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Summary The dual interrogation of the transcriptome and proteome with single-cell resolution provides exquisite insights into immune mechanisms in health and disease. Here, we describe a cutting-edge protocol wherein we combine Cellular Indexing of Transcriptomes and Epitopes by Sequencing (CITE-Seq), a technique utilizing antibody-oligonucleotide conjugates (AOCs), with fluorescence-activated cell sorting to enrich rare cell populations. Our protocol incorporates co-staining of cells with both fluorescent antibodies and AOCs simultaneously for subsequent input into the cell sorting and CITE-Seq pipeline. For complete details on the use and execution of this protocol, please refer to Mair et al. (2020)., Graphical abstract, Highlights • Flow cytometry analysis to evaluate signals from cells at co-staining • Step-by-step protocol for co-staining cells with fluorescent antibodies and AOCs • Strategy to choose clones for the same protein marker with two antibodies, The dual interrogation of the transcriptome and proteome with single-cell resolution provides exquisite insights into immune mechanisms in health and disease. Here, we describe a cutting-edge protocol wherein we combine Cellular Indexing of Transcriptomes and Epitopes by Sequencing (CITE-Seq), a technique utilizing antibody-oligonucleotide conjugates (AOCs), with fluorescence-activated cell sorting to enrich rare cell populations. Our protocol incorporates co-staining of cells with both fluorescent antibodies and AOCs simultaneously for subsequent input into the cell sorting and CITE-Seq pipeline.

Advancements in flow cytometry have led to a comprehensive characterization of T cells. While many markers can be used for a detailed immunophenotypic or functional analysis, design of a large multicolor flow cytometry panel is still hampered by the selection of optimal fluorochrome combinations. For example, expansion of existing flow cytometry panels with new markers of interest can result is suboptimal resolution and, in some cases, the need to design a new panel, impacting cost and increasing time to insight. To minimize these challenges and to provide increased flexibility, we have developed a human T cell backbone panel strategically designed to be complemented with 5-8 drop-in markers of choice, depending on instrument configuration. The backbone panel contains five T cell markers (CD3, CD4, CD8, CD45RA, CCR7) conventionally used to identify different maturational states of CD4+ and CD8+ T cells (naïve, central memory, effector memory, effector memory RA). We will show how this backbone panel meets four fundamental requirements: i) clear resolution of major T cell subsets; ii) the fluorochromes used in the backbone panel have minimal resolution impact on the detectors allocated for drop-ins; iii) the fluorochromes assigned to drop-ins have minimal impact on the resolution of the backbone panel; iv) the fluorochromes assigned to drop-ins do not impact each other. We will provide examples of different drop-in combinations for the study of T cell and regulatory T cell biology. Performance of the backbone panel on different instruments will be shown to demonstrate assay consistency across platforms. The compatibility of the backbone panel with intracellular cytokine stain and transcription factor analysis will be further demonstrated. This pre-optimized backbone panel represents a unique tool for researchers who need to study different aspects of T cell biology and want to easily increase their assay capabilities, while minimizing panel design challenges and impact to population resolution. For Research Use Only. Not for use in diagnostic or therapeutic procedures. Citation Format: Mirko Corselli, Chad Sisouvanthong, Nihan Kara, Stephanie Widmann. Development of a human T cell backbone flow cytometry panel enabling flexibility in reagent choice while minimizing panel design challenges [abstract]. In: Proceedings of the American Association for Cancer Research Annual Meeting 2022; 2022 Apr 8-13. Philadelphia (PA): AACR; Cancer Res 2022;82(12_Suppl):Abstract nr 1392.

In-depth understanding of the intrinsic properties and complexity of the tumor microenvironment is crucial to develop both diagnostic and therapeutic strategies for cancer treatment. The tumor microenvironment is composed of various cell types, all of which interact and collectively determine cancer progression and response to therapy. Additionally, tumor cells have a strong ability to adapt to environmental stimuli and can evade treatment modalities. As a result of those features, it is essential to understand the dynamic gene expression profile to decipher tumor heterogeneity and develop efficient and safe therapeutic strategies to fight cancer. Challenges are faced by downstream genomic assay design where tumor specimens cannot be processed immediately in the clinical site. In this case, samples need to be preserved properly to maintain good cell quality and transcriptomic profile. In this work, we propose a storage solution named BD® Tumor and Tissue Preservation Reagent (TTPR). We evaluated the RNA quality of sample storage in this solution up to three days. Expression of cellular stress-related genes were assessed over the storage time course. Importantly, samples stored in TTPR proved compatible with single cell capture workflow using BD RhapsodyTM system and the single-cell gene expression is comparable to that of cells from fresh sample. In conclusion, TTPR is a useful and convenient solution for short-term sample storage prior to downstream genomic assays including single-cell sequencing. 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. © 2021 BD. All rights reserved. MSA Approved 1121 Supported by NA

