A Na pump with reduced stoichiometry is up-regulated by brine shrimp in extreme salinities

Brine shrimp (Artemia) are the only animals to thrive at sodium concentrations above 4 M. Salt excretion is powered by the Na+,K+-ATPase (NKA), a heterodimeric (αβ) pump that usually exports 3Na+ in exchange for 2 K+ per hydrolyzed ATP. Artemia express several NKA catalytic α-subunit subtypes. High-salinity adaptation increases abundance of α2KK, an isoform that contains two lysines (Lys308 and Lys758 in transmembrane segments TM4 and TM5, respectively) at positions where canonical NKAs have asparagines (Xenopus α1's Asn333 and Asn785). Using de novo transcriptome assembly and qPCR, we found that Artemia express two salinity-independent canonical α subunits (α1NN and α3NN), as well as two β variants, in addition to the salinity-controlled α2KK. These β subunits permitted heterologous expression of the α2KK pump and determination of its CryoEM structure in a closed, ion-free conformation, showing Lys758 residing within the ion-binding cavity. We used electrophysiology to characterize the function of α2KK pumps and compared it to that of Xenopus α1 (and its α2KK-mimicking single- and double-lysine substitutions). The double substitution N333K/N785K confers α2KK-like characteristics to Xenopus α1, and mutant cycle analysis reveals energetic coupling between these two residues, illustrating how α2KK's Lys308 helps to maintain high affinity for external K+ when Lys758 occupies an ion-binding site. By measuring uptake under voltage clamp of the K+-congener 86Rb+, we prove that double-lysine-substituted pumps transport 2Na+ and 1 K+ per catalytic cycle. Our results show how the two lysines contribute to generate a pump with reduced stoichiometry allowing Artemia to maintain steeper Na+ gradients in hypersaline environments.

Atroposelective Brønsted Acid-Catalyzed Photocyclization to Access Chiral N-Aryl Quinolones with Low Rotational Barriers

Herein, a novel route to atropisomeric N-aryl quinolones with low rotational barriers is demonstrated, leveraging a dual photochemical/organocatalytic approach to the required ring closure in up to 94% yield and up to >99% ee. The use of a continuous flow system allows for impurity suppression and enables rapid scale-up to a decagram scale.

Affinity and cooperativity modulate ternary complex formation to drive targeted protein degradation

Targeted protein degradation via "hijacking" of the ubiquitin-proteasome system using proteolysis targeting chimeras (PROTACs) has evolved into a novel therapeutic modality. The design of PROTACs is challenging; multiple steps involved in PROTAC-induced degradation make it difficult to establish coherent structure-activity relationships. Herein, we characterize PROTAC-mediated ternary complex formation and degradation by employing von Hippel-Lindau protein (VHL) recruiting PROTACs for two different target proteins, SMARCA2 and BRD4. Ternary-complex attributes and degradation activity parameters are evaluated by varying components of the PROTAC's architecture. Ternary complex binding affinity and cooperativity correlates well with degradation potency and initial rates of degradation. Additionally, we develop a ternary-complex structure modeling workflow to calculate the total buried surface area at the interface, which is in agreement with the measured ternary complex binding affinity. Our findings establish a predictive framework to guide the design of potent degraders.

Protein-protein interfaces in molecular glue-induced ternary complexes: classification, characterization, and prediction

Molecular glues are a class of small molecules that stabilize the interactions between proteins. Naturally occurring molecular glues are present in many areas of biology where they serve as central regulators of signaling pathways. Importantly, several clinical compounds act as molecular glue degraders that stabilize interactions between E3 ubiquitin ligases and target proteins, leading to their degradation. Molecular glues hold promise as a new generation of therapeutic agents, including those molecular glue degraders that can redirect the protein degradation machinery in a precise way. However, rational discovery of molecular glues is difficult in part due to the lack of understanding of the protein-protein interactions they stabilize. In this review, we summarize the structures of known molecular glue-induced ternary complexes and the interface properties. Detailed analysis shows different mechanisms of ternary structure formation. Additionally, we also review computational approaches for predicting protein-protein interfaces and highlight the promises and challenges. This information will ultimately help inform future approaches for rational molecular glue discovery.

Modeling the CRL4A ligase complex to predict target protein ubiquitination induced by cereblon-recruiting PROTACs

PROteolysis TArgeting Chimeras (PROTACs) are hetero-bifunctional small molecules that can simultaneously recruit target proteins and E3 ligases to form a ternary complex, promoting target protein ubiquitination and degradation via the Ubiquitin-Proteasome System (UPS). PROTACs have gained increasing attention in recent years due to certain advantages over traditional therapeutic modalities and enabling targeting of previously “undruggable” proteins. To better understand the mechanism of PROTAC-induced Target Protein Degradation (TPD), several computational approaches have recently been developed to study and predict ternary complex formation. However, mounting evidence suggests that ubiquitination can also be a rate-limiting step in PROTAC-induced TPD. Here, we propose a structure-based computational approach to predict target protein ubiquitination induced by cereblon (CRBN)-based PROTACs by leveraging available structural information of the CRL4A ligase complex (CRBN/DDB1/CUL4A/Rbx1/NEDD8/E2/Ub). We generated ternary complex ensembles with Rosetta, modeled multiple CRL4A ligase complex conformations, and predicted ubiquitination efficiency by separating the ternary ensemble into productive and unproductive complexes based on the proximity of the ubiquitin to accessible lysines on the target protein. We validated our CRL4A ligase complex models with published ternary complex structures and additionally employed our modeling workflow to predict ubiquitination efficiencies and sites of a series of cyclin-dependent kinases (CDKs) after treatment with TL12–186, a pan-kinase PROTAC. Our predictions are consistent with CDK ubiquitination and site-directed mutagenesis of specific CDK lysine residues as measured using a NanoBRET ubiquitination assay in HEK293 cells. This work structurally links PROTAC-induced ternary formation and ubiquitination, representing an important step toward prediction of target “degradability.”

Elusive Intermediate State Key in the Conversion of ATP Hydrolysis into Useful Work Driving the Ca2+ Pump SERCA

A key event in the ATP-driven transport cycle of the calcium pump sarco/endoplasmic reticulum Ca²⁺-ATPase (SERCA) occurs when autophosphorylation of the pump with two bound ions Ca²⁺ triggers a large conformational change that opens a gate on the luminal side of the membrane allowing the release of the ions. It is believed that this conformational transition proceeds through a two-step mechanism, with an initial rearrangement of the three cytoplasmic domains of the pump responsible for ATP binding and hydrolysis followed by the opening of the gate toward the luminal side in the transmembrane region. Here, molecular dynamics computation of the free energy landscapes associated with this transition show how, in response to phosphorylation, the cytoplasmic domains are partially reconfigured into an intermediate state on the path toward the E2 state with a closed luminal gate. It is suggested that the free energy associated with this conformational reorganization must subsequently be used to drive the opening of the gate on the luminal side.

