A Novel 3DNA® Nanocarrier effectively delivers payloads to pancreatic tumors

INTRODUCTION

Standard-of-care systemic chemotherapies for pancreatic ductal adenocarcinoma (PDAC) currently have limited clinical benefits, in addition to causing adverse side effects in many patients. One factor known to contribute to the poor chemotherapy response is the poor drug diffusion into PDAC tumors. Novel treatment methods are therefore drastically needed to improve targeted delivery of treatments. Here, we evaluated the efficacy of the 3DNA® Nanocarrier (3DNA) platform to direct delivery of therapeutics to PDAC tumors in vivo.

MATERIALS AND METHODS

A panel of PDAC cell lines and a patient tissue microarray were screened for established tumor-specific proteins to identify targeting moieties for active targeting of the 3DNA. NRG mice with or without orthotopic MIA PaCa-2-luciferase PDAC tumors were treated intraperitoneally with 100 μl of fluorescently labeled 3DNA.

RESULTS

Folic acid and transferrin receptors were significantly elevated in PDAC compared to normal pancreas. Accordingly, both folic acid- and transferrin-conjugated 3DNA treatments significantly increased delivery of 3DNA specifically to tumors in comparison to unconjugated 3DNA treatment. In the absence of tumors, there was an increased clearance of both folic acid-conjugated 3DNA and unconjugated 3DNA, compared to the clearance rate in tumor-bearing mice. Lastly, delivery of siLuciferase by folic acid-conjugated 3DNA in an orthotopic model of luciferase-expressing PDAC showed significant and prolonged suppression of luciferase protein expression and activity.

CONCLUSION

Our study progresses the 3DNA technology as a reliable and effective treatment delivery platform for targeted therapeutic approaches in PDAC.

Epitope-Specific IgE at 1 Year of Age Can Predict Peanut Allergy Status at 5 Years

BACKGROUND

Currently, there is no laboratory test that can accurately identify children at risk of developing peanut allergy. Utilizing a subset of children randomized to the peanut avoidance arm of the LEAP trial, we monitored the development of epitope-specific (ses-)IgE and ses-IgG4 from 4-11 months to 5 years of age.

OBJECTIVE

The aim of the study was to evaluate the prognostic ability of epitope-specific antibodies to predict the result of an oral food challenge (OFC) at 5 years.

METHODS

A Bead-Based Epitope Assay was used to quantitate IgE and IgG4 to 64 sequential (linear) epitopes from Ara h 1-3 proteins at 4-11 months, 1 and 2.5 years of age in 74 subjects (38 of them with a positive OFC at 5 years). Specific IgE (sIgE) to peanut and component proteins was measured using ImmunoCAP. Machine learning methods were used to identify the earliest time point to predict 5-year outcome, developing prognostic algorithms based only on 4-11 month samples, 1-year or 2.5-year, and a combination of them. Data from 74 children were iteratively split 3:1 into training and validation sets, and machine learning models were developed to predict the 5-year outcome. A test set (n = 90) from an independent cohort was used for final evaluation.

RESULTS

Elastic-Net algorithm combining ses-IgE and IgE to Ara h 1, 2, 3, and 9 proteins could predict the 5-year peanut allergy status of LEAP participants with an average validation accuracy of 64% at baseline. Samples taken at 1 year accurately predicted a 5-year OFC outcome with 83% accuracy. This performance remained consistent when evaluated on an independent CoFAR2 cohort with an accuracy of 78% for the 1-year model.

CONCLUSION

IgE antibody profiles at 1 year of age are predictive of peanut OFC at 5 years in children avoiding peanuts. If further confirmed, this model may enable early identification of infants who may benefit from early immunotherapeutic interventions.

Predicting probability of tolerating discrete amounts of peanut protein in allergic children using epitope-specific IgE antibody profiling

BACKGROUND

IgE-epitope profiling can accurately diagnose clinical peanut allergy.

OBJECTIVE

We sought to determine whether sequential (linear) epitope-specific IgE (ses-IgE) profiling can provide probabilities of tolerating discrete doses of peanut protein in allergic subjects undergoing double-blind, placebo-controlled food challenges utilizing PRACTALL dosing.

METHODS

Sixty four ses-IgE antibodies were quantified in blood samples using a bead-based epitope assay. A pair of ses-IgEs that predicts Cumulative Tolerated Dose (CTD) was determined using regression in 75 subjects from the discovery cohort. This epitope-based predictor was validated on 331 subjects from five independent cohorts (ages 4-25 years). Subjects were grouped based on their predicted values and probabilities of reactions at each CTD threshold were calculated.

RESULTS

In discovery, an algorithm using two ses-IgE antibodies was correlated with CTDs (rho = 0.61, p < .05); this correlation was 0.51 (p < .05) in validation. Using the ses-IgE-based predictor, subjects were assigned into "high," "moderate," or "low" dose-reactivity groups. On average, subjects in the "high" group were four times more likely to tolerate a specific dose, compared with the "low" group. For example, predicted probabilities of tolerating 4, 14, 44, and 144 or 444 mg in the "low" group were 92%, 77%, 53%, 29%, and 10% compared with 98%, 95%, 94%, 88%, and 73% in the "high" group.

CONCLUSIONS

Accurate predictions of food challenge thresholds are complex due to factors including limited responder sample sizes at each dose and variations in study-specific challenge protocols. Despite these limitations, an epitope-based predictor was able to accurately identify CTDs and may provide a useful surrogate for peanut challenges.

