Advancements in single cell multiomic profiling of antigen-specific T cells with dCODE Dextramer&[trade] (RiO) and BD® AbSeq Reagents on the BD Rhapsody&[trade] Single-Cell Analysis System

The advancement of immunotherapies and drug development relies on the characterization of antigen-specific T cells. However, due to their low frequency among T cells and their inherent weak affinity to bind known MHC-peptide complexes, detection of these cells has been difficult. Furthermore, pairing this information with the corresponding variable (V), diversity (D), and joining (J) [V(D)J] sequences of the antigen-specific T cell receptors has also been challenging due to hurdles in sequencing these large regions, particularly at the single-cell level. Here, we have expanded our previous work of combining two powerful technologies, Immudex dCODE Dextramer™ (RiO) Reagents and the BD Rhapsody™ Single-Cell Analysis System, to detect and characterize low-frequency antigen-specific T cells, including the full sequences of the V(D)J gene segments of the T cell receptors, as well as profile transcriptome and protein expression. Specifically, thousands of sorted PBMCs were multiplexed to provide high-throughput detection of individual antigen-specific CD8+ T cells in combination with the corresponding full V(D)J sequences of the T cell receptors. In addition, we simultaneously obtained gene expression data for over 400 immune-related mRNAs as well as cell phenotypes using a panel of 30 cell surface BD® AbSeq Protein Markers. Together these data can be used to define T cell phenotypes associated with T cell activation states, alongside antigen specificity of enriched CD8+ dextramer+ cells from PBMC populations. This study showcases the importance of multiomic analysis for high-resolution T cell profiling that has broader implications and utility in immuno-oncology, infectious diseases and autoimmunity.

An integrated single-cell multiomics approach to characterize mRNA, intracellular, and surface proteins using intracellular AbSeq and BD® AbSeq Immune Discovery Panel

DNA-barcoded antibodies enable single-cell multiomics approaches that examine protein alongside mRNA in a single cell. Although it is a powerful approach, leading methods are currently limited to surface proteins, which limits understanding of signal-transduction and transcriptional pathways that are often governed by expression changes and posttranslational modifications of intracellular proteins. The ability to analyze intracellular proteins alongside the transcriptome is complicated by the fix and perm processes necessary to access intracellular epitopes, which can negatively impact RNA assay sensitivity. Furthermore, nonspecific binding of antibody-oligos to nucleic acids can generate high background signals.

To address these issues, we generated a protocol that can recover high-quality RNA alongside specific intracellular and surface protein information. Using this protocol in conjunction with the BD Rhapsody™ Single-Cell Analysis System, we simultaneously profiled over 50 protein markers including 14 intracellular proteins with the whole transcriptome. We identified predicted patterns, including increased phosphorylation of AKT protein correlated with the proliferation marker Ki67 upon immune stimulation, and transcription factor (T-bet) expression in a specific cell subset. Together these preliminary results suggest that analysis of intracellular proteins together with the transcriptome may be possible using single-cell sequencing technologies and can enable a deeper understanding of cellular states.

For Research Use Only. Not for use in diagnostic or therapeutic procedures.

Single cell multiomic analysis of T cell exhaustion in vitro

T-cell activation is a key step in the amplification of an immune response. Over the course of an immune response, cells may be chronically stimulated, with some proportion becoming exhausted; an enormous number of molecules are involved in this process. There remain a number of questions about the process, namely: 1) what degree of heterogeneity and plasticity do T-cells exhibit during stimulation? 2) how many unique cell states define chronic stimulation? and 3) what markers discriminate activated from exhausted cells? We addressed these questions by performing single-cell multiomic analysis to simultaneously measure expression of 38 proteins and 399 genes in human T cells expanded in vitro. This approach allowed us to study - with unprecedented depth - how T cells change over the course of chronic stimulation. Comprehensive immunophenotypic and transcriptomic analysis at day 0 enabled a refined characterization of T-cell maturational states and the identification of a donor-specific subset of terminally differentiated T-cells that would have been otherwise overlooked using canonical cell classification schema. As expected, activation downregulated naïve-cell markers and upregulated effector molecules, proliferation regulators, co-inhibitory and co-stimulatory receptors. Our deep kinetic analysis further revealed clusters of proteins and genes identifying unique states of activation, defined by markers temporarily expressed upon 3 days of stimulation (PD-1, CD69, LTA), markers constitutively expressed throughout chronic activation (CD25, GITR, LGALS1), and markers uniquely up-regulated upon 14 days of stimulation (CD39, ENTPD1, TNFDF10); expression of these markers could be associated with the emergence of short-lived cell types. Notably, different ratios of cells expressing activation or exhaustion markers were measured at each time point. These data reveal the high heterogeneity and plasticity of chronically stimulated T cells. Our study demonstrates the power of a single-cell multiomic approach to comprehensively characterize T-cells and to precisely monitor changes in differentiation, activation, and exhaustion signatures during cell stimulation.

Abstract 2788: Deep characterization of tumor infiltrating leukocytes using a combination of flow cytometry and single-cell multiomics

Cancer immunotherapies have the potential to induce durable anti-tumor immune responses; however the efficacy of these treatments varies among patients and partially depends on the complex interplay between malignant cells and non-malignant cells within the tumor microenvironment. In the tumor microenvironment, T cells play a crucial role in eliminating tumor cells and orchestrating anti-tumor immune responses; in contrast immunosuppressive cell types such as myeloid-derived suppressor cells can support tumor progression. Here we harnessed recent advances in single-cell multiomics that allow high-resolution functional characterization of intratumoral immune cells to improve our understanding of their dynamic relationships. Specifically, we utilized a One Solution Workflow to dissociate a solid tumor followed by in-depth dissection of the immune composition of the tumor microenvironment using both flow cytometry and the BD Rhapsody™ Single-Cell Analysis System. We characterized the cellular composition of tumor microenvironment using flow cytometry analysis. Importantly, by examining the expression of mRNA and surface protein markers at single-cell resolution, we unraveled the complexities of the tumor microenvironment, elucidated cellular heterogeneity and identified cell-type specific gene signatures. We propose this One Solution Workflow can be adopted to understand the transcriptional and proteomic phenotypes of tumor infiltrating leukocytes for development of novel immune therapeutic strategies for cancer.

For Research Use Only. Not for use in diagnostic or therapeutic procedures. Class 1 Laser Product.BD-23279 (v1.0) 1120BD, the BD Logo and Rhapsody are trademarks of Becton, Dickinson and Company or its affiliates. © 2020 BD. All rights reserved.

Citation Format: Xiaoshan Shi, Margaret Nakamoto, Aaron Middlebrook, Wei Huang, Evelyn Lo, Patrick T. Neuhoefer, Scott Bornheimer, Smita Ghanekar. Deep characterization of tumor infiltrating leukocytes using a combination of flow cytometry and single-cell multiomics [abstract]. In: Proceedings of the American Association for Cancer Research Annual Meeting 2021; 2021 Apr 10-15 and May 17-21. Philadelphia (PA): AACR; Cancer Res 2021;81(13_Suppl):Abstract nr 2788.