Barium blockade of the KcsA channel in open and closed conformation datasets

Barium is a potent blocker of the KcsA potassium channel. A strategy using x-ray crystallography and molecular dynamics (MD) simulation has been used to understand this phenomenon as described in Rohaim et al. [1]. Wild type KcsA is purified to homogeneity and crystallized in low and high K⁺ conditions. Crystals are grown using the hanging drop vapor diffusion method. To examine barium binding in the selectivity filter of KcsA, the crystals are systemically soaked in various concentrations of barium chloride solution. X-ray crystallography datasets are collected at the Advanced Photon Source. A total of 10 datasets are collected for various barium ion concentrations. Diffraction data are processed using the crystallography pipeline software RAPID. The crystal structures are solved by molecular replacement methods. The structure models are visualized using COOT and refined using REFMAC. Anomalous map coefficients are calculated using the phenix.maps tool in the PHENIX software suite. The datasets are deposited in the Protein Data Bank. The data provides a detailed picture of barium ion interaction with potassium channels. Structural analysis of the KcsA channel reveals two distinct configurations, open- and closed- state. Further MD simulation analysis suggests an energetically favorable binding mechanism for barium ion in the selectivity filter. The data could be used to interpret functional experiments related to barium blockade for potassium channels. Also, it is valuable for comparison and cross validation with other relevant potassium channel structures.

Open and Closed Structures of a Barium-Blocked Potassium Channel

Barium (Ba²⁺) is a classic permeant blocker of potassium (K⁺) channels. The "external lock-in effect" in barium block experiments, whereby the binding of external K⁺ impedes the forward translocation of the blocker, provides a powerful avenue to investigate the selectivity of the binding sites along the pore of potassium channels. Barium block experiments show that the external lock-in site is highly selective for K⁺ over Na⁺. Wild-type KcsA was crystallized in low K⁺ conditions, and the crystals were soaked in solutions containing various concentrations of barium. Structural analysis reveals open and closed gate conformations of the KcsA channel. Anomalous diffraction experiments show that Ba²⁺ primarily binds to the innermost site S4 of the selectivity filter of the open-gate conformation and also the site S2, but no binding is detected with the closed-gate conformation. Alchemical free-energy perturbation calculations indicate that the presence of a Ba²⁺ ion in the selectivity filter boosts the specificity of K⁺ binding relative to Na⁺ in the external sites S0-S2.

Correction: Crystal structures of human procathepsin H

[This corrects the article DOI: 10.1371/journal.pone.0200374.].

Crystal Structure and Conformational Dynamics of Pyrococcus furiosus Prolyl Oligopeptidase

Enzymes in the prolyl oligopeptidase family possess unique structures and substrate specificities that are important for their biological activity and for potential biocatalytic applications. The crystal structures of Pyrococcus furiosus ( Pfu) prolyl oligopeptidase (POP) and the corresponding S477C mutant were determined to 1.9 and 2.2 Å resolution, respectively. The wild type enzyme crystallized in an open conformation, indicating that this state is readily accessible, and it contained bound chloride ions and a prolylproline ligand. These structures were used as starting points for molecular dynamics simulations of Pfu POP conformational dynamics. The simulations showed that large-scale domain opening and closing occurred spontaneously, providing facile substrate access to the active site. Movement of the loop containing the catalytically essential histidine into a conformation similar to those found in structures with fully formed catalytic triads also occurred. This movement was modulated by chloride binding, providing a rationale for experimentally observed activation of POP peptidase catalysis by chloride. Thus, the structures and simulations reported in this study, combined with existing biochemical data, provide a number of insights into POP catalysis.

Proton Countertransport and Coupled Gating in the Sarcoplasmic Reticulum Calcium Pump

The calcium pump of the sarcoplasmic reticulum (SERCA) is an ATP-driven active transporter of Ca²⁺ ions that functions via an "alternating-access" cycle mechanism. In each cycle, SERCA transports two Ca²⁺ ions toward the lumen of the sarcoplasmic reticulum and two to three protons to the cytoplasm. How the latter conformational transition is coupled to cytoplasmic release of protons remains poorly understood. The present computational study shows how the mechanism of proton countertransport is coupled to the alternating access gating process in SERCA. Molecular dynamics simulation trajectories are generated starting from a series of configurations taken along the E2 to E1 transition pathway determined by the string method with swarms-of-trajectories. Simulations of different protonation configurations at the binding sites reveal how deprotonation events affect the opening of the cytoplasmic gate. The results show that there is a strong coupling between the chronological order of deprotonation, the entry of water molecules into the TM region, and the opening of the cytoplasmic gate. Deprotonation of E309 and E771 is sequential with E309 being the first to lose the proton. The deprotonation promotes the opening of the cytoplasmic gate but leads to a productive gating transition only if it occurs after the transmembrane domain has reached an intermediate conformation. Deprotonation of E309 and E771 is unproductive when it occurs too early because it causes the re-opening of the luminal gate.

Abstract P4-09-14: Analysis of breast cancer recurrence using gene set enrichment analysis

Background: Even after successful treatment of primary breast tumors, there is a continued risk of recurrence. The risk varies between subtypes and there are ongoing efforts that aim to improve prediction of such risks for individual patients. Detection of subclinical metastases might be achieved by biomarkers in blood. In this study, we profiled protein expression in blood plasma from patients with known clinical outcome (recurrence vs no recurrence) to identify prognostic markers of breast cancer recurrence.

Methods: The subjects and specimens were made available through the Clinical Breast Care Project using IRB-approved protocols. We analyzed blood plasma samples taken at the time of diagnosis from consented patients who subsequently relapsed (33 cases) as well as those with no disease recurrence (31 controls). Based on hormone receptor and lymph node status the samples were grouped as: ER-/HER2- (17 cases/15 controls), ER+/LN+ (10/10) and ER+/LN- (6/6). We used aptamer-based SOMAscan assay platform to study the expression of 1252 proteins. We analyzed the protein expression data by using their coding genes in order to apply the Gene Set Enrichment Analysis method (GSEA v.2, Broad Institute). Pathway databases of KEGG, REACTOME, BIOCARTA and C4 collection were used. Significant gene sets were called at 5% FDR, and overlaps and low coverage gene sets (Tags <70%) were removed. Statistical analysis and clustering were done using R.

Results: Unsupervised clustering showed some difference in signal in the ER+/LN- group. Even though there was a lack of significantly differentiated proteins between the cases and controls of this group, many significant gene sets were identified. After applying the cutoff filters and removing the overlaps, there were 5 gene sets enriched with the pathway collection, involved in B-cell receptor signaling, mRNA metabolism, tight junction and SCF-KIT signaling. Similarly, 9 gene sets from the MORF compendium were differentially expressed with the C4 collection and included neighborhood genes of NME2, ACTG1, EIF3S2, AP2M1, DAP3, UBE2I, NPM1, AATF and NPM1. In contrast, neither differentially expressed proteins nor gene sets were identified from the ER+/LN+ and ER-/HER2- groups. Since the sample size of the ER+/LN- group was small, we conducted a similar analysis by randomly choosing 6 case and control samples in the other two groups respectively. There were still no differentially expressed proteins or gene sets identified above the specified cutoff parameters.