Limited nutrient availability in the tumor microenvironment renders pancreatic tumors sensitive to allosteric IDH1 inhibitors

Nutrient-deprived conditions in the tumor microenvironment (TME) restrain cancer cell viability due to increased free radicals and reduced energy production. In pancreatic cancer cells a cytosolic metabolic enzyme, wild-type isocitrate dehydrogenase 1 (wtIDH1), enables adaptation to these conditions. Under nutrient starvation, wtIDH1 oxidizes isocitrate to generate α-ketoglutarate (αKG) for anaplerosis and NADPH to support antioxidant defense. In this study, we show that allosteric inhibitors of mutant IDH1 (mIDH1) are potent wtIDH1 inhibitors under conditions present in the TME. We demonstrate that low magnesium levels facilitate allosteric inhibition of wtIDH1, which is lethal to cancer cells when nutrients are limited. Furthermore, the Food & Drug Administration (FDA)-approved mIDH1 inhibitor ivosidenib (AG-120) dramatically inhibited tumor growth in preclinical models of pancreatic cancer, highlighting this approach as a potential therapeutic strategy against wild-type IDH1 cancers.

Sustained Release of Antibody-Conjugated DNA Nanocarriers from a Novel Injectable Hydrogel for Targeted Cell Depletion to Treat Cataract Posterior Capsule Opacification

Purpose: To compare a novel, sustained release formulation and a bolus injection of a targeted nanocarrier for the ability to specifically deplete cells responsible for the development of posterior capsule opacification (PCO) in week-long, dynamic cell cultures. Methods: A novel, injectable, thermosensitive poly(D,L-lactic-co-glycolic acid)-b-poly(ethylene glycol)-b-poly(D,L-lactic-co-glycolic acid) (PLGA-PEG-PLGA) triblock copolymer hydrogel was engineered for the sustained release of targeted, nucleic acid nanocarriers loaded with cytotoxic doxorubicin (G8:3DNA:Dox). Human rhabdomyosarcoma (RD) cells were used due to their expression of brain-specific angiogenesis inhibitor 1 (BAI1), a specific marker for the myofibroblasts responsible for PCO. Under constant media flow, nanocarriers were injected into cell cultures as either a bolus or within the hydrogel. Cells were fixed and stained every other day for 7 days to compare targeted depletion of BAI1⁺ cells. Results: The formulation transitions to a gel at physiological temperatures, is optically clear, noncytotoxic, and can release G8:3DNA:Dox nanocarriers for up to 4 weeks. In RD cell cultures, G8:3DNA:Dox nanocarriers specifically eliminated BAI1⁺ cells. The bolus nanocarrier dose showed significantly reduced cell depletion overtime, while the sustained release of nanocarriers showed increased cell depletion over time. By day 7, <2% of BAI1⁺ cells were depleted by the bolus injection and 74.2% BAI1⁺ cells were targeted by the sustained release of nanocarriers. Conclusions: The sustained release of nanocarriers from the hydrogel allows for improved therapeutic delivery in a dynamic system. This method can offer a more effective and efficient method of prophylactically treating PCO after cataract surgery.

Accurate and reproducible diagnosis of peanut allergy using epitope mapping

BACKGROUND

Accurate diagnosis of peanut allergy is a significant clinical challenge. Here, a novel diagnostic blood test using the peanut bead-based epitope assay ("peanut BBEA") was developed utilizing the LEAP cohort and then validated using two independent cohorts.

METHODS

The development of the peanut BBEA diagnostic test followed the National Academy of Medicine's established guidelines with discovery performed on 133 subjects from the non-interventional arm of the LEAP trial and an independent validation performed on 82 subjects from the CoFAR2 and 84 subjects from the POISED study. All samples were analyzed using the peanut BBEA methodology, which measures levels of IgE to two Ara h 2 sequential (linear) epitopes and compares their combination to a threshold pre-specified in the model development phase. When a patient has an inconclusive outcome by skin prick testing (or sIgE), IgE antibody levels to this combination of two epitopes can distinguish whether the patient is "Allergic" or "Not Allergic." Diagnoses of peanut allergy in all subjects were confirmed by double-blind placebo-controlled food challenge and subjects' ages were 7-55 years.

RESULTS

In the validation using CoFAR2 and POISED cohorts, the peanut BBEA diagnostic test correctly diagnosed 93% of the subjects, with a sensitivity of 92%, specificity of 94%, a positive predictive value of 91%, and negative predictive value of 95%.

CONCLUSIONS

In validation of the peanut BBEA diagnostic test, the overall accuracy was found to be superior to existing diagnostic tests for peanut allergy including skin prick testing, peanut sIgE, and peanut component sIgE testing.

Mapping Sequential IgE-Binding Epitopes on Major and Minor Egg Allergens

INTRODUCTION

Molecular studies of hen's egg allergens help define allergic phenotypes, with IgE to sequential (linear) epitopes on the ovomucoid (OVM) protein associated with a persistent disease. Epitope profiles of other egg allergens are largely unknown. The objective of this study was to construct an epitope library spanning across 7 allergens and further evaluate sequential epitope-specific (ses-)IgE and ses-IgG4 among baked-egg reactive or tolerant children.

METHODS

A Bead-Based Epitope Assay was used to identify informative IgE epitopes from 15-mer overlapping peptides covering the entire OVM and ovalbumin (OVA) proteins in 38 egg allergic children. An amalgamation of 12 B-cell epitope prediction tools was developed using experimentally identified epitopes. This ensemble was used to predict epitopes from ovotransferrin, lysozyme, serum albumin, vitellogenin-II fragment, and vitellogenin-1 precursor. Ses-IgE and ses-IgG4 repertoires of 135 egg allergic children (82 reactive to baked-egg, the remaining 52 tolerant), 46 atopic controls, and 11 healthy subjects were compared.

