND

Despite the use of aggressive multimodality treatment, most anaplastic thyroid carcinoma (ATC) patients die within a year of diagnosis. Although the combination of BRAF and MEK inhibitors has recently been approved for use in BRAF-mutated ATC, they remain effective in a minority of patients who are likely to develop drug resistance. There remains a critical clinical need for effective systemic agents for ATC with a reasonable toxicity profile to allow for rapid translational development.

MATERIAL AND METHODS

Twelve human thyroid cancer cell lines with comprehensive genomic characterization were used in a high-throughput screening (HTS) of 257 compounds to select agents with maximal growth inhibition. Cell proliferation, colony formation, orthotopic thyroid models, and patient-derived xenograft (PDX) models were used to validate the selected agents.

RESULTS

Seventeen compounds were effective, and docetaxel, LBH-589, and pralatrexate were selected for additional in vitro and in vivo analysis as they have been previously approved by the US Food and Drug Administration for other cancers. Significant tumor growth inhibition (TGI) was detected in all tested models treated with LBH-589; pralatrexate demonstrated significant TGI in the orthotopic papillary thyroid carcinoma model and 2 PDX models; and docetaxel demonstrated significant TGI only in the context of mutant TP53.

CONCLUSIONS

HTS identified classes of systemic agents that demonstrate preferential effectiveness against aggressive thyroid cancers, particularly those with mutant TP53. Preclinical validation in both orthotopic and PDX models, which are accurate in vivo models mimicking tumor microenvironment, may support initiation of early-phase clinical trials in non-BRAF mutated or refractory to BRAF/MEK inhibition ATC.

Mammary-specific expression of Trim24 establishes a mouse model of human metaplastic breast cancer

Conditional overexpression of histone reader Tripartite motif containing protein 24 (TRIM24) in mouse mammary epithelia (Trim24COE) drives spontaneous development of mammary carcinosarcoma tumors, lacking ER, PR and HER2. Human carcinosarcomas or metaplastic breast cancers (MpBC) are a rare, chemorefractory subclass of triple-negative breast cancers (TNBC). Comparison of Trim24COE metaplastic carcinosarcoma morphology, TRIM24 protein levels and a derived Trim24COE gene signature reveals strong correlation with human MpBC tumors and MpBC patient-derived xenograft (PDX) models. Global and single-cell tumor profiling reveal Met as a direct oncogenic target of TRIM24, leading to aberrant PI3K/mTOR activation. Here, we find that pharmacological inhibition of these pathways in primary Trim24COE tumor cells and TRIM24-PROTAC treatment of MpBC TNBC PDX tumorspheres decreased cellular viability, suggesting potential in therapeutically targeting TRIM24 and its regulated pathways in TRIM24-expressing TNBC.

Morphological screening of mesenchymal mammary tumor organoids to identify drugs that reverse epithelial-mesenchymal transition

The epithelial-mesenchymal transition (EMT) has been implicated in conferring stem cell properties and therapeutic resistance to cancer cells. Therefore, identification of drugs that can reprogram EMT may provide new therapeutic strategies. Here, we report that cells derived from claudin-low mammary tumors, a mesenchymal subtype of triple-negative breast cancer, exhibit a distinctive organoid structure with extended "spikes" in 3D matrices. Upon a miR-200 induced mesenchymal-epithelial transition (MET), the organoids switch to a smoother round morphology. Based on these observations, we developed a morphological screening method with accompanying analytical pipelines that leverage deep neural networks and nearest neighborhood classification to screen for EMT-reversing drugs. Through screening of a targeted epigenetic drug library, we identified multiple class I HDAC inhibitors and Bromodomain inhibitors that reverse EMT. These data support the use of morphological screening of mesenchymal mammary tumor organoids as a platform to identify drugs that reverse EMT.