Conclusion: Using plasma protein expression data we identified underlying gene sets differentially expressed between ER+/LN- patients who had cancer recurrence and no recurrence. Many genes in these sets were already known biomarkers (e.g. PTEN, AKT1, STAT3, SET etc.). These results can be used for understanding patterns of recurrence in different cancer subtypes. Further research is needed to estimate the clinical significance of these gene products.

The views expressed in this article are those of the author and do not reflect the official policy of the Department of Army/Navy/Air Force, the Department of Defense, or U.S. Government.

Citation Format: Praveen Kumar A, Kovatich AJ, Biancotto A, Cheung F, Davidson-Moncada JK, Kvecher L, Liu J, Ru Y, Kovatich AW, Deyarmin B, Fantacone-Campbell JL, Hooke JA, Raj Kumar PK, Rui H, Hu H, Shriver CD. Analysis of breast cancer recurrence using gene set enrichment analysis [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 P4-09-14.

Locking the Elbow: Improved Antibody Fab Fragments as Chaperones for Structure Determination

Antibody Fab fragments have been exploited with significant success to facilitate the structure determination of challenging macromolecules as crystallization chaperones and as molecular fiducial marks for single particle cryo-electron microscopy approaches. However, the inherent flexibility of the "elbow" regions, which link the constant and variable domains of the Fab, can introduce disorder and thus diminish their effectiveness. We have developed a phage display engineering strategy to generate synthetic Fab variants that significantly reduces elbow flexibility, while maintaining their high affinity and stability. This strategy was validated using previously recalcitrant Fab-antigen complexes where introduction of an engineered elbow region enhanced crystallization and diffraction resolution. Furthermore, incorporation of the mutations appears to be generally portable to other synthetic antibodies and may serve as a universal strategy to enhance the success rates of Fabs as structure determination chaperones.

SmgGDS is a transient nucleolar protein that protects cells from nucleolar stress and promotes the cell cycle by regulating DREAM complex gene expression

The chaperone protein and guanine nucleotide exchange factor SmgGDS (RAP1GDS1) is a key promoter of cancer cell proliferation and tumorigenesis. SmgGDS undergoes nucleocytoplasmic shuttling, suggesting that it has both cytoplasmic and nuclear functions that promote cancer. Previous studies indicate that SmgGDS binds cytoplasmic small GTPases and promotes their trafficking to the plasma membrane. In contrast, little is known about the functions of SmgGDS in the nucleus, or how these nuclear functions might benefit cancer cells. Here we show unique nuclear localization and regulation of gene transcription pathways by SmgGDS. Strikingly, SmgGDS depletion significantly reduces expression of over 600 gene products that are targets of the DREAM complex, which is a transcription factor complex that regulates expression of proteins controlling the cell cycle. The cell cycle regulators E2F1, MYC, MYBL2 (B-Myb) and FOXM1 are among the DREAM targets that are diminished by SmgGDS depletion. E2F1 is well known to promote G1 cell cycle progression, and the loss of E2F1 in SmgGDS-depleted cells provides an explanation for previous reports that SmgGDS depletion characteristically causes a G1 cell cycle arrest. We show that SmgGDS localizes in nucleoli, and that RNAi-mediated depletion of SmgGDS in cancer cells disrupts nucleolar morphology, signifying nucleolar stress. We show that nucleolar SmgGDS interacts with the RNA polymerase I transcription factor upstream binding factor (UBF). The RNAi-mediated depletion of UBF diminishes nucleolar localization of SmgGDS and promotes proteasome-mediated degradation of SmgGDS, indicating that nucleolar sequestration of SmgGDS by UBF stabilizes SmgGDS protein. The ability of SmgGDS to interact with UBF and localize in the nucleolus is diminished by expressing DiRas1 or DiRas2, which are small GTPases that bind SmgGDS and act as tumor suppressors. Taken together, our results support a novel nuclear role for SmgGDS in protecting malignant cells from nucleolar stress, thus promoting cell cycle progression and tumorigenesis.

Gramicidin A Channel Formation Induces Local Lipid Redistribution I: Experiment and Simulation

Integral membrane protein function can be modulated by the host bilayer. Because biological membranes are diverse and nonuniform, we explore the consequences of lipid diversity using gramicidin A channels embedded in phosphatidylcholine (PC) bilayers composed of equimolar mixtures of di-oleoyl-PC and di-erucoyl-PC (dC_18:1+dC_22:1, respectively), di-palmitoleoyl-PC and di-nervonoyl-PC (dC_16:1+dC_24:1, respectively), and di-eicosenoyl-PC (pure dC_20:1), all of which have the same average bilayer chain length. Single-channel lifetime experiments, molecular dynamics simulations, and a simple lipid compression model are used in tandem to gain insight into lipid redistribution around the channel, which partially alleviates the bilayer deformation energy associated with channel formation. The average single-channel lifetimes in the two-component bilayers (95 ± 10 ms for dC_18:1+dC_22:1 and 195 ± 20 ms for dC_16:1+dC_24:1) were increased relative to the single-component dC_20:1 control bilayer (65 ± 10 ms), implying lipid redistribution. Using a theoretical treatment of thickness-dependent changes in channel lifetimes, the effective local enrichment of lipids around the channel was estimated to be 58 ± 4% dC_18:1 and 66 ± 2% dC_16:1 in the dC_18:1+dC_22:1 and dC_16:1+dC_24:1 bilayers, respectively. 3.5-μs molecular dynamics simulations show 66 ± 2% dC_16:1 in the first lipid shell around the channel in the dC_16:1+dC_24:1 bilayer, but no significant redistribution (50 ± 4% dC_18:1) in the dC_18:1+dC_22:1 bilayer; these simulated values are within the 95% confidence intervals of the experimental averages. The strong preference for the better matching lipid (dC_16:1) near the channel in the dC_16:1+dC_24:1 mixture and lesser redistribution in the dC_18:1+dC_22:1 mixture can be explained by the energetic cost associated with compressing the lipids to match the channel's hydrophobic length.

CHARMM-GUI 10 years for biomolecular modeling and simulation

CHARMM-GUI, http://www.charmm-gui.org, is a web-based graphical user interface that prepares complex biomolecular systems for molecular simulations. CHARMM-GUI creates input files for a number of programs including CHARMM, NAMD, GROMACS, AMBER, GENESIS, LAMMPS, Desmond, OpenMM, and CHARMM/OpenMM. Since its original development in 2006, CHARMM-GUI has been widely adopted for various purposes and now contains a number of different modules designed to set up a broad range of simulations: (1) PDB Reader & Manipulator, Glycan Reader, and Ligand Reader & Modeler for reading and modifying molecules; (2) Quick MD Simulator, Membrane Builder, Nanodisc Builder, HMMM Builder, Monolayer Builder, Micelle Builder, and Hex Phase Builder for building all-atom simulation systems in various environments; (3) PACE CG Builder and Martini Maker for building coarse-grained simulation systems; (4) DEER Facilitator and MDFF/xMDFF Utilizer for experimentally guided simulations; (5) Implicit Solvent Modeler, PBEQ-Solver, and GCMC/BD Ion Simulator for implicit solvent related calculations; (6) Ligand Binder for ligand solvation and binding free energy simulations; and (7) Drude Prepper for preparation of simulations with the CHARMM Drude polarizable force field. Recently, new modules have been integrated into CHARMM-GUI, such as Glycolipid Modeler for generation of various glycolipid structures, and LPS Modeler for generation of lipopolysaccharide structures from various Gram-negative bacteria. These new features together with existing modules are expected to facilitate advanced molecular modeling and simulation thereby leading to an improved understanding of the structure and dynamics of complex biomolecular systems. Here, we briefly review these capabilities and discuss potential future directions in the CHARMM-GUI development project. © 2016 Wiley Periodicals, Inc.

