Large-Scale Atom Probe Tomography Data Mining: Methods and Application to Inform Hydrogen Behavior.

A large number of atom probe tomography (APT) datasets from past experiments were collected into a database to conduct statistical analyses. An effective way of handling the data is shown, and a study on hydrogen is conducted to illustrate the usefulness of this approach. We propose to handle a large collection of APT spectra as a point cloud and use a city block distance-based metric to measure dissimilarity between spectra. This enables quick and automated searching for spectra by similarity. Since spectra from APT experiments on similar materials are similar, the point cloud of spectra contains clusters. Analysis of these clusters of spectra in this point cloud allows us to infer the sample materials. The behavior of contaminant hydrogen is analyzed and correlated with voltage, electric field, and sample base material. Across several materials, the H2+ /H+ ratio is found to decrease with increasing field, likely an indication of postionization of H2+ ions. The absolute amounts of H2+ and H+ are found to frequently increase throughout APT experiments.

Processing APT Spectral Backgrounds for Improved Quantification.

We describe a method to estimate background noise in atom probe tomography (APT) mass spectra and to use this information to enhance both background correction and quantification. Our approach is mathematically general in form for any detector exhibiting Poisson noise with a fixed data acquisition time window, at voltages varying through the experiment. We show that this accurately estimates the background observed in real experiments. The method requires, as a minimum, the z-coordinate and mass-to-charge-state data as input and can be applied retrospectively. Further improvements are obtained with additional information such as acquisition voltage. Using this method allows for improved estimation of variance in the background, and more robust quantification, with quantified count limits at parts-per-million concentrations. To demonstrate applications, we show a simple peak detection implementation, which quantitatively suppresses false positives arising from random noise sources. We additionally quantify the detectability of 121-Sb in a standardized-doped Si microtip as (1.5 × 10−5, 3.8 × 10−5) atomic fraction, α = 0.95. This technique is applicable to all modes of APT data acquisition and is highly general in nature, ultimately allowing for improvements in analyzing low ionic count species in datasets.

Blockade of TGF-ß signaling to enhance the antitumor response is accompanied by dysregulation of the functional activity of CD4+CD25+Foxp3+ and CD4+CD25-Foxp3+ T cells.

BACKGROUND: The pleiotropic cytokine, transforming growth factor (TGF)-ß, and CD4+CD25+Foxp3+ regulatory T cells (Tregs) play a critical role in actively suppressing antitumor immune responses. Evidence shows that TGF-ß produced by tumor cells promotes tolerance via expansion of Tregs. Our group previously demonstrated that blockade of TGF-ß signaling with a small molecule TGF-ß receptor I antagonist (SM16) inhibited primary and metastatic tumor growth in a T cell dependent fashion. In the current study, we evaluated the effect of SM16 on Treg generation and function. METHODS: Using BALB/c, FoxP3eGFP and Rag-/- mice, we performed FACS analysis to determine if SM16 blocked de novo TGF-ß-induced Treg generation in vitro and in vivo. CD4+ T cells from lymph node and spleen were isolated from control mice or mice maintained on SM16 diet, and flow cytometry analysis was used to detect the frequency of CD4+CD25-FoxP3+ and CD4+CD25+FoxP3+ T cells. In vitro suppression assays were used to determine the ability to suppress naive T cell proliferation in vitro of both CD4+CD25+FoxP3+ and CD4+CD25-FoxP3+ T cell sub-populations. We then examined whether SM16 diet exerted an inhibitory effect on primary tumor growth and correlated with changes in FoxP3+expression. ELISA analysis was used to measure IFN-γ levels after 72 h co-culture of CD4+CD25+ T cells from tumor-bearing mice on control or SM16 diet with CD4+CD25- T cells from naive donors. RESULTS: SM16 abrogates TGF-ß-induced Treg generation in vitro but does not prevent global homeostatic expansion of CD4+ T cell sub-populations in vivo. Instead, SM16 treatment causes expansion of a population of CD4+CD25-Foxp3+ Treg-like cells without significantly altering the overall frequency of Treg in lymphoreplete naive and tumor-bearing mice. Importantly, both the CD4+CD25-Foxp3+ T cells and the CD4+CD25+Foxp3+ Tregs in mice receiving SM16 diet exhibited diminished ability to suppress naive T cell proliferation in vitro compared to Treg from mice on control diet. CONCLUSIONS: These findings suggest that blockade of TGF-ß signaling is a potentially useful strategy for blunting Treg function to enhance the anti-tumor response. Our data further suggest that the overall dampening of Treg function may involve the expansion of a quiescent Treg precursor population, which is CD4+CD25-Foxp3+.