Growing evidence suggests that tumor progression can interfere with normal hematopoiesis and skew the host system to undergo myeloid biased changes. Hematopoietic stem and progenitor cells (HSPCs) are a rare population of precursor cells giving rise to progeny that replenish blood cells throughout life. HSPCs are mainly localized in the bone marrow niche in healthy adults, however pathophysiological conditions such as cancer can cause extramedullary hematopoiesis in organs like the spleen. In this study, we investigated tumor-driven phenotypic and molecular alterations in the HSPC compartment at a single-cell level during extramedullary hematopoiesis using single-cell multiomics. We used a B16-F10 melanoma mouse model to uncover the tumor-mediated changes. Mice with tumor-burden showed splenomegaly and alterations in the composition of the HSPC compartment in the spleen consistent with extramedullary hematopoiesis. We then isolated four HSPC populations, including Lin- Sca1+ cKit+ (LSK), common myeloid progenitor (CMP), granulocyte-macrophage progenitor (GMP) and megakaryocyte-erythrocyte progenitor (MEP) cells from the spleen and bone marrow of melanoma-burdened mice using the BD FACSMelody™ Cell Sorter. Next, we used an integrated workflow on the BD Rhapsody™ Single-Cell Analysis System for the downstream single-cell multiomics analysis. We utilized oligo-conjugated antibodies for NGS-based sample multiplexing and protein detection (BD® Single-Cell Multiplexing Kit, BD® AbSeq Assay), along with whole transcriptome analysis for a comprehensive analysis of mRNA expression. Data analysis using the X-shift algorithm paired with single-cell force-directed layout visualization enabled delineation of the developmental trajectories of HSPC populations and exploration of phenotypic and transcriptomic changes across different hematopoietic subpopulations and across distinct anatomic sites. The analysis also identified unique hematopoietic cell clusters present during melanoma-driven extramedullary hematopoiesis in the spleen. Overall, our findings highlight melanoma-driven perturbations in hematopoiesis by utilizing advanced single-cell multiomics technology. Disclaimers: For Research Use Only. Not for use in diagnostic or therapeutic procedures. Class 1 Laser Product. BD-23277 (v1.0) 1120 BD, the BD Logo, FACSMelody and Rhapsody are trademarks of Becton, Dickinson and Company or its affiliates. © 2020 BD. All rights reserved. Citation Format: Nihan Kara, Nikolay Samusik, Xiaoshan Shi, Chip Lomas, Stephanie Widmann, Aaron J. Tyznik. Single-cell trajectory analysis reveals a melanoma-driven distinct hematopoietic response in murine spleen [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 3201.

Obesity creates a chronic inflammatory environment that can lead to an exhausted phenotype among T cells. Since exhausted T cells gradually lose their effector functions, obese patients may be at higher risk of developing different disorders, including infectious diseases and cancer. Using the BD FACSymphonyTM A5 Cell Analyzer, we applied a 21-color high-parameter flow cytometry panel to assess various immune cell types in a mouse model of obesity. Also, a flow-based functional assay provided insights into obesity-associated T cell dysfunction. To address progressive changes that might have been caused by a high-fat diet over time, C57BL/6 mice were fed with a high-fat diet for a period of 4 or 16 weeks. Cell populations were examined in blood, spleen and epididymal fat tissue with the latter being known as a location that harbors local inflammation in obese mice. Computational tools for high-dimensional data analysis allowed a thorough characterization of tissue-specific cell phenotypes and their relationship with obesity. Notably, the frequency of effector/memory CD8 T cells and TCRγδ T cells were increased in the fat of obese mice. However, assessment of T cell effector functions in vitro revealed an impairment in cell proliferation, suggesting that fat CD8 T cells from obese mice may not effectively respond to stimulation. Though further studies are required, these results support previous published evidence that low-grade chronic inflammation associated with obesity may impact T cell responses. The data also represent an efficient stepwise approach for staining of surface and intracellular markers and for evaluation of T cell function in vitro and demonstrates the utility of computational tools available in FlowJo™ v10 Software. For Research Use Only. Not for use in diagnostic or therapeutic procedures. Class 1 Laser Product.BD-23275 (v1.0) 1120BD, the BD Logo, FACSymphony and FlowJo are trademarks of Becton, Dickinson and Company or its affiliates. © 2020 BD. All rights reserved. Citation Format: Gisele V. Baracho, Stephanie Widmann, Aaron Tyznik. Defining cell population diversity and T cell dysfunction in a mouse model of obesity [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 1815.