Abstract 368: Aurora kinase inhibitors cause cell death in HPV+ cells: A plausible treatment option for HPV+ cancers

Human papilloma virus (HPV) driven cancers are common and lethal. The standard of care chemo-radiation treatment for HPV+ head and neck squamous cell carcinoma (HNSCC) results in permanent, often life-altering, toxicities in a relatively young population (aged ~45-55). Additionally, those who recur have poor outcomes. Therefore, there is an urgent need for better treatment options. No biomarker-driven targeted therapies are available. To address the current unmet need, we hypothesized that a large-scale High Throughput Drug Screen (HTDS) comparing drug efficacy in HPV+ and HPV- cell lines would identify biomarker driven, effective and less toxic options for HPV+ cancers. We tested the drug- sensitivity of 864 unique drugs (0-3.1 µM) in 51 classes based on their targets in 16 HPV+ and 17 HPV- squamous cancer cell lines. Cells were treated for 72 hours and DAPI+ nuclei counted before and after drug treatment. We used the Area Over the Curve_Lethal Dose (AOC_LD) to measure drug sensitivity because it is independent of cell division. We defined effective drugs as those that led to cell death (i.e., less cells at the end of drug treatment than prior to treatment) in at least one cell line. About half of the drugs tested (439) were effective and certain classes of drugs were enriched in either the effective or ineffective categories (Pearson residual). We found that Aurora kinase inhibitors were the most effective class overall. Other effective drug classes included anthracyclines, vinca-alkaloids, and inhibitors of HDAC, proteasome, EGFR, CDC7, and BTK1. Only 30 drugs had a differential effect based on HPV status. All 16 Aurora kinase inhibitors were more effective in HPV+ than in HPV- cells and the difference in sensitivity (dichotomous variable) was statistically significant in 7 of them. To determine if factors other than HPV status predict response to Aurora kinase inhibitors, we compared the expression of 304 proteins (RPPA) and mutational status for the 50 most commonly mutated genes in HNSCC to drug efficacy. The expression of eight proteins were associated with sensitivity to multiple Aurora kinase inhibitors. We validated RPPA data by immunoblotting and observed that only Rb, pRB(S807/811) and p16 correlated with drug sensitivity. For gene mutations, only TP53 mutations correlated with drug resistance with 7 Aurora kinase inhibitors. Interestingly, these two biomarkers, Rb and TP53, corroborate well with HPV status. To validate the screening results, we treated HPV+ cells with two clinically relevant Aurora kinase inhibitors, alisertib and barasertib, and observed significantly more cell death in HPV+ cells in comparison with HPV- cells. Therefore, our present study portrays Aurora kinase inhibitors as an effective strategy for HPV+ cancer cells. Multiple Aurora kinase inhibitors are currently in clinical development making the clinical application of our data possible soon.

Citation Format: Tuhina Mazumdar, Li Shen, Wei Xu, Soma Ghosh, Reid T. Powell, Clifford Stephan, Curtis R. Pickering, Jeffery N. Myers, Jing Wang, Faye M. Johnson. Aurora kinase inhibitors cause cell death in HPV+ cells: A plausible treatment option for HPV+ cancers [abstract]. In: Proceedings of the American Association for Cancer Research Annual Meeting 2021; 2021 Apr 10-15 and May 17-21. Philadelphia (PA): AACR; Cancer Res 2021;81(13_Suppl):Abstract nr 368.

Abstract 369: Identification of pathways that enhance cell death in NOTCH1-mutant HNSCC

Head and neck squamous carcinoma (HNSCC) is dominantly driven by mutations in tumor suppressor genes making it challenging to devise biomarker-based targeted therapy. In order to meet this pressing clinical need, our group recently demonstrated that HNSCCs with loss of function NOTCH1 mutations were more sensitive to phosphoinositide-3 kinase (PI3K) pathway inhibition than their wild-type counterparts.Modest clinical responses and acquired resistance are leading causes of failure for molecular targeted therapies that are otherwise well tolerated. In order to address this challenge and identify drugs that could work in combination with PI3K inhibitors against NOTCH1-mutant HNSCC, we performed a high throughput screen of 5669 drugs (0-1µM) with diverse targets. We used a laser-based confocal imaging platform to determine actual cell numbers using DAPI staining before and after drug treatment of NOTCH1-mutant HNSCC cells (HN31, UMSCC22A). We used 2 metrics of efficacy to identify potential candidates to combine with PI3K inhibition: an arbitrary cut off value of ≤ 0.9 for the area under the curve, growth rate index and area over the curve lethal dose (AOC_LD). We calculate both metrics using the normalized growth rate inhibition curve in order to avoid the confounding effect of the rate of cell division. The AOC_LD is &gt; 0 only when there are fewer cells after treatment than before (i.e., there was cell death). Of the resulting 340 candidates, we excluded chemotherapy, PI3K inhibitors, and non-specific drugs. When several candidates targeted the same pathway, we chose 2-3 of the most specific drugs to use in the combination screen. We combined the resulting 74 drugs with PI3K inhibitors, bimiralisib (0-1µM) or copanlisib (FDA approved, 0-100nM), for 72 h. Synergistic effects from these combinations were assessed using Bliss, HAS, Zip, and Loewe models. Trametinib (MEK inhibitor) and copanlisib were synergistic with the combination leading to 0.90 fraction of cells affected at concentrations of 30nM and 100nM respectively. These concentrations are target-specific and clinically achievable. Likewise, low concentrations of inhibitors of EGFR (10nM afatinib, 50nM AZ5104), HER2 (25nM sapitinib, 10nM poziotinib), and PLK1 (50nM BI2536, 50nM volasertib) were both effective and additive to synergistic with PI3K inhibitors. These combinations will further be validated in vitro using an independent approach to test for apoptosis (cleaved PARP and caspase-3 induction and TUNEL assay) and cell counts in multiple NOTCH1 mutant HNSCC cell lines. We will test the most promising combination in vivo. We have identified four drug classes that not only maximize the killing of NOTCH1-mutant HNSCC, but may also prevent resistance at clinically relevant concentrations. The identified pathways may give us insight into mechanisms of resistance. If validated, these combinations may lead to the first biomarker-specific, targeted therapy for HNSCC.

