In Vitro Culture Alters Cell Lineage Composition and Cellular Metabolism of Bovine Blastocyst

Profiling bovine blastocyst transcriptome at the single-cell level has enabled us to reveal the first cell lineage segregation, during which the inner cell mass (ICM), trophectoderm (TE), and an undefined population of transitional cells were identified. By comparing the transcriptome of blastocysts derived in vivo (IVV), in vitro from a conventional culture medium (IVC), and in vitro from an optimized reduced nutrient culture medium (IVR), we found a delay of the cell fate commitment to ICM in the IVC and IVR embryos. Developmental potential differences between IVV, IVC, and IVR embryos were mainly contributed by ICM and transitional cells. Pathway analysis of these non-TE cells between groups revealed highly active metabolic and biosynthetic processes, reduced cellular signaling, and reduced transmembrane transport activities in IVC embryos that may lead to reduced developmental potential. IVR embryos had lower activities in metabolic and biosynthetic processes but increased cellular signaling and transmembrane transport, suggesting these cellular mechanisms may contribute to improved blastocyst development compared to IVC embryos. However, the IVR embryos had compromised development compared to IVV embryos with notably over-active transmembrane transport activities that impaired ion homeostasis.

MAPKs signaling is obligatory for male reproductive function in a development-specific manner

Mitogen-activated protein kinases (MAPKs) represent widely expressed and evolutionarily conserved proteins crucial for governing signaling pathways and playing essential roles in mammalian male reproductive processes. These proteins facilitate the transmission of signals through phosphorylation cascades, regulating diverse intracellular functions encompassing germ cell development in testis, physiological maturation of spermatozoa within the epididymis, and motility regulation at ejaculation in the female reproductive tract. The conservation of these mechanisms appears prevalent across species, including humans, mice, and, to a limited extent, livestock species such as bovines. In Sertoli cells (SCs), MAPK signaling not only regulates the proliferation of immature SCs but also determines the appropriate number of SCs in the testes at puberty, thereby maintaining male fertility by ensuring the capacity for sperm cell production. In germ cells, MAPKs play a crucial role in dynamically regulating testicular cell-cell junctions, supporting germ cell proliferation and differentiation. Throughout spermatogenesis, MAPK signaling ensures the appropriate Sertoli-to-germ cell ratio by regulating apoptosis, controlling the metabolism of developing germ cells, and facilitating the maturation of spermatozoa within the cauda epididymis. During ejaculation in the female reproductive tract, MAPKs regulate two pivotal events-capacitation and the acrosome reaction essential for maintaining the fertility potential of sperm cells. Any disruptions in MAPK pathway signaling possibly may disturb the testicular microenvironment homeostasis, sperm physiology in the male body before ejaculation and in the female reproductive tract during fertilization, ultimately compromising male fertility. Despite decades of research, the physiological function of MAPK pathways in male reproductive health remains inadequately understood. The current review attempts to combine recent findings to elucidate the impact of MAPK signaling on male fertility and proposes future directions to enhance our understanding of male reproductive functions.

In Vitro Culture Alters Cell Lineage Composition and Cellular Metabolism of Bovine Blastocyst

Profiling transcriptome at single cell level of bovine blastocysts derived in vivo (IVV), in vitro from conventional culture medium (IVC), and reduced nutrient culture medium (IVR) has enabled us to reveal cell lineage segregation, during which forming inner cell mass (ICM), trophectoderm (TE), and an undefined population of transitional cells. Only IVV embryos had well-defined ICM, indicating in vitro culture may delay the first cell fate commitment to ICM. Differences between IVV, IVC and IVR embryos were mainly contributed by ICM and transitional cells. Pathway analysis by using the differentially expressed genes of these non-TE cells between groups pointed to highly active metabolic and biosynthetic processes, with reduced cellular signaling and membrane transport in IVC embryos, which may lead to reduced developmental potential. IVR embryos had lower activities in metabolic and biosynthetic processes, but increased cellular signaling and membrane transport, suggesting these cellular mechanisms may contribute to the improved blastocyst development compared to IVC embryos. However, the IVR embryos had compromised development when compared to IVV embryos with notably over-active membrane transport activities that led to impaired ion homeostasis.

Soft-Dielectron Excess in Proton-Proton Collisions at sqrt[s]=13 TeV

A measurement of dielectron production in proton-proton (pp) collisions at sqrt[s]=13  TeV, recorded with the ALICE detector at the CERN LHC, is presented in this Letter. The data set was recorded with a reduced magnetic solenoid field. This enables the investigation of a kinematic domain at low dielectron (ee) invariant mass m_{ee} and pair transverse momentum p_{T,ee} that was previously inaccessible at the LHC. The cross section for dielectron production is studied as a function of m_{ee}, p_{T,ee}, and event multiplicity dN_{ch}/dη. The expected dielectron rate from hadron decays, called hadronic cocktail, utilizes a parametrization of the measured η/π^{0} ratio in pp and proton-nucleus collisions, assuming that this ratio shows no strong dependence on collision energy at low transverse momentum. Comparison of the measured dielectron yield to the hadronic cocktail at 0.15<m_{ee}<0.6  GeV/c^{2} and for p_{T,ee}<0.4  GeV/c indicates an enhancement of soft dielectrons, reminiscent of the "anomalous" soft-photon and soft-dilepton excess in hadron-hadron collisions reported by several experiments under different experimental conditions. The enhancement factor over the hadronic cocktail amounts to 1.61±0.13(stat)±0.17(syst,data)±0.34(syst,cocktail) in the ALICE acceptance. Acceptance-corrected excess spectra in m_{ee} and p_{T,ee} are extracted and compared with calculations of dielectron production from hadronic bremsstrahlung and thermal radiation within a hadronic many-body approach.