RESULTS

183 peptides from OVM and OVA were screened and used to create an aggregate algorithm, improving predictions of 12 individual tools. A final library of 65 sequential epitopes from 7 proteins was constructed. Egg allergic children had higher ses-IgE and lower ses-IgG4 to predominantly OVM epitopes than both atopic and healthy controls. Baked-egg reactive children had similar ses-IgG4 but greater ses-IgE than tolerant group. A combination of OVA-sIgE with ses-IgEs to OVM-023 and OVA-028 was the best predictor of reactive phenotype.

CONCLUSION

We have created a comprehensive epitope library and showed that ses-IgE is a potential biomarker of baked-egg reactivity.

The immunomodulating enzyme indoleamine 2,3-dioxygenase 2 (IDO2) as a target for therapy in autoimmune disease

The enzyme indoleamine 2,3-dioxygenase 2 (IDO2) is an important mediator of inflammatory autoimmune responses. Unlike its better-known counterpart, IDO1, which is thought to act primarily in an immunosuppressive manner, IDO2 acts to promote inflammation via a B-cell intrinsic mechanism. Prior work has demonstrated that genetic knockout of IDO2 can inhibit both autoantibody production and joint inflammation in the KRN.g7 murine model of arthritis. IDO2 played a similar role in driving inflammation in collagen induced arthritis and contact hypersensitivity models. Given the clear role of IDO2 in mediating autoimmunity, we have worked to find novel ways to target IDO2 in vivo. In addition to previous research successfully targeting the intracellular IDO2 protein with a novel monoclonal antibody, we have recently described an innovative, targeted DNA nanostructure-based siRNA-delivery system to specifically inhibit IDO2 function in B cells. Treatment of KRN mice with this B cell-directed anti-IDO2 siRNA nanotherapy reduced autoantibodies and attenuated arthritis, mimicking the phenotype seen with genetic knockouts. These data provided preclinical proof-of-concept that IDO2 could be effectively targeted as a treatment strategy in murine arthritis and suggested a similar strategy could be used target IDO2 in human RA. Similar to our findings using murine B cells, we found that IDO2 expression was elevated in B cells isolated from RA patients and could be silenced using anti-IDO2 siRNA in vitro. These data provide the first indication for the relevance of IDO2 in human RA and suggest nanoparticle delivery systems are a potential therapeutic strategy to inhibit IDO2 in RA patient B cells.

Evolution of epitope-specific IgE and IgG4 antibodies in children enrolled in the LEAP trial

BACKGROUND

In the LEAP (Learning Early About Peanut Allergy) trial, early consumption of peanut in high-risk infants was found to decrease the rate of peanut allergy at 5 years of age. Sequential epitope-specific (ses-)IgE is a promising biomarker of clinical peanut reactivity.

OBJECTIVE

We sought to compare the evolution of ses-IgE and ses-IgG₄ in children who developed (or not) peanut allergy and to evaluate the immunomodulatory effects of early peanut consumption on these antibodies.

METHODS

Sera from 341 children (LEAP cohort) were assayed at baseline, 1, 2.5, and 5 years of age, with allergy status determined by oral food challenge at 5 years. A bead-based epitope assay was used to quantitate ses-IgE and ses-IgG₄ to 64 sequential epitopes from Ara h 1 to Ara h 3 and was analyzed using linear mixed-effect models.

RESULTS

In children avoiding peanut who became peanut allergic, the bulk of peanut ses-IgE did not develop until after 2.5 years. Minimal increases of ses-IgE occurred after 1 year in consumers, but not to the same epitopes as those in children developing peanut allergy. No major changes in ses-IgE were seen in nonallergic or sensitized children. IgE in sensitized consumers was detected against peanut proteins. ses-IgG₄ increased over time in most children regardless of consumption or allergy status.

CONCLUSIONS

Early peanut consumption in infants at high risk of developing peanut allergy appears to divert the immunologic response to a presumably "protective" effect. In general, consumers tend to generate ses-IgG₄ earlier and in greater quantities than nonconsumers do, whereas only avoiders tend to generate significant quantities of ses-IgE.

Ovomucoid epitope-specific repertoire of IgE, IgG4 , IgG1 , IgA1 , and IgD antibodies in egg-allergic children

BACKGROUND

Egg-white ovomucoid, that is, Gal d 1, is associated with IgE-mediated allergic reactions in most egg-allergic children. Epitope-specific IgE levels have been correlated with the severity of egg allergy, while emerging evidence suggests that other antibody isotypes (IgG₁ , IgG₄ , IgA, and IgD) may have a protective function; yet, their epitope-specific repertoires and associations with atopic comorbidities have not been studied.

METHODS

Bead-based epitope assay (BBEA) was used to quantitate the levels of epitope-specific (es)IgA, esIgE, esIgD, esIgG₁ , and esIgG₄ antibodies directed at 58 (15-mer) overlapping peptides, covering the entire sequence of ovomucoid, in plasma of 38 egg-allergic and 6 atopic children. Intraclass correlation (ICC) and coefficient of variation (CV) were used for the reliability assessment. The relationships across esIgs were evaluated using network analysis; linear and logistic regressions were used to compare groups based on egg allergy status and comorbidities.

RESULTS

BBEA had high reliability (ICC >0.75) and low variability (CV <20%) and could detect known IgE-binding epitopes. Egg-allergic children had lower esIgA₁ (P = .010) and esIgG₁ (P = .016) and higher esIgE (P < .001) and esIgD (P = .015) levels compared to the atopic controls. Interestingly, within the allergic group, children with higher esIgD had decreased odds of anaphylactic reactions (OR =0.48, P = .038). Network analysis identified most associations between esIgE with either esIgG₄ or esIgD; indicating that IgE-secreting plasma cells could originate from either sequential isotype switch from antigen-experienced intermediate isotypes or directly from the IgD⁺ B cells.