Conformational Transitions and Alternating-Access Mechanism in the Sarcoplasmic Reticulum Calcium Pump

Ion pumps are integral membrane proteins responsible for transporting ions against concentration gradients across biological membranes. Sarco/endoplasmic reticulum Ca2+-ATPase (SERCA), a member of the P-type ATPases family, transports two calcium ions per hydrolyzed ATP molecule via an "alternating-access" mechanism. High-resolution crystallographic structures provide invaluable insight on the structural mechanism of the ion pumping process. However, to understand the molecular details of how ATP hydrolysis is coupled to calcium transport, it is necessary to gain knowledge about the conformational transition pathways connecting the crystallographically resolved conformations. Large-scale transitions in SERCA occur at time-scales beyond the current reach of unbiased molecular dynamics simulations. Here, we overcome this challenge by employing the string method, which represents a transition pathway as a chainofstates linking two conformational endpoints. Using a multiscale methodology, we have determined all-atom transition pathways for three main conformational transitions responsible for the alternating-access mechanism. The present pathways provide a clear chronology and ordering of the key events underlying the active transport of calcium ions by SERCA. Important conclusions are that the conformational transition that leads to occlusion with bound ATP and calcium is highly concerted and cooperative, the phosphorylation of Asp351 causes areorganization of the cytoplasmic domains that subsequently drives the opening of the luminal gate, and thereclosing of luminal gate induces a shift in the cytoplasmic domains that subsequently enables the dephosphorylation of Asp351-P. Formation of transient residue-residue contacts along the conformational transitions predicted by the computations provide an experimental route to test the general validity of the computational pathways.

Serum levels of the immunomodulatory protein, the progesterone induced blocking factor (PIBF) which is found in high levels during pregnancy is not higher in women with progesterone (P) receptor (R) positive vs. negative breast cancer

PURPOSE

To determine if serum levels of the immunomodulatory protein, the progesterone induced blocking factor (PIBF), which is present in high levels during normal pregnancy, is present in higher levels in women with breast cancer positive for progesterone receptors. The study would also determine whether the presence or absence of the estrogen receptor in any way modifies PIBF expression.

MATERIALS AND METHODS

PIBF using a research ELISA was evaluated in the follicular phase in 21 women with receptor status as follows: seven with estrogen receptor (ER)+ and progesterone receptor (PR)+, seven with ER- and PR+, and seven with ER+ and PR.

RESULTS

The results showed no differences in serum PIBF in the three groups. The serum PIBF levels were no different than historical controls in the follicular phase.

CONCLUSIONS

Measurement of serum PIBF does not seem to be an important marker to use to either detect women with breast cancer or to help determine tumor virulence or potential specific therapies. If PIBF plays a role in helping cancer cells to escape immune surveillance, it seems that the intracytoplasmic PIBF would be the form most likely operative.

Structural and functional characterization of a calcium-activated cation channel from Tsukamurella paurometabola

The selectivity filter is an essential functional element of K⁺ channels that is highly conserved both in terms of its primary sequence and its three-dimensional structure. Here, we investigate the properties of an ion channel from the Gram-positive bacterium Tsukamurella paurometabola with a selectivity filter formed by an uncommon proline-rich sequence. Electrophysiological recordings show that it is a non-selective cation channel and that its activity depends on Ca²⁺ concentration. In the crystal structure, the selectivity filter adopts a novel conformation with Ca²⁺ ions bound within the filter near the pore helix where they are coordinated by backbone oxygen atoms, a recurrent motif found in multiple proteins. The binding of Ca²⁺ ion in the selectivity filter controls the widening of the pore as shown in crystal structures and in molecular dynamics simulations. The structural, functional and computational data provide a characterization of this calcium-gated cationic channel.

Tetrameric cationic channels specificity is determined by the sequence and structural conformation of their selectivity filter. Here, the authors show that a cationic channel from Tsukamurella paurometabola is non-selective due to a Ca²⁺-binding motif within its unusual proline-rich filter.

The selectivity of the Na(+)/K(+)-pump is controlled by binding site protonation and self-correcting occlusion

The Na⁺/K⁺-pump maintains the physiological K⁺ and Na⁺ electrochemical gradients across the cell membrane. It operates via an 'alternating-access' mechanism, making iterative transitions between inward-facing (E₁) and outward-facing (E₂) conformations. Although the general features of the transport cycle are known, the detailed physicochemical factors governing the binding site selectivity remain mysterious. Free energy molecular dynamics simulations show that the ion binding sites switch their binding specificity in E₁ and E₂. This is accompanied by small structural arrangements and changes in protonation states of the coordinating residues. Additional computations on structural models of the intermediate states along the conformational transition pathway reveal that the free energy barrier toward the occlusion step is considerably increased when the wrong type of ion is loaded into the binding pocket, prohibiting the pump cycle from proceeding forward. This self-correcting mechanism strengthens the overall transport selectivity and protects the stoichiometry of the pump cycle.

DOI:http://dx.doi.org/10.7554/eLife.16616.001

A protein called the sodium-potassium pump resides in the membrane that surrounds living cells. The role of this protein is to 'pump' sodium and potassium ions across the membrane to help restore their concentration inside and outside of the cell. About 25% of the body's energy is used to keep the pump going, rising to nearly 70% in the brain. Problems that affect the pump have been linked to several disorders, including heart, kidney and metabolic diseases, as well as severe neurological conditions.

The sodium-potassium pump must be able to effectively pick out the correct ions to transport from a mixture of many different types of ions. However, it was not clear how the pump succeeds in doing this efficiently. Rui et al. have now used a computational method called molecular dynamics simulations to model how the sodium-potassium pump transports the desired ions across the cell membrane.

The pump works via a so-called 'alternating-access' mechanism, repeatedly transitioning between inward-facing and outward-facing conformations. In each cycle, it binds three sodium ions from the cell’s interior and exports them to the outside. Then, the pump binds to two potassium ions from outside the cell and imports them inside. Although the bound sodium and potassium ions interact with similar binding sites in the pump, the pump sometimes preferentially binds sodium, and sometimes potassium. The study performed by Rui et al. shows that this preference is driven by how protons (hydrogen ions) bind to the amino acids that make up the binding site.

The simulations also suggest that the pump uses a ‘self-correcting’ mechanism to prevent the pump from transporting the wrong types of ions. When incorrect ions are present at the binding sites, the pump cycle pauses temporarily until the ions detach from the pump. Only when the correct ions are bound will the pump cycle continue again.