Immune phenotypic analysis using predesigned and lyophilized BD® AbSeq Immune Discovery Panel

High-throughput single cell RNA sequencing (scRNA-seq) has recently emerged as a powerful tool for profiling complex cell populations. While traditional scRNA-seq captures information at the transcript level, recent technology using DNA-barcoded antibodies enable multiomic analysis, examining protein alongside mRNA. Although this approach allows analyzing a large number of protein markers, the sequencing cost can escalate quickly for large panels, particularly ones with high antigen-density markers, and workflows can be long. Therefore, panels should be optimized to gain meaningful results efficiently and cost-effectively. Here, we introduce the BD® AbSeq Immune Discovery Panel (IDP), a lyophilized panel consisting of 30 antibodies against major human immune cell-types and immune response markers for analyzing multiple immune cell subsets. The BD® AbSeq IDP can be used to uncover phenotypic changes in cell subsets such as unique cell input differences or changes in the immune cell status. To test this capability, we used the IDP alongside a mRNA analysis using targeted mRNA panel and whole transcriptome assay to compare the immune phenotypes of cells from disease and in vitro stimulated samples at the single-cell level using the BD Rhapsody™ System. We propose that the BD® AbSeq IDP can be used to identify the cell types and molecular pathways impacted by the disease at the single cell level.

For Research Use Only. Not for use in diagnostic or therapeutic procedures.

BD, the BD Logo, and Rhapsody are trademarks of Becton, Dickinson and Company or its affiliates. © 2019 BD. All rights reserved.

Multiomic characterization of T-cell populations at the single-cell level utilizing sensitive dextramers and BD® AbSeq on the BD Rhapsody™ Single-Cell Analysis system

Adoptively transferred antigen-specific T cells have shown great efficacy in treatment of some virus-associated diseases and malignancies. A major driver of the development of adoptive T-cell therapy has been our ability to successfully characterize the functional status and antigen specificity of T cells. However, this has been limited by inefficient detection of antigen-specific T cells possibly due to their low frequency and low binding affinities to known MHC-peptide complexes. Here, we aim to combine two powerful technologies, advanced dCODE™ Dextramer® from Immudex and single-cell multiomics analysis using the BD Rhapsody™ Single-Cell Analysis system, to detect and characterize disease-specific CD8+ T cells within thousands of PBMCs. Currently, we are able to identify over 350 mRNAs alongside a panel of over 20 BD® AbSeq cell surface protein markers which can be associated with T cell activation states. These data can be used to define T-cell phenotypes alongside antigen specificity of enriched CD8+ dextramer+ cells from a PBMC population. This study outlines our ability for high-resolution T-cell profiling that has broader implications and utility in immuno-oncology, infectious diseases and autoimmunity.

For Research Use Only. Not for use in diagnostic or therapeutic procedures.

BD, the BD Logo, and Rhapsody are trademarks of Becton, Dickinson and Company or its affiliates. © 2019 BD. All rights reserved.

Deep characterization of tumor infiltrating leukocytes using a combination of flow cytometry and single-cell multiomics

Cancer immunotherapies have the potential to induce durable anti-tumor immune responses; however the efficacy of these treatments varies among patients and partially depends on the complex interplay between malignant cells and non-malignant cells within the tumor microenvironment. In the tumor microenvironment, T cells play a crucial role in eliminating tumor cells and orchestrating anti-tumor immune responses; in contrast immunosuppressive cell types can support tumor progression. Here we harnessed recent advances in single-cell multiomics that allow high-resolution functional characterization of intratumoral immune cells to improve our understanding of their dynamic relationships. Specifically, we utilized a One Solution Workflow to dissociate a solid tumor followed by in-depth dissection of the immune composition of the tumor microenvironment using both flow cytometry and the BD Rhapsody™ Single-Cell Analysis System. We characterized the cellular composition of tumor microenvironment using flow cytometry. Importantly, by examining the expression of mRNA and surface protein markers at single-cell resolution, we unraveled the complexities of the tumor microenvironment, elucidated cellular heterogeneity and identified cell-type specific gene signatures. We propose this One Solution Workflow can be adopted to understand the transcriptional and proteomic phenotypes of tumor infiltrating leukocytes for development of novel immune therapeutic strategies for cancer.

For Research Use Only. Not for use in diagnostic or therapeutic procedures.

Class 1 Laser Product.

BD-23279 (v1.0) 1120

BD, the BD Logo and Rhapsody are trademarks of Becton, Dickinson and Company or its affiliates. © 2020 BD. All rights reserved.

Abstract 3779: Multiomic single cell analysis of normal human bone marrow identifies a unique stem and progenitor population that expands in AML

Hematopoietic stem and progenitor cells (HSPCs) can generate a diversity of blood cells throughout the human lifespan. Although these cells have been evaluated using both sorted (Corces et al. Nat. Genet. 2016) and single cell assays (Pellin et al Nat. Commun. 2019), there remains uncertainty in the degree of heterogeneity within HSPC subpopulations and their associated differentiation trajectories. The phenotypic diversity within HSPCs needs to be better characterized in order to understand the pathogenesis of blood disorders including hematologic malignancies. To address this need, we characterized healthy bone marrow mononuclear cells (BMMCs) with whole transcriptome analysis (WTA) and surface marker evaluation. We hypothesized that by utilizing concurrent RNA and surface marker analysis (n=35), we can improve HSPC clustering and characterize specific phenotypic states along unique hematopoietic differentiation trajectories. Three healthy BMMC samples were stained with antibody conjugated oligonucleotides (BD® Abseq) and analyzed using BD Rhapsody™. We filtered 8,070 high quality cells for 2,508 HSPCs, myeloid cells, and lymphocyte precursors. The antibody-derived tags (ADTs) obtained from BD® Abseq comprised 33 of the most informative features (n=2000) and resulted in more stable clustering as determined by within sum of squares (WSS = 898 verses 934 for WTA alone for 20 clusters). Additionally, we designed a targeted HSPC panel (n=500 genes) with BD® Abseq which identified similar cell clusters compared to the WTA alone and WTA plus ADT data (rand index = 0.88). HSPC clustering identified putative hematopoietic stem cell (HSC), common myeloid progenitor (CMP), and megakaryocyte-erythroid progenitor (MEP) clusters that expressed canonical surface markers. Of interest, we identified candidate novel myeloid, T-cell, and B-cell primed precursors and new surface marker expression gradients that align with specific differentiation trajectories. The results of this analysis will be presented. The HSPC clusters were converted into a signature matrix using Cibersortx (Newman et al. Nat. Biotechnol. 2019), and bulk acute myeloid leukemia (AML) and healthy samples were deconvolved into respective healthy cell clusters. We subsequently performed multivariate Cox proportional hazard analysis, and observed that high levels of healthy cluster 8 (H8; HR 3.40, 95% confidence interval 1.24-9.34), the candidate lymphoid-primed multipotent progenitor (LMPP), and low levels of healthy cluster 6 (H6; HR 0.26, 95% confidence interval 0.12-0.58), a candidate erythrocyte precursor, at diagnosis were associated with worse overall survival. Deconvolution using sorted healthy sub-populations (Corces et al. Nat. Genet. 2016) only identified erythrocyte precursors as statistically relevant (HR 0.27, 95% confidence interval 0.12-0.61). Of note, H8 had a distinct gene expression profile compared to that identified for the sorted LMPP sub-population using differential gene expression analysis. In summary, we identified novel cell type clusters and surface marker associations using combined single cell WTA and surface marker analysis (BD® Abseq). We were able to correlate cell types with both canonical and novel surface markers, and deconvolution analysis provided preliminary insights into their clinical relevance in AML.