A Gas-Phase Reaction Cell for Modern Atom Probe Systems.

In this work, we demonstrate a new system for the examination of gas interactions with surfaces via atom probe tomography. This system provides capability of examining the surface and subsurface interactions of gases with a wide range of specimens, as well as a selection of input gas types. This system has been primarily developed to aid the investigation of hydrogen interactions with metallurgical samples, to better understand the phenomenon of hydrogen embrittlement. In its current form, it is able to operate at pressures from 10-6 to 1000 mbar (abs), can use a variety of gasses, and is equipped with heating and cryogenic quenching capabilities. We use this system to examine the interaction of hydrogen with Pd, as well as the interaction of water vapor and oxygen in Mg samples.

DF-Fit: A Robust Algorithm for Detection of Crystallographic Information in Atom Probe Tomography Data.

We report on a new algorithm for the detection of crystallographic information in three-dimensional, as retained in atom probe tomography (APT), with improved robustness and signal detection performance. The algorithm is underpinned by one-dimensional distribution functions (DFs), as per existing algorithms, but eliminates an unnecessary parameter as compared to current methods.By examining traditional DFs in an automated fashion in real space, rather than using Fourier transform approaches, we utilize an error metric based upon the expected value for a spatially random distribution for detecting crystallography. We show cases where the metric is able to successfully obtain orientation information, and show that it can function with high levels of additive and displacive background noise. We additionally compare this metric to Fourier transform methods, showing fewer artifacts when examining simulated datasets. An extension of the approach is used to aid the automatic detection of high-quality data regions within an entire dataset, albeit with a large increase in computational cost.This extension is demonstrated on acquired aluminum and tungsten APT datasets, and shown to be able to discern regions of the data which have relatively improved spatial data quality. Finally, this program has been made available for use in other laboratories undertaking their own analyses.

Autophagosome-based strategy to monitor apparent tumor-specific CD8 T cells in patients with prostate cancer.

The immune system plays an essential role in eradicating cancer in concert with various treatment modalities. In the absence of autologous tumor material, no standardized method exists to assess T cell responses against the many antigens that may serve as cancer rejection antigens. Thus, development of methods to screen for therapy-induced anti-tumor responses is a high priority that could help tailor therapy. Here we tested whether a tumor-derived antigen source called DRibbles®, which contain a pool of defective ribosomal products (DRiPs), long-lived and short-lived proteins (SLiPs) and danger-associated molecular patterns (DAMPs), can be used to identify tumor-associated antigen (TAA)-specific responses in patients before or after immunotherapy treatment. Protein content, gene expression and non-synonymous - single nucleotide variants (ns-SNVs) present in UbiLT3 DRibbles were compared with prostate adenocarcinomas and the prostate GVAX vaccine cell lines (PC3/LNCaP). UbiLT3 DRibbles were found to share proteins, as well as match tumor sequences for ns-SNVs with prostate adenocarcinomas and with the cell lines PC3 and LNCaP. UbiLT3 DRibbles were used to monitor anti-tumor responses in patients vaccinated with allogeneic prostate GVAX. UbiLT3-DRibble-reactive CD8+ T-cell responses were detected in post-vaccine PBMC of 6/12 patients (range 0.85-22% of CD8+ cells) after 1 week in vitro stimulation (p = 0.007 vs. pre-vaccine). In conclusion, a cancer-derived autophagosome-enriched preparation, packaging over 100 proteins over-expressed in prostate cancer into microvesicles containing DAMPs, could be used to identify CD8+ T cells in peripheral blood from patients after prostate GVAX vaccination and may represent a general method to monitor anti-cancer T cell responses following immunotherapy.

Single-Ion Deconvolution of Mass Peak Overlaps for Atom Probe Microscopy.