In the future, Rui et al. hope to use long time-scale molecular dynamics simulations to show the conformational transition in action. In addition, the 'self-correcting' mechanism will be directly tested by letting the wrong and correct ions compete for the binding sites to see whether the pump will transport only the correct ions.

DOI:http://dx.doi.org/10.7554/eLife.16616.002

Abstract P4-09-14: PhosphohistoneH3 as a prognostic marker in breast cancer: High expression is associated with younger age, triple negative subtype, and disease specific survival

BACKGROUND PhosphohistoneH3 (PPH3) is an emerging marker in breast cancer and has been linked to both patient survival and age. Phosphorylation of HistoneH3 is an important step during the cell cycle leading to proper compaction of the chromatin during late G2 and early mitosis. Here we assessed the use of PPH3 as a prognostic marker within a group of invasive breast cancers in the Clinical Breast Care Project (CBCP).

METHODS CBCP participants and their samples were collected following IRB-approved, HIPAA-compliant protocols. Samples from 157 CBCP patients were selected for tissue whole section immunohistochemistry (IHC), using antibodies to PPH3, ER, PR, Ki67, and Her2. For each sample, staining of PPH3 was assessed across 5 high powered microscope fields and was considered positive if there was on average >2 stained cells per field. ER and PR were considered positive when there was >5% nuclear staining, and Ki67 was positive when there was >15% nuclear staining. Her2 was considered positive with an IHC score of 3+ or 2+ with a FISH score above 2.2. The samples were subtyped as Luminal A (LA: ER+/HER2-/Ki67-), Luminal B1 (LB1: ER+/HER2-/Ki67+), Luminal B2 (LB2: ER+/HER2+), Her2+ (ER-/PR-/HER2+), and Triple Negative (TN: ER-/PR-/HER2-). PPH3 was tested for associations with age and subtype using a stratified univariate Wilcoxon rank-sum analysis and a multivariate analysis controlling for subtype. To test the efficacy of PPH3 as a prognostic marker, Kaplan-Meier curves for disease specific survival were analyzed and the cox proportional hazard regression model was calculated. Further analysis addressing population demographics and additional cancer characteristics is ongoing.

RESULTS Wilcoxon analysis revealed an association between higher PPH3 levels and younger age (P=.0038). Subtype was also found to be associated with PPH3, with the TN subtype 6.26 times more likely to have higher PPH3 expression than LA (P=.005). The association with age was confirmed by repeating the analysis and stratifying into non-TN subtypes (P=.05) and TN only subtype (P=.017). Non-TN subtypes positive for PPH3 expression had median age of 53.18 at diagnosis and 63.29 for negative PPH3 expression; TN subtypes that were positive for PPH3 had a median age of 50.44 and 72.9 for negative PPH3. Multivariate analysis with age and subtype as the variables also supported these results (age P=.017; TN vs LA P=.022). Disease specific survival analysis showed that a shorter survival time was associated with positive PPH3 protein levels (P=0.03; hazard ratio=6.97).

CONCLUSIONS High expression of PPH3 is associated with a younger age, poorer survival rate, and the TN subtype. These results corroborate the use of PPH3 as a prognostic marker for breast cancer patients.

The views expressed in this article are those of the author and do not reflect the official policy of the Department of Defense, or U.S. Government.

Citation Format: Craig J, Kovatich AJ, Hooke JA, Kvecher L, Liu J, Fantacone-Campbell JL, Rui H, Shriver CD, Hu H. PhosphohistoneH3 as a prognostic marker in breast cancer: High expression is associated with younger age, triple negative subtype, and disease specific survival. [abstract]. In: Proceedings of the Thirty-Eighth Annual CTRC-AACR San Antonio Breast Cancer Symposium: 2015 Dec 8-12; San Antonio, TX. Philadelphia (PA): AACR; Cancer Res 2016;76(4 Suppl):Abstract nr P4-09-14.

Abstract PD2-08: Potential role of prolactin signaling in development and growth of the lobular subtype of breast cancer

Invasive lobular carcinoma (ILC) is the eighth most frequently diagnosed cancer in any organ, and accounts for 8-11% of breast cancer. This histological subtype is characterized by loss of E-cadherin, and favorable prognostic factors, such as low Ki67 and high rates of ER/PR-positive tumors. Only recently is the lobular subtype gaining recognition as a distinct disease, displaying a unique growth pattern, unique molecular changes in addition to loss of E-cadherin, and evidence for late recurrences and reduced response to targeted endocrine therapy. It is widely accepted that a late age at first full term birth (FFTB) increases a women's risk for breast cancer. Interestingly, several published epidemiological studies have shown that the increased risk after a late age at FFTB is preferential for the lobular subtype of breast cancer compared to the ductal subtype. We therefore hypothesized that pregnancy hormones like prolactin play an integral role in the development and progression of ILC. Interrogation of the Cancer Genome Atlas (TCGA) data revealed a high expression of milk protein genes as well as prolactin signaling molecules, specifically Stat5a and Stat5b in lobular carcinomas compared to ductal carcinomas. We developed a lactation score including 7 milk protein genes and found that in the TCGA data set ILC tumors have a significantly higher lactation score than IDC tumors. Additionally, we found that ILC cell lines express increased prolactin receptor mRNA and protein levels compared to IDC cell lines. Prolactin treatment in ILC and IDC cells reveals divergent signaling pathways - prolactin stimulates ERK activation in IDC but not ILC cells. We are currently further delineating the prolactin signaling pathways, and resulting phenotypes, comparing ILC and IDC cells. We expect these experiments to move the field forward by establishing a relationship between prolactin and lobular carcinoma.

Citation Format: Oesterreich S, Katz TA, Logan G, Levine K, Nagle A, Huo Z, Tseng GC, Rui H, Lee AV, Butler LM. Potential role of prolactin signaling in development and growth of the lobular subtype of breast cancer. [abstract]. In: Proceedings of the Thirty-Eighth Annual CTRC-AACR San Antonio Breast Cancer Symposium: 2015 Dec 8-12; San Antonio, TX. Philadelphia (PA): AACR; Cancer Res 2016;76(4 Suppl):Abstract nr PD2-08.