T cell immunity is vital for the control of viral infections. Cytotoxic CD8 T cells play a crucial role in eliminating virus-infected cells while CD4 helper T cells mediate host immune responses and promote B cells to secrete antibodies. For both, T cell recognition of viral antigens in the form of short peptides presented by HLA complexes is a prerequisite for T cell activation. Severe Acute Respiratory Syndrome Corona Virus 2 (SARS-CoV-2), the causative agent of coronavirus disease 2019 (COVID-19), has become a global pandemic that has disrupted economies and resulted in an enormous burden on health care systems. Despite the worldwide intensive efforts on development of COVID-19 therapeutics, a safe and effective COVID-19 treatment or vaccine is not yet available. In this study, we established an in vitro stimulation system in which peripheral blood mononuclear cells were treated with putative SARS-CoV-2 immunogenic peptides. T cell immune responses were measured using different quantitative flow cytometry panels that were designed for evaluating cytokine production or identifying T cell subsets. Evaluation of host immune responses with a suite of flow cytometric panels may prove to be useful in the study of COVID-19. For Research Use Only. Not for use in diagnostic or therapeutic procedures. Class 1 Laser Product.BD-23276 (v1.0) 1120BD and the BD Logo are trademarks of Becton, Dickinson and Company. © 2020 BD. All rights reserved. Citation Format: Xiaoshan Shi, Scott J. Bornheimer, Suraj Saksena, Stephanie Widmann, Aaron Tyznik. Flow cytometry analysis of immune response to COVID-19 vaccine candidates using an in vitro stimulation model [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 715.

T cell immunity is vital for the control of viral infections. Cytotoxic CD8 T cells play a crucial role in eliminating virus-infected cells while CD4 helper T cells mediate host immune responses and promote B cells to secrete antibodies. For both, T cell recognition of viral antigens in the form of short peptides presented by HLA complexes is a prerequisite for T cell activation. Severe Acute Respiratory Syndrome Corona Virus 2 (SARS-CoV-2), the causative agent of coronavirus disease 2019 (COVID-19), has become a global pandemic that has disrupted economies and resulted in an enormous burden on health care systems. Despite the worldwide intensive efforts on development of COVID-19 therapeutics, a safe and effective COVID-19 treatment is not yet available. In this study, we established an in vitro stimulation system in which peripheral blood mononuclear cells were treated with putative SARS-CoV-2 immunogenic peptides. T cell immune responses were measured using different quantitative flow cytometry panels that were designed for evaluating cytokine production or identifying T cell subsets. Evaluation of host immune responses with a suite of flow cytometric panels may prove to be useful in the study of COVID-19. For Research Use Only. Not for use in diagnostic or therapeutic procedures. Class 1 Laser Product. BD-23276 (v1.0) 1120 BD and the BD Logo are trademarks of Becton, Dickinson and Company. © 2020 BD. All rights reserved.