Elliptic Flow of Electrons from Beauty-Hadron Decays in Pb-Pb Collisions at sqrt[s_{NN}]=5.02 TeV

The elliptic flow of electrons from beauty hadron decays at midrapidity (|y|<0.8) is measured in Pb-Pb collisions at sqrt[s_{NN}]=5.02  TeV with the ALICE detector at the LHC. The azimuthal distribution of the particles produced in the collisions can be parametrized with a Fourier expansion, in which the second harmonic coefficient represents the elliptic flow, v_{2}. The v_{2} coefficient of electrons from beauty hadron decays is measured for the first time in the transverse momentum (p_{T}) range 1.3-6  GeV/c in the centrality class 30%-50%. The measurement of electrons from beauty-hadron decays exploits their larger mean proper decay length cτ≈500  μm compared to that of charm hadrons and most of the other background sources. The v_{2} of electrons from beauty hadron decays at midrapidity is found to be positive with a significance of 3.75  σ. The results provide insights into the degree of thermalization of beauty quarks in the medium. A model assuming full thermalization of beauty quarks is strongly disfavored by the measurement at high p_{T}, but is in agreement with the results at low p_{T}. Transport models including substantial interactions of beauty quarks with an expanding strongly interacting medium describe the measurement within uncertainties.

A Priori Activation of Apoptosis Pathways of Tumor (AAAPT) technology: Development of targeted apoptosis initiators for cancer treatment

Cancer cells develop tactics to circumvent the interventions by desensitizing themselves to interventions. Amongst many, the principle routes of desensitization include a) activation of survival pathways (e.g. NF-kB, PARP) and b) downregulation of cell death pathways (e.g. CD95/CD95L). As a result, it requires high therapeutic dose to achieve tumor regression which, in turn damages normal cells through the collateral effects. Methods are needed to sensitize the low and non-responsive resistant tumor cells including cancer stem cells (CSCs) in order to evoke a better response from the current treatments. Current treatments including chemotherapy can induce cell death only in bulk cancer cells sparing CSCs and cancer resistant cells (CRCs) which are shown to be responsible for high recurrence of disease and low patient survival. Here, we report several novel tumor targeted sensitizers derived from the natural Vitamin E analogue (AMP-001-003). The drug design is based on a novel concept "A priori activation of apoptosis pathways of tumor technology (AAAPT) which is designed to activate specific cell death pathways and inhibit survival pathways simultaneously and selectively in cancer cells sparing normal cells. Our results indicate that AMP-001-003 sensitize various types of cancer cells including MDA-MB-231 (triple negative breast cancer), PC3 (prostate cancer) and A543 (lung cancer) cells resulting in reducing the IC-50 of doxorubicin in vitro when used as a combination. At higher doses, AMP-001 acts as an anti-tumor agent on its own. The synergy between AMP-001 and doxorubicin could pave a new pathway to use AAAPT leading molecules as neoadjuvant to chemotherapy to achieve better efficacy and reduced off-target toxicity compared to the current treatments.

Developmental and molecular response of bovine embryos to reduced nutrients in vitro

Recent studies in our laboratory have indicated that bovine embryos only use a small amount of the nutrients available to them in culture. Our objective was to evaluate the developmental and molecular response of bovine embryos when nutrient concentrations in the culture medium were significantly reduced. Following IVM and IVF, embryos were cultured in media containing 75, 50, and 25% (experiment 1) or 25, 12.5, and 6.25% (experiment 2) of the concentrations of nutrients (carbohydrates, amino acids, and vitamins) present in our control medium (100%). Blastocyst formation, hatching, and allocation of cells to the inner cell mass (ICM) and trophectoderm (TE) were evaluated on day 7. Although the number of TE cells was decreased (P < 0.05) when nutrient concentrations were ≤25% (73.8–124.1 cells), it was not until nutrient concentrations were reduced to 6.25% that blastocyst formation (18.3 ± 3.0%) and hatching (3.0 ± 1.3%) were inhibited (P < 0.05) compared to embryos cultured in the control medium (156.1 ± 14.1 cells, 40.0 ± 3.8%, 20.0 ± 3.1%, respectively). Inhibition of fatty acid oxidation (etomoxir) reduced (P < 0.05) blastocyst development, with more pronounced effects at lower nutrient concentrations (≤12.5%). Reducing nutrient concentrations was associated with increased activity of AMPK, decreased activity of mTOR, and altered abundance of transcripts for hexokinase 1 (HK1), carnitine palmitoyl transferase 2 (CPT2), lactate dehydrogenase A (LDHA), and pyruvate dehydrogenase kinase 1 (PDK1), consistent with an increase in glucose and fatty acid metabolism. Reduced nutrient conditions provide a unique perspective on embryo metabolism that may facilitate the optimization of culture media.

Lay summary

To support early embryo development in the first week after fertilisation, an appropriate mixture of nutrients (carbohydrates, amino acids, and vitamins) is needed in the culturing solution. However, refining these solutions to support optimal embryo health remains challenging. In this study, bovine (cow) embryos derived from abattoir material were used as a model for the development of other mammalian embryos, including humans. These embryos were cultured in the presence of 75, 50, 25, 12.5, or 6.25% of the nutrients present in control conditions (100%), which are similar to those reported for the fluids of the fallopian tubes and uterus. Embryo development was largely unaffected in the 75, 50, and 25% treatments, with some embryos developing in the presence of only 6.25% nutrients. Cow embryos are remarkably resilient to reduced concentrations of nutrients in their environment because they can utilize internal stores of fat as a source of energy.

Measurement of the Low-Energy Antideuteron Inelastic Cross Section

In this Letter, we report the first measurement of the inelastic cross section for antideuteron-nucleus interactions at low particle momenta, covering a range of 0.3≤p<4  GeV/c. The measurement is carried out using p-Pb collisions at a center-of-mass energy per nucleon-nucleon pair of sqrt[s_{NN}]=5.02  TeV, recorded with the ALICE detector at the CERN LHC and utilizing the detector material as an absorber for antideuterons and antiprotons. The extracted raw primary antiparticle-to-particle ratios are compared to the results from detailed ALICE simulations based on the geant4 toolkit for the propagation of (anti)particles through the detector material. The analysis of the raw primary (anti)proton spectra serves as a benchmark for this study, since their hadronic interaction cross sections are well constrained experimentally. The first measurement of the inelastic cross section for antideuteron-nucleus interactions averaged over the ALICE detector material with atomic mass numbers ⟨A⟩=17.4 and 31.8 is obtained. The measured inelastic cross section points to a possible excess with respect to the Glauber model parametrization used in geant4 in the lowest momentum interval of 0.3≤p<0.47  GeV/c up to a factor 2.1. This result is relevant for the understanding of antimatter propagation and the contributions to antinuclei production from cosmic ray interactions within the interstellar medium. In addition, the momentum range covered by this measurement is of particular importance to evaluate signal predictions for indirect dark-matter searches.