CONCLUSIONS

Collectively, these data point toward a contribution of epitope-specific antibody repertoires to the pathogenesis of egg allergy.

B-Cell-Targeted 3DNA Nanotherapy Against Indoleamine 2,3-Dioxygenase 2 (IDO2) Ameliorates Autoimmune Arthritis in a Preclinical Model

The tryptophan catabolizing enzyme indoleamine 2,3-dioxygenase 2 (IDO2) has been identified as an immunomodulatory agent promoting autoimmunity in preclinical models. As such, finding ways to target the expression of IDO2 in B cells promises a new avenue for therapy for debilitating autoimmune disorders such as rheumatoid arthritis. IDO2, like many drivers of disease, is an intracellular protein expressed in a range of cells, and thus therapeutic inhibition of IDO2 requires a mechanism for targeting this intracellular protein in specific cell types. DNA nanostructures are a promising novel way of delivering small molecule drugs, antibodies, or siRNAs to the cytoplasm of a cell. These soluble, branched structures can carry cell-specific targeting moieties along with their therapeutic deliverable. Here, we examined a 3DNA nanocarrier specifically targeted to B cells with an anti-CD19 antibody. We find that this 3DNA is successfully delivered to and internalized in B cells. To test whether these nanostructures can deliver an efficacious therapeutic dose to alter autoimmune responses, a modified anti-IDO2 siRNA was attached to B-cell-directed 3DNA nanocarriers and tested in an established preclinical model of autoimmune arthritis, KRN.g7. The anti-IDO2 3DNA formulation ameliorates arthritis in this system, delaying the onset of joint swelling and reducing total arthritis severity. As such, a 3DNA nanocarrier system shows promise for delivery of targeted, specific, low-dose therapy for autoimmune disease.

Early epitope-specific IgE antibodies are predictive of childhood peanut allergy

BACKGROUND

Peanut allergy is characterized by the development of IgE against peanut antigen.

OBJECTIVE

We sought to evaluate the evolution of epitope-specific (es)IgE and esIgG₄ in a prospective cohort of high-risk infants to determine whether antibody profiles can predict peanut allergy after age 4 years.

METHODS

The end point was allergy status at age 4⁺ years; samples from 293 children were collected at age 3 to 15 months and 2 to 3 and 4⁺ years. Levels of specific (s)IgE and sIgG₄ to peanut and component proteins, and 50 esIgE and esIgG₄ were quantified. Changes were analyzed with mixed-effects models. Machine learning algorithms were developed to identify a combination of antigen- and epitope-specific antibodies that using 3- to 15-month or 2- to 3-year samples can predict allergy status at age 4⁺ years.

RESULTS

At age 4⁺ years, 38% of children were Tolerant or 14% had Possible, 8% Convincing, 24% Serologic, and 16% Confirmed allergy. At age 3 to 15 months, esIgE profiles were similar among groups, whereas marked increases were evident at age 2 and 4⁺ years only in Confirmed and Serologic groups. In contrast, peanut sIgE level was significantly lower in the Tolerant group at age 3 to 15 months, increased in Confirmed and Serologic groups but decreased in Convincing and Possibly Allergic groups over time. An algorithm combining esIgEs with peanut sIgE outperformed different clinically relevant IgE cutoffs, predicting allergy status on an "unseen" set of patients with area under the curves of 0.84 at age 3 to 15 months and 0.87 at age 2 to 3 years.

CONCLUSIONS

Early epitope-specific plus peanut-specific IgE is predictive of allergy status at age 4⁺ years.

Brain-specific angiogenesis inhibitor 1 is expressed in the Myo/Nog cell lineage

The Myo/Nog cell lineage was discovered in the chick embryo and is also present in adult mammalian tissues. The cells are named for their expression of mRNA for the skeletal muscle specific transcription factor MyoD and bone morphogenetic protein inhibitor Noggin. A third marker for Myo/Nog cells is the cell surface molecule recognized by the G8 monoclonal antibody (mAb). G8 has been used to detect, track, isolate and kill Myo/Nog cells. In this study, we screened a membrane proteome array for the target of the G8 mAb. The array consisted of >5,000 molecules, each synthesized in their native confirmation with appropriate post-translational modifications in a single clone of HEK-293T cells. G8 mAb binding to the clone expressing brain-specific angiogenesis inhibitor 1 (BAI1) was detected by flow cytometry, re-verified by sequencing and validated by transfection with the plasmid construct for BAI1. Further validation of the G8 target was provided by enzyme-linked immunosorbent assay. The G8 epitope was identified by screening a high-throughput, site directed mutagenesis library designed to cover 95–100% of the 954 amino acids of the extracellular domain of the BAI1 protein. The G8 mAb binds within the third thrombospondin repeat of the extracellular domain of human BAI1. Immunofluorescence localization experiments revealed that G8 and a commercially available BAI1 mAb co-localize to the subpopulation of Myo/Nog cells in the skin, eyes and brain. Expression of the multi-functional BAI1 protein in Myo/Nog cells introduces new possibilities for the roles of Myo/Nog cells in normal and diseased tissues.

A new Luminex-based peptide assay to identify reactivity to baked, fermented, and whole milk

BACKGROUND

The majority of children with cow's milk allergy (CMA) tolerate baked milk. However, reactivity to fermented milk products such as yogurt/cheese has not been previously evaluated. We sought to determine whether children with CMA could tolerate yogurt/cheese and whether a patient's IgE and IgG4-binding pattern to milk protein epitopes could distinguish clinical reactivity.