Due to the intrinsic evaporation properties of the material studied, insufficient mass-resolving power and lack of knowledge of the kinetic energy of incident ions, peaks in the atom probe mass-to-charge spectrum can overlap and result in incorrect composition measurements. Contributions to these peak overlaps can be deconvoluted globally, by simply examining adjacent peaks combined with knowledge of natural isotopic abundances. However, this strategy does not account for the fact that the relative contributions to this convoluted signal can often vary significantly in different regions of the analysis volume; e.g., across interfaces and within clusters. Some progress has been made with spatially localized deconvolution in cases where the discrete microstructural regions can be easily identified within the reconstruction, but this means no further point cloud analyses are possible. Hence, we present an ion-by-ion methodology where the identity of each ion, normally obscured by peak overlap, is resolved by examining the isotopic abundance of their immediate surroundings. The resulting peak-deconvoluted data are a point cloud and can be analyzed with any existing tools. We present two detailed case studies and discussion of the limitations of this new technique.

Atom Probe Analysis of Ex Situ Gas-Charged Stable Hydrides.

In this work, we report on the atom probe tomography analysis of two metallic hydrides formed by pressurized charging using an ex situ hydrogen charging cell, in the pressure range of 200-500 kPa (2-5 bar). Specifically we report on the deuterium charging of Pd/Rh and V systems. Using this ex situ system, we demonstrate the successful loading and subsequent atom probe analysis of deuterium within a Pd/Rh alloy, and demonstrate that deuterium is likely present within the oxide-metal interface of a native oxide formed on vanadium. Through these experiments, we demonstrate the feasibility of ex situ hydrogen analysis for hydrides via atom probe tomography, and thus a practical route to three-dimensional imaging of hydrogen in hydrides at the atomic scale.

An atom probe perspective on phase separation and precipitation in duplex stainless steels.

Three-dimensional chemical imaging of Fe-Cr alloys showing Fe-rich (α)/Cr-rich (α') phase separation is reported using atom probe tomography techniques. The extent of phase separation, i.e., amplitude and wavelength, has been quantitatively assessed using the Langer-Bar-on-Miller, proximity histogram, and autocorrelation function methods for two separate Fe-Cr alloys, designated 2101 and 2205. Although the 2101 alloy possesses a larger wavelength and amplitude after annealing at 427 °C for 100-10 000 h, it exhibits a lower hardness than the 2205 alloy. In addition to this phase separation, ultra-fine Ni-Mn-Si-Cu-rich G-phase precipitates form at the α/α' interfaces in both alloys. For the 2101 alloy, Cu clusters act to form a nucleus, around which a Ni-Mn-Si shell develops during the precipitation process. For the 2205 alloy, the Ni and Cu atoms enrich simultaneously and no core-shell chemical distribution was found. This segregation phenomenon may arise from the exact Ni/Cu ratio inside the ferrite. After annealing for 10 000 h, the number density of the G-phase within the 2205 alloy was found to be roughly one order of magnitude higher than in the 2101 alloy. The G-phase precipitates have an additional deleterious effect on the thermal embrittlement, as evaluated by the Ashby-Orowan equation, which explains the discrepancy between the hardness and the rate of phase separation with respect to annealing time (Gladman T 1999 Mater. Sci. Tech. Ser. 15 30-36).

A Semi-automated Approach to Preparing Antibody Cocktails for Immunophenotypic Analysis of Human Peripheral Blood.

Immunophenotyping of peripheral blood by flow cytometry determines changes in the frequency and activation status of peripheral leukocytes during disease and treatment. It has the potential to predict therapeutic efficacy and identify novel therapeutic targets. Whole blood staining utilizes unmanipulated blood, which minimizes artifacts that can occur during sample preparation. However, whole blood staining must also be done on freshly collected blood to ensure the integrity of the sample. Additionally, it is best to prepare antibody cocktails on the same day to avoid potential instability of tandem-dyes and prevent reagent interaction between brilliant violet dyes. Therefore, whole blood staining requires careful standardization to control for intra and inter-experimental variability. Here, we report deployment of an automated liquid handler equipped with a two-dimensional (2D) barcode reader into a standard process of making antibody cocktails for flow cytometry. Antibodies were transferred into 2D barcoded tubes arranged in a 96 well format and their contents compiled in a database. The liquid handler could then locate the source antibody vials by referencing antibody names within the database. Our method eliminated tedious coordination for positioning of source antibody tubes. It provided versatility allowing the user to easily change any number of details in the antibody dispensing process such as specific antibody to use, volume, and destination by modifying the database without rewriting the scripting in the software method for each assay. A proof of concept experiment achieved outstanding inter and intra- assay precision, demonstrated by replicate preparation of an 11-color, 17-antibody flow cytometry assay. These methodologies increased overall throughput for flow cytometry assays and facilitated daily preparation of the complex antibody cocktails required for the detailed phenotypic characterization of freshly collected anticoagulated peripheral blood.