Probing the Effects of Strong Electromagnetic Fields with Charge-Dependent Directed Flow in Pb-Pb Collisions at the LHC

The first measurement at the LHC of charge-dependent directed flow (v_{1}) relative to the spectator plane is presented for Pb-Pb collisions at sqrt[s_{NN}]=5.02  TeV. Results are reported for charged hadrons and D^{0} mesons for the transverse momentum intervals p_{T}>0.2  GeV/c and 3<p_{T}<6  GeV/c in the 5%-40% and 10%-40% centrality classes, respectively. The difference between the positively and negatively charged hadron v_{1} has a positive slope as a function of pseudorapidity η, dΔv_{1}/dη=[1.68±0.49(stat)±0.41(syst)]×10^{-4}. The same measurement for D^{0} and D[over ¯]^{0} mesons yields a positive value dΔv_{1}/dη=[4.9±1.7(stat)±0.6(syst)]×10^{-1}, which is about 3 orders of magnitude larger than the one of the charged hadrons. These measurements can provide new insights into the effects of the strong electromagnetic field and the initial tilt of matter created in noncentral heavy ion collisions on the dynamics of light (u, d, and s) and heavy (c) quarks. The large difference between the observed Δv_{1} of charged hadrons and D^{0} mesons may reflect different sensitivity of the charm and light quarks to the early time dynamics of a heavy ion collision. These observations challenge some recent theoretical calculations, which predicted a negative and an order of magnitude smaller value of dΔv_{1}/dη for both light flavor and charmed hadrons.

Evidence of Spin-Orbital Angular Momentum Interactions in Relativistic Heavy-Ion Collisions

The first evidence of spin alignment of vector mesons (K^{*0} and ϕ) in heavy-ion collisions at the Large Hadron Collider (LHC) is reported. The spin density matrix element ρ_{00} is measured at midrapidity (|y|<0.5) in Pb-Pb collisions at a center-of-mass energy (sqrt[s_{NN}]) of 2.76 TeV with the ALICE detector. ρ_{00} values are found to be less than 1/3 (1/3 implies no spin alignment) at low transverse momentum (p_{T}<2  GeV/c) for K^{*0} and ϕ at a level of 3σ and 2σ, respectively. No significant spin alignment is observed for the K_{S}^{0} meson (spin=0) in Pb-Pb collisions and for the vector mesons in pp collisions. The measured spin alignment is unexpectedly large but qualitatively consistent with the expectation from models which attribute it to a polarization of quarks in the presence of angular momentum in heavy-ion collisions and a subsequent hadronization by the process of recombination.

Scattering Studies with Low-Energy Kaon-Proton Femtoscopy in Proton-Proton Collisions at the LHC

The study of the strength and behavior of the antikaon-nucleon (K[over ¯]N) interaction constitutes one of the key focuses of the strangeness sector in low-energy quantum chromodynamics (QCD). In this Letter a unique high-precision measurement of the strong interaction between kaons and protons, close and above the kinematic threshold, is presented. The femtoscopic measurements of the correlation function at low pair-frame relative momentum of (K^{+}p⊕K^{-}p[over ¯]) and (K^{-}p⊕K^{+}p[over ¯]) pairs measured in pp collisions at sqrt[s]=5, 7, and 13 TeV are reported. A structure observed around a relative momentum of 58  MeV/c in the measured correlation function of (K^{-}p⊕K^{+}p[over ¯]) with a significance of 4.4σ constitutes the first experimental evidence for the opening of the (K[over ¯]^{0}n⊕K^{0}n[over ¯]) isospin breaking channel due to the mass difference between charged and neutral kaons. The measured correlation functions have been compared to Jülich and Kyoto models in addition to the Coulomb potential. The high-precision data at low relative momenta presented in this work prove femtoscopy to be a powerful complementary tool to scattering experiments and provide new constraints above the K[over ¯]N threshold for low-energy QCD chiral models.

Measurement of ϒ(1S) Elliptic Flow at Forward Rapidity in Pb-Pb Collisions at sqrt[s_{NN}]=5.02 TeV

The first measurement of the ϒ(1S) elliptic flow coefficient (v_{2}) is performed at forward rapidity (2.5<y<4) in Pb-Pb collisions at sqrt[s_{NN}]=5.02  TeV with the ALICE detector at the LHC. The results are obtained with the scalar product method and are reported as a function of transverse momentum (p_{T}) up to 15  GeV/c in the 5%-60% centrality interval. The measured ϒ(1S)v_{2} is consistent with 0 and with the small positive values predicted by transport models within uncertainties. The v_{2} coefficient in 2<p_{T}<15  GeV/c is lower than that of inclusive J/ψ mesons in the same p_{T} interval by 2.6 standard deviations. These results, combined with earlier suppression measurements, are in agreement with a scenario in which the ϒ(1S) production in Pb-Pb collisions at LHC energies is dominated by dissociation limited to the early stage of the collision, whereas in the J/ψ case there is substantial experimental evidence of an additional regeneration component.

Investigations of Anisotropic Flow Using Multiparticle Azimuthal Correlations in pp, p-Pb, Xe-Xe, and Pb-Pb Collisions at the LHC

Measurements of anisotropic flow coefficients (v_{n}) and their cross-correlations using two- and multiparticle cumulant methods are reported in collisions of pp at sqrt[s]=13  TeV, p-Pb at a center-of-mass energy per nucleon pair sqrt[s_{NN}]=5.02  TeV, Xe-Xe at sqrt[s_{NN}]=5.44  TeV, and Pb-Pb at sqrt[s_{NN}]=5.02  TeV recorded with the ALICE detector. The multiplicity dependence of v_{n} is studied in a very wide range from 20 to 3000 particles produced in the midrapidity region |η|<0.8 for the transverse momentum range 0.2<p_{T}<3.0  GeV/c. An ordering of the coefficients v_{2}>v_{3}>v_{4} is found in pp and p-Pb collisions, similar to that seen in large collision systems, while a weak v_{2} multiplicity dependence is observed relative to nucleus-nucleus collisions in the same multiplicity range. Using a novel subevent method, v_{2} measured with four-particle cumulants is found to be compatible with that from six-particle cumulants in pp and p-Pb collisions. The magnitude of the correlation between v_{n}^{2} and v_{m}^{2}, evaluated with the symmetric cumulants SC(m,n) is observed to be positive at all multiplicities for v_{2} and v_{4}, while for v_{2} and v_{3} it is negative and changes sign for multiplicities below 100, which may indicate a different v_{n} fluctuation pattern in this multiplicity range. The observed long-range multiparticle azimuthal correlations in high multiplicity pp and p-Pb collisions can neither be described by pythia 8 nor by impact-parameter-Glasma, music, and ultrarelativistic quantum molecular dynamics model calculations, and hence, provide new insights into the understanding of collective effects in small collision systems.