The mRNA-binding protein HuR promotes hypoxia-induced chemoresistance through posttranscriptional regulation of the proto-oncogene PIM1 in pancreatic cancer cells

Previously, it has been shown that pancreatic ductal adenocarcinoma (PDA) tumors exhibit high levels of hypoxia, characterized by low oxygen pressure (pO2) and decreased O2 intracellular perfusion. Chronic hypoxia is strongly associated with resistance to cytotoxic chemotherapy and chemoradiation in an understudied phenomenon known as hypoxia-induced chemoresistance. The hypoxia-inducible, pro-oncogenic, serine-threonine kinase PIM1 (Proviral Integration site for Moloney murine leukemia virus 1) has emerged as a key regulator of hypoxia-induced chemoresistance in PDA and other cancers. Although its role in therapeutic resistance has been described previously, the molecular mechanism behind PIM1 overexpression in PDA is unknown. Here, we demonstrate that cis-acting AU-rich elements (ARE) present within a 38-base pair region of the PIM1 mRNA 3'-untranslated region mediate a regulatory interaction with the mRNA stability factor HuR (Hu antigen R) in the context of tumor hypoxia. Predominantly expressed in the nucleus in PDA cells, HuR translocates to the cytoplasm in response to hypoxic stress and stabilizes the PIM1 mRNA transcript, resulting in PIM1 protein overexpression. A reverse-phase protein array revealed that HuR-mediated regulation of PIM1 protects cells from hypoxic stress through phosphorylation and inactivation of the apoptotic effector BAD and activation of MEK1/2. Importantly, pharmacological inhibition of HuR by MS-444 inhibits HuR homodimerization and its cytoplasmic translocation, abrogates hypoxia-induced PIM1 overexpression and markedly enhances PDA cell sensitivity to oxaliplatin and 5-fluorouracil under physiologic low oxygen conditions. Taken together, these results support the notion that HuR has prosurvival properties in PDA cells by enabling them with growth advantages in stressful tumor microenvironment niches. Accordingly, these studies provide evidence that therapeutic disruption of HuR's regulation of PIM1 may be a key strategy in breaking an elusive chemotherapeutic resistance mechanism acquired by PDA cells that reside in hypoxic PDA microenvironments.

CHARMM all-atom additive force field for sphingomyelin: elucidation of hydrogen bonding and of positive curvature

The C36 CHARMM lipid force field has been extended to include sphingolipids, via a combination of high-level quantum mechanical calculations on small molecule fragments, and validation by extensive molecular dynamics simulations on N-palmitoyl and N-stearoyl sphingomyelin. NMR data on these two molecules from several studies in bilayers and micelles played a strong role in the development and testing of the force field parameters. Most previous force fields for sphingomyelins were developed before the availability of the detailed NMR data and relied on x-ray diffraction of bilayers alone for the validation; these are shown to be too dense in the bilayer plane based on published chain order parameter data from simulations and experiments. The present simulations reveal O-H:::O-P intralipid hydrogen bonding occurs 99% of the time, and interlipid N-H:::O=C (26-29%, depending on the lipid) and N-H:::O-H (17-19%). The interlipid hydrogen bonds are long lived, showing decay times of 50 ns, and forming strings of lipids, and leading to reorientational correlation time of nearly 100 ns. The spontaneous radius of curvature for pure N-palmitoyl sphingomyelin bilayers is estimated to be 43-100 Å, depending on the assumptions made in assigning a bending constant; this unusual positive curvature for a two-tailed neutral lipid is likely associated with hydrogen bond networks involving the NH of the sphingosine group.

Steroid induction of therapy-resistant cytokeratin-5-positive cells in estrogen receptor-positive breast cancer through a BCL6-dependent mechanism

Therapy resistance remains a major problem in estrogen receptor-α (ERα)-positive breast cancer. A subgroup of ERα-positive breast cancer is characterized by mosaic presence of a minor population of ERα-negative cancer cells expressing the basal cytokeratin-5 (CK5). These CK5-positive cells are therapy resistant and have increased tumor-initiating potential. Although a series of reports document induction of the CK5-positive cells by progestins, it is unknown if other 3-ketosteroids share this ability. We now report that glucocorticoids and mineralocorticoids effectively expand the CK5-positive cell population. CK5-positive cells induced by 3-ketosteroids lacked ERα and progesterone receptors, expressed stem cell marker, CD44, and displayed increased clonogenicity in soft agar and broad drug-resistance in vitro and in vivo. Upregulation of CK5-positive cells by 3-ketosteroids required induction of the transcriptional repressor BCL6 based on suppression of BCL6 by two independent BCL6 small hairpin RNAs or by prolactin. Prolactin also suppressed 3-ketosteroid induction of CK5+ cells in T47D xenografts in vivo. Survival analysis with recursive partitioning in node-negative ERα-positive breast cancer using quantitative CK5 and BCL6 mRNA or protein expression data identified patients at high or low risk for tumor recurrence in two independent patient cohorts. The data provide a mechanism by which common pathophysiological or pharmacologic elevations in glucocorticoids or other 3-ketosteroids may adversely affect patients with mixed ERα+/CK5+ breast cancer. The observations further suggest a cooperative diagnostic utility of CK5 and BCL6 expression levels and justify exploring efficacy of inhibitors of BCL6 and 3-ketosteroid receptors for a subset of ERα-positive breast cancers.

Significantly improving enzymatic saccharification of high crystallinity index's corn stover by combining ionic liquid [Bmim]Cl-HCl-water media with dilute NaOH pretreatment

In this study, a pretreatment by combining acidified aqueous ionic liquid 1-butyl-3-methylimidazolium chloride (IL [Bmim]Cl) solution with dilute NaOH extraction was employed to pretreat high crystallinity index (CrI) of corn stover before its enzymatic saccharification. After NaOH extraction, [Bmim]Cl-HCl-water (78.8:1.2:20, w/w/w) media was used for further pretreatment at 130 °C for 30 min. After being enzymatically hydrolyzed for 48 h, corn stover pretreated could be biotransformed into reducing sugars in the yield of 95.1%. Furthermore, SEM, XRD and FTIR analyses of untreated and pretreated corn stovers were examined. It was found that the intact structure was disrupted by combination pretreatment and resulted in a porous and amorphous regenerated cellulosic material that greatly improved enzymatic hydrolysis. Finally, the recovered hydrolyzates obtained from the enzymatic hydrolysis of pretreated corn stovers could be fermented into ethanol efficiently. In conclusion, the combination pretreatment shows high potential application in future.

Improved biosynthesis of ethyl (S)-4-chloro-3-hydroxybutanoate by adding L-glutamine plus glycine instead of NAD+ in β-cyclodextrin-water system

To reduce dependence on the expensive cofactor and effectively biotransform ethyl 4-chloro-3-oxobutanoate, L-glutamine and glycine were found to enhance the content of intracellular NADH and the reductase activity. Adding the mixture of 200 mM of L-glutamine and 500 mM of glycine to the reaction media, a 1.67-fold of reductase activity was increased over the control without the addition of the two compounds. Moreover, β-cyclodextrin (0.4 mol β-cyclodextrin/mol ethyl 4-chloro-3-oxobutanoate) was also added into this reaction media, and the biocatalytic activity of the whole-cell biocatalyst of Escherichia coli CCZU-K14 was increased by 1.34-fold than that without β-cyclodextrin. In this β-cyclodextrin-water media containing L-glutamine (200 mM) plus glycine (500 mM), ethyl (S)-4-chloro-3-hydroxybutanoate (>99% ee) could be obtained from 3000 mM ethyl 4-chloro-3-oxobutanoate in the yield of 98.0% after 8h. All the positive features demonstrate the potential applicability of the bioprocess for the large-scale production of ethyl (S)-4-chloro-3-hydroxybutanoate.

