Prognostic impact of cooccurring mutations in FLT3-ITD pediatric acute myeloid leukemia

ABSTRACT

We sought to define the cooccurring mutational profile of FLT3-ITD-positive (ITDpos) acute myeloid leukemia (AML) in pediatric and young adult patients and to define the prognostic impact of cooperating mutations. We identified 464 patients with FLT3-ITD mutations treated on Children's Oncology Group trials with available sequencing and outcome data. Overall survival, event-free survival (EFS), and relapse risk were determined according to the presence of cooccurring risk stratifying mutations. Among the cohort, 79% of patients had cooccurring alterations across 239 different genes that were altered through mutations or fusions. Evaluation of the prognostic impact of the cooccurring mutations demonstrated that patients with ITDpos AML experienced significantly different outcomes according to the cooccurring mutational profile. Patients with ITDpos AML harboring a cooccurring favorable-risk mutation of NPM1, CEBPA, t(8;21), or inv(16) experienced a 5-year EFS of 64%, which was significantly superior to of 22.2% for patients with ITDpos AML and poor-risk mutations of WT1, UBTF, or NUP98::NSD1 as well to 40.9% for those who lacked either favorable-risk or poor-risk mutation (ITDpos intermediate; P < .001 for both). Multivariable analysis demonstrated that cooccurring mutations had significant prognostic impact, whereas allelic ratio had no impact. Therapy intensification, specifically consolidation transplant in remission, resulted in significant improvements in survival for ITDpos AML. However, patients with ITDpos/NUP98::NSD1 continued to have poor outcomes with intensified therapy, including sorafenib. Cooccurring mutational profile in ITDpos AML has significant prognostic impacts and is critical to determining risk stratification and therapeutic allocation. These clinical trials were registered at www.clinicaltrials.gov as NCT00002798, NCT00070174, NCT00372593, and NCT01371981.

Study of High-Transverse-Momentum Higgs Boson Production in Association with a Vector Boson in the qqbb Final State with the ATLAS Detector

This Letter presents the first study of Higgs boson production in association with a vector boson (V=W or Z) in the fully hadronic qqbb final state using data recorded by the ATLAS detector at the LHC in proton-proton collisions at sqrt[s]=13  TeV and corresponding to an integrated luminosity of 137  fb^{-1}. The vector bosons and Higgs bosons are each reconstructed as large-radius jets and tagged using jet substructure techniques. Dedicated tagging algorithms exploiting b-tagging properties are used to identify jets consistent with Higgs bosons decaying into bb[over ¯]. Dominant backgrounds from multijet production are determined directly from the data, and a likelihood fit to the jet mass distribution of Higgs boson candidates is used to extract the number of signal events. The VH production cross section is measured inclusively and differentially in several ranges of Higgs boson transverse momentum: 250-450, 450-650, and greater than 650 GeV. The inclusive signal yield relative to the standard model expectation is observed to be μ=1.4_{-0.9}^{+1.0} and the corresponding cross section is 3.1±1.3(stat)_{-1.4}^{+1.8}(syst)  pb.

Measurement of the Centrality Dependence of the Dijet Yield in p+Pb Collisions at sqrt[s_{NN}]=8.16 TeV with the ATLAS Detector

ATLAS measured the centrality dependence of the dijet yield using 165  nb^{-1} of p+Pb data collected at sqrt[s_{NN}]=8.16  TeV in 2016. The event centrality, which reflects the p+Pb impact parameter, is characterized by the total transverse energy registered in the Pb-going side of the forward calorimeter. The central-to-peripheral ratio of the scaled dijet yields, R_{CP}, is evaluated, and the results are presented as a function of variables that reflect the kinematics of the initial hard parton scattering process. The R_{CP} shows a scaling with the Bjorken x of the parton originating from the proton, x_{p}, while no such trend is observed as a function of x_{Pb}. This analysis provides unique input to understanding the role of small proton spatial configurations in p+Pb collisions by covering parton momentum fractions from the valence region down to x_{p}∼10^{-3} and x_{Pb}∼4×10^{-4}.

Search for New Phenomena in Two-Body Invariant Mass Distributions Using Unsupervised Machine Learning for Anomaly Detection at sqrt[s]=13 TeV with the ATLAS Detector

Searches for new resonances are performed using an unsupervised anomaly-detection technique. Events with at least one electron or muon are selected from 140  fb^{-1} of pp collisions at sqrt[s]=13  TeV recorded by ATLAS at the Large Hadron Collider. The approach involves training an autoencoder on data, and subsequently defining anomalous regions based on the reconstruction loss of the decoder. Studies focus on nine invariant mass spectra that contain pairs of objects consisting of one light jet or b jet and either one lepton (e,μ), photon, or second light jet or b jet in the anomalous regions. No significant deviations from the background hypotheses are observed. Limits on contributions from generic Gaussian signals with various widths of the resonance mass are obtained for nine invariant masses in the anomalous regions.

Observation of WZγ Production in pp Collisions at sqrt[s]=13 TeV with the ATLAS Detector

This Letter reports the observation of WZγ production and a measurement of its cross section using 140.1±1.2  fb^{-1} of proton-proton collision data recorded at a center-of-mass energy of 13 TeV by the ATLAS detector at the Large Hadron Collider. The WZγ production cross section, with both the W and Z bosons decaying leptonically, pp→WZγ→ℓ^{'}^{±}νℓ^{+}ℓ^{-}γ (ℓ^{(^{'})}=e, μ), is measured in a fiducial phase-space region defined such that the leptons and the photon have high transverse momentum and the photon is isolated. The cross section is found to be 2.01±0.30(stat)±0.16(syst)  fb. The corresponding standard model predicted cross section calculated at next-to-leading order in perturbative quantum chromodynamics and at leading order in the electroweak coupling constant is 1.50±0.06  fb. The observed significance of the WZγ signal is 6.3σ, compared with an expected significance of 5.0σ.

Combined Measurement of the Higgs Boson Mass from the H→γγ and H→ZZ^{*}→4ℓ Decay Channels with the ATLAS Detector Using sqrt[s]=7, 8, and 13 TeV pp Collision Data

A measurement of the mass of the Higgs boson combining the H→ZZ^{*}→4ℓ and H→γγ decay channels is presented. The result is based on 140  fb^{-1} of proton-proton collision data collected by the ATLAS detector during LHC run 2 at a center-of-mass energy of 13 TeV combined with the run 1 ATLAS mass measurement, performed at center-of-mass energies of 7 and 8 TeV, yielding a Higgs boson mass of 125.11±0.09(stat)±0.06(syst)=125.11±0.11  GeV. This corresponds to a 0.09% precision achieved on this fundamental parameter of the Standard Model of particle physics.

Search for Dark Photons in Rare Z Boson Decays with the ATLAS Detector

A search for events with a dark photon produced in association with a dark Higgs boson via rare decays of the standard model Z boson is presented, using 139  fb^{-1} of sqrt[s]=13  TeV proton-proton collision data recorded by the ATLAS detector at the Large Hadron Collider. The dark boson decays into a pair of dark photons, and at least two of the three dark photons must each decay into a pair of electrons or muons, resulting in at least two same-flavor opposite-charge lepton pairs in the final state. The data are found to be consistent with the background prediction, and upper limits are set on the dark photon's coupling to the dark Higgs boson times the kinetic mixing between the standard model photon and the dark photon, α_{D}ϵ^{2}, in the dark photon mass range of [5, 40] GeV except for the ϒ mass window [8.8, 11.1] GeV. This search explores new parameter space not previously excluded by other experiments.

Observation of Single-Top-Quark Production in Association with a Photon Using the ATLAS Detector

This Letter reports the observation of single top quarks produced together with a photon, which directly probes the electroweak coupling of the top quark. The analysis uses 139  fb^{-1} of 13 TeV proton-proton collision data collected with the ATLAS detector at the Large Hadron Collider. Requiring a photon with transverse momentum larger than 20 GeV and within the detector acceptance, the fiducial cross section is measured to be 688±23(stat) _{-71}^{+75}(syst)  fb, to be compared with the standard model prediction of 515_{-42}^{+36}  fb at next-to-leading order in QCD.

Measurement of Suppression of Large-Radius Jets and Its Dependence on Substructure in Pb+Pb Collisions at sqrt[s_{NN}]=5.02 TeV with the ATLAS Detector

This letter presents a measurement of the nuclear modification factor of large-radius jets in sqrt[s_{NN}]=5.02  TeV Pb+Pb collisions by the ATLAS experiment. The measurement is performed using 1.72  nb^{-1} and 257  pb^{-1} of Pb+Pb and pp data, respectively. The large-radius jets are reconstructed with the anti-k_{t} algorithm using a radius parameter of R=1.0, by reclustering anti-k_{t} R=0.2 jets, and are measured over the transverse momentum (p_{T}) kinematic range of 158 Collapse

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Measurement of the Sensitivity of Two-Particle Correlations in pp Collisions to the Presence of Hard Scatterings

A key open question in the study of multiparticle production in high-energy pp collisions is the relationship between the "ridge"-i.e., the observed azimuthal correlations between particles in the underlying event that extend over all rapidities-and hard or semihard scattering processes. In particular, it is not known whether jets or their soft fragments are correlated with particles in the underlying event. To address this question, two-particle correlations are measured in pp collisions at sqrt[s]=13  TeV using data collected by the ATLAS experiment at the LHC, with an integrated luminosity of 15.8  pb^{-1}, in two different configurations. In the first case, charged particles associated with jets are excluded from the correlation analysis, while in the second case, correlations are measured between particles within jets and charged particles from the underlying event. Second-order flow coefficients, v_{2}, are presented as a function of event multiplicity and transverse momentum. These measurements show that excluding particles associated with jets does not affect the measured correlations. Moreover, particles associated with jets do not exhibit any significant azimuthal correlations with the underlying event, ruling out hard processes contributing to the ridge.