First Observation of an Attractive Interaction between a Proton and a Cascade Baryon

This Letter presents the first experimental observation of the attractive strong interaction between a proton and a multistrange baryon (hyperon) Ξ^{-}. The result is extracted from two-particle correlations of combined p-Ξ^{-}⊕p[over ¯]-Ξ[over ¯]^{+} pairs measured in p-Pb collisions at sqrt[s_{NN}]=5.02  TeV at the LHC with ALICE. The measured correlation function is compared with the prediction obtained assuming only an attractive Coulomb interaction and a standard deviation in the range [3.6, 5.3] is found. Since the measured p-Ξ^{-}⊕p[over ¯]-Ξ[over ¯]^{+} correlation is significantly enhanced with respect to the Coulomb prediction, the presence of an additional, strong, attractive interaction is evident. The data are compatible with recent lattice calculations by the HAL-QCD Collaboration, with a standard deviation in the range [1.8, 3.7]. The lattice potential predicts a shallow repulsive Ξ^{-} interaction within pure neutron matter and this implies stiffer equations of state for neutron-rich matter including hyperons. Implications of the strong interaction for the modeling of neutron stars are discussed.

Magnetocaloric effects from an interplay of magnetic sublattices in Nd2NiMnO6

We present a combined experimental and theoretical study to understand the magnetism and magnetocaloric behavior of the double perovskite Nd₂NiMnO₆. The magnetic susceptibility data confirms a ferromagnetic transition with [Formula: see text] K. An additional feature at T  =  25 K, indicative of antiferromagnetic correlations, is present. A positive magnetocaloric effect (MCE) near [Formula: see text] and a negative MCE around T  =  25 K is inferred from the temperature dependence of the change in magnetic entropy at low magnetic fields. The negative MCE peak is suppressed on the application of a magnetic field and can be made to switch to a conventional positive MCE upon increasing magnetic field. We understand and reproduce these features in Monte Carlo simulations of a phenomenological Heisenberg model for Nd₂NiMnO₆. The validity of the model is tested using density functional theory calculations. We argue that this simple understanding of the experimental observations in terms of two antiferromagnetically coupled sublattices allows these results to be useful across a broader class of magnetocaloric materials.

PI3K inhibition enhances the anti-tumor effect of eribulin in triple negative breast cancer

Loss of the tumor suppressor phosphatase and tensin homolog (PTEN) is commonly observed in triple negative breast cancer (TNBC), leading to activation of the phosphoinositide 3-kinase (PI3K) signaling to promote tumor cell growth and chemotherapy resistance. In this study, we investigated whether adding a pan-PI3K inhibitor could improve the cytotoxic effect of eribulin, a non-taxane microtubule inhibitor, in TNBC patient-derived xenograft models (PDX) with loss of PTEN, and the underlying molecular mechanisms. Three TNBC-PDX models (WHIM6, WHIM12 and WHIM21), all with loss of PTEN expression, were tested for their response to BKM120 and eribulin, alone or in combination in vivo. In addition, the effect of drug treatment on cell proliferation and cell cycle progression were also performed in vitro using a panel of TNBC cell lines, including 2 derived from PDX models. The combination of eribulin and BKM120 led to additive or synergistic anti-tumor effect in 2 of the 3 PDX models, accompanied by an enhanced mitotic arrest and apoptosis in sensitive PDX models. In addition, the combination was synergistic in reducing mammosphere formation, and markers for epithelial-mesenchymal transition (EMT). In conclusion, PI3K inhibition induces synergistic anti-tumor effect when combined with eribulin, by enhancing mitotic arrest and apoptosis, as well as, reducing the cancer stem cell population. This study provides a preclinical rationale to investigate the therapeutic potential for the combination of PI3K inhibition and eribulin in the difficult to treat TNBC. Further studies are needed to identify the biomarkers of response for target patient selection.

Azimuthal Anisotropy of Heavy-Flavor Decay Electrons in p-Pb Collisions at sqrt[s_{NN}]=5.02 TeV

Angular correlations between heavy-flavor decay electrons and charged particles at midrapidity (|η|<0.8) are measured in p-Pb collisions at sqrt[s_{NN}]=5.02  TeV. The analysis is carried out for the 0%-20% (high) and 60%-100% (low) multiplicity ranges. The jet contribution in the correlation distribution from high-multiplicity events is removed by subtracting the distribution from low-multiplicity events. An azimuthal modulation remains after removing the jet contribution, similar to previous observations in two-particle angular correlation measurements for light-flavor hadrons. A Fourier decomposition of the modulation results in a positive second-order coefficient (v_{2}) for heavy-flavor decay electrons in the transverse momentum interval 1.5<p_{T}<4  GeV/c in high-multiplicity events, with a significance larger than 5σ. The results are compared with those of charged particles at midrapidity and those of inclusive muons at forward rapidity. The v_{2} measurement of open heavy-flavor particles at midrapidity in small collision systems could provide crucial information to help interpret the anisotropies observed in such systems.

Abstract P3-10-18: Elucidating the role of functional signal transduction pathway activity in sensitivity and response of triple negative breast cancer to PI3K inhibition

Introduction

The PI3K signaling pathway is frequently active in triple negative breast cancer (TNBC), but response to PI3K inhibition is still poorly understood. To gain insights in therapy response and resistance, it is important not only to assess genetic alterations of these tumors, but also their phenotypic characteristics. Furthermore, not only is the functional status of the PI3K pathway important to know, but also other signal transduction pathways that may drive tumor growth, as they may explain primary or acquired therapy resistance.