Mining information from atom probe data.

Whilst atom probe tomography (APT) is a powerful technique with the capacity to gather information containing hundreds of millions of atoms from a single specimen, the ability to effectively use this information creates significant challenges. The main technological bottleneck lies in handling the extremely large amounts of data on spatial-chemical correlations, as well as developing new quantitative computational foundations for image reconstruction that target critical and transformative problems in materials science. The power to explore materials at the atomic scale with the extraordinary level of sensitivity of detection offered by atom probe tomography has not been not fully harnessed due to the challenges of dealing with missing, sparse and often noisy data. Hence there is a profound need to couple the analytical tools to deal with the data challenges with the experimental issues associated with this instrument. In this paper we provide a summary of some key issues associated with the challenges, and solutions to extract or "mine" fundamental materials science information from that data.

Detailed characterization of tumor infiltrating lymphocytes in two distinct human solid malignancies show phenotypic similarities.

BACKGROUND: We examined the phenotype and function of lymphocytes collected from the peripheral blood (PBL) and tumor (TIL) of patients with two different solid malignancies: colorectal cancer liver metastases (CRLM) and ovarian cancer (OVC). METHODS: Tumor and corresponding peripheral blood were collected from 16 CRLM and 22 OVC patients; immediately following resection they were processed and analyzed using a multi-color flow cytometry panel. Cytokine mRNA from purified PBL and TIL CD4(+) T cells were also analyzed by qPCR. RESULTS: Overall, we found similar changes in the phenotypic and cytokine profiles when the TIL were compared to PBL from patients with two different malignancies. The percentage of Treg (CD4(+)/CD25(+)/FoxP3(+)) in PBL and TIL was similar: 8.1% versus 10.2%, respectively in CRLM patients. However, the frequency of Treg in primary OVC TIL was higher than PBL: 19.2% versus 4.5% (p <0.0001). A subpopulation of Treg expressing HLA-DR was markedly increased in TIL compared to PBL in both tumor types, CRLM: 69.0% versus 31.7% (p = 0.0002) and OVC 74.6% versus 37.0% (p <0.0001), which suggested preferential Treg activation within the tumor. The cytokine mRNA profile showed that IL-6, a cytokine known for its immunosuppressive properties through STAT3 upregulation, was increased in TIL samples in patients with OVC and CRLM. Both TIL populations also contained a significantly higher proportion of activated CD8(+) T cells (HLA-DR(+)/CD38(+)) compared to PBL (CRLM: 30.2% vs 7.7%, (p = 0.0012), OVC: 57.1% vs 12.0%, (p <0.0001)). CONCLUSION: This study demonstrates that multi-color flow cytometry of freshly digested tumor samples reveals phenotypic differences in TIL vs PBL T cell sub-populations. The TIL composition in primary and metastatic tumors from two distinct histologies were remarkably similar, showing a greater proportion of activated/suppressive Treg (HLA-DR(+), CD39(+), CTLA-4(+) and Helios(+)) and activated cytotoxic T cells (CD8(+)/HLA-DR(+)/CD38(+)) when compared to PBL and an increase in IL-6 mRNA from CD4 TIL.

OX40 is a potent immune-stimulating target in late-stage cancer patients.

OX40 is a potent costimulatory receptor that can potentiate T-cell receptor signaling on the surface of T lymphocytes, leading to their activation by a specifically recognized antigen. In particular, OX40 engagement by ligands present on dendritic cells dramatically increases the proliferation, effector function, and survival of T cells. Preclinical studies have shown that OX40 agonists increase antitumor immunity and improve tumor-free survival. In this study, we performed a phase I clinical trial using a mouse monoclonal antibody (mAb) that agonizes human OX40 signaling in patients with advanced cancer. Patients treated with one course of the anti-OX40 mAb showed an acceptable toxicity profile and regression of at least one metastatic lesion in 12 of 30 patients. Mechanistically, this treatment increased T and B cell responses to reporter antigen immunizations, led to preferential upregulation of OX40 on CD4(+) FoxP3(+) regulatory T cells in tumor-infiltrating lymphocytes, and increased the antitumor reactivity of T and B cells in patients with melanoma. Our findings clinically validate OX40 as a potent immune-stimulating target for treatment in patients with cancer, providing a generalizable tool to favorably influence the antitumor properties of circulating T cells, B cells, and intratumoral regulatory T cells.