Observation of an Excess of Dicharmonium Events in the Four-Muon Final State with the ATLAS Detector

A search is made for potential ccc[over ¯]c[over ¯] tetraquarks decaying into a pair of charmonium states in the four muon final state using proton-proton collision data at sqrt[s]=13  TeV, corresponding to an integrated luminosity of 140  fb^{-1} recorded by the ATLAS experiment at LHC. Two decay channels, J/ψ+J/ψ→4μ and J/ψ+ψ(2S)→4μ, are studied. Backgrounds are estimated based on a hybrid approach involving Monte Carlo simulations and data-driven methods. Statistically significant excesses with respect to backgrounds dominated by the single parton scattering are seen in the di-J/ψ channel consistent with a narrow resonance at 6.9 GeV and a broader structure at lower mass. A statistically significant excess is also seen in the J/ψ+ψ(2S) channel. The fitted masses and decay widths of the structures are reported.

Observation of the γγ→ττ Process in Pb+Pb Collisions and Constraints on the τ-Lepton Anomalous Magnetic Moment with the ATLAS Detector

This Letter reports the observation of τ-lepton-pair production in ultraperipheral lead-lead collisions Pb+Pb→Pb(γγ→ττ)Pb and constraints on the τ-lepton anomalous magnetic moment a_{τ}. The dataset corresponds to an integrated luminosity of 1.44  nb^{-1} of LHC Pb+Pb collisions at sqrt[s_{NN}]=5.02  TeV recorded by the ATLAS experiment in 2018. Selected events contain one muon from a τ-lepton decay, an electron or charged-particle track(s) from the other τ-lepton decay, little additional central-detector activity, and no forward neutrons. The γγ→ττ process is observed in Pb+Pb collisions with a significance exceeding 5 standard deviations and a signal strength of μ_{ττ}=1.03_{-0.05}^{+0.06} assuming the standard model value for a_{τ}. To measure a_{τ}, a template fit to the muon transverse-momentum distribution from τ-lepton candidates is performed, using a dimuon (γγ→μμ) control sample to constrain systematic uncertainties. The observed 95% confidence-level interval for a_{τ} is -0.057 Collapse

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Efficacy of immune checkpoint inhibitors for the treatment of advanced melanoma in patients with concomitant chronic lymphocytic leukemia

BACKGROUND

Immune checkpoint inhibitors (ICIs) have revolutionized the management of advanced melanoma (AM). However, data on ICI effectiveness have largely been restricted to clinical trials, thereby excluding patients with co-existing malignancies. Chronic lymphocytic leukemia (CLL) is the most prevalent adult leukemia and is associated with increased risk of melanoma. CLL alters systemic immunity and can induce T-cell exhaustion, which may limit the efficacy of ICIs in patients with CLL. We, therefore, sought to examine the efficacy of ICI in patients with these co-occurring diagnoses.

PATIENTS AND METHODS

In this international multicenter study, a retrospective review of clinical databases identified patients with concomitant diagnoses of CLL and AM treated with ICI (US-MD Anderson Cancer Center, N = 24; US-Mayo Clinic, N = 15; AUS, N = 19). Objective response rates (ORRs), assessed by RECIST v1.1, and survival outcomes [overall survival (OS) and progression-free survival (PFS)] among patients with CLL and AM were assessed. Clinical factors associated with improved ORR and survival were explored. Additionally, ORR and survival outcomes were compared between the Australian CLL/AM cohort and a control cohort of 148 Australian patients with AM alone.

RESULTS

Between 1997 and 2020, 58 patients with concomitant CLL and AM were treated with ICI. ORRs were comparable between AUS-CLL/AM and AM control cohorts (53% versus 48%, P = 0.81). PFS and OS from ICI initiation were also comparable between cohorts. Among CLL/AM patients, a majority were untreated for their CLL (64%) at the time of ICI. Patients with prior history of chemoimmunotherapy treatment for CLL (19%) had significantly reduced ORRs, PFS, and OS.

CONCLUSIONS

Our case series of patients with concomitant CLL and melanoma demonstrate frequent, durable clinical responses to ICI. However, those with prior chemoimmunotherapy treatment for CLL had significantly worse outcomes. We found that CLL disease course is largely unchanged by treatment with ICI.

Chromatin Profiling of CBFA2T3-GLIS2 AMLs Identifies Key Transcription Factor Dependencies and BRG1 Inhibition as a Novel Therapeutic Strategy

Oncogenic fusions involving transcription factors are present in the majority of pediatric leukemias; however, the context-specific mechanisms they employ to drive cancer remain poorly understood. CBFA2T3-GLIS2 (C/G) fusions occur in treatment-refractory acute myeloid leukemias and are restricted to young children. To understand how the C/G fusion drives oncogenesis we applied CUT&RUN chromatin profiling to an umbilical cord blood/endothelial cell (EC) co-culture model of C/G AML that recapitulates the biology of this malignancy. We find C/G fusion binding is mediated by its zinc finger domains. Integration of fusion binding sites in C/G- transduced cells with Polycomb Repressive Complex 2 (PRC2) sites in control cord blood cells identifies MYCN, ZFPM1, ZBTB16 and LMO2 as direct C/G targets. Transcriptomic analysis of a large pediatric AML cohort shows that these genes are upregulated in C/G patient samples. Single cell RNA-sequencing of umbilical cord blood identifies a population of megakaryocyte precursors that already express many of these genes despite lacking the fusion. By integrating CUT&RUN data with CRISPR dependency screens we identify BRG1/SMARCA4 as a vulnerability in C/G AML. BRG1 profiling in C/G patient-derived cell lines shows that the CBFA2T3 locus is a binding site, and treatment with clinically-available BRG1 inhibitors reduces fusion levels and downstream C/G targets including N-MYC, resulting in C/G leukemia cell death and extending survival in a murine xenograft model.

Strong Constraints on Jet Quenching in Centrality-Dependent p+Pb Collisions at 5.02 TeV from ATLAS

Jet quenching is the process of color-charged partons losing energy via interactions with quark-gluon plasma droplets created in heavy-ion collisions. The collective expansion of such droplets is well described by viscous hydrodynamics. Similar evidence of collectivity is consistently observed in smaller collision systems, including pp and p+Pb collisions. In contrast, while jet quenching is observed in Pb+Pb collisions, no evidence has been found in these small systems to date, raising fundamental questions about the nature of the system created in these collisions. The ATLAS experiment at the Large Hadron Collider has measured the yield of charged hadrons correlated with reconstructed jets in 0.36  nb^{-1} of p+Pb and 3.6  pb^{-1} of pp collisions at 5.02 TeV. The yields of charged hadrons with p_{T}^{ch}>0.5  GeV near and opposite in azimuth to jets with p_{T}^{jet}>30 or 60 GeV, and the ratios of these yields between p+Pb and pp collisions, I_{pPb}, are reported. The collision centrality of p+Pb events is categorized by the energy deposited by forward neutrons from the struck nucleus. The I_{pPb} values are consistent with unity within a few percent for hadrons with p_{T}^{ch}>4  GeV at all centralities. These data provide new, strong constraints that preclude almost any parton energy loss in central p+Pb collisions.

Test of CP Invariance in Higgs Boson Vector-Boson-Fusion Production Using the H→γγ Channel with the ATLAS Detector

A test of CP invariance in Higgs boson production via vector-boson fusion has been performed in the H→γγ channel using 139  fb^{-1} of proton-proton collision data at sqrt[s]=13  TeV collected by the ATLAS detector at the LHC. The optimal observable method is used to probe the CP structure of interactions between the Higgs boson and electroweak gauge bosons, as described by an effective field theory. No sign of CP violation is observed in the data. Constraints are set on the parameters describing the strength of the CP-odd component in the coupling between the Higgs boson and the electroweak gauge bosons in two effective field theory bases: d[over ˜] in the HISZ basis and c_{HW[over ˜]} in the Warsaw basis. The results presented are the most stringent constraints on CP violation in the coupling between Higgs and weak bosons. The 95% C.L. constraint on d[over ˜] is derived for the first time and the 95% C.L. constraint on c_{HW[over ˜]} has been improved by a factor of 5 compared to the previous measurement.

Long Noncoding RNA Expression Independently Predicts Outcome in Pediatric Acute Myeloid Leukemia

PURPOSE

Optimized strategies for risk classification are essential to tailor therapy for patients with biologically distinctive disease. Risk classification in pediatric acute myeloid leukemia (pAML) relies on detection of translocations and gene mutations. Long noncoding RNA (lncRNA) transcripts have been shown to associate with and mediate malignant phenotypes in acute myeloid leukemia (AML) but have not been comprehensively evaluated in pAML.

METHODS

To identify lncRNA transcripts associated with outcomes, we evaluated the annotated lncRNA landscape by transcript sequencing of 1,298 pediatric and 96 adult AML specimens. Upregulated lncRNAs identified in the pAML training set were used to establish a regularized Cox regression model of event-free survival (EFS), yielding a 37 lncRNA signature (lncScore). Discretized lncScores were correlated with initial and postinduction treatment outcomes using Cox proportional hazards models in validation sets. Predictive model performance was compared with standard stratification methods by concordance analysis.

RESULTS

Training set cases with positive lncScores had 5-year EFS and overall survival rates of 26.7% and 42.7%, respectively, compared with 56.9% and 76.3% with negative lncScores (hazard ratio, 2.48 and 3.16; P < .001). Pediatric validation cohorts and an adult AML group yielded comparable results in magnitude and significance. lncScore remained independently prognostic in multivariable models, including key factors used in preinduction and postinduction risk stratification. Subgroup analysis suggested that lncScores provide additional outcome information in heterogeneous subgroups currently classified as indeterminate risk. Concordance analysis showed that lncScore adds to overall classification accuracy with at least comparable predictive performance to current stratification methods that rely on multiple assays.