METHODS

Four groups of reactivity were identified by Oral food challenge: baked milk reactive, fermented milk reactive, whole milk reactive, and outgrown. sIgE and sIgG4 binding to milk protein epitopes were assessed with a novel Luminex-based peptide assay (LPA). Using machine learning techniques, a model was developed to predict different degrees of CMA.

RESULTS

The baked milk reactive patients demonstrated the highest degree of IgE epitope binding, which was followed sequentially by fermented milk reactive, whole milk reactive, and outgrown. Data were randomly divided into two groups with 75% of the data utilized for model development (n = 68) and 25% for testing (n = 21). All 68 children used for training were correctly classified with models using IgE and IgG4 epitopes. The average cross-validation accuracy was much higher for models using IgE plus IgG4 epitopes by LPA (84.8%), twice the performance of the serum component proteins assayed by UniCAP (41.9%). The performance of the model on "unseen data" was tested using the 21 withheld patients, and the accuracy of IgE was 86% (AUC = 0.89) while of IgE+IgG4 model was 81% (AUC = 0.94).

CONCLUSION

Using a novel high-throughput LPA, we were able to distinguish the diversity of IgE/IgG4 binding to epitopes in the varying CMA phenotypes. LPA is a promising tool to predict correctly different degrees of CMA.

Predicting development of sustained unresponsiveness to milk oral immunotherapy using epitope-specific antibody binding profiles

BACKGROUND

In a recent trial of milk oral immunotherapy (MOIT) with or without omalizumab in 55 patients with milk allergy treated for 28 months, 44 of 55 subjects passed a 10-g desensitization milk protein challenge; 23 of 55 subjects passed the 10-g sustained unresponsiveness (SU) challenge 8 weeks after discontinuing MOIT.

OBJECTIVE

We sought to determine whether IgE and IgG₄ antibody binding to allergenic milk protein epitopes changes with MOIT and whether this could predict the development of SU.

METHODS

By using a novel high-throughput Luminex-based assay to quantitate IgE and IgG₄ antibody binding to 66 sequential epitopes on 5 milk proteins, serum samples from 47 subjects were evaluated before and after MOIT. Machine learning strategies were used to predict whether a subject would have SU after 8 weeks of MOIT discontinuation.

RESULTS

MOIT profoundly altered IgE and IgG₄ binding to epitopes, regardless of treatment outcome. At the initiation of MOIT, subjects achieving SU exhibited significantly less antibody binding to 40 allergenic epitopes than subjects who were desensitized only (false discovery rate ≤ 0.05 and fold change > 1.5). Based on baseline epitope-specific antibody binding, we developed predictive models of SU. Using simulations, we show that, on average, IgE-binding epitopes alone perform significantly better than models using standard serum component proteins (average area under the curve, >97% vs 80%). The optimum model using 6 IgE-binding epitopes achieved a 95% area under the curve and 87% accuracy.

CONCLUSION

Despite the relatively small sample size, we have shown that by measuring the epitope repertoire, we can build reliable models to predict the probability of SU after MOIT. Baseline epitope profiles appear more predictive of MOIT response than those based on serum component proteins.

Abstract 1961: Gaps in the armor: Targeting HuR to sensitize pancreatic cancer

HuR is an RNA binding protein involved in a coordinated cellular response to stressors. Upon insults such as chemotherapy or radiation treatment, HuR translocates from the nucleus to the cytoplasm where it binds the 3'UTR of target mRNAs. HuR's interaction with target mRNAs leads to the upregulation of target genes and ultimately treatment resistance. This is particularly relevant in the case of pancreatic ductal adenocarcinoma (PDA). PDA is highly resistant to standard chemotherapy such as FOLFIRINOX or gemcitabine/nab-paclitaxel. Using a tumor microarray (TMA), we found 79% of patient tumor samples (n=70) were positive for active cytoplasmic HuR, while little to no cytoplasmic localization was detected in normal tissue. In addition, HuR CRISPR knockout cell lines have a xenograft lethal phenotype. Previously published data also demonstrated that reduction of HuR in xenografts with a DOX-inducible shRNA system caused a 3.6 fold decrease in tumor size. HuR reduction was also shown to potentiate a PARP-inhibitor (olaparib) treatment from a 5.6-fold reduction alone to 9.3-fold reduction in tumor size when combined with shHuR, demonstrating the role of HuR in drug resistance. The aim of our current study was: A) to target HuR directly using nanoparticle delivery of siRNA against HuR; and B) to use the FDA approved small molecule pyrvinium pamoate (PP) to inhibit HuR's translocation and sensitize PDA cells to concurrent therapies. Using 3DNA, a 60nm nanoparticle composed of a sphere of crosslinked DNA, we have successfully delivered siRNA against HuR in vivo utilizing targeting moieties against receptors known to be overexpressed on the surface of PDA cells: EGFR, folic acid receptor, and transferrin receptor. Bi-weekly IP treatment of siHuR bound to 3DNA was safe and effective at extending life in a xenograft model as indicated by Kaplan Meier analysis (p=0.01). We are currently testing siHuR-3DNA dendrimer therapy's ability to sensitize PDA cells to oxaliplatin or olaparib in vivo. We are also investigating the use of PP to target HuR's localization. PP has previously been shown in bladder cancer to inhibit the translocation of HuR in vitro and in vivo. We have reproduced this finding in PDA cells, and have shown impressive drug potency with IC50s as low as 38nM in 2D cultures and 16nM in a 3D mouse PDA organoid model. Combination index (CI) values determine drugs interactions where 1 is additive, &lt;1 is synergistic and &gt;1 is antagonistic. We have determined that PP can enhance therapies such as gemcitabine (CI of 0.55), olaparib (CI of 0.40) and palbociclib (CI of 0.37) in vitro, and are currently validating these findings in vivo. Taken together, our data demonstrate that HuR inhibition via 3DNA delivery of siHuR and/or PP treatment can sensitize PDA cells to chemotherapy and targeted therapies. By inhibiting a resistance driver (HuR) in pancreatic cancer we aim to improve current therapies for this devastating disease.