Material & Method

We analyzed 17 patient derived xenograft (PDX) models of TNBC with varying response to buparlisib treatment. Long-term response (˜30 days) was assessed by comparing growth rates between buparlisib and vehicle treated PDXs. For characterization, mRNA expression analysis was performed on tumor material post 3 days of vehicle or buparlisib treatment of each PDX model. Functional pathway activity was determined using computational Bayesian networks that look at mRNA levels of pathway target genes resulting from activation (Verhaegh et al, Cancer Res 2014), amongst others for the FOXO-PI3K (van Ooijen et al, Am J Pathol, in press), ER, AR, Hedgehog, TGFbeta and Wnt pathways. These computational networks were calibrated on samples with known pathway activity, and biologically validated on various healthy and diseased cell and tissue types.

Results

On an initial set of 6 PDX models, pathway activity clearly varied between different TNBC PDXs, and between vehicle and buparlisib treatment. ER pathway activity was low in all samples, as expected in TNBC. Two PDX models with the most growth reduction by buparlisib showed high PI3K activity, of which one based on low FOXO activity and the other on oxidative stress. The former, best responding PDX showed a clear reduction in PI3K activity (restoring FOXO activity), when comparing 3 days buparlisib to vehicle treatment. Of the two PDX models with least growth reduction, one had low PI3K activity, while the other one, carrying a PIK3CA mutation, did show high PI3K activity (low FOXO), but this remained after treatment.

Other differences in pathway activity that were found, included slightly elevated AR and Wnt activity in one PDX with good response, and somewhat higher TGFbeta activity in four PDXs (good, medium and poor response). Analysis of the remaining 11 PDXs is ongoing, including other signal transduction pathways, to investigate the variation in pathway activity across the entire panel and to shed more light on the differences in tumor biology between the PDX models.

Conclusion

Our computational Bayesian networks measured differences in functional activity of signal transduction pathways across a collection of TNBC PDX models, which may be expected due to the large variation between TNBC tumors. Functional PI3K activity was related to growth inhibition by buparlisib treatment, and reduction of PI3K pathway activity was observed upon treatment in responding PDX models. Other pathways also showed variation across PDXs. Further clinical evaluation of our signal transduction pathway activity measurement is ongoing. RT-qPCR based analysis is available, optimized for FFPE tissue and small samples.

Citation Format: Guo Z, Verhaegh W, Hoog J, Rajput S, van Strijp D, van de Stolpe A, Li S, Ma C. Elucidating the role of functional signal transduction pathway activity in sensitivity and response of triple negative breast cancer to PI3K inhibition [abstract]. In: Proceedings of the 2018 San Antonio Breast Cancer Symposium; 2018 Dec 4-8; San Antonio, TX. Philadelphia (PA): AACR; Cancer Res 2019;79(4 Suppl):Abstract nr P3-10-18.

127 Temporal regulation of molecular pathways, metabolic enzymes and growth factor receptors during bovine oocyte maturation in vitro

Although great efforts have been made to improve in vitro oocyte maturation (IVM) medium, we have yet to achieve competence equivalent to in vivo-matured oocytes. The failure in development of culture conditions for IVM yielding high quality eggs is attributed to an incomplete understanding of molecular pathways regulating oocyte and cumulus cell metabolism. The objective of the present study was to characterise the expression and functional activity of cell signalling pathways (mTOR, AKT, 4EBP1, ERK1/2), metabolic enzymes (PKM2, PDH, LDHA, AMPK), and growth factor receptors (IGF1R, IGFIIR, EGFR, FGFR1) in bovine oocytes and cumulus cells before and after in vitro maturation. In vitro-derived cumulus-oocyte complexes were collected at germinal vesicle (GV) and metaphase II (MII) stages (20 cumulus-oocyte complexes per stage; n=3 replicates) and subjected separately to Western blot analysis using antibodies against both phosphorylated (p) and total (t) protein abundance; the ratio p:t was used to determine the activity of each pathway. Results demonstrate increased (P&lt;0.05) mTOR and ERK1/2 signalling, with no change in AKT and 4EBP1 activity, in oocytes during IVM. We observed increased (P&lt;0.05) abundance of oocyte t-ERK from the GV to MII stage, but total expression of AKT, mTOR and 4EBP1 did not change. In cumulus cells, there was a significant (P&lt;0.05) reduction in mTOR and 4EBP1, an increase in AKT, and no significant change in ERK activity. Analysis of metabolic enzymes in oocytes demonstrated increased (P&lt;0.05) PDH, reduced AMPK, and unchanged PKM2 and LDHA phosphorylation during IVM. However, increased expression of t-PKM2 abundance was observed from the GV to MII stage. In cumulus cells, tAMPK abundance was reduced (P&gt;0.05), but no significant change was observed in the activity of other metabolic enzymes analysed during IVM. Finally, we observed abundant expression of IGF2R in the oocyte compared with other growth factor receptors analysed, although IGF2R was significantly (P&lt;0.05) reduced from GV to MII oocytes. In cumulus cells, both IGF1R and IGF2R were highly abundant compared with EGFR and FGFR but did not change during IVM. Data were analysed using one-way ANOVA. Results suggest that regulatory mechanisms including AKT/mTOR/4EBP1 and ERK are entirely different in oocytes and cumulus cells during maturation. An increase in the inhibitory phosphorylation of oocyte PDH (S293) toward the end of maturation suggests low metabolism of pyruvate via the Krebs cycle at that time. Similarly, dephosphorylation of AMPK (T172) suggests reduced AMPK activity and reduced fatty acid oxidation in mature oocytes. In addition, temporal regulation of IGF1R in the oocyte and EGFR in cumulus cells suggests an important role for these growth factor receptors during maturation and that these growth factors could be used to improve IVM medium in the bovine. Collectively, these results increase our understanding of the molecular pathways regulating oocyte metabolism during maturation and provide a strategy to improve the IVM environment for assisted reproductive technology.