Citation Format: Pooja A. Shah, Tuhina Mazumdar, Reid T. Powell, Li Shen, Jing Wang, Clifford C. Stephen, Mitchell J. Frederick, Faye M. Johnson. Identification of pathways that enhance cell death in NOTCH1-mutant HNSCC [abstract]. In: Proceedings of the American Association for Cancer Research Annual Meeting 2021; 2021 Apr 10-15 and May 17-21. Philadelphia (PA): AACR; Cancer Res 2021;81(13_Suppl):Abstract nr 369.

High-throughput screening against protein:protein interaction interfaces reveals anti-cancer therapeutics as potent modulators of the voltage-gated Na+ channel complex

Multiple voltage-gated Na⁺ (Nav) channelopathies can be ascribed to subtle changes in the Nav macromolecular complex. Fibroblast growth factor 14 (FGF14) is a functionally relevant component of the Nav1.6 channel complex, a causative link to spinocerebellar ataxia 27 (SCA27) and an emerging risk factor for neuropsychiatric disorders. Yet, how this protein:channel complex is regulated in the cell is still poorly understood. To search for key cellular pathways upstream of the FGF14:Nav1.6 complex, we have developed, miniaturized and optimized an in-cell assay in 384-well plates by stably reconstituting the FGF14:Nav1.6 complex using the split-luciferase complementation assay. We then conducted a high-throughput screening (HTS) of 267 FDA-approved compounds targeting known mediators of cellular signaling. Of the 65 hits initially detected, 24 were excluded based on counter-screening and cellular toxicity. Based on target analysis, potency and dose-response relationships, 5 compounds were subsequently repurchased for validation and confirmed as hits. Among those, the tyrosine kinase inhibitor lestaurtinib was highest ranked, exhibiting submicromolar inhibition of FGF14:Nav1.6 assembly. While providing evidence for a robust in-cell HTS platform that can be adapted to search for any channelopathy-associated regulatory proteins, these results lay the potential groundwork for repurposing cancer drugs for neuropsychopharmacology.

Abstract 1402: Single cell transcriptomic profiling of ex vivo tumoroid models reveal therapeutic vulnerabilities of pancreatic ductal adenocarcinoma