Citation Format: Christopher W. Schultz, Kevin O'Hayer, Teena Dhir, Oloruntoba Bolaji, Kathryn M. Bormes, Samantha Z. Brown, Henry Thomsett, Saswati Chand, Aditi Jain, Wei Jiang, Grace McCarthy, Charles J. Yeo, Austin Goetz, Avinoam Nevler, Jonathan R. Brody, Jordan M. Winter, Ranjan Preet, Dan Dixon, Jessica Bowers, Kelly Rhodes, Robert Getts. Gaps in the armor: Targeting HuR to sensitize pancreatic cancer [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 1961.

Myo/Nog cells are present in the ciliary processes, on the zonule of Zinn and posterior capsule of the lens following cataract surgery

Myo/Nog cells, named for their expression of MyoD and noggin, enter the eye during early stages of embryonic development. Their release of noggin is critical for normal morphogenesis of the lens and retina. Myo/Nog cells are also present in adult eyes. Single nucleated skeletal muscle cells designated as myofibroblasts arise from Myo/Nog cells in cultures of lens tissue. In this report we document the presence of Myo/Nog cells in the lens, ciliary body and on the zonule of Zinn in mice, rabbits and humans. Myo/Nog cells were rare in all three structures. Their prevalence increased in the lens and ciliary body of rabbits 24 h following cataract surgery. Rabbits developed posterior capsule opacification (PCO) within one month of surgery. The number of Myo/Nog cells continued to be elevated in the lens and ciliary body. Myo/Nog cells containing alpha smooth muscle actin and striated muscle myosin were present on the posterior capsule and overlaid deformations in the capsule. Myo/Nog cells also were present on the zonule fibers and external surface of the posterior capsule. These findings suggest that Myo/Nog contribute to PCO and may use the zonule fibers to migrate between the ciliary processes and lens.

Abstract LB-B19: Re-sensitizing Pancreatic Cancer, targeted siRNA inhibition of HuR

We have demonstrated that 3DNA nanocarriers can specifically, effectively, and safely deliver siRNA oligos targeted against a pro-survival hub, HuR (the ELAVL1 gene) in an in vivo, pre-clinical model of pancreatic cancer. Pancreatic cancer remains one of the deadliest cancers with an overall 5 year survival rate of 9%; and is on pace to become the second leading cause of cancer related deaths in the U.S. by 2020. Pancreatic cancer is so deadly, in part, because it is highly refractory to standard chemotherapeutics. In fact, new standard of care regiments such as FOLFIRINOX have only improved survival by a few months. Our previous work has established HuR as a target in pancreatic cancer. HuR is an RNA binding protein that is primarily retained in the nucleus, but upon exposure to cancer associated stressors translocates to the cytoplasm. In the cytoplasm, HuR functions to bind, stabilize, and up-regulate expression of pro-survival target mRNAs. CRISPR-mediated deletion of HuR causes a xenograft lethal phenotype in vivo and increases sensitivity to a variety of drugs, particularly PARP inhibitor therapy, enhancing Olaparib therapy over 20-fold in vitro. In an independent doxycycline inducible knockdown model, HuR depletion combined with Olaparib treatment resulted in a 9.3 fold (p&lt;.001) decrease in tumor volume in vivo. Based on these findings and our previous published work, we have launched into a line of investigation attempting to target HuR in pancreatic cancer cells. We have delivered siHuR oligos tethered to 3DNA nanostructures (Genisphere, LLC) in a targeted fashion using either a folic acid targeting moiety, a transferrin receptor targeted antibody, or an EGFR targeted antibody (i.e., siHuR nanotherapy). Additionally, we are working to combine siHuR nanotherapy with conventional therapeutics. 3DNA nanocarriers are constructed using stable DNA strands assembled and crosslinked in a stepwise fashion, to create a layered nanoscaffold capable of attaching multiple different targeting moieties and deliverables. The siRNA oligos hybridized to the 3DNA were modified in order to withstand systemic RNases during treatment. We first validated the modified siHuR nanotherapy in vitro by evaluating protein and RNA levels of HuR. Second, we validated the expression of our intended targeting moieties in both human cell lines and a tissue microarray consisting of patient derived pancreatic cancer tumors. For the mouse studies, athymic female nude mice were injected with 4 million MIA PaCa-2 cells per flank, and randomized to treatment arms when tumors reached 100mm3. Mice were then treated intraperitoneally twice weekly with either siHuR or siControl nanotherapies (3ug siRNA per treatment) with one of the three targeting moieties. We demonstrated efficacy of systemic targeted delivery of siHuR nanotherapy which improved average overall survival by 35% (p=.012) compared to the control arm, with an increase in survival using a Kaplan-Meier survival analysis (p=.01). We are currently setting up treatments with siHuR nanotherapy in conjunction with a targeted treatment strategy, Olaparib, which has previously been shown to work in conjunction with dox-inducible HuR silencing (i.e.,shRNA targeting) in vivo. Herein, we describe the development of siHuR nanotherapy that, as a monotherapy or most likely with clinically available drugs, may improve outcomes for patients with pancreatic cancer.