Citation Format: Asiri Ediriwickrema, Sreejith Ramakrishnan, Margaret Nakamoto, Smita Ghanekar, Bogdan Luca, Aaron Newman, Andrew Gentles, Ravindra Majeti. Multiomic single cell analysis of normal human bone marrow identifies a unique stem and progenitor population that expands in AML [abstract]. In: Proceedings of the Annual Meeting of the American Association for Cancer Research 2020; 2020 Apr 27-28 and Jun 22-24. Philadelphia (PA): AACR; Cancer Res 2020;80(16 Suppl):Abstract nr 3779.

Abstract 1344: Simultaneous mRNA, protein, and immune repertoire profiling of antigen-specific T cells by single cell sequencing

High-throughput single cell RNA-seq (scRNA-seq) has transformed our understanding of complex and heterogenous immune populations. New advances in scRNA-seq are expanding the molecules that can be profiled at the single cell level, such as oligo-conjugated antibody technologies that enable protein expression profiling alongside mRNA. Although the ability to sequence the immune repertoire can provide crucial insights into understanding the complexities of the adaptive immune system and advancing discoveries in immuno-oncology, the ability to extract this information from single cells requires new technology to profile regions of the mRNA that are missed by conventional 3' scRNA-seq. In this study we utilized an ex vivo antigen stimulation system to measure antigen-specific T-cell activation and clonal amplification. Stimulated T cells from two donors were loaded onto the BD Rhapsody™ Single-Cell Analysis System to extract immune repertoire information in addition to gene and protein expression information from the same cells. In a single workflow, we profiled a panel of 400 mRNA targets, 20 BD® AbSeq protein markers associated with different status of T-cell activation, and the hypervariable region of T-cell receptors at the single cell resolution. The study is a proof of concept of combining mRNA, protein and immune repertoire analysis at the single cell level to deconvolute the heterogeneity and different activation of stimulated T cells.

For Research Use Only. Not for use in diagnostic or therapeutic procedures.

BD, the BD Logo, and Rhapsody are trademarks of Becton, Dickinson and Company or its affiliates. © 2019 BD. All rights reserved.

Citation Format: Imteaz Siddique, Xiaoshan Shi, Margaret Nakamoto, Stefanie Mortimer. Simultaneous mRNA, protein, and immune repertoire profiling of antigen-specific T cells by single cell sequencing [abstract]. In: Proceedings of the Annual Meeting of the American Association for Cancer Research 2020; 2020 Apr 27-28 and Jun 22-24. Philadelphia (PA): AACR; Cancer Res 2020;80(16 Suppl):Abstract nr 1344.

Abstract 6197: Improving sample preparation workflows for single cell multiomic analysis of infiltrating leukocytes from solid tumors

Single cell multiomic (scM) methods are powerful tools to characterize patient-specific tumor-immune microenvironment, but current methods of sample handling and preparation can introduce bias. Obtaining non-biased results is particularly important in studies to identify new biomarkers for patient stratification of responders versus non-responders for immunotherapies in oncology. This problem is becoming acute as the number of immune-therapy modalities and combinations in clinical trials and in medical practice continue to expand. Current methodologies used to analyze patient specimens in routine pathology are not adequate to address heterogeneity and complexity of immune cell ecosystem of individuals. SCM analysis of immune cells from tumor microenvironment using technologies that allow high parameter analysis of genes and proteins will allow a comprehensive atlas of immune cells in the tumor tissue, however the quality of single cell sample preparation is critical. Here, we report evaluation of several available solid tumor dissociation methods, including mechanical dissociation by scalpel, BD™ Medimachine System, Miltenyi gentleMACS™ dissociator. Mechanical dissociation was followed by enzymatic dissociation using BD Horizon™ Dri Tumor & Tissue Dissociation Reagent or, in the case of gentleMACS™, the Miltenyi Tumor Dissociation Kit. Metrics evaluated were cell recovery, viability, and proportion of various cell lineage populations using flow cytometry; and expression of 399 mRNA transcripts and 31 proteins using single cell multiomics (BD Rhapsody™, BD Rhapsody™ Immune Response Targeted Panel, and BD™ AbSeq). Tumor tissues were from a mouse a pancreatic (PDAC) tumor model and humanized Patient-Derived Xenograft (PDX; from Onco-hu® mice) models of colon and lung cancer. Method dependent differences in viable cell yield and proportions of immune vs. tumor cells were observed. SCM analysis of FACS sorted CD45+ tumor-infiltrating lymphocytes (TILs) showed differences in gene and protein expression profiles, particularly for expression of rare vs. abundant genes depending on the dissociation method. Our data identify protocols to interrogate tumor immune microenvironment starting from tumor tissue specimen through scM all the way to informatics analysis with consistent results. Similar studies and further optimization are recommended for other tumor types. Consistent adoption of standardized protocols will enable robust findings in research and clinical trials, with the ultimate goal of improved therapies, biomarkers and outcomes.

For Research Use Only. Not for use in diagnostic or therapeutic procedures. GentleMACS™ is trademark of Miltenyi Biotec. Onco-hu® is a registered trademark of The Jackson Laboratory. BD, the BD Logo, Horizon, Medimachine, and Rhapsody are trademarks of Becton, Dickinson and Company or its affiliates.

© 2019 BD. All rights reserved.

Citation Format: Aaron J. Middlebrook, Wei Huang, Margaret Nakamoto, Xiaoshan Shi, Evelyn Lo, Patrick Neuhoefer, Scott Bornheimer, Smita Ghanekar. Improving sample preparation workflows for single cell multiomic analysis of infiltrating leukocytes from solid tumors [abstract]. In: Proceedings of the Annual Meeting of the American Association for Cancer Research 2020; 2020 Apr 27-28 and Jun 22-24. Philadelphia (PA): AACR; Cancer Res 2020;80(16 Suppl):Abstract nr 6197.

Abstract 2166: Deep characterization of in vitro chronically stimulated T cells via single-cell multiomic analysis