By 2030, pancreatic ductal adenocarcinoma (PDAC) will likely become the second leading cause of cancer-related death. A lack of actionable mutations continues to be a significant challenge in addressing the disease in a precision medicine setting. As a result, current treatment options are often limited to genotype-independent cytotoxic agents. Patient derived tumor organoid (PDOs) models have gained traction as potential tools for therapeutic stratification. We characterized single cell gene expression profiles of PDOs and applied an in silico therapeutic drug prediction model to identify and validate combinatorial strategies targeting heterogeneous subpopulations. Four established PDOs from PDAC were profiled through single cell RNA-Seq analysis in order to identify subpopulations of cancer cells with differing therapeutic response. The PDOs were then subjected to a high-throughput drug screen of 764 agency approved candidates. Top candidates, including combinatorial drug selections, were orthogonally validated through single cell gene expression analysis and evaluated for efficacy and synergistic interactions. Single-cell transcriptomic profiling of PDOs revealed unique subpopulations of cancer cells with differential expression of DNA Damage response, protein and fatty acid metabolism, and inflammatory related pathways. Effective combinatorial therapies were projected based on pharmacogenomic predictions targeting opposite gene expression patterns of each subpopulation and validated through drug library screens. In a PDO, common sensitivity nodes utilizing epigenetic modifiers were detected among all tumor derived subpopulations. A synergy matrix seeded with PDOs and evaluated using Bliss independence revealed that combinatorial treatment with HDAC-inhibitors and PARP1-inhibitors produced the most profound synergistic result. Mechanistically, HDAC inhibitors limit the activity of DNA repair proteins which in conjunction with PARP-inhibition leads to synergistic outcomes. We have demonstrated the utility of single cell transcriptomic profiling from PDOs in identifying viable treatment options using a pharmacogenomic strategy. The sophisticated heterogeneity of PDOs, revealed the necessity of using combinatorial strategies to target all relevant subpopulations. Furthermore, this strategy revealed an exciting synergistic interplay between HDAC and PARP1 inhibitors, an interaction that has never before been shown in a PDAC case. Looking forward, our model not only may be a vehicle used to discover new drug candidates and elucidate novel mechanisms, but may also be the first step towards the establishment of a true precision medicine paradigm for PDAC.

Citation Format: Vincent Bernard, F. Anthony San Lucas, Jonathan Huang, Reid T. Powell, Paola A. Guerrero, Alexander Semaan, Clifford C. Stephan, Peter Davies, Gauri R. Varadhachary, Matthew H. Katz, Cullen M. Taniguchi, Hector A. Alvarez, Senthil Muthuswamy, Anirban Maitra. Single cell transcriptomic profiling of ex vivo tumoroid models reveal therapeutic vulnerabilities of pancreatic ductal adenocarcinoma [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 1402.

Bacteria-to-Human Protein Networks Reveal Origins of Endogenous DNA Damage

DNA damage provokes mutations and cancer and results from external carcinogens or endogenous cellular processes. However, the intrinsic instigators of endogenous DNA damage are poorly understood. Here, we identify proteins that promote endogenous DNA damage when overproduced: the DNA "damage-up" proteins (DDPs). We discover a large network of DDPs in Escherichia coli and deconvolute them into six function clusters, demonstrating DDP mechanisms in three: reactive oxygen increase by transmembrane transporters, chromosome loss by replisome binding, and replication stalling by transcription factors. Their 284 human homologs are over-represented among known cancer drivers, and their RNAs in tumors predict heavy mutagenesis and a poor prognosis. Half of the tested human homologs promote DNA damage and mutation when overproduced in human cells, with DNA damage-elevating mechanisms like those in E. coli. Our work identifies networks of DDPs that provoke endogenous DNA damage and may reveal DNA damage-associated functions of many human known and newly implicated cancer-promoting proteins.

Bexarotene - a novel modulator of AURKA and the primary cilium in VHL-deficient cells

Loss of the gene von Hippel–Lindau (VHL) is associated with loss of primary cilia and is causally linked to elevated levels of Aurora kinase A (AURKA). We developed an image-based high-throughput screening (HTS) assay using a dual-labeling image analysis strategy that identifies both the cilium and the basal body. By using this strategy, we screened small-molecule compounds for the targeted rescue of cilia defects associated with VHL deficiency with high accuracy and reproducibility. Bexarotene was identified and validated as a positive regulator of the primary cilium. Importantly, the inability of an alternative retinoid X receptor (RXR) agonist to rescue ciliogenesis, in contrast to bexarotene, suggested that multiple bexarotene-driven mechanisms were responsible for the rescue. We found that bexarotene decreased AURKA expression in VHL-deficient cells, thereby restoring the ability of these cells to ciliate in the absence of VHL. Finally, bexarotene treatment reduced the propensity of subcutaneous lesions to develop into tumors in a mouse xenograft model of renal cell carcinoma (RCC), with a concomitant decrease in activated AURKA, highlighting the potential of bexarotene treatment as an intervention strategy in the clinic to manage renal cystogenesis associated with VHL deficiency and elevated AURKA expression.

Highlighted Article: An image-based screen using a dual labeling strategy identified bexarotene, a rexinoid, as a novel modulator of the primary cilium in VHL-deficient cells.