CONCLUSION

Inclusion of the lncScore enhances predictive power of traditional cytogenetic and mutation-defined stratification in pAML with potential, as a single assay, to replace these complex stratification schemes with comparable predictive accuracy.

Etiology of oncogenic fusions in 5,190 childhood cancers and its clinical and therapeutic implication

Oncogenic fusions formed through chromosomal rearrangements are hallmarks of childhood cancer that define cancer subtype, predict outcome, persist through treatment, and can be ideal therapeutic targets. However, mechanistic understanding of the etiology of oncogenic fusions remains elusive. Here we report a comprehensive detection of 272 oncogenic fusion gene pairs by using tumor transcriptome sequencing data from 5190 childhood cancer patients. We identify diverse factors, including translation frame, protein domain, splicing, and gene length, that shape the formation of oncogenic fusions. Our mathematical modeling reveals a strong link between differential selection pressure and clinical outcome in CBFB-MYH11. We discover 4 oncogenic fusions, including RUNX1-RUNX1T1, TCF3-PBX1, CBFA2T3-GLIS2, and KMT2A-AFDN, with promoter-hijacking-like features that may offer alternative strategies for therapeutic targeting. We uncover extensive alternative splicing in oncogenic fusions including KMT2A-MLLT3, KMT2A-MLLT10, C11orf95-RELA, NUP98-NSD1, KMT2A-AFDN and ETV6-RUNX1. We discover neo splice sites in 18 oncogenic fusion gene pairs and demonstrate that such splice sites confer therapeutic vulnerability for etiology-based genome editing. Our study reveals general principles on the etiology of oncogenic fusions in childhood cancer and suggests profound clinical implications including etiology-based risk stratification and genome-editing-based therapeutics.

Mortality and histopathology in sheepshead minnow (Cyprinodon variegatus) larvae exposed to pectenotoxin-2 and Dinophysis acuminata

Toxic species of the dinoflagellate genus Dinophysis can produce diarrheic toxins including okadaic acid (OA) and dinophysistoxins (DTXs), and the non-diarrheic pectenotoxins (PTXs). Okadaic acid and DTXs cause diarrheic shellfish poisoning (DSP) in human consumers, and also cause cytotoxic, immunotoxic and genotoxic effects in a variety of mollusks and fishes at different life stages in vitro. The possible effects of co-produced PTXs or live cells of Dinophysis to aquatic organisms, however, are less understood. Effects on an early life stage of sheepshead minnow (Cyprinodon variegatus), a common finfish in eastern USA estuaries, were evaluated using a 96-h toxicity bioassay. Three-week old larvae were exposed to PTX2 concentrations from 50 to 4000 nM, live Dinophysis acuminata culture (strain DAVA01), live cells resuspended in clean medium or culture filtrate. This D. acuminata strain produced mainly intracellular PTX2 (≈ 21 pg cell^-1), with much lower levels of OA and dinophysistoxin-1. No mortality or gill damages were observed in larvae exposed to D. acuminata (from 5 to 5500 cells mL^-1), resuspended cells and culture filtrate. However, exposure to purified PTX2 at intermediate to high concentrations (from 250 to 4000 nM) resulted in 8 to 100% mortality after 96 h (24-h LC₅₀ of 1231 nM). Histopathology and transmission electron microscopy of fish exposed to intermediate to high PTX2 concentrations revealed important gill damage, including intercellular edema, necrosis and sloughing of gill respiratory epithelia, and damage to the osmoregulatory epithelium, including hypertrophy, proliferation, redistribution and necrosis of chloride cells. Tissue damage in gills is likely caused by the interaction of PTX2 with the actin cytoskeleton of the affected gill epithelia. Overall, the severe gill pathology observed following the PTX2 exposure suggested death was due to loss of respiratory and osmoregulatory functions in C. variegatus larvae.

Verification of prognostic expression biomarkers is improved by examining enriched leukemic blasts rather than mononuclear cells from acute myeloid leukemia patients

BACKGROUND

Studies have not systematically compared the ability to verify performance of prognostic transcripts in paired bulk mononuclear cells versus viable CD34-expressing leukemic blasts from patients with acute myeloid leukemia. We hypothesized that examining the homogenous leukemic blasts will yield different biological information and may improve prognostic performance of expression biomarkers.

METHODS

To assess the impact of cellular heterogeneity on expression biomarkers in acute myeloid leukemia, we systematically examined paired mononuclear cells and viable CD34-expressing leukemic blasts from SWOG diagnostic specimens. After enrichment, patients were assigned into discovery and validation cohorts based on availability of extracted RNA. Analyses of RNA sequencing data examined how enrichment impacted differentially expressed genes associated with pre-analytic variables, patient characteristics, and clinical outcomes.

RESULTS

Blast enrichment yielded significantly different expression profiles and biological pathways associated with clinical characteristics (e.g., cytogenetics). Although numerous differentially expressed genes were associated with clinical outcomes, most lost their prognostic significance in the mononuclear cells and blasts after adjusting for age and ELN risk, with only 11 genes remaining significant for overall survival in both cell populations (CEP70, COMMD7, DNMT3B, ECE1, LNX2, NEGR1, PIK3C2B, SEMA4D, SMAD2, TAF8, ZNF444). To examine the impact of enrichment on biomarker verification, these 11 candidate biomarkers were examined by quantitative RT/PCR in the validation cohort. After adjusting for ELN risk and age, expression of 4 genes (CEP70, DNMT3B, ECE1, and PIK3CB) remained significantly associated with overall survival in the blasts, while none met statistical significance in mononuclear cells.

CONCLUSIONS

This study provides insights into biological information gained/lost by examining viable CD34-expressing leukemic blasts versus mononuclear cells from the same patient and shows an improved verification rate for expression biomarkers in blasts.

Comprehensive molecular and clinical characterization of NUP98 fusions in pediatric acute myeloid leukemia

NUP98 fusions c omprise a family o f rare r ecurrent a lterations i n A ML, associated w ith adverse outcomes. To define the underlying biology and clinical implications of this family of fusions, we performed comprehensive transcriptome, epigenome, and immunophenotypic profiling of 2,235 children and young adults with AML and identified 160 NUP98 rearrangements (7.2%), including 108 NUP98-NSD1 (4.8%), 32 NUP98-KDM5A (1.4%) and 20 NUP98-X cases (0.9%) with 13 different fusion partners. Fusion partners defined disease characteristics and biology; patients with NUP98-NSD1 or NUP98-KDM5A had distinct immunophenotypic, transcriptomic, and epigenomic profiles. Unlike the two most prevalent NUP98 fusions, NUP98-X variants are typically not cryptic. Furthermore, NUP98-X cases are associated with WT1 mutations, and have epigenomic profiles that resemble either NUP98- NSD1 or NUP98-KDM5A. Cooperating FLT3-ITD and WT1 mutations define NUP98-NSD1, and chromosome 13 aberrations are highly enriched in NUP98-KDM5A. Importantly, we demonstrate that NUP98 fusions portend dismal overall survival, with the noteworthy exception of patients bearing abnormal chr13.

Global gene expression of human malaria parasite liver stages throughout intrahepatocytic development

Plasmodium falciparum (Pf) is causing the greatest malaria burden, yet the liver stages (LS) of this most important parasite species have remained poorly studied. Here, we used a human liver-chimeric mouse model in combination with a novel fluorescent PfNF54 parasite line (PfNF54cspGFP) to isolate PfLS-infected hepatocytes and generate transcriptomes that cover the major LS developmental phases in human hepatocytes. RNA-seq analysis of early Pf LS trophozoites two days after infection, revealed a central role of translational regulation in the transformation of the extracellular invasive sporozoite into intracellular LS. The developmental time course gene expression analysis indicated that fatty acid biosynthesis, isoprenoid biosynthesis and iron metabolism are sustaining LS development along with amino acid metabolism and biosynthesis. Countering oxidative stress appears to play an important role during intrahepatic LS development. Furthermore, we observed expression of the variant PfEMP1 antigen-encoding var genes, and we confirmed expression of PfEMP1 protein during LS development. Transcriptome comparison of the late Pf liver stage schizonts with P. vivax (Pv) late liver stages revealed highly conserved gene expression profiles among orthologous genes. A notable difference however was the expression of genes regulating sexual stage commitment. While Pv schizonts expressed markers of sexual commitment, the Pf LS parasites were not sexually committed and showed expression of gametocytogenesis repression factors. Our results provide the first comprehensive gene expression profile of the human malaria parasite Pf LS isolated during in vivo intrahepatocytic development. This data will inform biological studies and the search for effective intervention strategies that can prevent infection.

CBFA2T3-GLIS2 model of pediatric acute megakaryoblastic leukemia identifies FOLR1 as a CAR T cell target

Fusion oncoproteins are the initiating event in the pathogenesis of many pediatric AML. The CBFA2T3-GLIS2 (C/G) fusion is a product of a cryptic translocation primarily seen in infants and early childhood and is associated with dismal outcome. Here, we demonstrate that the expression of the C/G oncogenic fusion protein promotes the transformation of human cord blood hematopoietic stem/progenitor cells (CB HSPCs) in an endothelial cell (EC) co-culture system, that recapitulates the transcriptome, morphology and immunophenotype of C/G AML and induces highly aggressive leukemia in xenograft models. Interrogating the transcriptome of C/G-CB cells and primary C/G AML identified a library of C/G fusion-specific genes that are potential targets for therapy. We developed chimeric antigen receptor (CAR) T cells directed against one of the targets, FOLR1, and demonstrated their pre-clinical efficacy against C/G AML using in vitro and xenograft models. FOLR1 is also expressed in renal and pulmonary epithelium, raising concerns for toxicity that must be addressed for the clinical application of this therapy. Our findings underscore the role of the endothelial niche in promoting leukemic transformation of C/G-transduced CB HSPCs. Furthermore, this work has broad implications for studies of leukemogenesis applicable to a variety of oncogenic fusion-driven pediatric leukemias, providing a robust and tractable model system to characterize the molecular mechanisms of leukemogenesis and identify biomarkers for disease diagnosis and targets for therapy.