79 CRISPR gene editing in bovine zygotes — mutation confirmation by integration of protein expression and DNA sequencing analyses

Confirmation of gene editing in livestock following CRISPR/Cas9 zygotic microinjection is often limited to either protein expression or gene sequencing analyses of unfixed embryos, but not both, due to the challenges of extracting DNA from fixed samples suitable for genotyping. Bovine embryos have been derived from gene-edited cell lines to screen for mutations followed by nuclear transfer, but these techniques limit embryo production efficiency, include technical challenges, and alter physiological relevance. Herein we report an integrative approach to evaluate both protein expression and the genotype of individual, fixed bovine embryos subjected to CRISPR/Cas9 microinjection. Bovine zygotes were derived from IVF and parthenogenetic activation of in vitro-matured oocytes followed by intracytoplasmic injection of CRISPR/Cas9 targeting embryonic POU5F1. Embryos were cultured for 7 days and fixed in 4% paraformaldehyde and stored at 5°C for up to 4 weeks. Fixed embryos were first subjected to immunohistochemistry to determine POU5F1 mutation success by protein expression. Binder reinforcement labels were affixed to glass slides as a substitute for adhesive spacers. Single embryos were added to 9µL of PBS with a coverslip for imaging. Individual embryos were then recovered and placed in 10µL of QuickExtract (Lucigen, Middleton, WI, USA) for DNA extraction by heating samples to 65°C for 6min and 95°C for 2min. Two rounds of PCR were applied to templates in 20-µL reactions consisting of 10µL of GoTaq Hot Start Green Master Mix (2×; Promega, Madison, WI, USA) with the addition of 0.4µL (10µM) of forward and reverse primer each and 9.2µL of template. The second PCR reaction contained 5µL of PCR product from the first reaction, nested primers, and 4.2µL of H2O. The PCR conditions were |95°C, 3 min| and 35 cycles of |95°C, 30s |56°C, 30 s|72°C, 30 s|72°C, 7 min|. The PCR product was run on an agarose gel to confirm DNA amplification of a single band, and the remainder was purified (QIAquick PCR Purification Kit, Qiagen, Hilden, Germany) and submitted (100ng) for Sanger sequencing. The CRISPR-injected embryos were aligned to wild-type embryo sequences using SnapGene (http://www.snapgene.com/) and TIDE software (https://tide.nki.nl/). Both DNA extraction (n=18/19) and Sanger sequencing (n=19/23) proved highly efficient and repeatable (83 and 95%, respectively). These methods provide an efficient, cost effective, and reproducible approach for confirmation of CRISPR gene editing in individual and fixed bovine embryos by both protein expression and gene sequencing. In addition, these techniques complement the production of gene editing in livestock after zygotic CRISPR microinjection by conclusively determining mutation efficiency through both proteomic and genomic analyses. This research was supported by a USDA NIFA AFRI ELI Postdoctoral Fellowship 2016-67012-25254 to BWD and NIFA multistate research project W3171 to PJR. BD is currently supported by a grant from the Eunice Kennedy Shiver National Institute of Child Health and Human Development of the National Institutes of Health under the award numbers T32HD087166.

Embryonic POU5F1 is Required for Expanded Bovine Blastocyst Formation

POU5F1 is a transcription factor and master regulator of cell pluripotency with indispensable roles in early embryo development and cell lineage specification. The role of embryonic POU5F1 in blastocyst formation and cell lineage specification differs between mammalian species but remains completely unknown in cattle. The CRISPR/Cas9 system was utilized for targeted disruption of the POU5F1 gene by direct injection into zygotes. Disruption of the bovine POU5F1 locus prevented blastocyst formation and was associated with embryonic arrest at the morula stage. POU5F1 knockout morulas developed at a similar rate as control embryos and presented a similar number of blastomeres by day 5 of development. Initiation of SOX2 expression by day 5 of development was not affected by lack of POU5F1. On the other hand, CDX2 expression was aberrant in embryos lacking POU5F1. Notably, the phenotype observed in bovine POU5F1 knockout embryos reveals conserved functions associated with loss of human embryonic POU5F1 that differ from Pou5f1- null mice. The similarity observed in transcriptional regulation of early embryo development between cattle and humans combined with highly efficient gene editing techniques make the bovine a valuable model for human embryo biology with expanded applications in agriculture and assisted reproductive technologies.

Mass Spectrometry-Based Proteomics Reveals Potential Roles of NEK9 and MAP2K4 in Resistance to PI3K Inhibition in Triple-Negative Breast Cancers

Activation of PI3K signaling is frequently observed in triple-negative breast cancer (TNBC), yet PI3K inhibitors have shown limited clinical activity. To investigate intrinsic and adaptive mechanisms of resistance, we analyzed a panel of patient-derived xenograft models of TNBC with varying responsiveness to buparlisib, a pan-PI3K inhibitor. In a subset of patient-derived xenografts, resistance was associated with incomplete inhibition of PI3K signaling and upregulated MAPK/MEK signaling in response to buparlisib. Outlier phosphoproteome and kinome analyses identified novel candidates functionally important to buparlisib resistance, including NEK9 and MAP2K4. Knockdown of NEK9 or MAP2K4 reduced both baseline and feedback MAPK/MEK signaling and showed synthetic lethality with buparlisib in vitro A complex in/del frameshift in PIK3CA decreased sensitivity to buparlisib via NEK9/MAP2K4-dependent mechanisms. In summary, our study supports a role for NEK9 and MAP2K4 in mediating buparlisib resistance and demonstrates the value of unbiased omic analyses in uncovering resistance mechanisms to targeted therapy.Significance: Integrative phosphoproteogenomic analysis is used to determine intrinsic resistance mechanisms of triple-negative breast tumors to PI3K inhibition. Cancer Res; 78(10); 2732-46. ©2018 AACR.

D-Meson Azimuthal Anisotropy in Midcentral Pb-Pb Collisions at sqrt[s]_{NN}=5.02 TeV

The azimuthal anisotropy coefficient v_{2} of prompt D^{0}, D^{+}, D^{*+}, and D_{s}^{+} mesons was measured in midcentral (30%-50% centrality class) Pb-Pb collisions at a center-of-mass energy per nucleon pair sqrt[s_{NN}]=5.02  TeV, with the ALICE detector at the LHC. The D mesons were reconstructed via their hadronic decays at midrapidity, |y|<0.8, in the transverse momentum interval 1<p_{T}<24  GeV/c. The measured D-meson v_{2} has similar values as that of charged pions. The D_{s}^{+} v_{2}, measured for the first time, is found to be compatible with that of nonstrange D mesons. The measurements are compared with theoretical calculations of charm-quark transport in a hydrodynamically expanding medium and have the potential to constrain medium parameters.