SETD2 Haploinsufficiency for Microtubule Methylation Is an Early Driver of Genomic Instability in Renal Cell Carcinoma

Loss of the short arm of chromosome 3 (3p) occurs early in >95% of clear cell renal cell carcinoma (ccRCC). Nearly ubiquitous 3p loss in ccRCC suggests haploinsufficiency for 3p tumor suppressors as early drivers of tumorigenesis. We previously reported methyltransferase SETD2, which trimethylates H3 histones on lysine 36 (H3K36me3) and is located in the 3p deletion, to also trimethylate microtubules on lysine 40 (αTubK40me3) during mitosis, with αTubK40me3 required for genomic stability. We now show that monoallelic, Setd2-deficient cells retaining H3K36me3, but not αTubK40me3, exhibit a dramatic increase in mitotic defects and micronuclei count, with increased viability compared with biallelic loss. In SETD2-inactivated human kidney cells, rescue with a pathogenic SETD2 mutant deficient for microtubule (αTubK40me3), but not histone (H3K36me3) methylation, replicated this phenotype. Genomic instability (micronuclei) was also a hallmark of patient-derived cells from ccRCC. These data show that the SETD2 tumor suppressor displays a haploinsufficiency phenotype disproportionately impacting microtubule methylation and serves as an early driver of genomic instability.Significance: Loss of a single allele of a chromatin modifier plays a role in promoting oncogenesis, underscoring the growing relevance of tumor suppressor haploinsufficiency in tumorigenesis. Cancer Res; 78(12); 3135-46. ©2018 AACR.

PanCancer insights from The Cancer Genome Atlas: the pathologist's perspective

The Cancer Genome Atlas (TCGA) represents one of several international consortia dedicated to performing comprehensive genomic and epigenomic analyses of selected tumour types to advance our understanding of disease and provide an open-access resource for worldwide cancer research. Thirty-three tumour types (selected by histology or tissue of origin, to include both common and rare diseases), comprising >11 000 specimens, were subjected to DNA sequencing, copy number and methylation analysis, and transcriptomic, proteomic and histological evaluation. Each cancer type was analysed individually to identify tissue-specific alterations, and make correlations across different molecular platforms. The final dataset was then normalized and combined for the PanCancer Initiative, which seeks to identify commonalities across different cancer types or cells of origin/lineage, or within anatomically or morphologically related groups. An important resource generated along with the rich molecular studies is an extensive digital pathology slide archive, composed of frozen section tissue directly related to the tissues analysed as part of TCGA, and representative formalin-fixed paraffin-embedded, haematoxylin and eosin (H&E)-stained diagnostic slides. These H&E image resources have primarily been used to verify diagnoses and histological subtypes with some limited extraction of standard pathological variables such as mitotic activity, grade, and lymphocytic infiltrates. Largely overlooked is the richness of these scanned images for more sophisticated feature extraction approaches coupled with machine learning, and ultimately correlation with molecular features and clinical endpoints. Here, we document initial attempts to exploit TCGA imaging archives, and describe some of the tools, and the rapidly evolving image analysis/feature extraction landscape. Our hope is to inform, and ultimately inspire and challenge, the pathology and cancer research communities to exploit these imaging resources so that the full potential of this integral platform of TCGA can be used to complement and enhance the insightful integrated analyses from the genomic and epigenomic platforms. Copyright © 2017 Pathological Society of Great Britain and Ireland. Published by John Wiley & Sons, Ltd.

Methylated α-tubulin antibodies recognize a new microtubule modification on mitotic microtubules

Posttranslational modifications (PTMs) on microtubules differentiate these cytoskeletal elements for a variety of cellular functions. We recently identified SETD2 as a dual-function histone and microtubule methyltransferase, and methylation as a new microtubule PTM that occurs on lysine 40 of α-tubulin, which is trimethylated (α-TubK40me3) by SETD2. In the course of these studies, we generated polyclonal (α-TubK40me3 pAb) and monoclonal (α-TubK40me3 mAb) antibodies to a methylated α-tubulin peptide (GQMPSD-Kme3-TIGGGDC). Here, we characterize these antibodies, and the specific mono-, di- or tri-methylated lysine residues they recognize. While both the pAb and mAb antibodies recognized lysines methylated by SETD2 on microtubules and histones, the clone 18 mAb was more specific for methylated microtubules, with little cross-reactivity for methylated histones. The clone 18 mAb recognized specific subsets of microtubules during mitosis and cytokinesis, and lacked the chromatin staining seen by immunocytochemistry with the pAb. Western blot analysis using these antibodies revealed that methylated α-tubulin migrated faster than unmethylated α-tubulin, suggesting methylation may be a signal for additional processing of α-tubulin and/or microtubules. As the first reagents that specifically recognize methylated α-tubulin, these antibodies are a valuable tool for studying this new modification of the cytoskeleton, and the function of methylated microtubules.