Level set methods for modelling field evaporation in atom probe.

Atom probe is a nanoscale technique for creating three-dimensional spatially and chemically resolved point datasets, primarily of metallic or semiconductor materials. While atom probe can achieve local high-level resolution, the spatial coherence of the technique is highly dependent upon the evaporative physics in the material and can often result in large geometric distortions in experimental results. The distortions originate from uncertainties in the projection function between the field evaporating specimen and the ion detector. Here we explore the possibility of continuum numerical approximations to the evaporative behavior during an atom probe experiment, and the subsequent propagation of ions to the detector, with particular emphasis placed on the solution of axisymmetric systems, such as isolated particles and multilayer systems. Ultimately, this method may prove critical in rapid modeling of tip shape evolution in atom probe tomography, which itself is a key factor in the rapid generation of spatially accurate reconstructions in atom probe datasets.

Defining clusters in APT reconstructions of ODS steels.

Oxide nanoclusters in a consolidated Fe-14Cr-2W-0.3Ti-0.3Y2O3 ODS steel and in the alloy powder after mechanical alloying (but before consolidation) are investigated by atom probe tomography (APT). The maximum separation method is a standard method to define and characterise clusters from within APT data, but this work shows that the extent of clustering between the two materials is sufficiently different that the nanoclusters in the mechanically alloyed powder and in the consolidated material cannot be compared directly using the same cluster selection parameters. As the cluster selection parameters influence the size and composition of the clusters significantly, a procedure to optimise the input parameters for the maximum separation method is proposed by sweeping the d(max) and N(min) parameter space. By applying this method of cluster parameter selection combined with a 'matrix correction' to account for trajectory aberrations, differences in the oxide nanoclusters can then be reliably quantified.

Tumor-derived autophagosome vaccine: mechanism of cross-presentation and therapeutic efficacy.

PURPOSE: We previously reported that autophagy in tumor cells plays a critical role in cross-presentation of tumor antigens and that autophagosomes are efficient antigen carriers for cross-priming of tumor-reactive CD8(+) T cells. Here, we sought to characterize further the autophagosome-enriched vaccine named DRibble (DRiPs-containing blebs), which is derived from tumor cells after inhibition of protein degradation, and to provide insights into the mechanisms responsible for their efficacy as a novel cancer immunotherapy. EXPERIMENTAL DESIGN: DRibbles were characterized by Western blot and light or transmission electron microscopy. The efficiency of cross-presentation mediated by DRibbles was first compared with that of whole-tumor cells and pure proteins. The mechanisms of antigen cross-presentation by DRibbles were analyzed, and the antitumor efficacy of the DRibble vaccine was tested in 3LL Lewis lung tumors and B16F10 melanoma. RESULTS: The DRibbles sequester both long-lived and short-lived proteins, including defective ribosomal products (DRiP), and damage-associated molecular pattern molecules exemplified by HSP90, HSP94, calreticulin, and HMGB1. DRibbles express ligands for CLEC9A, a newly described C-type lectin receptor expressed by a subset of conventional and plasmacytoid dendritic cells (DC), and cross-presentation was partially CLEC9A dependent. Furthermore, this autophagy-assisted antigen cross-presentation pathway involved both caveolae- and clathrin-mediated endocytosis and endoplasmic reticulum-associated degradation machinery. It depends on proteasome and TAP1, but not lysosome functions of antigen-presenting cells. Importantly, DCs loaded with autophagosome-enriched DRibbles can eradicate 3LL Lewis lung tumors and significantly delay the growth of B16F10 melanoma. CONCLUSIONS: These data documented the unique characteristics and potent antitumor efficacy of the autophagosome-based DRibble vaccine. The efficacy of DRibble cancer vaccine will be further tested in clinical trials.

Crystallographic structural analysis in atom probe microscopy via 3D Hough transformation.