Citation Format: Chris W. Schultz, Kevin O'Hayer, Kathryn M. Bormes, Teena Dhir, Samantha Brown, Avinoam Nevlar, Saswati Chand, Henry Thomsett, Wei Jiang, Jessica Bowers, Kelly Rhodes, Michael Pishvaian, Robert Getts, Jonathan Brody. Re-sensitizing Pancreatic Cancer, targeted siRNA inhibition of HuR [abstract]. In: Proceedings of the AACR-NCI-EORTC International Conference: Molecular Targets and Cancer Therapeutics; 2017 Oct 26-30; Philadelphia, PA. Philadelphia (PA): AACR; Mol Cancer Ther 2018;17(1 Suppl):Abstract nr LB-B19.

DNA-Based Drug Carriers: The Paradox of a Classical "Cargo" Material Becoming a Versatile "Carrier" to Overcome Barriers in Drug Delivery

Drug delivery strategies help cope with drawbacks of classical pharmaceuticals, including increasing their solubility, diminishing side effects and improving biodistribution. A multitude of vehicles have been envisioned to this end, encompassing a variety of materials, architectures, and functionalities. DNA-built carriers are relatively new, yet promising devices to help overcome some of the current barriers in drug delivery. Its easy fabrication, reproducibility and tunability make DNA a unique material for building devices ranging from macro-scale depot systems to nano-scale vehicles tailored as nanoparticles, containers, dendrimers, tubes, etc. Although this DNA application is relatively novel and knowledge is building up, current advances suggest great potential. Intracellular delivery is a promising option, whereby access of cargoes (from small molecules to large biotherapeutics) to the cytosol has been demonstrated in many cell types, without apparent side effects or need for additional actuators. This is paradoxical since "natural" DNA cannot access cells and nucleic acids are among the most difficult cargoes to be delivered within cells; yet this property arises from engineering DNA into particular configurations. Their biocompatibility and safety also holds potential, since this natural material is biodegradable and nucleotides are biological metabolites. Using modified nucleotides and properly designing their sequence, along with classical chemical means, make it feasible to tune the stability and degradation rates of DNA devices. Taken together, although much research is still necessary to understand the in vivo behaviour of DNA-based vehicles, the design parameters ruling their optimization, and the biological pathways regulating their function, DNA represents a unique material to help in future drug delivery applications.

Abstract 700: Systemic administration of DNA nanoparticles containing the diphtheria toxin gene reduces pancreatic tumor load in mice

Despite years of research and hundreds of clinical trials, our ability to treat metastatic pancreatic ductal adenocarcinoma (PDA) effectively has been thwarted due to the numerous genetic mutations in multiple core pathways that are characteristically present in pancreatic tumors, as well as the ability of tumors to develop resistance to chemotherapeutic drugs and small molecules. To avoid these complications, we have developed a suicide gene therapy that targets the death of PDA tumor cells regardless of their genetic mutation profile while avoiding unwanted harmful effects to healthy cells. A novel DNA nanoparticle, 3DNA, serving as a delivery vector is derivatized by conjugation to a DNA construct (MSLN promoter-driven diphtheria toxin A, pMSLN/DTA) as well as to a tumor-targeting molecule. Targeted DTA-induced tumor cell death is achieved in two ways: targeted nanoparticle delivery to tumor cells via docking and internalization, and targeted expression to cells that have an active mesothelin (MSLN) promoter (MSLN is highly overexpressed in ∼50% of PDA tumors). In preclinical tests, these formulations are systemically administered to PDA tumor-bearing mice. In an initial experiment, after confirming that MSLN is highly expressed in murine Pan02-luc PDA cells, we generated Pan02-luc orthografts in C57BL/6 mice and treated mice 2X/week with ∼50μg cargo DNA/i.v. injection for 4 weeks with either MSLN/DTA-TFP (n=7) or with MSLN/XX-TFP (n=5) dendrimer formulations (TFP is a peptide with strong affinity for the human transferrin receptor (TR), and weaker affinity for murine TR; XX = no coding sequence). Tumor load was assessed weekly by optical imaging and luciferase bioluminescence quantitation. Fold increase in relative light units (RLU) (baseline to 4 days after the last injection) was used to measure therapeutic efficacy. After 4 weeks of treatment, the mean RLU ratio for the MSLN/DTA-TFP treated mice was 0.51 +/-0.20 while that of the MSLN/XX-TFP treated mice was 7.1 +/-8.22, a significant 15-fold difference in tumor load (p=0.04). This quantitative analysis of tumor load as well as gross observations of tumors upon sacrifice of the mice showed that tumors in mice systemically treated with MSLN/DTA-TFP dendrimer formulation shrunk significantly to the point where tumor load was negligible in contrast to rapid growth of tumors in mice treated with the MSLN/XX-TFP formulation. This experiment demonstrates that systemically-administered DNA nanoparticle-delivered DTA effectively kills tumor cells with little to no apparent systemic toxicity as assessed by body weight and TUNEL assays of multiple normal tissues. In ongoing experiments to further validate this approach for the treatment of metastatic PDA, other targeting molecules such as folate and TFP are being used to target delivery to Pan02-luc orthografts and human BxPC3-luc2 xenografts.

Citation Format: Janet A. Sawicki, Weidan Peng, Kelly Rhodes, Robert Getts. Systemic administration of DNA nanoparticles containing the diphtheria toxin gene reduces pancreatic tumor load in mice. [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 700. doi:10.1158/1538-7445.AM2014-700

Identification of methods for use of formalin-fixed, paraffin-embedded tissue samples in RNA expression profiling

Formalin-fixed paraffin-embedded (FFPE) tissue samples are a potentially valuable resource of expression information for medical research, but are under-utilized due to degradation and modification of the RNA. Using a random primer-based RNA amplification strategy, we have evaluated multiple protocols for the extraction and isolation of RNA from FFPE samples. We found that the RecoverAll RNA isolation procedure with three or four slices (ten-microns in thickness), supplemented with additional DNAse, gave optimal results. RNA integrity as assessed by Agilent Bioanalyzer, and amplification of the 28S ribosomal RNA, were predictive for the number of genes detected on Affymetrix arrays. We obtained expression data for colon and lung tumor and normal FFPE samples and matched frozen samples and found a high correlation between frozen and matched FFPE samples (R(2) between 0.82 and 0.89), while the signature sets in tumor versus normal comparisons were also quite similar. QPCR confirmed all 16 of the differential expression results from the microarrays that we tested. Differentially expressed signature genes from tumor versus matched normal FFPE tissue from colon and lung were identified as cancer-related, with 95 colon tumor and 67 lung tumor genes identified, respectively.