ATM functions at the peroxisome to induce pexophagy in response to ROS

Peroxisomes are highly metabolic, autonomously replicating organelles that generate ROS as a by product of fatty acid β-oxidation. Consequently, cells must maintain peroxisome homeostasis, or risk pathologies associated with too few peroxisomes, such as peroxisome biogenesis disorders, or too many peroxisomes, inducing oxidative damage and promoting diseases such as cancer. We report that the PEX5 peroxisome import receptor binds ataxia-telangiectasia mutated (ATM) and localizes this kinase to the peroxisome. In response to reactive oxygen species (ROS), ATM signaling activates ULK1 and inhibits mTORC1 to induce autophagy. Specificity for autophagy of peroxisomes (pexophagy) is provided by ATM phosphorylation of PEX5 at Ser141, which promotes PEX5 mono-ubiquitination at K209, and recognition of ubiquitinated PEX5 by the autophagy adapter protein p62, directing the autophagosome to peroxisomes to induce pexophagy. These data reveal an important new role for ATM in metabolism as a sensor of ROS that regulates pexophagy.

Defining estrogenic mechanisms of bisphenol A analogs through high throughput microscopy-based contextual assays

Environmental exposures to chemically heterogeneous endocrine-disrupting chemicals (EDCs) mimic or interfere with hormone actions and negatively affect human health. Despite public interest and the prevalence of EDCs in the environment, methods to mechanistically classify these diverse chemicals in a high throughput (HT) manner have not been actively explored. Here, we describe the use of multiparametric, HT microscopy-based platforms to examine how a prototypical EDC, bisphenol A (BPA), and 18 poorly studied BPA analogs (BPXs), affect estrogen receptor (ER). We show that short exposure to BPA and most BPXs induces ERα and/or ERβ loading to DNA changing target gene transcription. Many BPXs exhibit higher affinity for ERβ and act as ERβ antagonists, while they act largely as agonists or mixed agonists and antagonists on ERα. Finally, despite binding to ERs, some BPXs exhibit lower levels of activity. Our comprehensive view of BPXs activities allows their classification and the evaluation of potential harmful effects. The strategy described here used on a large-scale basis likely offers a faster, more cost-effective way to identify safer BPA alternatives.

Linking ecological impact to metal concentrations and speciation: a microcosm experiment using a salt marsh meiofaunal community

Microcosm experiments addressed the impact of a mixture of Cu, Cr, Cd, Pb, and Hg at three concentrations after 36 h, 12 d, and 30 d on a meiofauna-dominated salt marsh community. In addition to analyzing effects on meiofaunal abundances, the study quantified the sediment metal concentrations of all five metals and pore-water concentrations, speciation, and ligand complexation of Cu. Abundances of deposit feeders such as the polychaete Streblospio benedicti, gastropods, and bivalves were impacted at lower metal concentrations than the mainly algal-feeding copepods, ostracods, and nematodes. We suggest that this might be due to bulk ingestion of metal-contaminated sediments resulting in relatively higher metal exposure in the deposit feeders than in the other, nondeposit feeding taxa. Copepod and ostracod abundances decreased only in the highest metal treatment, where levels of inorganic Cu ([Cu']) in pore waters were similar to levels associated with both acute and subacute toxicity in published in vivo toxicity studies of marine copepods. The higher metal treatments yielded disproportionately higher pore-water [Cu] compared with sediment [Cu], suggesting saturation of sediment-associated ligands with increased additions of Cu. Similarly, the higher metal treatments appeared to reach saturation of the organic Cu ligands, with the excess pore-water [Cu] present in the more toxic, inorganic species of Cu. Acid-volatile sulfide (AVS) concentrations at sediment horizons inhabited by meiofauna were low and AVS was not considered a significant metal ligand at these depths. Since meiofauna are predominantly associated with oxic surface sediments, it is doubtful that AVS is a major factor controlling availability of free metal for exposure to these taxa.