A key step in the clinical production of CAR T cells is the expansion of engineered T cells. To generate enough cells for viable adoptive cell therapy, cells must be robustly stimulated, which raises the risk of inducing T-cell exhaustion and reducing therapeutic efficacy. As protocols for T-cell expansion are being developed to optimize CAR T-cell yield, function and persistence, fundamental questions about the impact of in vitro manipulation on T-cell identity are important to answer. Namely: 1) what types of cells are generated during chronic stimulation? 2) how many unique cell states can be defined during chronic stimulation? We sought to answer these fundamental questions by performing single-cell multiomic analysis using BD® AbSeq and BD Rhapsody™ Single-Cell Analysis system to simultaneously measure expression of 38 proteins and 399 genes in human T cells expanded in vitro. This approach allowed us to study - with unprecedented depth - how T cells change throughout chronic stimulation. Human PBMCs from three healthy donors were stimulated for 14 days in the presence of CD3/CD28 antibody-coated beads and recombinant human IL-2. This model system resembles culture conditions that may be used for CAR T-cell expansion. Cells were collected at different time points (day 0, 3, 7 and 14) prior to downstream analysis. Comprehensive immunophenotypic and transcriptomic analysis at day 0 enabled a refined characterization of T-cell maturational states (from naïve to TEMRA cells) and the identification of a donor-specific subset of terminally differentiated T cells that would have been otherwise overlooked using canonical cell classification schema. As expected, T-cell activation induced downregulation of naïve-associated markers and upregulation of effector molecules, proliferation regulators, co-inhibitory and co-stimulatory receptors. Our deep kinetic analysis further revealed clusters of proteins and genes identifying unique states of activation defined by markers temporarily expressed upon 3 days of stimulation (PD-1, CD69, LTA), markers constitutively expressed throughout chronic activation (CD25, GITR, LGALS1), and markers uniquely up-regulated upon 14 days of stimulation (CD39, ENTPD1, TNFSF10). Notably, different ratios of cells expressing activation or exhaustion markers were measured at each time point. These data indicate heterogeneity and plasticity of chronically stimulated T cells in response to different kinetics of activation. We demonstrate the power of a single-cell multiomic approach to comprehensively characterize T cells and to precisely monitor changes in differentiation, activation and exhaustion signatures in response to different activation protocols. For Research Use Only. Not for use in diagnostic or therapeutic procedures. BD, the BD Logo, and Rhapsody are trademarks of Becton, Dickinson and Company or its affiliates. © 2019 BD. All rights reserved.

Citation Format: Mirko Corselli, Suraj Saksena, Margaret Nakamoto, Woodrow E. Lomas, Ian Taylor, Pratip K. Chattopadhyay. Deep characterization of in vitro chronically stimulated T cells via single-cell multiomic analysis [abstract]. In: Proceedings of the Annual Meeting of the American Association for Cancer Research 2020; 2020 Apr 27-28 and Jun 22-24. Philadelphia (PA): AACR; Cancer Res 2020;80(16 Suppl):Abstract nr 2166.

Abstract 1348: Optimizing experimental design for high-parameter protein analysis using BD AbSeq technology

High-throughput single cell RNA sequencing (RNA-seq) has recently emerged as a powerful tool for profiling complex cell populations. While traditional single cell RNA-seq captures information about transcript expression, recent technological advances using oligo-conjugated antibodies enable simultaneous detection of proteins alongside mRNA in high-throughput sequencing. This multiomic technology enables high parameter protein analysis that can simultaneously discriminate 100 protein markers. However, experiment workflow time and cost can escalate quickly with high plexy assays. To address these issues we investigated a number of methods to decrease cost and assay time while maintaining data quality using the BD® AbSeq on the BD Rhapsody™ Single-Cell Analysis sequencing system. To begin, we investigated the performance of 20 core proteins when used in a 20plex, 40plex, 60plex, 80plex, or 100plex in model cells. Results from 3 experiments showed that performance was maintained as plexy increased, however rigorous experimental approaches must be followed to minimize impact on specificity or sensitivity. After establishing performance of this 20plex we investigated pre-cocktailing of antibodies as a method to shorten the day-of-experiment workflow, and mixing of oligo-labeled and unlabeled antibodies to high-expressing proteins (“signal muting”) as a way to decrease sequencing costs. Results showed a decrease in specificity as soon as 24 hours after the cocktailing of antibodies and increasing non-specific binding with longer cocktail storage times. On the other hand, signal muting was effective at decreasing sequencing requirements by up to 70%, without impacting data for high expressors. Together these results can be used to aid in optimizing experimental design when working with high-plex AbSeq protein panels, to better harness the information gained from multiomic single cell sequencing data. For Research Use Only. Not for use in diagnostic or therapeutic procedures.BD, the BD Logo, and Rhapsody are trademarks of Becton, Dickinson and Company or its affiliates. © 2019 BD. All rights reserved.

Citation Format: Punya Narayan, Hye-Won Song, Margaret Nakamoto, Elisabeth Walczak, Katherine Lazaruk, Stefanie Mortimer. Optimizing experimental design for high-parameter protein analysis using BD AbSeq technology [abstract]. In: Proceedings of the Annual Meeting of the American Association for Cancer Research 2020; 2020 Apr 27-28 and Jun 22-24. Philadelphia (PA): AACR; Cancer Res 2020;80(16 Suppl):Abstract nr 1348.

Abstract 1345: Advances in single cell whole transcriptome analysis: Single nucleus RNAseq and simultaneous protein and mRNA profiling using the BD RhapsodyTM Single-Cell Analysis system and BD® AbSeq

Advances in high-throughput single cell whole transcriptome analysis (WTA) have enabled the discovery of biomarkers and cellular pathways critical to resolving diversity in diseases. Despite these advances, challenges still remain in comprehensively profiling single cells. Here we address two challenges, limited use of frozen tissues, and inability to resolve post-transcriptional differences from cell to cell.

Single-cell RNAseq often requires intact single cells to get good resolution of signal, preventing the use of archival frozen samples. To overcome this limitation, we have tested the possibility to use dissociated nuclei that can be isolated from frozen samples in the BD RhapsodyTM Single-Cell Analysis system. As a proof of concept, we compared high throughput single-nucleus WTA data to that produced from single-cell RNAseq from the same cell type. Our data showed that mRNAs from single nuclei can be captured, and amplified using the BD RhapsodyTM system. Furthermore although the number of molecules detected is lower in nucleus, probably due to lower mRNA content, their expression profiles are well correlated with Pearson's correlation coefficient over 0.9. This opens up the possibility to conduct single cell transcriptomic analysis on the large pool of archived frozen specimens, expanding the variety and number of disease samples that can be examined at the single cell level in the BD RhapsodyTM system.

A second limitation of WTA analysis is that it only provides information about gene regulation at the transcript level. Given that regulation critical for cellular pathways is often found not only at the transcriptional level but also at the post-transcriptional level, quantitative analysis of proteins and mRNAs at the single cell level can provide deeper understanding of the disease cells. Here, we used DNA-barcoded antibodies BD® AbSeq to enable multiomic analysis, examining protein alongside mRNA expression and enabling simultaneous transcriptional and post-transcriptional gene profiling in single cells. Our data show that upon activation human peripheral blood mononuclear cells and isolated T cells undergo regulation of markers at the protein level that cannot be resolved at the mRNA level. Several key markers used to define activation states including CD69 and L-Selectin were found to be regulated at the protein level confirming that addition of protein analysis to WTA can generate more comprehensive cell profiling.

These approaches offer flexibility and choice in experimental design and allow users to utilize archived frozen samples or to obtain mRNA and protein profiles from single cells.

For Research Use Only. Not for use in diagnostic or therapeutic procedures.

BD, the BD Logo, and Rhapsody are trademarks of Becton, Dickinson and Company or its affiliates. © 2019 BD. All rights reserved.

Citation Format: Hye-Won Song, Gretchen Y. Lam, Margaret Nakamoto, Punya Narayan, Ian Taylor, Stefanie Mortimer. Advances in single cell whole transcriptome analysis: Single nucleus RNAseq and simultaneous protein and mRNA profiling using the BD RhapsodyTM Single-Cell Analysis system and BD® AbSeq [abstract]. In: Proceedings of the Annual Meeting of the American Association for Cancer Research 2020; 2020 Apr 27-28 and Jun 22-24. Philadelphia (PA): AACR; Cancer Res 2020;80(16 Suppl):Abstract nr 1345.