Concerted motions networking pores and distant ferroxidase centers enable bacterioferritin function and iron traffic

X-ray crystallography, molecular dynamics (MD) simulations, and biochemistry were utilized to investigate the effect of introducing hydrophobic interactions in the 4-fold (N148L and Q151L) and B-pores (D34F) of Pseudomonas aeruginosa bacterioferritin B (BfrB) on BfrB function. The structures show only local structural perturbations and confirm the anticipated hydrophobic interactions. Surprisingly, structures obtained after soaking crystals in Fe2+-containing crystallization solution revealed that although iron loads into the ferroxidase centers of the mutants, the side chains of ferroxidase ligands E51 and H130 do not reorganize to bind the iron ions, as is seen in the wt BfrB structures. Similar experiments with a double mutant (C89S/K96C) prepared to introduce changes outside the pores show competent ferroxidase centers that function akin to those in wt BfrB. MD simulations comparing wt BfrB with the D34F and N148L mutants show that the mutants exhibit significantly reduced flexibility and reveal a network of concerted motions linking ferroxidase centers and 4-fold and B-pores, which are important for imparting ferroxidase centers in BfrB with the required flexibility to function efficiently. In agreement, the efficiency of Fe2+ oxidation and uptake of the 4-fold and B-pore mutants in solution is significantly compromised relative to wt or C89S/K96C BfrB. Finally, our structures show a large number of previously unknown iron binding sites in the interior cavity and B-pores of BfrB, which reveal in unprecedented detail conduits followed by iron and phosphate ions across the BfrB shell, as well as paths in the interior cavity that may facilitate nucleation of the iron phosphate mineral.

Probing the U-shaped conformation of caveolin-1 in a bilayer

Caveolin induces membrane curvature and drives the formation of caveolae that participate in many crucial cell functions such as endocytosis. The central portion of caveolin-1 contains two helices (H1 and H2) connected by a three-residue break with both N- and C-termini exposed to the cytoplasm. Although a U-shaped configuration is assumed based on its inaccessibility by extracellular matrix probes, caveolin structure in a bilayer remains elusive. This work aims to characterize the structure and dynamics of caveolin-1 (D82-S136; Cav182-136) in a DMPC bilayer using NMR, fluorescence emission measurements, and molecular dynamics simulations. The secondary structure of Cav182-136 from NMR chemical shift indexing analysis serves as a guideline for generating initial structural models. Fifty independent molecular dynamics simulations (100 ns each) are performed to identify its favorable conformation and orientation in the bilayer. A representative configuration was chosen from these multiple simulations and simulated for 1 μs to further explore its stability and dynamics. The results of these simulations mirror those from the tryptophan fluorescence measurements (i.e., Cav182-136 insertion depth in the bilayer), corroborate that Cav182-136 inserts in the membrane with U-shaped conformations, and show that the angle between H1 and H2 ranges from 35 to 69°, and the tilt angle of Cav182-136 is 27 ± 6°. The simulations also reveal that specific faces of H1 and H2 prefer to interact with each other and with lipid molecules, and these interactions stabilize the U-shaped conformation.

CHARMM-GUI PDB manipulator for advanced modeling and simulations of proteins containing nonstandard residues

CHARMM-GUI, http://www.charmm-gui.org, is a web-based graphical user interface to prepare molecular simulation systems and input files to facilitate the usage of common and advanced simulation techniques. Since it is originally developed in 2006, CHARMM-GUI has been widely adopted for various purposes and now contains a number of different modules designed to setup a broad range of simulations including free energy calculation and large-scale coarse-grained representation. Here, we describe functionalities that have recently been integrated into CHARMM-GUI PDB Manipulator, such as ligand force field generation, incorporation of methanethiosulfonate spin labels and chemical modifiers, and substitution of amino acids with unnatural amino acids. These new features are expected to be useful in advanced biomolecular modeling and simulation of proteins.

CHARMM-GUI Membrane Builder toward realistic biological membrane simulations

CHARMM-GUI Membrane Builder, http://www.charmm-gui.org/input/membrane, is a web-based user interface designed to interactively build all-atom protein/membrane or membrane-only systems for molecular dynamics simulations through an automated optimized process. In this work, we describe the new features and major improvements in Membrane Builder that allow users to robustly build realistic biological membrane systems, including (1) addition of new lipid types, such as phosphoinositides, cardiolipin (CL), sphingolipids, bacterial lipids, and ergosterol, yielding more than 180 lipid types, (2) enhanced building procedure for lipid packing around protein, (3) reliable algorithm to detect lipid tail penetration to ring structures and protein surface, (4) distance-based algorithm for faster initial ion displacement, (5) CHARMM inputs for P21 image transformation, and (6) NAMD equilibration and production inputs. The robustness of these new features is illustrated by building and simulating a membrane model of the polar and septal regions of E. coli membrane, which contains five lipid types: CL lipids with two types of acyl chains and phosphatidylethanolamine lipids with three types of acyl chains. It is our hope that CHARMM-GUI Membrane Builder becomes a useful tool for simulation studies to better understand the structure and dynamics of proteins and lipids in realistic biological membrane environments.

Abstract P5-04-05: Preclinical modeling of luminal breast cancer: Recapitulating progression to lethal and tamoxifen-resistant lung metastases in novel patient-derived xenotransplant models in prolactin-humanized mice

Seventy to eighty percent of newly diagnosed breast cancer cases are estrogen receptor(ER)-positive and are classified as luminal. Despite hormone therapy, 25-30% of luminal breast cancers will recur within 15 years of surgical removal of the primary tumor, and many of these patients will die from currently incurable distant metastases. Lung and bone are the most common organ sites for distant breast cancer metastases, with either site affected in approximately 70% of patients based on autopsy studies. A major hurdle for therapeutic progress with luminal breast cancer is the historical difficulty to establish xenograft models of human luminal breast cancer in mice. In particular, there is a need for experimental ER-positive breast cancer models that recapitulate distant metastasis formation from orthotopic tumor implants in mammary glands. Such experimental models will allow surgical resection of the primary tumor followed by clinically relevant testing of targeted adjuvant agents against distant residual disease.

We have engineered prolactin-humanized mice that have been backcrossed for ten generations into the Nod-SCOD-IL2Rgamma (NSG) immunodeficient background. These prolactin-humanized mice display improved take rates of patient-derived luminal breast cancer. Using prolactin-humanized mice we have established patient-derived serially transplantable luminal breast cancer models that metastasize to distant sites when grown as primary tumors in the mammary gland. One of the ER-positive lines, PDX2, effectively metastasizes to lungs in 100% of animals within 55 days of grafting into mammary glands. PDX2 lung metastases retain ER and progesterone receptor (PR) expression as well as expression of the luminal marker, GATA3, and display high degree of Ki67 positivity indicating rapidly proliferative lesions. Importantly, metastatic PDX2 lesions show only limited dormancy. In fact, when primary PDX2 tumors are surgically removed at Day 55, mice will die from lung metastases around Day 150. Estrogen supplementation is required for establishment of PDX2 tumors in mice. After primary PDX2 tumors are established in mammary glands in the presence of estradiol, primary tumors respond to tamoxifen with growth suppression but do not undergo tumor regression, and develop resistance to tamoxifen. Treatment of mice with adjuvant tamoxifen following surgical removal of primary PDX2 tumors led to extensive regression of existing lung metastases to barely detectable levels within 30 days of surgery. However, tamoxifen-refractory PDX2 lung metastases regrew during the next 30 day-period in the continued exposure to tamoxifen. Molecular phenotyping of the PDX2 model and other new luminal breast cancer models are ongoing, with the goal of characterizing tamoxifen-responsive and tamoxifen-refractory primary and metastatic lesions. Long-term, our intent is to use the PDX2 and other preclinical xenograft models in prolactin-humanized mice to systematically explore agents for synergy with anti-estrogens to establish curative combination treatments for metastatic luminal breast cancer.