Whereas the atom probe is regarded almost exclusively as a technique for 3D chemical microanalysis of solids with the highest chemical and spatial resolution, we demonstrate that the technique can be used for detailed crystallographic determinations. We present a new method for the quantitative determination of crystal structure (plane spacings and angles) using a Hough transformation of the reconstructed atom probe data. The resolving power is shown to be high enough to identify poorly established, discontinuous planes that are typical in semiconducting materials. We demonstrate the determination of crystal geometry around a grain boundary and the use of the technique for the optimisation of tomographic reconstruction. We propose that this method will enable automatic spatial analysis and, ultimately, automated tomographic reconstruction in atom probe microscopy.

Exhaustive expansion: A novel technique for analyzing complex data generated by higher-order polychromatic flow cytometry experiments.

BACKGROUND: The complex data sets generated by higher-order polychromatic flow cytometry experiments are a challenge to analyze. Here we describe Exhaustive Expansion, a data analysis approach for deriving hundreds to thousands of cell phenotypes from raw data, and for interrogating these phenotypes to identify populations of biological interest given the experimental context. METHODS: We apply this approach to two studies, illustrating its broad applicability. The first examines the longitudinal changes in circulating human memory T cell populations within individual patients in response to a melanoma peptide (gp100209-2M) cancer vaccine, using 5 monoclonal antibodies (mAbs) to delineate subpopulations of viable, gp100-specific, CD8+ T cells. The second study measures the mobilization of stem cells in porcine bone marrow that may be associated with wound healing, and uses 5 different staining panels consisting of 8 mAbs each. RESULTS: In the first study, our analysis suggests that the cell surface markers CD45RA, CD27 and CD28, commonly used in historical lower order (2-4 color) flow cytometry analysis to distinguish memory from naïve and effector T cells, may not be obligate parameters in defining central memory T cells (TCM). In the second study, we identify novel phenotypes such as CD29+CD31+CD56+CXCR4+CD90+Sca1-CD44+, which may characterize progenitor cells that are significantly increased in wounded animals as compared to controls. CONCLUSIONS: Taken together, these results demonstrate that Exhaustive Expansion supports thorough interrogation of complex higher-order flow cytometry data sets and aids in the identification of potentially clinically relevant findings.

Spatial resolution in atom probe tomography.

This article addresses gaps in definitions and a lack of standard measurement techniques to assess the spatial resolution in atom probe tomography. This resolution is known to be anisotropic, being better in-depth than laterally. Generally the presence of atomic planes in the tomographic reconstruction is considered as being a sufficient proof of the quality of the spatial resolution of the instrument. Based on advanced spatial distribution maps, an analysis methodology that interrogates the local neighborhood of the atoms within the tomographic reconstruction, it is shown how both the in-depth and the lateral resolution can be quantified. The influences of the crystallography and the temperature are investigated, and models are proposed to explain the observed results. We demonstrate that the absolute value of resolution is specimen specific.

Depletion of tumor-induced Treg prior to reconstitution rescues enhanced priming of tumor-specific, therapeutic effector T cells in lymphopenic hosts.

We reported previously that vaccination of reconstituted, lymphopenic mice resulted in a higher frequency of tumor-specific effector T cells with therapeutic activity than vaccination of normal mice. Here, we show that lymphopenic mice reconstituted with spleen cells from tumor-bearing mice (TBM), a situation that resembles the clinical condition, failed to generate tumor-specific T cells with therapeutic efficacy. However, depletion of CD25(+) Treg from the spleen cells of TBM restored tumor-specific priming and therapeutic efficacy. Adding back TBM CD25(+) Treg to CD25(-) naïve and TBM donor T cells prior to reconstitution confirmed their suppressive role. CD25(+) Treg from TBM prevented priming of tumor-specific T cells since subsequent depletion of CD4(+) T cells did not restore therapeutic efficacy. This effect may not be antigen-specific as three histologically distinct tumors generated CD25(+) Treg that could suppress the T-cell immune response to a melanoma vaccine. Importantly, since ex vivo depletion of CD25(+) Treg from TBM spleen cells prior to reconstitution and vaccination fully restored the generation of therapeutic effector T cells, even in animals with established tumor burden, we have initiated a translational clinical trial of this strategy in patients with metastatic melanoma.