Hematopoietic stem and progenitor cells (HSPCs) are a rare population of precursor cells residing in bone marrow that replenish blood cells throughout adult life. Growing evidence suggests that tumor progression can interfere with normal hematopoiesis, skew the host system to undergo myeloid biased changes and cause extramedullary hematopoiesis (EMH) in organs such as the spleen. In this study, we investigated tumor-driven phenotypic and molecular alterations in HSPCs during EMH using single-cell multiomics. We used a B16-F10 melanoma mouse model which showed splenomegaly and alterations in the composition of the HSPCs in the spleen consistent with EMH. We then isolated four HSPC populations from the spleen and bone marrow of melanoma-burdened mice using the BD FACSMelody™ Cell Sorter and used the BD Rhapsody™ Single-Cell Analysis System for the downstream single-cell multiomics analysis. We utilized oligo-conjugated antibodies for NGS-based sample multiplexing (BD® Single-Cell Multiplexing Kit) and protein detection (BD® AbSeq Assay), along with whole transcriptome analysis for a comprehensive analysis of mRNA expression. We observed tumor-driven distinct hematopoietic response and alterations in developmental trajectories of HSPCs during EMH using the X-shift algorithm paired with single-cell force-directed layout visualization. Our findings highlight melanoma-driven perturbations in hematopoiesis by utilizing single-cell multiomics in a murine model. Class 1 Laser Product. For Research Use Only. Not for use in diagnostic or therapeutic procedures. BD-24477 (v1.0) 1220 BD, the BD Logo, FACSMelody, Rhapsody and AbSeq are trademarks of Becton, Dickinson and Company or its affiliates ©2020 BD. All rights reserved.

Cytotoxic T lymphocytes (CTLs) and natural killer (NK) cells have become attractive therapeutic targets for cancer immunotherapy because of their efficient mechanisms for killing cancerous cells. Both effector CTLs and mature NK cells are endowed with secretory granules containing pre-formed cytolytic proteins that, once released at the immunological synapse, initiate a cascade of reactions leading to the apoptosis of the target cell. CTLs and NK cells may also promote cell killing through death-receptor-mediated and cytokine-induced cell death mechanisms. Here we show a 16-color flow cytometry panel allowing clear identification of CTLs, NK cells and related cell subsets in whole blood. We also describe an optimized intracellular staining protocol for analysis of granules content, including granzyme B, granzyme K and perforin. Optimal resolution of cell populations was achieved by employing a selection of BD Horizon Brilliant™ Reagents and BD Horizon™ Red 718 Reagent, a new small molecule fluorochrome option for the red laser. Cell fixation and permeabilization were carried out directly in whole blood using the BD Phosflow™ Reagents, adding convenience to the workflow and practical analysis of cell frequencies. The data also showed the expression of selected activation and inhibitory surface receptors. These results combined with the analysis of intracellular proteins contribute to characterization of the functional status of cytotoxic cells. Class 1 Laser Product. For Research Use Only. Not for use in diagnostic or therapeutic procedures. BD 25443 (v1.0) 0121 BD, the BD Logo, FACSymphony, Horizon, Horizon Brilliant and Phosflow are trademarks of Becton, Dickinson and Company or its affiliates. © 2021 BD. All rights reserved.

Obesity can weaken the body's immune system and reduce its ability to fight off infections. Current analysis on immune cells from obese mouse models suggests that the immune cells suffer from chronic inflammation. To understand the root cause of this problem, we used single cell sequencing to examine thousands of immune cells isolated from primary and secondary lymphoid organs as well as adipose tissue and compared a diet-induced obesity mouse model with control mice. Cells were stained with 30 BD® AbSeq DNA-barcoded antibodies to enable multiomic analysis, i.e. examining protein alongside mRNA expression in tandem. We also utilized DNA-barcoded universal antibodies from the BD® Single-Cell Multiplexing Kit, which allowed us to combine 8 samples from different mice and tissue types into a single pooled sample, significantly reducing experimental scale and cost while eliminating potential batch effects. The pooled samples were loaded on the BD Rhapsody™ system to perform cell lysis and individual mRNA and cell barcoding, allowing measurement of ~400 immune-related mRNAs and 30 proteins at the single cell level. We were able to efficiently de-multiplex the pooled samples after sequencing. The targeted mRNA and AbSeq panel provided robust clustering of immune cell types and showed that genes related to critical immune responses, including inflammation and lymphocyte activation, are differentially regulated in specific immune-cell subsets in the obese mouse model. Using this multiomic analysis of genes differentially regulated in immune cells from different tissues, we propose a model to explain the immuno-phenotype we observed in obese mouse. 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, Gisele Baracho, Ian Taylor, Stephanie Widmann, Stefanie Mortimer. An efficient multiplexing approach to avoid batch effects in single cell RNA- and Ab-seq studies demonstrated in a mouse model of chronic inflammation and obesity [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 2750.