Citation Information: Cancer Res 2013;73(24 Suppl): Abstract nr P5-04-05.

Abstract P4-06-03: Assays on core biopsies and surgically resected tumors may result in different subtyping of the invasive breast cancer from the same patient

Background Core biopsies (CBs) are often used for biomarker expression assays to determine the treatment regimen. However, a number of other clinically important analyses (e.g. OncoType Dx), are performed on surgically resected tumors (SRTs). A previous study has shown that biomarkers ER, PR, and Ki67 expressed higher in CBs than in SRTs. Here we analyze how this difference impacts the subtyping of ER+ breast tumors.

Methods Female patients enrolled in the Clinical Breast Care Project (CBCP) from a civilian site were selected for this study, where expression of ER, PR, HER2, and Ki67 were assayed by IHC in a reference lab on CBs; the same 4 assays were performed on SRTs by a CBCP central lab. Both labs are CLIA-certified. Patients treated with neoadjuvant chemotherapy and those with multiple tumors were excluded. 167 cases were identified for this study to compare assays performed on CBs and SRTs from the same patients. ER and PR were positive if >1% nuclear staining, HER2 was negative if IHC = 0 or 1+, positive if IHC = 3+, and for IHC = 2+ FISH was used for the final call. Ki67 was positive if > = 15% nuclear staining. LA was ER+/HER2-/Ki67-, LB1 was ER+/HER2-/Ki67+, and LB2 was ER+/HER2+. For histologic grades, only readings from the central lab on SRTs were used. Statistical analyses were performed using SAS.

Results This analysis confirmed that Ki67, ER, and PR showed higher percent nuclear staining in CBs than in SRTs from the same patients. The difference for Ki67 was more striking and unidirectional. ER and PR cases clustered at the upper percent levels. Histograms with a bin-width of 15% show a peak at 15% for Ki67 difference between CBs and SRTs, whereas the peaks for ER and PR differences were at 0%. McNemar's (or Exact McNemar’s) test showed significant differences between the binary status calls for Ki67 (p = 3.2E-15) and ER (p = 0.012), but not for PR (p = 0.65). Assays on CBs and SRTs resulted in different subtype calls for the cases (Table 1). Grade distributions were different between LA and LB (p<0.001 for both CB- and SRT-based subtypes, Chi-Square or Fisher's Exact test), but not so between LB1 and LB2 (p = 0.23 for CB, 0.31 for SRT). However, SRT-based LB1 cases concentrate more on higher grades compared to CB-based cases (p = 0.048).

Table 1. ER+ subtypes based on IHC assays (from CBs and SRTs) and corresponding grades (from SRTs) CBSRTSubtypeG1G2G3G1G2G3LA2126034518LB11435342820LB2036032

Discussion On IHC assays, Ki67 expression is strikingly higher in CBs than in SRTs, and ER expression is also higher in CBs than in SRTs. This directly resulted in more LB than LA subtypes based on CBs. SRT-based LB1 cases concentrate more on higher grades compared to CB-based cases, which is more consistent with the observation that LB subtypes have worse outcomes. A limitation of this study is that technical differences between the labs may contribute to the observed differences between CBs and SRTs. Further studies need to be performed to determine whether SRT should also be assayed in addition to CB for treatment regimen decision-making.

The views expressed in this abstract are those of the authors and do not reflect the official policy of the Department of Defense, or US Government.

Citation Information: Cancer Res 2013;73(24 Suppl): Abstract nr P4-06-03.

Abstract P1-06-10: Characterization of novel activated human mammary fibroblast lines and their protumorigenic effect on human breast cancer xenotransplants in mice

Human breast cancer is typically characterized by an extensive stromal compartment enriched in fibroblasts. In contrast, xenotransplants of human breast cancer cell lines are typically epithelial-rich and characterized by sparse in-growth of murine fibroblast stroma. Stromal fibroblasts are important for structural integrity of normal tissue and constitute a major element of the stromal microenvironment of invasive cancer. Cancer associated fibroblasts (CAFs) frequently undergo activation as they co-evolve with cancer cells, serving to promote tumor growth and angiogenesis through secretion of multiple paracrine factors. Presence of activated CAFs in solid malignancies is generally associated with higher grade tumors and poor prognosis. Activated CAFs are resistant to apoptosis and display a myofibroblastic phenotype, including expression of a-smooth muscle actin (α-SMA). To more accurately model human tumor-stroma interactions in human breast cancer xenograft lines in mice, we aimed to develop immortalized activated human mammary fibroblasts for admixture xenografting with human breast cancer cells. Human mammary fibroblasts (HMFs) were isolated from multiple surgically excised tissues of reduction mammoplasties or mastectomies. Five isolated primary HMF lines were screened for α-SMA expression. HMF1 expressed the highest levels of α-SMA and was immortalized by stable lentiviral-delivered hTERT. Quantitative real-time PCR, anchorage-independent growth assay, and in vivo studies were used to further characterize selected HMFs. hTERT-HMF1 and HMF2, despite lower level of α-SMA expression in HMF2, displayed significantly elevated levels of mRNA of proteins commonly associated with activated fibroblasts, including SDF-α, SDF-β, HGF, IL-6, VEGF and podoplanin, as well as promoted a 10-fold increase in anchorage-independent growth of MCF7 breast cancer cells in vitro. To evaluate the ability of these HMF lines to promote tumor growth in vivo, MCF7 human breast cancer cells were orthotopically injected into murine mammary fat pads in the presence or absence of hTERT-HMF1 or HMF2. Both HMF lines facilitated in vivo MCF7-xenograft growth and induced histological changes, including higher grade and greater stromal development, when compared to pure MCF7 cell xenografts. IHC for SMA and collagen confirmed the presence of activated fibroblasts in all tumors; however HMF/MCF7 xenografts showed a distinct distribution of fibroblast stroma throughout the tumor in contrast to sparser stroma between larger epithelial aggregates in tumors grafted from MCF7 cells alone. hTERT-HFM1 cells promoted tumor growth in vivo more robustly than HFM2 cells. By 60 days post xenografting, hTERT-HMF1/MCF7 tumors were significantly larger (∼4-fold) than control MCF7 tumors. In addition, admixture with hTERT-HMF1 cells promoted increased tumor angiogenesis and cancer cell proliferation as measured by Ki67 expression. hTERT-HMF1 represents a novel mammary myofibroblast line that may be useful for improved preclinical xenotransplant modeling and tumor drug response testing of human breast cancer in vivo.

Citation Information: Cancer Res 2013;73(24 Suppl): Abstract nr P1-06-10.