Integrated stem cell signature and cytomolecular risk determination in pediatric acute myeloid leukemia

Relapsed or refractory pediatric acute myeloid leukemia (AML) is associated with poor outcomes and relapse risk prediction approaches have not changed significantly in decades. To build a robust transcriptional risk prediction model for pediatric AML, we perform RNA-sequencing on 1503 primary diagnostic samples. While a 17 gene leukemia stem cell signature (LSC17) is predictive in our aggregated pediatric study population, LSC17 is no longer predictive within established cytogenetic and molecular (cytomolecular) risk groups. Therefore, we identify distinct LSC signatures on the basis of AML cytomolecular subtypes (LSC47) that were more predictive than LSC17. Based on these findings, we build a robust relapse prediction model within a training cohort and then validate it within independent cohorts. Here, we show that LSC47 increases the predictive power of conventional risk stratification and that applying biomarkers in a manner that is informed by cytomolecular profiling outperforms a uniform biomarker approach.

Relapsed pediatric acute myeloid leukemia is associated with poor prognosis. Here, the authors use RNA-seq data from 1503 primary samples to create a combined transcriptional and cytomolecular signature to improve relapse risk prediction.

Targeting improved resilience in Merino sheep - Correlations between immune competence and health and fitness traits

Resilience can be defined as the ability of an animal to remain productive in the face of diverse environmental challenges. Several factors contribute to an animal's resilience including its ability to resist disease, cope with climatic extremes and respond to stressors. Immune competence, a proxy trait for general disease resistance, is expected to contribute to an animal's resilience. This research aimed to develop a practical method to assess immune competence in Merino sheep which would not restrict the future sale of tested animals, and to estimate genetic parameters associated with the novel trait. We also aimed to explore associations between immune competence and other industry-relevant disease resistance and fitness-related traits and to assess the ability of immune competence phenotypes to predict health outcomes. Here, the ability of Merino wethers (n = 1 339) to mount both an antibody-mediated and cell-mediated immune response was used to define their immune competence phenotype. For that purpose, antigens in a commercial vaccine were administered at the commencement of weaning and their responses were assessed. Univariate sire models were used to estimate variance components and heritabilities for immune competence and its component traits. Bivariate sire models were used to estimate genetic correlations between immune competence and a range of disease resistance and fitness-related traits. The heritability of immune competence and its component traits, antibody-mediated immune response and cell-mediated immune response were estimated at 0.49 ± 0.14, 0.52 ± 0.14 and 0.36 ± 0.11, respectively. Immune competence was favourably genetically correlated with breech flystrike incidence (-0.44 ± 0.39), worm egg count (-0.19 ± 0.23), dag score (-0.26 ± 0.31) and fitness compromise (-0.35 ± 0.24) but not fleece rot (0.17 ± 0.23). Results suggest that selection for immune competence has the potential to improve the resilience of Merino sheep; however, due to the large standard errors associated with correlation estimates reported here, further studies will be required in larger populations to validate associations between immune competence and disease resistance and fitness traits in Australian Merino sheep.

Abstract 3479: UBTF tandem duplications (UBTF-TD) in childhood AML: Enrichment in FLT3-ITD and association with clinical outcome

Childhood AML is an aggressive disease with high rates of failures and poor survival. We have demonstrated that the molecular landscape of AML in children is distinct, and co-occurrence of variants modulate outcomes. Recent discovery of tandem duplication (TD) of the UBTF gene in AML, with enrichment in FLT3-ITD has implicated yet another mutation whose cooperation with FLT3-ITD may modify outcome. Here, we provide a comprehensive evaluation of UBTF-TD in de novo AML and define its clinical implications within FLT3-ITD patients. Initial interrogation of transcriptome data from 1,158 children enrolled on COG AAML1031 identified 50 cases of UBTF-TD (4.3%). Overwhelming majority of UBTF-TD cases were observed in FLT3-ITD cases (77%), vs. that of 1.2% in those without FLT3-ITD (p&lt;0.001). Given extreme enrichment of UBTF-TD in FLT3-ITD, we inquired whether cooperation of UBTF-TD and FLT3-ITD creates a distinct clinical entity. To this end we screened diagnostic DNA from 400 FLT3-ITD patients treated on three consecutive CCG/COG trials (COG AAML1031, COG AAML0531, and CCG-2961) by PCR and fragment analysis. UBTF-TD was identified in 61 FLT3-ITD cases (15.3%).

The data presented here forth focuses on evaluation of implications of UBTF-TD in FLT3-ITD positive patients only. Within the FLT3-ITD patients, initial correlation of UBTF-TD with demographics, disease characteristics, and associated genomic variants was conducted. Patients with and without UBTF-TD had a similar median age at diagnosis (p=0.322), lower diagnostic WBC (p=0.010) and higher marrow blast % (p&lt;0.001). There was a stark paucity of cooperating variants that commonly co-occur with FLT3-ITD, with a single NPM1 mutation (1.6% vs. 29%, p&lt;0.001) and no NUP98 fusions (0% vs. 23%, p&lt;0.001). There was a significant enrichment of WT1 mutations, with 45% UBTF-TD patients with a WT1 mutation (FLT3-ITD/UBTF-TD/WT1), vs. 11% in UBTF-WT (p&lt;0.001). Trisomy 8 (Tri8) was seen in 15% of UBTF-TD. Patients with UBTF-TD had a lower CR rate (44% vs. 60%, p = 0.018), and Higher MRD rate (38% vs. 21%, p&lt;0.001). Patients with and without UBTF-TD had an EFS of 28% vs. 42% (p=0.047) with a corresponding OS of 40% and 57% (p=0.019). Given enrichment of WT1 mutations and Tri8 in patients with UBTF-TD, we studied the outcome UBTF-TD patients in the context of these two variants. FLT3-ITD/UBTF-TD/WT1 patients had a 5-year EFS of 17% vs. 38% for similar patients without WT1 mutations (p=0.0062). Patients with UBTF-TD with additional Tri8 had a similarly poor outcome with an EFS of 23% with a corresponding OS of 33%, providing a distinct high risk UBTF-TD cohort (+WT1 or Tri8), whereas the remaining UBTF-TD patients had a more favorable outcome with EFS and OS of 64% and 86%, respectively (p&lt;0.0001, and p&lt;0.0001). UBTF-TD is a novel genomic entity with high enrichment in patients with FLT3-ITD and a distinct clinical outcome driven by cooperating WT1 mutation and Tri8.

Citation Format: Leila Robinson, Amanda Leonti, Todd A. Alonzo, Yi-Cheng Wang, Michele S. Redell, Rhonda E. Ries, Jenny L. Smith, Tiffany A. Hylkema, Quy Le, E Anders Kolb, Richard Aplenc, Xiaotu Ma, Jeffrey Klco, Katherine Tarlock, Soheil Meshinchi. UBTF tandem duplications (UBTF-TD) in childhood AML: Enrichment in FLT3-ITD and association with clinical outcome [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 3479.

Integrated Genomic Analysis Identifies UBTF Tandem Duplications as a Recurrent Lesion in Pediatric Acute Myeloid Leukemia

The genetics of relapsed pediatric acute myeloid leukemia (AML) has yet to be comprehensively defined. Here, we present the spectrum of genomic alterations in 136 relapsed pediatric AMLs. We identified recurrent exon 13 tandem duplications (TD) in upstream binding transcription factor (UBTF) in 9% of relapsed AML cases. UBTF-TD AMLs commonly have normal karyotype or trisomy 8 with cooccurring WT1 mutations or FLT3-ITD but not other known oncogenic fusions. These UBTF-TD events are stable during disease progression and are present in the founding clone. In addition, we observed that UBTF-TD AMLs account for approximately 4% of all de novo pediatric AMLs, are less common in adults, and are associated with poor outcomes and MRD positivity. Expression of UBTF-TD in primary hematopoietic cells is sufficient to enhance serial clonogenic activity and to drive a similar transcriptional program to UBTF-TD AMLs. Collectively, these clinical, genomic, and functional data establish UBTF-TD as a new recurrent mutation in AML.

SIGNIFICANCE

We defined the spectrum of mutations in relapsed pediatric AML and identified UBTF-TDs as a new recurrent genetic alteration. These duplications are more common in children and define a group of AMLs with intermediate-risk cytogenetic abnormalities, FLT3-ITD and WT1 alterations, and are associated with poor outcomes. See related commentary by Hasserjian and Nardi, p. 173. This article is highlighted in the In This Issue feature, p. 171.

Robust bulk micro-nano hierarchical copper structures possessing exceptional bactericidal efficacy

Conventional copper (Cu) metal surfaces are well recognized for their bactericidal properties. However, their slow bacteria-killing potency has historically excluded them as a rapid bactericidal material. We report the development of a robust bulk superhydrophilic micro-nano hierarchical Cu structure that possesses exceptional bactericidal efficacy. It resulted in a 4.41 log₁₀ reduction (>99.99%) of the deadly Staphylococcus aureus (S. aureus) bacteria within 2 min vs. a 1.49 log₁₀ reduction (96.75%) after 240 min on common Cu surfaces. The adhered cells exhibited extensive blebbing, loss of structural integrity and leakage of vital intracellular material, demonstrating the rapid efficacy of the micro-nano Cu structure in destructing bacteria membrane integrity. The mechanism was attributed to the synergistic degradation of the cell envelope through enhanced release and therefore uptake of the cytotoxic Cu ions and the adhesion-driven mechanical strain due to its rapid ultimate superhydrophilicity (contact angle drops to 0° in 0.18 s). The scalable fabrication of this micro-nano Cu structure was enabled by integrating bespoke precursor alloy design with microstructure preconditioning for dealloying and demonstrated on 2000 mm² Cu surfaces. This development paves the way to the practical exploitation of Cu as a low-cost antibiotic-free fast bactericidal material.