As for most neoplasms, the pathogenesis and progression of B-cell malignancies is a dynamic process involving reciprocal interactions between malignant cells and surrounding components in the tumor microenvironment. In the case of certain B-cell lymphomas, neoplastic cells migrate to lymphoid sites and prompt the infiltration of non-malignant immune cells. The infiltration of cytotoxic lymphocytes correlates with tumor cell killing and good prognosis. However, most immune cell types in the tumor niche often become unresponsive or end up promoting tumor growth. In this study we present a sorting strategy using the BD FACSymphony™ S6 Cell Sorter that enables concurrent isolation of six cell populations from a tumor niche in a model of B-cell lymphoma. Downstream application of single-cell sequencing was used to unravel the respective roles of each cell subset for the tumor's progression and/or evasion. The six cell subsets were isolated from two groups of mice that had been inoculated with an OVA-expressing B-cell lymphoma cell line and subsequently with either wild-type or BTLA-deficient OVA-specific CD8+ T cells. Prior to sorting, each tissue was labeled with a unique BD™ AbSeq Oligo barcode, allowing us to combine biological replicates (2 mice per group) for a higher throughput. After sorting, cells from both groups were pooled and loaded onto cartridges from the BD™ Rhapsody Single-Cell Analysis System, followed by library preparations for Next-Generation Sequencing. In addition to 34 surface proteins, marked with BD™ AbSeq Oligos, sequencing of 399 target mRNA transcripts enabled a detailed examination of the cellular responses that were triggered in the presence of the tumor. During cell analysis, various algorithms in SeqGeq™ segregated the cells from each individual mouse and identified the sorted populations based on their specific phenotypic and molecular signatures. Importantly, because sequencing is biased toward detecting high frequency proteins and mRNAs, the cell sorting aided more robust single-cell profiling of rare cell subsets within the sorted populations. These analyses also contributed to a better understanding of the conditions underlying the differences between the two mice groups. In sum, we demonstrated a scalable and high-throughput approach that enabled a comprehensive characterization of critical cell populations in tumor responses. Since these cell populations constitute potential targets for the treatment of B-cell lymphomas, this platform, notably through the analysis of protein expression, offers an opportunity for identification of new therapeutic targets. For Research Use Only. Not for use in diagnostic or therapeutic procedures. Class 1 laser product. BD, the BD Logo, FACSymphony and Rhapsody are trademarks of Becton, Dickinson and Company. © 2019 BD and its subsidiaries. All rights reserved. Citation Format: Gisele V. Baracho, Xhiaoshan Shi, Wai Lin, John Sedy, Chip Lomas, Stephanie Widmann, Aaron Tyznik. Leveraging the power of high parameter cell sorting and single-cell multi-omics to profile intratumoral immune cells in a model of B-cell lymphoma [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 4967.

Cancer treatment has been revolutionized with the development of immunomodulatory therapies. These therapies have primarily focused on enhancing T-cell responses: whether it is unleashing T cells through blockade of regulatory checkpoint inhibitors or generation of chimeric antigen receptor (CAR) T cells. However, there has been recent interest in harnessing the immunotherapeutic potential of other cytotoxic cells such as Natural Killer (NK) cells. Similar to NK cells, innate lymphoid cells (ILCs) may offer another target of these immunotherapy approaches. Before the potential of these cells can be realized, there is a need for better understanding of these recently described cell populations. ILCs act as the immune system's first responders and have been shown to play a key role in tissue homeostasis, chronic inflammation and cancer. Three main groups of non-cytotoxic ILCs (ILC1, ILC2 and ILC3) have been broadly defined based on developmental trajectories and function, driven by expression of specific transcription factors. Deeper characterization of these cells through either high parameter protein analysis or single-cell RNA sequencing has revealed a more complex and heterogeneous nature of ILCs across different tissues and donors. Therefore, the identity of ILCs is still elusive and controversial. In this study, we developed a comprehensive approach to further refine the signatures of human circulating ILC subsets. Total ILCs (Lineage- CD127+ cells) were enriched from 4 normal donors by flow sorting using the BD FACSAria™ Fusion cell sorter and processed for downstream single-cell multiomic characterization. BD® AbSeq reagents and a targeted BD Rhapsody™ Immune Response Panel were used to enable simultaneous detection of 42 proteins and 399 genes using the BD Rhapsody™ Single-Cell Analysis System. Differential protein and gene expression analysis in addition to combinatorial expression of CD294 and CD117 confirmed 3 conventional ILC populations as well as the signatures of three distinct subsets within ILC1. This discovery approach provided information about relative expression of a small selection of proteins or surface marker-coding genes that enable the discrimination of these ILC subsets. These data were used to design high-parameter flow cytometry panels for high-throughput analysis of different healthy donors. ILC subsets differentially distributed across donors were detected and defined using unsupervised computational analysis confirming the result of multiomic analysis, while the functional and biological relevance of the identified subsets remains to be assessed. For Research Use Only. Not for use in diagnostic or therapeutic procedures. Class 1 laser product. BD, the BD Logo, FACSymphony and Rhapsody are trademarks of Becton, Dickinson and Company or its affiliates. © 2019 BD. All rights reserved. Citation Format: Aaron J. Tyznik, Mirko Corselli, Gisle V. Baracho, Chip Lomas, Silin Sa, Stephanie Widmann, Suraj Saksena, Smita Ghanekar. Resolving the heterogeneity of human circulating innate lymphoid cells via simultaneous, high-dimensional analysis of protein and gene expression [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 3310.