J/ψ Elliptic Flow in Pb-Pb Collisions at sqrt[s_{NN}]=5.02 TeV

We report a precise measurement of the J/ψ elliptic flow in Pb-Pb collisions at sqrt[s_{NN}]=5.02  TeV with the ALICE detector at the LHC. The J/ψ mesons are reconstructed at midrapidity (|y|<0.9) in the dielectron decay channel and at forward rapidity (2.5<y<4.0) in the dimuon channel, both down to zero transverse momentum. At forward rapidity, the elliptic flow v_{2} of the J/ψ is studied as a function of the transverse momentum and centrality. A positive v_{2} is observed in the transverse momentum range 2<p_{T}<8  GeV/c in the three centrality classes studied and confirms with higher statistics our earlier results at sqrt[s_{NN}]=2.76  TeV in semicentral collisions. At midrapidity, the J/ψ  v_{2} is investigated as a function of the transverse momentum in semicentral collisions and found to be in agreement with the measurements at forward rapidity. These results are compared to transport model calculations. The comparison supports the idea that at low p_{T} the elliptic flow of the J/ψ originates from the thermalization of charm quarks in the deconfined medium but suggests that additional mechanisms might be missing in the models.

Anomalous Evolution of the Near-Side Jet Peak Shape in Pb-Pb Collisions at sqrt[s_{NN}]=2.76 TeV

The measurement of two-particle angular correlations is a powerful tool to study jet quenching in a p_{T} region inaccessible by direct jet identification. In these measurements pseudorapidity (Δη) and azimuthal (Δφ) differences are used to extract the shape of the near-side peak formed by particles associated with a higher p_{T} trigger particle (1<p_{T,trig}<8  GeV/c). A combined fit of the near-side peak and long-range correlations is applied to the data allowing the extraction of the centrality evolution of the peak shape in Pb-Pb collisions at sqrt[s_{NN}]=2.76  TeV. A significant broadening of the peak in the Δη direction at low p_{T} is found from peripheral to central collisions, which vanishes above 4  GeV/c, while in the Δφ direction the peak is almost independent of centrality. For the 10% most central collisions and 1<p_{T,assoc}<2  GeV/c, 1<p_{T,trig}<3  GeV/c a novel feature is observed: a depletion develops around the center of the peak. The results are compared to pp collisions at the same center of mass energy and ampt model simulations. The comparison to the investigated models suggests that the broadening and the development of the depletion is connected to the strength of radial and longitudinal flow.

Abstract 1078: Dinaciclib overcomes resistance to BKM120 in triple negative breast cancer patient-derived xenograft models

Purpose: Triple negative breast cancer (TNBC) is one of the most lethal subtypes of breast cancer with limited therapeutic options. Development of molecularly targeted agents for TNBC is an unmet clinical need. The phosphoinositide 3-kinase (PI3K) pathway, which is a major cell growth and survival pathway, is frequently activated in TNBC as a result of genetic aberrations such as loss of the negative regulator PTEN or gain of function mutations in PIK3CA, therefore an attractive therapeutic target. However, single agent PI3K inhibitors have shown limited anti-tumor activity in both preclinical models and in clinical trials. One of the most important mechanisms of resistance to PI3K inhibitor is amplification of Myc. Dinaciclib, a potent inhibitor of cyclin-dependent kinases (CDKs)1, 2, 5 and 9, has shown to be particularly effective in Myc dependent tumors in preclinical studies and in TNBC. We therefore hypothesized that dinaciclib could overcome tumor cell resistance to PI3K inhibitors and improve the therapeutic efficacy in TNBC. In this study, we evaluated the anti-tumor and molecular effect of dinaciclib and BKM120 (Pan-PI3K inhibitor), either alone or in combination, in a panel of patient derived xenograft (PDX) models of TNBC.

Methods: Four TNBC PDXs models were selected for the study for in-vivo and ex-vivo response to vehicle, BKM120, dinaciclib, or the combination of BKM120 and dinaciclib. Tumor volume changes over time in each group were documented to calculate the percentage of tumor growth inhibition by either agent alone or in combination. Tumor tissues harvested post treatment were examined by immunohistochemistry for cleaved PARP to determine the extent of apoptosis and phospho-Histone H3 for G2 to M phase cell cycle progression. Western blot analysis and reverse protein phase array (RPPA) were also performed to determine treatment effect on PI3K downstream targets and cell cycle molecules.

Results: The combination of BKM120 and dinaciclib induced significantly greater growth inhibitory effect on tumor growth than either single agent alone in TNBC PDX models. This is accompanied by an enhanced apoptotic induction and reduced cell cycle progression. In addition, the combination of dinaciclib and BKM120 significantly reduced the level of cyclin B and the key anti-apoptotic protein survivin as well as significant downregulation of pAKT, and pS6.

Conclusions: These data suggest that dinaciclib and BKM120 combination is an effective approach in treating TNBC. Additional mechanistic investigation for the efficacy of this combination is underway.

Citation Format: Sandeep Rajput, Fang Guo, Li Shun, Cynthia Ma. Dinaciclib overcomes resistance to BKM120 in triple negative breast cancer patient-derived xenograft models [abstract]. In: Proceedings of the American Association for Cancer Research Annual Meeting 2017; 2017 Apr 1-5; Washington, DC. Philadelphia (PA): AACR; Cancer Res 2017;77(13 Suppl):Abstract nr 1078. doi:10.1158/1538-7445.AM2017-1078

Energy dependence of forward-rapidity [Formula: see text] and [Formula: see text] production in pp collisions at the LHC

We present results on transverse momentum ([Formula: see text]) and rapidity ([Formula: see text]) differential production cross sections, mean transverse momentum and mean transverse momentum square of inclusive [Formula: see text] and [Formula: see text] at forward rapidity ([Formula: see text]) as well as [Formula: see text]-to-[Formula: see text] cross section ratios. These quantities are measured in pp collisions at center of mass energies [Formula: see text] and 13 TeV with the ALICE detector. Both charmonium states are reconstructed in the dimuon decay channel, using the muon spectrometer. A comprehensive comparison to inclusive charmonium cross sections measured at [Formula: see text], 7 and 8 TeV is performed. A comparison to non-relativistic quantum chromodynamics and fixed-order next-to-leading logarithm calculations, which describe prompt and non-prompt charmonium production respectively, is also presented. A good description of the data is obtained over the full [Formula: see text] range, provided that both contributions are summed. In particular, it is found that for [Formula: see text] GeV/c the non-prompt contribution reaches up to 50% of the total charmonium yield.