Simultaneous mRNA, protein, and immune repertoire profiling of antigen-specific T cells by single cell sequencing

High-throughput single cell RNA-seq (scRNA-seq) has transformed our understanding of complex and heterogenous immune populations. New advances in scRNA-seq are expanding the molecules that can be profiled at the single cell level, such as oligo-conjugated antibody technologies that enable protein expression profiling alongside mRNA. Although the ability to sequence the immune repertoire can provide crucial insights into understanding the complexities of the adaptive immune system and advancing discoveries in immuno-oncology, the ability to extract this information from single cells requires new technology to profile regions of the mRNA that are missed by conventional 3′ scRNA-seq. In this study we utilized an ex vivo antigen stimulation system to measure antigen-specific T-cell activation and clonal amplification. Stimulated T cells from two donors were loaded onto the BD Rhapsody™ Single-Cell Analysis System to extract immune repertoire information in addition to gene and protein expression information from the same cells. In a single workflow, we profiled a panel of 400 mRNA targets, 20 BD® AbSeq protein markers associated with different status of T-cell activation, and the hypervariable region of T-cell receptors at the single cell resolution. The study is a proof of concept of combining mRNA, protein and immune repertoire analysis at the single cell level to deconvolute the heterogeneity and different activation of stimulated T cells.

For Research Use Only. Not for use in diagnostic or therapeutic procedures.

BD, the BD Logo, and Rhapsody are trademarks of Becton, Dickinson and Company or its affiliates. © 2019 BD. All rights reserved.

Deep characterization of in vitro chronically stimulated T cells via single-cell multiomic analysis

To generate enough cells for viable adoptive cell therapy, cells must be robustly stimulated, which raises the risk of inducing T-cell exhaustion and reducing therapeutic efficacy. To comprehensively characterize in vitro chronically expanded human T cells, we performed single-cell multiomic analysis using BD® AbSeq and BD Rhapsody™ Single-Cell Analysis system for simultaneous measurement of the expression of 38 proteins and 399 genes. Comprehensive immunophenotypic and transcriptomic analysis at day 0 enabled a refined characterization of T-cell maturational states. T-cell activation induced by anti-CD3/CD28 beads and recombinant human IL-2 led to downregulation of naïve-associated markers and upregulation of effector molecules, proliferation regulators, co-inhibitory and co-stimulatory receptors. Our deep kinetic analysis further revealed clusters of proteins and genes identifying unique states of activation defined by markers temporarily expressed upon 3 days of stimulation, markers constitutively expressed throughout chronic activation, and markers uniquely up-regulated upon 14 days of stimulation. These data indicate heterogeneity and plasticity of chronically stimulated T cells in response to different kinetics of activation. We demonstrate the power of a single-cell multiomic approach to comprehensively characterize T cells and to precisely monitor changes in differentiation, activation and exhaustion signatures in response to different activation protocols.

For Research Use Only. Not for use in diagnostic or therapeutic procedures.

BD, the BD Logo, and Rhapsody are trademarks of Becton, Dickinson and Company or its affiliates. © 2019 BD. All rights reserved.

Molecular cytometry identifies a wide range of translationally relevant markers in tumor and peripheral immune cells of lung cancer patients

Many immunotherapy drugs, used singly or in combination, are emerging. To realize precision oncology, and better design clinical trials, in-depth immune profiling is key. Many new technologies are available; the most promising simultaneously analyzes >102 proteins and 400 mRNA cell-by-cell (molecular cytometry). Using this technology, we deeply profiled TIL, from freshly resected lung tissue, and PBMC collected at surgery (n=10).

Antibody staining was robust, with all canonical cell populations at expected frequency. We identified markers uniquely upregulated in TIL, including CXCR6, CD39, CD26, CD69, CD103, and RGS. We also asked what markers were uniquely enriched in PD1-TIL, in order to find other drug targets for patients who fail Nivolumab. We found many molecules upregulated in PD1-TIL, including CD326, CD98, LGALS3, TIM3, CD54, CD235ab, CXCL8, CD141, and CD117. We further identified precise combinations of these markers that inform design of combination immunotherapy.

We also characterized immune landscapes in metastatic disease vs. localized adenocarcinoma, finding drug targets and tumor-immune interactions are different across these settings. For example, T-cell activation markers are downregulated in metastatic tissue, e.g., HLADR (p = 1.5E-16), CD69 (p=2.9e-10), and CD38 (p=3.2e-16). CD103 was also highly downregulated (p=1.9E-14). Notably, in metastatic disease various myeloid proteins are elevated, including CD206 (p=0.002), CD32 (p=0.02), and CD61 (p=0.006). We also characterized the degree of immune exhaustion, using ratios of ZBED2:LGALS in cells. In summary, we demonstrate the utility of molecular cytometry for providing unique (and translationally-relevant) insight into lung cancer.

Multiomic characterization of T-cell populations at the single-cell level utilizing sensitive dextramers and BD® AbSeq on the BD Rhapsody™ Single-Cell Analysis system

Adoptively transferred antigen-specific T cells have shown great efficacy in treatment of some virus-associated diseases and malignancies. A major driver of the development of adoptive T-cell therapy has been our ability to successfully characterize the functional status and antigen specificity of T cells. However, this has been limited by inefficient detection of antigen-specific T cells possibly due to their low frequency and low binding affinities to known MHC-peptide complexes. Here, we aim to combine two powerful technologies, advanced dCODE™ Dextramer® from Immudex and single-cell multiomics analysis using the BD Rhapsody™ Single-Cell Analysis system, to detect and characterize disease-specific CD8+ T cells within thousands of PBMCs. Currently, we are able to identify over 350 mRNAs alongside a panel of over 20 BD® AbSeq cell surface protein markers which can be associated with T cell activation states. These data can be used to define T-cell phenotypes alongside antigen specificity of enriched CD8+ dextramer+ cells from a PBMC population. This study outlines our ability for high-resolution T-cell profiling that has broader implications and utility in immuno-oncology, infectious diseases and autoimmunity.

Abstract B90: Deep characterization of in vitro chronically stimulated T cells through single-cell multiomic analysis