Cancer is associated with concomitant myeloid cell responses that are characterized by an expansion of tumor associated myeloid cells including, myeloid derived suppressor cells (MDSCs), tumor associated macrophages (TAMs) and neutrophils (TANs). These myeloid derived cells are known to modulate immune responses that enhance cancer cell stemness, angiogenesis, metastasis, invasion and immune escape. The prevailing paradigm is that cancer interferes with hematopoiesis and skews the host system to generate cells of myeloid origin with tumor-promoting functions. Intriguingly, tumor derived factors can perturbate normal bone marrow hematopoiesis and promote extramedullary hematopoiesis in organs such as the spleen. Advances in single cell multiomic technologies now enable the analysis of high dimensional protein and mRNA expression from thousands of cells simultaneously. Using the power of the BD Rhapsody™ Single-Cell Analysis system, we have carefully investigated melanoma associated extramedullary hematopoiesis in mice. To do this, we isolated four hematopoietic stem and progenitor cell populations simultaneously, including Lin- Sca-1+ c-Kit+ (LSK), common myeloid progenitor (CMP), granulocyte-macrophage progenitor (GMP) and megakaryocyte-erythrocyte progenitor (MEP) cells from the spleen and bone marrow of melanoma-bearing mice using the BD FACSMelody™ cell sorter in combination with a multiplex BD® AbSeq Oligos panel for surface protein expression and a single-cell whole transcriptome analysis. Using advanced analysis plugins in SeqGeq™ software, we were able to delineate the developmental trajectories of these hematopoietic stem and progenitor cells in this systemic immuno-suppressive myeloid environment. These advanced technologies are critical to uncover tumor mediated abnormalities in hematopoiesis. Disclaimers: For Research Use Only. Not for use in diagnostic or therapeutic procedures. Class 1 Laser Product. BD, the BD Logo, FACSMelody and Rhapsody are trademarks of Becton, Dickinson and Company or its affiliates. © 2019 BD. All rights reserved. Citation Format: Nihan Kara, Xiaoshan Shi, Nikolay Samusik, Stephanie Widmann, Aaron J. Tyznik. A single-cell multiomics approach to study tumor-driven perturbations during hematopoiesis in mice [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 4497.

The pathogenesis and progression of B-cell lymphomas is a dynamic process involving reciprocal interactions between malignant cells and surrounding components in the tumor microenvironment. Neoplastic B cells migrate to lymphoid sites and prompt the immune cell infiltration. The infiltrated cytotoxic lymphocytes potentially contribute to tumor cell killing and good prognosis. However, most immune cell types in the tumor niche often become unresponsive or end up promoting tumor growth. In this study we present a sorting strategy using the BD FACSymphony™ S6 Cell Sorter that enables concurrent isolation of six cell populations from a tumor niche in a murine B-cell lymphoma model. Single-cell sequencing was used downstream to unravel the respective roles of each cell subset for the tumor’s progression and/or evasion. The six cell subsets were isolated from mice that had been inoculated with an OVA-expressing B-cell lymphoma cell line and subsequently with either wild-type or BTLA-deficient OVA-specific CD8+ T cells. The cell sorting aided more robust single-cell profiling of rare cell subsets within the sorted populations. In summary, we demonstrated a high-throughput approach that enabled a comprehensive characterization of critical cell populations in tumor responses. Since these cell populations constitute potential targets for the treatment of B-cell lymphomas, this platform, notably through the analysis of protein expression, offers an opportunity for identification of new therapeutic targets. For Research Use Only. Class 1 laser product. BD, the BD Logo, FACSymphony and Rhapsody are trademarks of Becton, Dickinson and Company. © 2019 BD and its subsidiaries. All rights reserved.