Abstract P143: Development of siRNA-loaded lipid nanoparticles targeting long non-coding RNA LINC01257 as a novel and safe therapeutic approach for paediatric acute myeloid leukaemia

Introduction: Standard of care therapies for children with acute myeloid leukemia (AML) cause potent off-target toxicity to healthy cells, highlighting the need to develop new therapeutic approaches that are safe and specific for leukemia cells. Long non-coding RNAs (lncRNAs) are an emerging and highly attractive therapeutic target in the treatment of cancer due to their oncogenic functions and selective expression in cancer cells. However, lncRNAs have historically been considered ‘undruggable’ targets because they do not encode for a protein product. Therefore, the discovery of novel lncRNA targets and the development of efficient methods to silence them is critical for developing new therapies for AML. In this study, we describe the development of an siRNA-loaded lipid nanoparticle (LNP) for the therapeutic silencing of the novel oncogenic lncRNA LINC01257. Materials and Methods: Transcriptomic analysis of children with AML from both the Therapeutically Applicable Research to Generate Effective Treatments (TARGET) initiative and AAML1031 study was performed to identify AML specific lncRNAs. The subsequently identified lncRNA LINC01257 was knocked down in AML Kasumi-1 cells via electroporation of siRNA targeting LINC01257 (si-LINC01257). Changes in proliferation and cell viability were assessed via cell count and Annexin V/7AAD staining 48 hours post-transfection. LNPs incorporating non-targeting si-SCR or si-LINC01257 were synthesized through NxGen non-turbulent microfluidics. LNPs were formulated reproducing the FDA-approved Onpattro® siRNA delivery vector, D-Lin-MC3-DMA:DSPC:cholesterol:PEG-DMG. LNP-si-LINC01257 uptake was measured by confocal microscopy and flow cytometry. Kasumi-1 cells and healthy peripheral blood mononuclear cells (PBMCs) were treated with 250nM LNP-si-SCR or LNP-si-LINC01257 for 48 hours. Changes in proliferation and cell viability were assessed with cell counts and Annexin V/7AAD staining 48 hours post-treatment. Results: LINC01257 was significantly overexpressed in patients carrying the t(8;21) translocation compared to healthy controls ( P = &lt;0.001). Compared to si-SCR controls, siRNA knockdown of LINC01257 in Kasumi-1 cells resulted in a 62% reduction in the total cell count after 48 hours (P = &lt;0.001) , which was accompanied by a 70% decrease in overall cell viability (P = &lt;0.004). LNP-siRNA production yielded a mean LNP size of ~65 nm along with a &gt;85% siRNA encapsulation rate. LNP-siRNAs were efficiently taken up by Kasumi-1 cells (&gt;95% of cells) and LNP-si-LINC01257 treatment successfully ablated LINC01257 expression, which was accompanied by a 55% reduction in total cell count following 48 hours of treatment (P= 0.02). In contrast, healthy PBMCs, which do not express LINC01257, were unaffected by LNP-si-LINC01257 treatment despite comparable levels of LNP-siRNA uptake. Conclusion: Our data demonstrate the effective use of LNP-based RNA interference modalities for the silencing of cancer-driving lncRNAs and highlight their potential as a viable therapeutic and non-toxic approach in the management of AML.

Citation Format: Patrick Connerty, Ernest Moles, Charles deBock, Nisitha Jayatilleke, Jenny L. Smith, Soheil Meshinchi, Chelsea Mayoh, Maria Kavallaris, Richard B. Lock. Development of siRNA-loaded lipid nanoparticles targeting long non-coding RNA LINC01257 as a novel and safe therapeutic approach for paediatric acute myeloid leukaemia [abstract]. In: Proceedings of the AACR-NCI-EORTC Virtual International Conference on Molecular Targets and Cancer Therapeutics; 2021 Oct 7-10. Philadelphia (PA): AACR; Mol Cancer Ther 2021;20(12 Suppl):Abstract nr P143.

A B-cell developmental gene regulatory network is activated in infant AML

Infant Acute Myeloid Leukemia (AML) is a poorly-addressed, heterogeneous malignancy distinguished by surprisingly few mutations per patient but accompanied by myriad age-specific translocations. These characteristics make treatment of infant AML challenging. While infant AML is a relatively rare disease, it has enormous impact on families, and in terms of life-years-lost and life limiting morbidities. To better understand the mechanisms that drive infant AML, we performed integrative analyses of genome-wide mRNA, miRNA, and DNA-methylation data in diagnosis-stage patient samples. Here, we report the activation of an onco-fetal B-cell developmental gene regulatory network in infant AML. AML in infants is genomically distinct from AML in older children/adults in that it has more structural genomic aberrations and fewer mutations. Differential expression analysis of ~1500 pediatric AML samples revealed a large number of infant-specific genes, many of which are associated with B cell development and function. 18 of these genes form a well-studied B-cell gene regulatory network that includes the epigenetic regulators BRD4 and POU2AF1, and their onco-fetal targets LIN28B and IGF2BP3. All four genes are hypo-methylated in infant AML. Moreover, micro-RNA Let7a-2 is expressed in a mutually exclusive manner with its target and regulator LIN28B. These findings suggest infant AML may respond to bromodomain inhibitors and immune therapies targeting CD19, CD20, CD22, and CD79A.

Development of siRNA-Loaded Lipid Nanoparticles Targeting Long Non-Coding RNA LINC01257 as a Novel and Safe Therapeutic Approach for t(8;21) Pediatric Acute Myeloid Leukemia

Standard of care therapies for children with acute myeloid leukemia (AML) cause potent off-target toxicity to healthy cells, highlighting the need to develop new therapeutic approaches that are safe and specific for leukemia cells. Long non-coding RNAs (lncRNAs) are an emerging and highly attractive therapeutic target in the treatment of cancer due to their oncogenic functions and selective expression in cancer cells. However, lncRNAs have historically been considered ‘undruggable’ targets because they do not encode for a protein product. Here, we describe the development of a new siRNA-loaded lipid nanoparticle for the therapeutic silencing of the novel oncogenic lncRNA LINC01257. Transcriptomic analysis of children with AML identified LINC01257 as specifically expressed in t(8;21) AML and absent in healthy patients. Using NxGen microfluidic technology, we efficiently and reproducibly packaged anti-LINC01257 siRNA (LNP-si-LINC01257) into lipid nanoparticles based on the FDA-approved Patisiran (Onpattro^®) formulation. LNP-si-LINC01257 size and ζ-potential were determined by dynamic light scattering using a Malvern Zetasizer Ultra. LNP-si-LINC01257 internalization and siRNA delivery were verified by fluorescence microscopy and flow cytometry analysis. lncRNA knockdown was determined by RT-qPCR and cell viability was characterized by flow cytometry-based apoptosis assay. LNP-siRNA production yielded a mean LNP size of ~65 nm with PDI ≤ 0.22 along with a >85% siRNA encapsulation rate. LNP-siRNAs were efficiently taken up by Kasumi-1 cells (>95% of cells) and LNP-si-LINC01257 treatment was able to successfully ablate LINC01257 expression which was accompanied by a significant 55% reduction in total cell count following 48 h of treatment. In contrast, healthy peripheral blood mononuclear cells (PBMCs), which do not express LINC01257, were unaffected by LNP-si-LINC01257 treatment despite comparable levels of LNP-siRNA uptake. This is the first report demonstrating the use of LNP-assisted RNA interference modalities for the silencing of cancer-driving lncRNAs as a therapeutically viable and non-toxic approach in the management of AML.

CEBPA-bZip mutations are associated with favorable prognosis in de novo AML: a report from the Children's Oncology Group

Biallelic CEBPA mutations are associated with favorable outcomes in acute myeloid leukemia (AML). We evaluated the clinical and biologic implications of CEBPA-basic leucine zipper (CEBPA-bZip) mutations in children and young adults with newly diagnosed AML. CEBPA-bZip mutation status was determined in 2958 patients with AML enrolled on Children's Oncology Group trials (NCT00003790, NCT0007174, NCT00372593, NCT01379181). Next-generation sequencing (NGS) was performed in 1863 patients (107 with CEBPA mutations) to characterize the co-occurring mutations. CEBPA mutational status was correlated with disease characteristics and clinical outcomes. CEBPA-bZip mutations were identified in 160 (5.4%) of 2958 patients, with 132 (82.5%) harboring a second CEBPA mutation (CEBPA-double-mutated [CEBPA-dm]) and 28 (17.5%) had a single CEBPA-bZip only mutation. The clinical and laboratory features of the 2 CEBPA cohorts were very similar. Patients with CEBPA-dm and CEBPA-bZip experienced identical event-free survival (EFS) of 64% and similar overall survival (OS) of 81% and 89%, respectively (P = .259); this compared favorably to EFS of 46% and OS of 61% in patients with CEBPA-wild-type (CEBPA-WT) (both P < .001). Transcriptome analysis demonstrated similar expression profiles for patients with CEBPA-bZip and CEBPA-dm. Comprehensive NGS of patients with CEBPA mutations identified co-occurring CSF3R mutations in 13.1% of patients and GATA2 mutations in 21.5% of patients. Patients with dual CEBPA and CSF3R mutations had an EFS of 17% vs 63% for patients with CEBPA-mutant or CSF3R-WT (P < .001) with a corresponding relapse rate (RR) of 83% vs 22%, respectively (P < .001); GATA2 co-occurrence did not have an impact on outcome. CEBPA-bZip domain mutations are associated with favorable clinical outcomes, regardless of monoallelic or biallelic status. Co-occurring CSF3R and CEBPA mutations are associated with a high RR that nullifies the favorable prognostic impact of CEBPA mutations.