A key step in the clinical production of CAR T cells is the expansion of engineered T cells. To generate enough cells for a therapeutic product, cells must be robustly stimulated, which raises the risk of inducing T-cell exhaustion and reducing therapeutic efficacy. As protocols for T-cell expansion are being developed to optimize CAR T cell yield, function, and persistence, fundamental questions about the impact of in vitro manipulation on T-cell identity are important to answer. Namely: 1) What types of cells are generated during chronic stimulation? 2) How many unique cell states can be defined during chronic stimulation? We sought to answer these fundamental questions by performing single-cell multiomic analysis to simultaneously measure expression of 38 proteins and 399 genes in human T cells expanded in vitro. This approach allowed us to study—with unprecedented depth—how T cells change over the course of chronic stimulation. Human PBMCs from three healthy donors were continuously stimulated for 14 days in the presence of CD3/CD28 antibody-coated beads and recombinant human IL-2. This model system was developed to resemble culture conditions that may be used for CAR T cell expansion. Cells were collected at different time points (day 0, 3, 7, and 14) prior to downstream analysis. Comprehensive immunophenotypic and transcriptomic analysis at day 0 enabled a refined characterization of T-cell maturational states (from naive to TEMRA cells) and the identification of a donor-specific subset of terminally differentiated T-cells that would have been otherwise overlooked using canonical cell classification schema. As expected, T-cell activation induced downregulation of naive-associated markers and upregulation of effector molecules, proliferation regulators, coinhibitory and costimulatory receptors. Our deep kinetic analysis further revealed clusters of proteins and genes identifying unique states of activation defined by markers temporarily expressed upon 3 days of stimulation (PD-1, CD69, LTA), markers constitutively expressed throughout chronic activation (CD25, GITR, LGALS1), and markers uniquely upregulated upon 14 days of stimulation (CD39, ENTPD1, TNFSF10). Notably, different ratios of cells expressing activation or exhaustion markers were measured at each time point. These data indicate high heterogeneity and plasticity of chronically stimulated T cells in response to different kinetics of activation. In this study, we demonstrate the power of a single-cell multiomic approach to comprehensively characterize T cells and to precisely monitor changes in differentiation, activation, and exhaustion signatures in response to different activation protocols.

Citation Format: Mirko Corselli, Margaret Nakamoto, Chip Lomas, Ian Taylor, Suraj Saksena, Tariq Arshad, Pratip K. Chattopadhyay. Deep characterization of in vitro chronically stimulated T cells through single-cell multiomic analysis [abstract]. In: Proceedings of the AACR Special Conference on Tumor Immunology and Immunotherapy; 2019 Nov 17-20; Boston, MA. Philadelphia (PA): AACR; Cancer Immunol Res 2020;8(3 Suppl):Abstract nr B90.

Abstract 3531: Modular RNA expression analysis using whole transcriptome and targeted analysis in single cells on BD Rhapsody

Advances in genomics have allowed high-throughput single-cell whole transcriptome analysis (WTA) to enable the discovery of biomarkers and cellular pathways that may be important in diseases. As a complementary tool to WTA, targeted analysis can provide high sensitivity of single cell gene expression data with lower sequencing cost. Here we demonstrate using the BD Rhapsody platform in a modular fashion to generate both WTA and targeted sequencing libraries from the same sample. Utilizing the archivability of the BD Rhapsody beads, we first subsampled a portion of the beads to generate WTA data, from which we identified genes that are important for T cell exhaustion. We then designed a targeted panel to profile the rest of the beads from the same experiment. The study demonstrates the versatility of the BD Rhapsody single cell platform and the ability to conduct different workflows on the same sample. This approach offers flexibility and choice for users in experimental design and allows users to easily transition from novel target discovery to robust data validation using targeted panels.

Citation Format: Margaret Nakamoto, Gretchen Lam, Christina Chang, Eleen Shum. Modular RNA expression analysis using whole transcriptome and targeted analysis in single cells on BD Rhapsody [abstract]. In: Proceedings of the American Association for Cancer Research Annual Meeting 2019; 2019 Mar 29-Apr 3; Atlanta, GA. Philadelphia (PA): AACR; Cancer Res 2019;79(13 Suppl):Abstract nr 3531.

Abstract 4118: Molecular cytometry for immunotherapy trials

The ability to simultaneously query both protein and mRNA expression on tens of thousands of single cells has emerged only recently, with the development of CITE-seq, REAP-seq, and Ab-seq platforms. Each technology relies on antibodies conjugated to oligonucleotide tags, followed by capture of antibody-stained cells for single cell RNA-sequencing. The technologies have important advantages over flow cytometry, chiefly in that they allow study of a limitless number of parameters, and single cell RNA sequencing, which cannot identify cell populations with as much verity as protein/antibody-based analysis. We characterized the newest molecular cytometry technique (Ab-seq, BD Biosciences) by titrating nearly 100 antibodies (in a single staining experiment and sequencing run), and demonstrated that oligonucleotide antibodies exhibit the same staining characteristics and patterns as flow cytometry antibodies. We also comprehensively examined cells discordant for protein and mRNA expression, in order to discriminate true features of immune cell biology from artifacts caused by drop-out in sequencing assays. Importantly, we also found that mRNA expression could guide the discrimination of cells expressing a protein versus those lacking expression, and define a remarkably low limit of detection for the technology: 1-5 molecules. This remarkable sensitivity will allow detection of cells expressing even the lowest levels of immune exhaustion and checkpoint molecules in cancer immunotherapy trials, and could enable better biomarker discovery than existing technologies. Moreover, this approach allows more detailed characterization of the tumor microenvironment and periphery than ever before. Indeed, in a lymphoma patient, we show that cells expressing both PD1 and CTLA4 carry a unique and specific signature that includes markers never revealed by flow cytometry or other technologies, which might represent new targets for immunotherapy. In sum, this presentation will characterize this new technology and demonstrate the power and promise of new molecular cytometry tools.

Citation Format: Woodrow E. Lomas, Aidan F. Winters, Jason Alexandre, Jody Martin, Nidhanjali Bansal, Margaret Nakamoto, Brent Gaylord, Suraj Saksena, Pratip K. Chattopadhyay. Molecular cytometry for immunotherapy trials [abstract]. In: Proceedings of the American Association for Cancer Research Annual Meeting 2019; 2019 Mar 29-Apr 3; Atlanta, GA. Philadelphia (PA): AACR; Cancer Res 2019;79(13 Suppl):Abstract nr 4118.

Simultaneous mRNA, protein, and immune-repertoire profiling of thousands of single cells

High-throughput single cell RNA-seq (scRNA-seq) has transformed our understanding of heterogenous immune populations. Advances in scRNA-seq, such as oligo-conjugated antibody technologies that enable protein expression profiling alongside mRNA, are expanding the range of molecules that can be profiled at the single cell level. Although sequencing the T-cell and B-cell immune repertoire can provide crucial insights into the complexities of the adaptive immune system, thus advancing discoveries in immunology and immune-oncology, the ability to extract this information from single cells requires new technology to profile regions of the mRNA missed by conventional 3′ scRNA-seq. Here we demonstrate a novel approach using the BD Rhapsody™ system to extract immune-repertoire information in addition to gene-expression information from the same cells. In a single workflow, we profiled a panel of 400 mRNA targets and 40 protein markers as well as the CDR3 region of T- and B-cell receptors in thousands of human PBMCs. After using the mRNA and protein information to robustly annotate different lymphocyte populations, we examined the T- and B-cell repertoires for differences in their clonal diversity. We were able to identify clonally expanded T cells and B cells and examine how their gene-expression profiles differ from that of non-expanded cells. This study demonstrates the power of combining mRNA, protein, and immune repertoire analysis at the single cell level to answer complex and important biological and clinical questions.

For Research Use Only. Not for use in diagnostic or therapeutic procedures.

BD, the BD Logo, and Rhapsody are trademarks of Becton, Dickinson and Company. © 2019 BD and its subsidiaries. All rights reserved.