Production of Σ(1385)± and Ξ(1530)0 in p-Pb collisions at sNN=5.02 TeV

The transverse momentum distributions of the strange and double-strange hyperon resonances (Σ ( 1385 ) ± , Ξ ( 1530 ) 0 ) produced in p-Pb collisions at s NN = 5.02 TeV were measured in the rapidity range - 0.5 < y CMS < 0 for event classes corresponding to different charged-particle multiplicity densities, ⟨ dN ch /dη lab ⟩ . The mean transverse momentum values are presented as a function of ⟨ dN ch /dη lab ⟩ , as well as a function of the particle masses and compared with previous results on hyperon production. The integrated yield ratios of excited to ground-state hyperons are constant as a function of ⟨ dN ch /dη lab ⟩ . The equivalent ratios to pions exhibit an increase with ⟨ dN ch /dη lab ⟩ , depending on their strangeness content.

Production of [Formula: see text] and [Formula: see text] mesons up to high transverse momentum in pp collisions at 2.76 TeV

The invariant differential cross sections for inclusive [Formula: see text] and [Formula: see text] mesons at midrapidity were measured in pp collisions at [Formula: see text] TeV for transverse momenta [Formula: see text] GeV/c and [Formula: see text] GeV/c, respectively, using the ALICE detector. This large range in [Formula: see text] was achieved by combining various analysis techniques and different triggers involving the electromagnetic calorimeter (EMCal). In particular, a new single-cluster, shower-shape based method was developed for the identification of high-[Formula: see text] neutral pions, which exploits that the showers originating from their decay photons overlap in the EMCal. Above 4 GeV/[Formula: see text], the measured cross sections are found to exhibit a similar power-law behavior with an exponent of about 6.3. Next-to-leading-order perturbative QCD calculations differ from the measured cross sections by about 30% for the [Formula: see text], and between 30-50% for the [Formula: see text] meson, while generator-level simulations with PYTHIA 8.2 describe the data to better than 10-30%, except at [Formula: see text] GeV/[Formula: see text]. The new data can therefore be used to further improve the theoretical description of [Formula: see text] and [Formula: see text] meson production.

Flow Dominance and Factorization of Transverse Momentum Correlations in Pb-Pb Collisions at the LHC

We present the first measurement of the two-particle transverse momentum differential correlation function, P_{2}≡⟨Δp_{T}Δp_{T}⟩/⟨p_{T}⟩^{2}, in Pb-Pb collisions at sqrt[s_{NN}]=2.76  TeV. Results for P_{2} are reported as a function of the relative pseudorapidity (Δη) and azimuthal angle (Δφ) between two particles for different collision centralities. The Δϕ dependence is found to be largely independent of Δη for |Δη|≥0.9. In the 5% most central Pb-Pb collisions, the two-particle transverse momentum correlation function exhibits a clear double-hump structure around Δφ=π (i.e., on the away side), which is not observed in number correlations in the same centrality range, and thus provides an indication of the dominance of triangular flow in this collision centrality. Fourier decompositions of P_{2}, studied as a function of the collision centrality, show that correlations at |Δη|≥0.9 can be well reproduced by a flow ansatz based on the notion that measured transverse momentum correlations are strictly determined by the collective motion of the system.

Measurement of azimuthal correlations of D mesons with charged particles in pp collisions at [Formula: see text] TeV and p-Pb collisions at [Formula: see text] TeV

The azimuthal correlations of D mesons with charged particles were measured with the ALICE apparatus in pp collisions at [Formula: see text] and p-Pb collisions at [Formula: see text] at the Large Hadron Collider. [Formula: see text], [Formula: see text], and [Formula: see text] mesons and their charge conjugates with transverse momentum [Formula: see text] and rapidity in the nucleon-nucleon centre-of-mass system [Formula: see text] (pp collisions) and [Formula: see text] (p-Pb collisions) were correlated to charged particles with [Formula: see text]. The yield of charged particles in the correlation peak induced by the jet containing the D meson and the peak width are compatible within uncertainties in the two collision systems. The data are described within uncertainties by Monte-Carlo simulations based on PYTHIA, POWHEG, and EPOS 3 event generators.

Effect of Surface Morphology and Magnetic Impurities on the Electronic Structure in Cobalt-Doped BaFe2As2 Superconductors

Combined scanning tunneling microscopy, spectroscopy, and local barrier height (LBH) studies show that low-temperature-cleaved optimally doped Ba(Fe_1-xCo_x)₂As₂ crystals with x = 0.06, with T_c = 22 K, have complicated morphologies. Although the cleavage surface and hence the morphologies are variable, the superconducting gap maps show the same gap widths and nanometer size inhomogeneities irrelevant to the morphology. Based on the spectroscopy and LBH maps, the bright patches and dark stripes in the morphologies are identified as Ba- and As-dominated surface terminations, respectively. Magnetic impurities, possibly due to Co or Fe atoms, are believed to create local in-gap state and, in addition, suppress the superconducting coherence peaks. This study will clarify the confusion on the cleavage surface terminations of the Fe-based superconductors and its relation with the electronic structures.

Correlated Event-by-Event Fluctuations of Flow Harmonics in Pb-Pb Collisions at sqrt[s_{NN}]=2.76 TeV

We report the measurements of correlations between event-by-event fluctuations of amplitudes of anisotropic flow harmonics in nucleus-nucleus collisions, obtained for the first time using a new analysis method based on multiparticle cumulants in mixed harmonics. This novel method is robust against systematic biases originating from nonflow effects and by construction any dependence on symmetry planes is eliminated. We demonstrate that correlations of flow harmonics exhibit a better sensitivity to medium properties than the individual flow harmonics. The new measurements are performed in Pb-Pb collisions at the center-of-mass energy per nucleon pair of sqrt[s_{NN}]=2.76  TeV by the ALICE experiment at the Large Hadron Collider. The centrality dependence of correlation between event-by-event fluctuations of the elliptic v_{2} and quadrangular v_{4} flow harmonics, as well as of anticorrelation between v_{2} and triangular v_{3} flow harmonics are presented. The results cover two different regimes of the initial state configurations: geometry dominated (in midcentral collisions) and fluctuation dominated (in the most central collisions). Comparisons are made to predictions from Monte Carlo Glauber, viscous hydrodynamics, ampt, and hijing models. Together with the existing measurements of the individual flow harmonics the presented results provide further constraints on the initial conditions and the transport properties of the system produced in heavy-ion collisions.