'Stat' workflow modifications to expedite care after needlestick injuries

BACKGROUND

Post-exposure prophylaxis (PEP) for human immunodeficiency virus (HIV) is recommended to start within hours of needlestick injuries (NSIs) among healthcare workers (HCWs). Delays associated with awaiting the results of testing from the source patient (whose blood was involved in the NSI) can lead to psychological consequences for the exposed HCW as well as symptomatic toxicities from empiric PEP.

AIMS

After developing a 'stat' (immediate) workflow that prioritized phlebotomy and resulting of source patient bloodwork for immediate handling and processing, we retrospectively investigated whether our new workflow had (i) decreased HIV order-result interval times for source patient HIV bloodwork and (ii) decreased the frequency of HIV PEP prescriptions being dispensed to exposed HCWs.

METHODS

We retrospectively analysed NSI records to identify source patient HIV order-result intervals and PEP dispensing frequencies across a 6-year period (encompassing a 54-month pre-intervention period and 16-month post-intervention period).

RESULTS

We identified 251 NSIs, which occurred at similar frequencies before versus after our intervention (means 3.54 NSIs and 3.75 NSIs per month, respectively). Median HIV order-result intervals decreased significantly (P < 0.05) from 195 to 156 min after our intervention, while the proportion of HCWs who received one or more doses of PEP decreased significantly (P < 0.001) from 50% (96/191) to 23% (14/60).

CONCLUSION

Using a 'stat' workflow to prioritize source patient testing after NSIs, we achieved a modest decrease in order-result intervals and a dramatic decrease in HIV PEP dispensing rates. This simple intervention may improve HCWs' physical and psychological health during a traumatic time.

Altered Processing of Complex Visual Stimuli in Patients with Postconcussive Visual Motion Sensitivity

BACKGROUND AND PURPOSE

Vestibular symptoms are common after concussion. Vestibular Ocular Motor Screening identifies vestibular impairment, including postconcussive visual motion sensitivity, though the underlying functional brain alterations are not defined. We hypothesized that alterations in multisensory processing are responsible for postconcussive visual motion sensitivity, are detectable on fMRI, and correlate with symptom severity.

MATERIALS AND METHODS

Twelve patients with subacute postconcussive visual motion sensitivity and 10 healthy control subjects underwent vestibular testing and a novel fMRI visual-vestibular paradigm including 30-second "neutral" or "provocative" videos. The presence of symptoms/intensity was rated immediately after each video. fMRI group-level analysis was performed for a "provocative-neutral" condition. Z-statistic images were nonparametrically thresholded using clusters determined by Z > 2.3 and a corrected cluster significance threshold of P = .05. Symptoms assessed on Vestibular Ocular Motor Screening were correlated with fMRI mean parameter estimates using Pearson correlation coefficients.

RESULTS

Subjects with postconcussive visual motion sensitivity had significantly more Vestibular Ocular Motor Screening abnormalities and increased symptoms while viewing provocative videos. While robust mean activation in the primary and secondary visual areas, the parietal lobe, parietoinsular vestibular cortex, and cingulate gyrus was seen in both groups, selective increased activation was seen in subjects with postconcussive visual motion sensitivity in the primary vestibular/adjacent cortex and inferior frontal gyrus, which are putative multisensory visual-vestibular processing centers. Moderate-to-strong correlations were found between Vestibular Ocular Motor Screening scores and fMRI activation in the left frontal eye field, left middle temporal visual area, and right posterior hippocampus.

CONCLUSIONS

Increased fMRI brain activation in visual-vestibular multisensory processing regions is selectively seen in patients with postconcussive visual motion sensitivity and is correlated with Vestibular Ocular Motor Screening symptom severity, suggesting that increased visual input weighting into the vestibular network may underlie postconcussive visual motion sensitivity.

Sweet Corn Sentinel Monitoring for Lepidopteran Field-Evolved Resistance to Bt Toxins

As part of an insect resistance management plan to preserve Bt transgenic technology, annual monitoring of target pests is mandated to detect susceptibility changes to Bt toxins. Currently Helicoverpa zea (Boddie) monitoring involves investigating unexpected injury in Bt crop fields and collecting larvae from non-Bt host plants for laboratory diet bioassays to determine mortality responses to diagnostic concentrations of Bt toxins. To date, this monitoring approach has not detected any significant change from the known range of baseline susceptibility to Bt toxins, yet practical field-evolved resistance in H. zea populations and numerous occurrences of unexpected injury occur in Bt crops. In this study, we implemented a network of 73 sentinel sweet corn trials, spanning 16 U.S. states and 4 Canadian provinces, for monitoring changes in H. zea susceptibility to Cry and Vip3A toxins by measuring differences in ear damage and larval infestations between isogenic pairs of non-Bt and Bt hybrids over three years. This approach can monitor susceptibility changes and regional differences in other ear-feeding lepidopteran pests. Temporal changes in the field efficacy of each toxin were evidenced by comparing our current results with earlier published studies, including baseline data for each Bt trait when first commercialized. Changes in amount of ear damage showed significant increases in H. zea resistance to Cry toxins and possibly lower susceptibility to Vip3a. Our findings demonstrate that the sentinel plot approach as an in-field screen can effectively monitor phenotypic resistance and document field-evolved resistance in target pest populations, improving resistance monitoring for Bt crops.

Development and Validation of a Deep Learning Algorithm for Gleason Grading of Prostate Cancer From Biopsy Specimens

Question

How does a deep learning system for assessing prostate biopsy specimens compare with interpretations determined by specialists in urologic pathology and by general pathologists?

Findings

In a validation data set of 752 biopsy specimens obtained from 2 independent medical laboratories and a tertiary teaching hospital, this study found that rate of agreement with subspecialists was significantly higher for the deep learning system than it was for a cohort of general pathologists.

Meaning

The deep learning system warrants evaluation as an assistive tool for improving prostate cancer diagnosis and treatment decisions, especially where subspecialist expertise is unavailable.

Importance

For prostate cancer, Gleason grading of the biopsy specimen plays a pivotal role in determining case management. However, Gleason grading is associated with substantial interobserver variability, resulting in a need for decision support tools to improve the reproducibility of Gleason grading in routine clinical practice.

Objective

To evaluate the ability of a deep learning system (DLS) to grade diagnostic prostate biopsy specimens.

Design, Setting, and Participants

The DLS was evaluated using 752 deidentified digitized images of formalin-fixed paraffin-embedded prostate needle core biopsy specimens obtained from 3 institutions in the United States, including 1 institution not used for DLS development. To obtain the Gleason grade group (GG), each specimen was first reviewed by 2 expert urologic subspecialists from a multi-institutional panel of 6 individuals (years of experience: mean, 25 years; range, 18-34 years). A third subspecialist reviewed discordant cases to arrive at a majority opinion. To reduce diagnostic uncertainty, all subspecialists had access to an immunohistochemical-stained section and 3 histologic sections for every biopsied specimen. Their review was conducted from December 2018 to June 2019.

Main Outcomes and Measures

The frequency of the exact agreement of the DLS with the majority opinion of the subspecialists in categorizing each tumor-containing specimen as 1 of 5 categories: nontumor, GG1, GG2, GG3, or GG4-5. For comparison, the rate of agreement of 19 general pathologists’ opinions with the subspecialists’ majority opinions was also evaluated.

Results

For grading tumor-containing biopsy specimens in the validation set (n = 498), the rate of agreement with subspecialists was significantly higher for the DLS (71.7%; 95% CI, 67.9%-75.3%) than for general pathologists (58.0%; 95% CI, 54.5%-61.4%) (P < .001). In subanalyses of biopsy specimens from an external validation set (n = 322), the Gleason grading performance of the DLS remained similar. For distinguishing nontumor from tumor-containing biopsy specimens (n = 752), the rate of agreement with subspecialists was 94.3% (95% CI, 92.4%-95.9%) for the DLS and similar at 94.7% (95% CI, 92.8%-96.3%) for general pathologists (P = .58).

Conclusions and Relevance

In this study, the DLS showed higher proficiency than general pathologists at Gleason grading prostate needle core biopsy specimens and generalized to an independent institution. Future research is necessary to evaluate the potential utility of using the DLS as a decision support tool in clinical workflows and to improve the quality of prostate cancer grading for therapy decisions.

The α2,3-selective potentiators of GABAA receptors, KRM-II-81 and MP-III-80, produce anxiolytic-like effects and block chemotherapy-induced hyperalgesia in mice without tolerance development

Opiate analgesics are one of the treatment options for severe chronic pain, including late-stage cancer, chronic back pain and other disorders. The recent resurgence in opioid overdose has highlighted the serious need for alternative medicines for pain management. While a role for potentiators of α2/3-containing GABA_A receptors in the modulation of pain has been known for several years, advancements in this area required data from selective compounds. KRM-II-81(5-(8-ethynyl-6-(pyridin-2-yl)-4H-benzo[f]imidazo[1,5-a][1,4]diazepin-3- yl)oxazole) and analogs selectively potentiate GABA_A receptors containing α2/3 subunits and have recently been shown to attenuate pain behaviors in several acute and chronic pain models in rodents. The present study was designed to ascertain whether KRM-II-81 and the structural analog MP-III-80 (3-ethyl-5-(8-ethynyl-6-(pyridin-2-yl)-4H-benzo[f]imidazo[1,5-a][1,4]diazepin-3-yl)-1,2,4-oxadiazole) would block chemotherapeutic agent paclitaxel-induced pain in male, C57BL/6 mice. Both compounds significantly inhibited pain behaviors evoked by cold and tactile stimulation in paclitaxel-treated mice as did the neuropathic pain drug gabapentin. Subchronic dosing for 22 days with KRM-II-81 and MP-III-80 demonstrated enduring analgesic efficacy without tolerance development, while the effects of gabapentin showed evidence of tolerance development. KRM-II-81 and MP-III-80 also decreased marble-burying behavior in this mouse strain as did the anxiolytic drug chlordiazepoxide. In contrast to KRM-II-81 and MP-III-80, chlordiazepoxide had motor-impairing effects at anxiolytic-like doses. The data add to the literature documenting that these selective potentiators of α2/3-containing GABA_A receptors are effective in a host of animal models used to detect novel analgesic drugs. The anxiolytic-like efficacy of these compounds fits well with the comorbidity of anxiety in patients with chronic pain and cancer.