Optimized high-throughput microRNA expression profiling provides novel biomarker assessment of clinical prostate and breast cancer biopsies

BACKGROUND

Recent studies indicate that microRNAs (miRNAs) are mechanistically involved in the development of various human malignancies, suggesting that they represent a promising new class of cancer biomarkers. However, previously reported methods for measuring miRNA expression consume large amounts of tissue, prohibiting high-throughput miRNA profiling from typically small clinical samples such as excision or core needle biopsies of breast or prostate cancer. Here we describe a novel combination of linear amplification and labeling of miRNA for highly sensitive expression microarray profiling requiring only picogram quantities of purified microRNA.

RESULTS

Comparison of microarray and qRT-PCR measured miRNA levels from two different prostate cancer cell lines showed concordance between the two platforms (Pearson correlation R2 = 0.81); and extension of the amplification, labeling and microarray platform was successfully demonstrated using clinical core and excision biopsy samples from breast and prostate cancer patients. Unsupervised clustering analysis of the prostate biopsy microarrays separated advanced and metastatic prostate cancers from pooled normal prostatic samples and from a non-malignant precursor lesion. Unsupervised clustering of the breast cancer microarrays significantly distinguished ErbB2-positive/ER-negative, ErbB2-positive/ER-positive, and ErbB2-negative/ER-positive breast cancer phenotypes (Fisher exact test, p = 0.03); as well, supervised analysis of these microarray profiles identified distinct miRNA subsets distinguishing ErbB2-positive from ErbB2-negative and ER-positive from ER-negative breast cancers, independent of other clinically important parameters (patient age; tumor size, node status and proliferation index).

CONCLUSION

In sum, these findings demonstrate that optimized high-throughput microRNA expression profiling offers novel biomarker identification from typically small clinical samples such as breast and prostate cancer biopsies.

Multiplexed, particle-based detection of DNA using flow cytometry with 3DNA dendrimers for signal amplification

BACKGROUND

Complex mixtures of DNA may be found in environmental and medical samples. There is a need for techniques that can measure low concentrations of target DNAs. For a multiplexed, flow cytometric assay, we show that the signal-to-noise ratio for fluorescence detection may be increased with the use of 3DNA dendrimers. A single fluorescent DNA molecule per bead could be detected with conventional flow cytometry instrumentation.

METHODS

The analyte consisted of single-stranded (ss) DNA amplicons that were hybridized to capture probes on the surface of fluorescent polystyrene microspheres (beads) and initially labeled with streptavidin-R-phycoerythrin (single-step labeling). These beads have a low reporter fluorescence background and high efficiency of DNA hybridization. The DNA/SA-RPE complex was then labeled with 3DNA dendrimers and SA-RPE. The bead complexes were detected with a Luminex 100 flow cytometer. Bead standards were developed to convert the intensity to the number of SA-RPE labels per bead and the number of dendrimers per bead.

RESULTS

The dendrimer assay resulted in 10-fold fluorescence amplification compared with single-step SA-RPE labeling. Based on concentration curves of pure target ss-amplicons, the signal-to-noise ratio of the dendrimer assay was greater by a factor of 8.5 over single-step SA-RPE labeling. The dendrimer assay was tested on 16S ribosomal DNA amplified from filter retentates of contaminated groundwater. Multiplexed detection of a single dendrimer-labeled DNA molecule per bead was demonstrated.

CONCLUSIONS

Multiplexed detection of DNA hybridization on a single molecule level per bead was achieved with conventional flow cytometry instrumentation. This assay is useful for detecting target DNAs at low concentrations.

Visualizing the Needle in the Haystack: In Situ Hybridization With Fluorescent Dendrimers

In situ hybridization with 3DNA™ dendrimers is a novel tool for detecting low levels of mRNA in tissue sections and whole embryos. Fluorescently labeled dendrimers were used to identify cells that express mRNA for the skeletal muscle transcription factor MyoD in the early chick embryo. A small population of MyoD mRNA positive cells was found in the epiblast prior to the initiation of gastrulation, two days earlier than previously detected using enzymatic or radiolabeled probes for mRNA. When isolated from the epiblast and placed in culture, the MyoD mRNA positive cells were able to differentiate into skeletal muscle cells. These results demonstrate that DNA dendrimers are sensitive and precise tools for identifying low levels of mRNA in single cells and tissues.

DNA dendrimers localize MyoD mRNA in presomitic tissues of the chick embryo

MyoD expression is thought to be induced in somites in response to factors released by surrounding tissues; however, reverse transcription-PCR and cell culture analyses indicate that myogenic cells are present in the embryo before somite formation. Fluorescently labeled DNA dendrimers were used to identify MyoD expressing cells in presomitic tissues in vivo. Subpopulations of MyoD positive cells were found in the segmental plate, epiblast, mesoderm, and hypoblast. Directly after laying, the epiblast of the two layered embryo contained approximately 20 MyoD positive cells. These results demonstrate that dendrimers are precise and sensitive reagents for localizing low levels of mRNA in tissue sections and whole embryos, and that cells with myogenic potential are present in the embryo before the initiation of gastrulation.