Single cell multiomic analysis of chronically stimulated T cells displaying hallmarks of T-cell exhaustion

T-cell exhaustion is a dysfunctional state caused by persistent antigen stimulation mediated by chronic infections or cancer. Current immunotherapy approaches focus on reinvigorating exhausted T cells through immune-receptor-blocking antibodies. A deeper understanding of the exhausted T-cell state is crucial for identification of new therapeutic targets. Single cell RNA-sequencing (scRNA-seq) is a powerful tool for resolving heterogeneity in complex systems like these; however the lack of protein information for the same cells can make it difficult to identify cells of interest or detect cellular responses. To resolve both mRNA and protein information in the same assay, we utilized DNA-conjugated BD™ AbSeq antibodies to profile protein and mRNA expression, using high-throughput sequencing analysis at the single cell level. Sorted T cells that had been transiently and chronically stimulated were multiplexed using the BD™ Single-Cell Multiplexing Kit and pooled before undergoing cell partitioning and cDNA capture on the BD Rhapsody™ system; this minimized batch effects and saved time and reagents. A panel of 400 mRNA targets alongside the 39-plex antibody panel was used for the study. We showed that cell-type resolution increased with higher protein plex, and the addition of mRNA information alongside protein markers revealed candidate protein markers for specific cell states. This study showcased the power of multiomics in analyzing heterogenous cell populations and cell states and answering complex biological questions.

Research Use Only. Not for use in diagnostic or therapeutic procedures.

BD, the BD Logo, and Rhapsody are trademarks of Becton, Dickinson and Company. © 2019 BD and its subsidiaries. All rights reserved.

Direct Selection of Fluorescence-Enhancing RNA Aptamers

RNA aptamers that generate a strong fluorescence signal upon binding a nonfluorescent small-molecule dye offer a powerful means for the selective imaging of individual RNA species. Unfortunately, conventional in vitro discovery methods are not efficient at generating such fluorescence-enhancing aptamers, because they primarily exert selective pressure based on target affinity-a characteristic that correlates poorly with fluorescence enhancement. Thus, only a handful of fluorescence-enhancing aptamers have been reported to date. In this work, we describe a method for converting DNA libraries into "gene-linked RNA aptamer particles" (GRAPs) that each display ∼10⁵ copies of a single RNA sequence alongside the DNA that encodes it. We then screen large libraries of GRAPs in a high-throughput manner using the FACS instrument based directly on their fluorescence-enhancing properties. Using this strategy, we demonstrate the capability to generate fluorescence-enhancing aptamers that produce a variety of different emission wavelengths upon binding the dye of interest.

Age-related Changes in Energy Intake and Weight in Community-dwelling Middle-aged and Elderly Japanese

OBJECTIVE

This study attempts to describe trends in energy intake and weight change over 12 years according to age at first participation in the study.

DESIGN

Prospective cohort study.

SETTING

The National Institute for Longevity Sciences - Longitudinal Study of Aging (NILS-LSA), a community-based study.

PARTICIPANTS

Participants included 922 men and 879 women who participated in the first study-wave (age 40-79 years) and also participated in at least one study-wave from the second to seventh study-wave. Each study-wave was conducted biennially. For individuals, the entire follow-up period was 12 years.

MEASUREMENTS

Energy intake was calculated from 3-day dietary records with photographs. Weight and height were measured under a fasting state. To estimate linear changes in energy intake and weight over 12 years according to age at first study-wave, we used the mixed-effects model.

RESULTS

Mean (SD) follow-up time and number of study-wave visits were 9.5 (3.7) years and 5.4 (1.8) times, respectively. The fixed effect of the interaction of age and time in energy intake and weight was statistically or marginally statistically significant both in men (p<0.01) and in women (p<0.06). In men, when energy intake was estimated according to age, the rate of decrease in energy intake increased from -6.8 to -33.8 kcal/year for ages 40-79 years. In women, the rate of decrease in energy intake slightly increased in older age groups (-9.1 to -16.7 kcal/year for ages 40-79 years). Weight increased in males in their 40s (0.07 kg/year from age 40) and started to decline by age 53. In women, weight started to decline around age 47 (-0.04 kg/year).

CONCLUSION

Twelve-year longitudinal data showed energy intake declined both in men and women in their 40s, and the rate of decrease increased in older males. Weight started to decline in men in their mid-50s and women in their late 40s. Further studies that focus on energy intake and weight reduction are needed to prevent weight loss or underweight in an increasingly aging society.

Direct detection of resonant electron pitch angle scattering by whistler waves in a laboratory plasma

Resonant interactions between energetic electrons and whistler mode waves are an essential ingredient in the space environment, and in particular in controlling the dynamic variability of Earth's natural radiation belts, which is a topic of extreme interest at the moment. Although the theory describing resonant wave-particle interaction has been present for several decades, it has not been hitherto tested in a controlled laboratory setting. In the present Letter we report on the first laboratory experiment to directly detect resonant pitch angle scattering of energetic (∼keV) electrons due to whistler mode waves. We show that the whistler mode wave deflects energetic electrons at precisely the predicted resonant energy, and that varying both the maximum beam energy, and the wave frequency, alters the energetic electron beam very close to the resonant energy.

Cereal Intake Increases and Dairy Products Decrease Risk of Cognitive Decline among Elderly Female Japanese

BACKGROUND

If cognitive decline can be prevented through changes in daily diet with no medical intervention, it will be highly significant for dementia prevention.

OBJECTIVES

This longitudinal study examined the associations of different food intakes on cognitive decline among Japanese subjects.

DESIGN

Prospective cohort study.

SETTING

The National Institute for Longevity Sciences - Longitudinal Study of Aging, a community-based study.

PARTICIPANTS

Participants included 298 males and 272 females aged 60 to 81 years at baseline who participated in the follow-up study (third to seventh wave) at least one time.

MEASUREMENTS

Cognitive function was assessed with the Mini-Mental State Examination (MMSE) in all study waves. Nutritional intake was assessed using a 3-day dietary record in the second wave. Cumulative data among participants with an MMSE >27 in the second wave were analyzed using a generalized estimating equation. Multivariate adjusted odds ratios (OR) and 95% confidence intervals (CI) for an MMSE score ≤27 in each study wave according to a 1 standard deviation (SD) increase of each food intake at baseline were estimated, after adjusting for age, follow-up time, MMSE score at baseline, education, body mass index, annual household income, current smoking status, energy intake, and history of diseases.

RESULTS

In men, after adjusting for age, and follow-up period, MMSE score at baseline, the adjusted OR for a decline in MMSE score was 1.20 (95% CI, 1.02-1.42; p=0.032) with a 1-SD increase in cereal intake. After adjusting for education and other confounding variables, the OR for a decrease in MMSE score did not reach statistical significance for this variable. In women, multivariate adjusted OR for MMSE decline was 1.43 (95% CI, 1.15-1.77; p=0.001) with a 1-SD increase in cereal intake and 0.80 (95% CI, 0.65-0.98; p=0.034) with a 1-SD increase in milk and dairy product intake.

CONCLUSIONS

This study indicates that a 1-SD (108 g/day) decrease in cereal intake and a 1-SD (128 g/day) increase in milk and dairy product intake may have an influence of cognitive decline in community-dwelling Japanese women aged 60 years and older. Further studies are needed in order to explore the potential causal relationship.

Abundant daily non-sedentary activity is associated with reduced prevalence of metabolic syndrome and insulin resistance

BACKGROUND

Non-exercise activity thermogenesis has recently drawn attention because of its potential to prevent weight gain.