R-(-)-ketamine modifies behavioral effects of morphine predicting efficacy as a novel therapy for opioid use disorder1

Substance abuse disorder continues to have devastating consequences for individuals and society and current therapies are not sufficient to provide the magnitude of medical impact required. Although some evidence suggests the use of ketamine in treating various substance use related- symptoms, its adverse event profile including dissociation, dysphoria, and abuse liability limit its potential as a therapy. Here, we outline experiments to test our hypothesis that (R)-ketamine can both alleviate withdrawal symptoms and produce effects that help sustain abstinence. In morphine-dependent rats, (R)-ketamine alleviated naloxone-precipitated withdrawal signs. (R)-ketamine also blocked morphine-induced place preference in mice without inducing place preference on its own. We also evaluated whether (R)-ketamine would induce anhedonia, a counter-indicated effect for a drug abuse treatment agent. S-(+)- but not R-(-)-ketamine produced anhedonia-like responses in rats that electrically self-stimulated the medial forebrain bundle (ICSS). However, time-course studies of ICSS are needed to fully appreciate these differences. These data begin to support the claim that (R)-ketamine will dampen withdrawal symptoms and drug liking, factors known to contribute to the cycle of drug addiction. In addition, these data suggest that (R)-ketamine would not produce negative mood or anhedonia that could interfere with treatment. It is suggested that continued investigation of (R)-ketamine as a novel therapeutic for substance abuse disorder be given consideration by the preclinical and clinical research communities. This suggestion is further encouraged by a recent report on the efficacy of (R)-ketamine in treatment-resistant depressed patients at a dose with little measurable dissociative side-effects.

Genome wide association study of 5 agronomic traits in olive (Olea europaea L.)

Olive (Olea europaea L.) is one of the most economically and historically important fruit crops worldwide. Genetic progress for valuable agronomic traits has been slow in olive despite its importance and benefits. Advances in next generation sequencing technologies provide inexpensive and highly reproducible genotyping approaches such as Genotyping by Sequencing, enabling genome wide association study (GWAS). Here we present the first comprehensive GWAS study on olive using GBS. A total of 183 accessions (FULL panel) were genotyped using GBS, 94 from the Turkish Olive GenBank Resource (TOGR panel) and 89 from the USDA-ARS National Clonal Germplasm Repository (NCGR panel) in the USA. After filtering low quality and redundant markers, GWAS was conducted using 24,977 SNPs in FULL, TOGR and NCGR panels. In total, 52 significant associations were detected for leaf length, fruit weight, stone weight and fruit flesh to pit ratio using the MLM_K. Significant GWAS hits were mapped to their positions and 19 candidate genes were identified within a 10-kb distance of the most significant SNP. Our findings provide a framework for the development of markers and identification of candidate genes that could be used in olive breeding programs.

Myeloid lineage enhancers drive oncogene synergy in CEBPA/CSF3R mutant acute myeloid leukemia

Acute Myeloid Leukemia (AML) develops due to the acquisition of mutations from multiple functional classes. Here, we demonstrate that activating mutations in the granulocyte colony stimulating factor receptor (CSF3R), cooperate with loss of function mutations in the transcription factor CEBPA to promote acute leukemia development. The interaction between these distinct classes of mutations occurs at the level of myeloid lineage enhancers where mutant CEBPA prevents activation of a subset of differentiation associated enhancers. To confirm this enhancer-dependent mechanism, we demonstrate that CEBPA mutations must occur as the initial event in AML initiation. This improved mechanistic understanding will facilitate therapeutic development targeting the intersection of oncogene cooperativity.

Comprehensive Transcriptome Profiling of Cryptic CBFA2T3-GLIS2 Fusion-Positive AML Defines Novel Therapeutic Options: A COG and TARGET Pediatric AML Study

PURPOSE

A cryptic inv(16)(p13.3q24.3) encoding the CBFA2T3-GLIS2 fusion is associated with poor outcome in infants with acute megakaryocytic leukemia. We aimed to broaden our understanding of the pathogenesis of this fusion through transcriptome profiling.

EXPERIMENTAL DESIGN

Available RNA from children and young adults with de novo acute myeloid leukemia (AML; N = 1,049) underwent transcriptome sequencing (mRNA and miRNA). Transcriptome profiles for those with the CBFA2T3-GLIS2 fusion (N = 24) and without (N = 1,025) were contrasted to define fusion-specific miRNAs, genes, and pathways. Clinical annotations defined distinct fusion-associated disease characteristics and outcomes.

RESULTS

The CBFA2T3-GLIS2 fusion was restricted to infants <3 years old (P < 0.001), and the presence of this fusion was highly associated with adverse outcome (P < 0.001) across all morphologic classifications. Further, there was a striking paucity of recurrent cooperating mutations, and transduction of cord blood stem cells with this fusion was sufficient for malignant transformation. CBFA2T3-GLIS2 positive cases displayed marked upregulation of genes with cell membrane/extracellular matrix localization potential, including NCAM1 and GABRE. Additionally, miRNA profiling revealed significant overexpression of mature miR-224 and miR-452, which are intronic miRNAs transcribed from the GABRE locus. Gene-set enrichment identified dysregulated Hippo, TGFβ, and hedgehog signaling, as well as NCAM1 (CD56) interaction pathways. Therapeutic targeting of fusion-positive leukemic cells with CD56-directed antibody-drug conjugate caused significant cytotoxicity in leukemic blasts.

CONCLUSIONS

The CBFA2T3-GLIS2 fusion defines a highly refractory entity limited to infants that appears to be sufficient for malignant transformation. Transcriptome profiling elucidated several highly targetable genes and pathways, including the identification of CD56, providing a highly plausible target for therapeutic intervention.

Development and validation of a deep learning algorithm for improving Gleason scoring of prostate cancer

For prostate cancer patients, the Gleason score is one of the most important prognostic factors, potentially determining treatment independent of the stage. However, Gleason scoring is based on subjective microscopic examination of tumor morphology and suffers from poor reproducibility. Here we present a deep learning system (DLS) for Gleason scoring whole-slide images of prostatectomies. Our system was developed using 112 million pathologist-annotated image patches from 1226 slides, and evaluated on an independent validation dataset of 331 slides. Compared to a reference standard provided by genitourinary pathology experts, the mean accuracy among 29 general pathologists was 0.61 on the validation set. The DLS achieved a significantly higher diagnostic accuracy of 0.70 (p = 0.002) and trended towards better patient risk stratification in correlations to clinical follow-up data. Our approach could improve the accuracy of Gleason scoring and subsequent therapy decisions, particularly where specialist expertise is unavailable. The DLS also goes beyond the current Gleason system to more finely characterize and quantitate tumor morphology, providing opportunities for refinement of the Gleason system itself.

The α2,3-selective potentiator of GABAA receptors, KRM-II-81, reduces nociceptive-associated behaviors induced by formalin and spinal nerve ligation in rats

Clinical evidence indicates that positive allosteric modulators (PAMs) of GABAA receptors have analgesic benefit in addition to efficacy in anxiety disorders. However, the utility of GABAA receptor PAMs as analgesics is compromised by the central nervous system side effects of non-selective potentiators. A selective potentiator of GABAA receptors associated with α2/3 subunits, KRM-II-81(5-(8-ethynyl-6-(pyridin-2-yl)-4H-benzo[f]imidazo[1,5-a][1,4]diazepin-3-yl)oxazole), has demonstrated anxiolytic, anticonvulsant, and antinociceptive effects in rodents with reduced motoric side effects. The present study evaluated the potential of KRM-II-81 as a novel analgesic. Oral administration of KRM-II-81 attenuated formalin-induced flinching; in contrast, diazepam was not active. KRM-II-81 attenuated nociceptive-associated behaviors engendered by chronic spinal nerve ligation (L5/L6). Diazepam decreased locomotion of rats at the dose tested in the formalin assay (10 mg/kg) whereas KRM-II-81 produced small decreases that were not dose-dependent (10-100 mg/kg). Plasma and brain levels of KRM-II-81 were used to demonstrate selectivity for α2/3- over α1-associated GABAA receptors and to define the degree of engagement of these receptors. Plasma and brain concentrations of KRM-II-81 were positively-associated with analgesic efficacy. GABA currents from isolated rat dorsal-root ganglion cultures were potentiated by KRM-II-81 with an ED50 of 32 nM. Measures of respiratory depression were reduced by alprazolam whereas KRM-II-81 was either inactive or produced effects with lower potency and efficacy. These findings add to the growing body of data supporting the idea that α2/3-selective GABAA receptor PAMs will have efficacy and tolerability as pain medications including those for neuropathic pain. Given their predicted anxiolytic effects, α2/3-selective GABAA receptor PAMs offer an additional inroad into the management of pain.

Leptospirosis: An important infectious disease in North American horses

North American horses are commonly exposed to Leptospira organisms. Leptospira Bratislava is the most common infecting serovar but this serovar has not been confirmed to cause clinical disease in North American horses. Leptospira Pomona type kennewicki is responsible for most of the clinical diseases (leptospirosis) in North American horses. Leptospirosis is most commonly associated with diseases of the placenta and fetus, the kidneys and the eyes in horses. In-utero infections in pregnant mares may result in abortion, neonatal illness or birth of an antibody positive healthy foal. Acute renal failure in younger horses and recurrent uveitis in adult horses are other well documented clinical syndromes of leptospirosis. Abortions, neonatal disease and acute renal failure are caused by a subacute infection, while horses with Leptospira associated recurrent uveitis develop ocular disease months or years after the initial Leptospira infection. Diagnosis of Leptospirosis is made by a combination of antigen or antibody testing methods. Mares that abort following Leptospira infection have no additional clinical signs at the time of abortion but may shed the offending Leptospira spp. in the urine for several weeks. Antibiotic treatments are sometimes used in hopes of decreasing Leptospira shedding in infected horses or prophylactically in exposed pregnant mares but documentation of efficacy is lacking. Horses with Leptospira - associated acute renal failure can be successfully treated with antibiotics and supportive care. Recurrent uveitis is commonly associated with leptospirosis in North American horses and although horses may have chronic intraocular infection triggering an immune disease, systemic antimicrobial therapy has not been effective in eliminating the organism from the eye. An equine approved Leptospira Pomona type kennewicki vaccine is now available in North America.