In chronic conditions, notably cancers, CD8+ cytotoxic T cells gradually lose their effector functions due to constant exposure to antigens and consequent upregulation of inhibitory receptors like PD-1. In this regard, PD-1 blockade therapy was shown to bolster cytotoxic T-cell response and improve disease prognosis in some cases. PD-1 mediated T cell dysfunction is also involved in obesity-induced tumorigenesis. In this study, we used a molecular cytometry approach to better understand the disturbances caused by obesity in immune cells. A detailed single-cell analysis of various cell compartments revealed a unique population of CD8+ cytotoxic T cells in the epididymal fat of mice consuming a high fat diet for 16 weeks. These cells showed high expression of proteins and/or mRNA transcripts for various inhibitory receptors, including PD-1. Based on these results, we created a 28-color panel for high-throughput cell analysis at multiple time points over the 16-week period, using a BD FACSymphony™. The frequency of CD8+PD-1+ T cells in the fat correlated with the numbers of inflammatory cells, suggesting that the dysfunctional phenotype resulted from a growth in inflammation over time. The functional state of the CD8+PD-1+ cells was also examined by challenging these cells with or without PD-1 blockade. Taken together the data delineated a refined application for a broad analysis of immune cells in the fat and provided insights into the effects of obesity-induced T-cell dysfunction in mice. For Research Use Only. Not for use in diagnostic or therapeutic procedures. Class 1 laser product. BD, the BD Logo, FACSymphony is trademark of Becton, Dickinson and Company. © 2019 BD and its subsidiaries. All rights reserved.

Cancer treatment has been revolutionized with the development of immunomodulatory therapies. While these therapies have primarily focused on enhancing T-cell responses, there has been interest in harnessing the potential of other cytotoxic cells such as Natural Killer (NK) cells. Similar to NK cells, innate lymphoid cells (ILCs) may offer another target of these immunotherapy approaches. However, there is a need for better understanding of these recently described cells. In this study, we developed a comprehensive approach to further refine the signatures of human circulating ILC subsets. Total ILCs were enriched using the BD FACSAria™ Fusion cell sorter and processed for downstream single-cell multiomic characterization. BD® AbSeq reagents and a targeted BD Rhapsody™ Immune Response Panel enabled simultaneous detection of 42 proteins and 399 genes using the BD Rhapsody™ Single-Cell Analysis System. Differential protein and gene expression analysis in addition to combinatorial expression of CD294 and CD117 confirmed 3 conventional ILC populations as well as the signatures of 3 distinct subsets within ILC1. This discovery approach provided information about relative expression of a small selection of proteins or surface marker-coding genes that enable the discrimination of these ILC subsets. These data were used to design high-parameter flow cytometry panels for high-throughput analysis. ILC subsets differentially distributed across donors were detected and defined using unsupervised computational analysis confirming the result of multiomic analysis. For Research Use Only. Class 1 laser product. BD, the BD Logo, and Rhapsody are trademarks of Becton, Dickinson and Company or its affiliates. © 2019 BD. All rights reserved.