AIM

This study evaluated the relationships between the duration of daily non-sedentary activities and the prevalence of metabolic syndrome and insulin resistance (IR) in the Japanese population.

MATERIAL/SUBJECTS AND METHODS

A total of 518 eligible subjects (380 men and 138 women) who attended the Tokushima Prefectural General Health Checkup Center and participated in the baseline survey of a cohort study conducted in Tokushima Prefecture, Japan were analyzed. Information about lifestyle characteristics including leisure-time exercise and daily non-exercise activities was obtained from a questionnaire. Logistic and multiple linear regression analyses were performed to evaluate the associations between the duration of daily non-exercise non-sedentary activities (beyond sitting) and prevalence of metabolic syndrome (and its components) and IR.

RESULTS

Subjects with longer duration of daily non-sedentary activities had significantly lower adjusted odds ratios for metabolic syndrome (p for trend =0.024), abdominal obesity (p for trend =0.023), and low HDLcholesterol levels (p for trend =0.002), after adjustment for sex, age, and other probable covariates including leisure-time exercise. Longer duration of daily non-sedentary activities was further associated with lower homeostasis model of assessment- IR (HOMA-IR) values (p for trend =0.009).

CONCLUSIONS

Our results suggest that abundant daily non-sedentary activity might be associated with a lower prevalence of metabolic syndrome, especially for the components of central obesity and low HDL-cholesterol levels, and with a lower prevalence of IR, independent of leisure-time exercise.

Estrogen oversees the maintenance of the female genetic program in terminally differentiated gonochorists

The sexual plasticity of the gonads is not retained after the completion of sex differentiation in vertebrates, except in some hermaphroditic species. Here, we report that the depletion of estradiol-17β (E2) by aromatase inhibitors (AI) for up to six months resulted in a functional female-to-male sex reversal in sexually-mature adults of two gonochoristic fish species, Nile tilapia and medaka. The sex-reversed fish showed a typical male pattern of E2 and androgen levels, secondary sexual characteristics, and male-like sex behavior, producing fertile sperm. Conversely, co-treatment of E2 inhibited AI-induced sex reversal. In situ hybridization of medaka gonads during AI-induced sex reversal indicated that cysts on the dorsal side of the adult ovaries are the origin of germ cells and Sertoli cells in the newly formed testicular tissue. Gonochoristic fish maintain their sexual plasticity until adulthood and E2 plays a critical role in maintaining the female phenotype.

Robotic laparoscopic distal gastrectomy: a comparison of the da Vinci and Zeus systems

BACKGROUND

The robotic surgical systems working on a master-slave principle have been developed and used in the worldwide in cardiac, urologic, and general surgery.

METHODS

The two robotic systems, the da Vinci and the Zeus Robotic Surgical System (Intuitive Surgical, Calif., USA), were compared with the aim of evaluating operative feasibility and technical efficacy in distal gastrectomy.

RESULTS

During laparoscopic gastrectomy, the da Vinci System (n = 2) had a shorter total operative time (445 versus 656 minutes; p = 0.09) and less blood loss (65 versus 277 mL; p = 0.08) compared with the Zeus System (n = 3). The articulated instruments of both systems were useful in lymph node dissection, isolation of vessels in fat tissue, ligation of vessels, and intraabdominal anastomosis of the gastrointestinal tract. Robotic laparoscopic procedures can be performed effectively using either the da Vinci or Zeus System.

CONCLUSION

In this limited study, the robotic instruments, especially those of da Vinci system, made it easier to complete tissue dissection including lymph nodes, complicated endoscopic anastomoses, and ligatures in a closed cavity.

Prevalence and specificity of LKB1 genetic alterations in lung cancers

Germline LKB1 mutations cause Peutz-Jeghers syndrome, a hereditary disorder that predisposes to gastrointestinal hamartomatous polyposis and several types of malignant tumors. Somatic LKB1 alterations are rare in sporadic cancers, however, a few reports showed the presence of somatic alterations in a considerable fraction of lung cancers. To determine the prevalence and the specificity of LKB1 alterations in lung cancers, we examined a large number of lung cancer cell lines and lung adenocarcinoma (AdC) specimens for the alterations. LKB1 genetic alterations were frequently detected in the cell lines (21/70, 30%), especially in non-small cell lung cancers (NSCLCs) (20/51, 39%), and were significantly more frequent in cell lines with KRAS mutations. Point mutations were detected only in AdCs and large cell carcinomas, whereas homozygous deletions were detected in all histological types of lung cancer. Among lung AdC specimens, LKB1 mutations were found in seven (8%) of 91 male smokers but in none of 64 females and/or nonsmokers, and were significantly more frequent in poorly differentiated tumors. The difference in the frequency of LKB1 alterations between cell lines and tumor specimens was likely to be owing to masking of deletions by the contamination of noncancerous cells in the tumor specimens. These results indicate that somatic LKB1 genetic alterations preferentially occur in a subset of poorly differentiated lung AdCs that appear to correlate with smoking males.

Identification of tumor markers and differentiation markers for molecular diagnosis of lung adenocarcinoma

To identify tumor markers and differentiation markers for lung adenocarcinoma (AdC), we analysed expression profiles of 14,500 genes against three cases of type II alveolar epithelial cells, bronchiolar epithelial cells, and bronchial epithelial cells, respectively, and 10 cases of AdC cells isolated by laser capture microdissection. Hierarchical clustering analysis indicated that AdC cells and noncancerous lung epithelial cells are significantly different in their expression profiles, and that different sets of differentiation markers are expressed among alveolar, bronchiolar and bronchial epithelial cells. Nine genes were identified as being highly expressed in AdC cells, but not expressed in noncancerous lung epithelial cells. Sixteen genes were identified as differentiation markers for lung epithelial cells. Real-time RT-PCR analysis of 45 lung AdC cases further revealed that expression of four tumor markers in AdC cells was significantly higher than that in noncancerous lung cells and that expression of ten differentiation markers was retained in a considerable fraction of lung AdC cases. Five tumor markers and seven differentiation markers were not expressed in peripheral blood cells. Similarities and differences in expression profiles between normal epithelial cells from different lung respiratory compartments and AdC cells demonstrated in this study will be informative for the molecular diagnosis of lung AdC.

Sodium sulfite and N-acetylcysteine: new additives to dialysate for inhibiting formation of glucose degradation products and advanced glycation end-products

The present study evaluated the inhibiting effect of various chemicals on the advanced glycation end-product (AGEs) cross-linking caused in protein by glucose degradation products (GDPs). We evaluated a few dozen organic and inorganic chemicals--in addition to previously reported AGE inhibitors, such as thiazolium derivatives and aminoguanidine--for their inhibiting effect. Collagen IV (from human placenta) or human serum albumin (HSA) was incubated with an AGE accelerator and one of the selected chemicals in phosphate buffer solution at 37 degrees C for as long as 14 days. Fluorescence intensity (440 nm) was determined after a given incubation time. Among 36 chemicals tested, 8 new chemicals and 5 previously known AGE inhibitors significantly suppressed the increase in fluorescence intensity seen after incubation of HSA with methylglyoxal. We believe that 6 chemicals may effectively quench GDPs and inhibit AGE cross-link formation, in a manner different from that of aminoguanidine and thiazolium.