Artificial Intelligence-Based Breast Cancer Nodal Metastasis Detection: Insights Into the Black Box for Pathologists

CONTEXT.—

Nodal metastasis of a primary tumor influences therapy decisions for a variety of cancers. Histologic identification of tumor cells in lymph nodes can be laborious and error-prone, especially for small tumor foci.

OBJECTIVE.—

To evaluate the application and clinical implementation of a state-of-the-art deep learning-based artificial intelligence algorithm (LYmph Node Assistant or LYNA) for detection of metastatic breast cancer in sentinel lymph node biopsies.

DESIGN.—

Whole slide images were obtained from hematoxylin-eosin-stained lymph nodes from 399 patients (publicly available Camelyon16 challenge dataset). LYNA was developed by using 270 slides and evaluated on the remaining 129 slides. We compared the findings to those obtained from an independent laboratory (108 slides from 20 patients/86 blocks) using a different scanner to measure reproducibility.

RESULTS.—

LYNA achieved a slide-level area under the receiver operating characteristic (AUC) of 99% and a tumor-level sensitivity of 91% at 1 false positive per patient on the Camelyon16 evaluation dataset. We also identified 2 "normal" slides that contained micrometastases. When applied to our second dataset, LYNA achieved an AUC of 99.6%. LYNA was not affected by common histology artifacts such as overfixation, poor staining, and air bubbles.

CONCLUSIONS.—

Artificial intelligence algorithms can exhaustively evaluate every tissue patch on a slide, achieving higher tumor-level sensitivity than, and comparable slide-level performance to, pathologists. These techniques may improve the pathologist's productivity and reduce the number of false negatives associated with morphologic detection of tumor cells. We provide a framework to aid practicing pathologists in assessing such algorithms for adoption into their workflow (akin to how a pathologist assesses immunohistochemistry results).

Establishment of Striacosta albicosta (Lepidoptera: Noctuidae) as a Primary Pest of Corn in the Great Lakes Region

Western bean cutworm, Striacosta albicosta Smith (Lepidoptera: Noctuidae), is a pest of corn, Zea maize L., and dry edible beans, Phaseolus sp. L., native to the western United States. Following the range expansion into the U.S. Corn Belt, pheromone trap monitoring began in the Great Lakes region in 2006. The first S. albicosta was captured in Michigan in 2006 and in Ontario, Canada in 2008. Pheromone traps were used to document spread and increasing captures of S. albicosta across Michigan and Ontario until 2012. Trapping confirmed the univoltine life cycle of S. albicosta in this region and identified peak flight, typically occurring in late July. Overwintering of S. albicosta in this region was confirmed by emergence from infested fields and overwintering experiments. Multiple soil textures were infested with prepupae, and recovery was assessed throughout the winter. Overwintering success was not affected by soil texture; however, prepupae were found at greater depths in coarse-textured soils. Soil temperatures at overwintering depths did not reach the supercooling point. Injury to corn by S. albicosta increased in incidence, severity and geographic range from 2010 to 2014 in field plots. Decreasing control of injury by Cry1F corn hybrids was observed over time. These findings show that S. albicosta has established as a perennial corn pest in the Great Lakes region due to observations of overwintering success and unmanaged injury. We recommend S. albicosta obtain primary pest status in this region within regulatory framework and a resistance management plan be required for traits targeting this pest.

Assessment of the relationship between a written measure of empathy and an independently rated interview of Motivational Interviewing

Motivational Interviewing (MI) is an evidence-based practice shown to be effective when working with people in treatment for substance use disorders. However, MI is a complex treatment modality optimized by training with feedback. Feedback, assessment and monitoring of treatment fidelity require measurement, which is typically done using audiotaped sessions. The gold standard for such measurement of MI skill has been an audiotaped interview, scored by a rater with a detailed structured instrument such as the Motivational Interviewing Treatment Integrity 2.0 (MITI 2.0) Coding System (Moyers, et al., 2005). The Helpful Responses Questionnaire (HRQ) (Miller, Hedrick, & Orlofsky, 1991) is a pen-and-paper test of empathy (a foundational MI skill) that does not require an audiotaped session. A randomized trial of three different regimens for training counselors in MI (live supervision using Teleconferencing, Tape-based supervision and Workshop only) (Smith et al., 2012) offered the opportunity to evaluate the performance of the HRQ as a measure of MI ability, compared to the several MITI 2.0 global scores and subscales. Participants were counselors (N=97) working at community-based substance use treatment programs, whose MI proficiency was measured at four time points: baseline (before an initial 2-day MI workshop), post-workshop, 8weeks post-workshop (i.e., post-supervision), and 20weeks post-workshop with both MITI 2.0 and HRQ. HRQ total scores correlated significantly with the Reflection to Question Ratio from the MITI 2.0 at post-workshop (r=0.33), week 8 (r=0.34), and week 20 (r=0.38), and with the Spirit (r=0.32) and Empathy (r=0.32) global scores at week 20. Correlations of HRQ with other MITI 2.0 subscales and time points after workshop were small and not significant. As predicted, HRQ scores differed between training conditions (X²(2)=7.88, p=0.02), with counselors assigned to live supervision achieving better HRQ scores than those in Workshop only. In summary, HRQ is a modestly accurate measure, mainly of the Reflection to Question Ratio, considered a core marker of MI skill. It is sensitive to training effects and may help identify counselors needing more intensive supervision. Given its ease of administration and scoring, HRQ may be a useful marker of MI skill during training efforts.

Abstract P3-05-01: Immune and transcriptional signatures of dendritic dell (DC) vaccination combined with chemotherapy in locally advanced, triple-negative breast cancer (TNBC) patients

BACKGROUND: Women with TNBC who do not achieve a pathologic complete response (pCR) with preoperative (preop) chemotherapy have a high risk of recurrence and death from BC. Immunotherapy is an attractive strategy as human BCs can be immunogenic, and enhancing the immune effector function may augment the cytotoxic effects of standard therapies.

CLINICAL TRIAL: Following IRB-approved informed consent, 10 pts with locally advanced TNBC received preop dose-dense doxorubicin/cyclophosphamide (AC) followed by paclitaxel and carboplatin (TCb) chemotherapy, combined with antigen-loaded (TNBC antigens: Cyclin B1, WT1, and control viral antigens: CEF) autologous monocyte-derived DC vaccinations administered intratumorally and subcutaneously. DCs were generated with GM-CSF and type I interferon, loaded with antigen in the form of long peptides and activated with innate ligands (LPS and Clo75) and CD40 ligand. Vaccines were given at 4 time points prior to definitive surgery, and 3 times post-surgery, pre- and post-radiation therapy (RT). Safety was the primary study endpoint, and pCR rate in breast and axilla was a secondary endpoint. Correlative studies included assessment of immune response via ELISpot and transcriptional profiling of blood samples collected over time.

RESULTS: All pts received the 4 vaccines during preop chemotherapy, and 7/10 received all 7 vaccines. At the time of definitive surgery, 4 pts achieved a pCR, 3 pts had macroscopic residual disease in the breast and axillary lymph nodes, and 3 pts had residual cancer burden scores of 1. As of June 1, 2017, all pts have been in follow-up for at least 1 year s/p completion of all vaccines, and 7/10 patients have no evidence of disease.

To assess immune signatures with IFN-γ-ELISpot, PBMCs from baseline (BL) and several time points during vaccine treatment were cultured with control peptides or with peptide libraries covering vaccine antigens. Using a linear mixed model to account for repeated and missing observations we found statistically significant (α = 0.05) increases in Cyclin B1, WT1, and CEF ELISpots in at least 1 time point post-DC vaccination and in follow-up. Compared to BL, Cyclin B1 and WT1 increased at 3 day pre-RT in 8/10 and 7/10 pts, respectively. To assess transcriptional signatures, a linear mixed model was utilized to determine statistically significant differences in fold-change over time compared to the BL and healthy controls. Modular analysis of differentially expressed transcripts at BL revealed downregulation of transcripts related to the monocyte lineage in 7/10 pts. Longitudinal analysis revealed profound transcriptional changes during AC with downregulation of lymphocyte modules and upregulation of innate and inflammation modules. While the latter ones have normalized during TCb and follow-up, T cell module remained substantially downregulated throughout treatment and follow-up.

CONCLUSIONS: Combination of preop chemotherapy and intratumoral and subcutaneous autologous DC vaccination is safe in locally advanced TNBC pts and is linked with profound changes in immune transcription signatures and with expansion of antigen-specific immune responses that can be detected in IFN-γ ELISpot.

Citation Format: Palucka AK, Roberts LK, Zurawski SM, Tarnowski J, Turner J, Wang X, Blankenship D, Smith JL, Levin MK, Finholt JP, Burkeholder SB, Timis R, Muniz LS, Dao T, Grant M, Banchereau J, Zurawski G, Pascual V, O'Shaughnessy JA. Immune and transcriptional signatures of dendritic dell (DC) vaccination combined with chemotherapy in locally advanced, triple-negative breast cancer (TNBC) patients [abstract]. In: Proceedings of the 2017 San Antonio Breast Cancer Symposium; 2017 Dec 5-9; San Antonio, TX. Philadelphia (PA): AACR; Cancer Res 2018;78(4 Suppl):Abstract nr P3-05-01.