Cancer is associated with concomitant myeloid cell responses that are characterized by an expansion of tumor associated myeloid cells, including myeloid derived suppressor cells, tumor associated macrophages and neutrophils. The prevailing paradigm is that cancer interferes with normal hematopoiesis by skewing the generation of myeloid cells with tumor promoting functions and promoting extramedullary hematopoiesis in organs such as the spleen. Advances in single cell multiomic technologies now enable the analysis of high dimensional protein and mRNA expression from thousands of cells simultaneously. Using the power of the BD Rhapsody™ Single-Cell Analysis System, we have carefully investigated melanoma associated extramedullary hematopoiesis in mice. To do this, we isolated 4 hematopoietic stem and progenitor cell populations simultaneously, including Lin− Sca-1+ c-Kit+, common myeloid progenitor, granulocyte-macrophage progenitor, and megakaryocyte-erythrocyte progenitor cells from the spleen and bone marrow of melanoma bearing mice using the BD FACSMelody™ cell sorter in combination with a multiplex BD® AbSeq Oligos panel for surface protein expression and a single-cell whole transcriptome analysis. Using advanced analysis plugins in SeqGeq™ software, we were able to delineate the developmental trajectories of these hematopoietic stem and progenitor cells in this systemic immuno-suppressive myeloid environment. These advanced technologies are critical to uncover tumor mediated abnormalities in hematopoiesis. Disclaimers: For Research Use Only. Class 1 Laser Product. BD, the BD Logo, FACSMelody and Rhapsody are trademarks of Becton, Dickinson and Company or its affiliates. © 2019 BD. All rights reserved.

Single cell RNA-sequencing (scRNA-seq) is a powerful tool for understanding the sample heterogeneity of individual cells. Many methods rely on whole transcriptome analysis (WTA) to get a snapshot of the entire cellular landscape. Although WTA analysis can be used to discover novel biomarkers, this technique can be expensive. To enable scaling of experiments, WTA data can be mined to design targeted gene panels. To showcase this, we used single cell sequencing to examine thousands of B cells isolated from the bone marrow and peripheral blood of chronic lymphocytic leukemia (CLL) and healthy donors. B cells that had been sorted using the BD FACSMelody™ cell sorter were multiplexed using the BD™ Human Single-Cell Multiplexing Kit and pooled before being processed on the BD Rhapsody™ system, thereby minimizing batch effects. The resulting data was mined to design a panel of differentially expressed genes between CLL and healthy B cells that could be used for subsequent CLL phenotyping. By combining this panel with the BD Rhapsody™ Immune Response Panel (together comprising ~500 mRNAs), along with 36 DNA-barcoded BD™ AbSeq antibodies, we were able to simultaneously analyze mRNA and protein targets from a new subset of CLL and healthy B cells for additional high-resolution analysis. This study showcases the power of using WTA data to design specific gene panels that can be used alone or in combination with existing targeted panels for routine and cost-effective transcriptional profiling at a single cell level. For Research Use Only. Not for use in diagnostic or therapeutic procedures. BD, the BD Logo, FACSMelody, and Rhapsody are trademarks of Becton, Dickinson and Company. © 2019 BD and its subsidiaries. All rights reserved.

Multiparameter flow cytometric analysis of single cells allows the enumeration and characterization of heterogeneous cell populations in a variety of infections, blood cancers, immunodeficiencies and other disorders. Supported by advances in reagent development and instrumentation, this approach has increased dimensionality in single-cell data collection, and accelerated the discovery and testing of new therapies. Here we show a broad immunophenotyping panel that identifies the major leucocyte populations and various sub-populations from different mouse tissues. The panel can also be divided into focused modules for specific analysis of T cell, B cell or myeloid/natural killer cell lineages. BD FACSymphony combined with BD Horizon Brilliant Dyes allowed for high resolution identification of known leucocyte populations. Dimensionality reduction with t-SNE and automated clustering algorithms simplified cell analysis, enabling a faster and more efficient comparison of cell phenotypes across the tissues. Importantly, automated cell clustering analyses, while recognizing the predicted cell populations, also identified cell subsets missed during supervised analysis of the dataset. Thus, we describe a comprehensive single-cell profiling application capable of identifying well-characterized leucocyte populations and that has the potential to discover unique cell phenotypes.

Obesity can weaken the body’s immune system and trigger chronic inflammation. To understand the root cause of this problem, we used single cell sequencing to examine thousands of immune cells isolated from primary and secondary lymphoid organs as well as adipose tissue and compared a diet-induced obesity mouse model with control mice. Cells were stained with 30 DNA-barcoded antibodies from BD™ AbSeq reagents to enable multiomic analysis, i.e. examining protein alongside mRNA expression in tandem. We also utilized DNA-barcoded universal antibodies from the BD™ Single-Cell Multiplexing Kit, which allowed us to combine 8 samples from different mice and tissue types into a single pooled sample, significantly reducing experimental scale and cost while eliminating potential batch effects. The pooled samples were loaded on the BD Rhapsody™ system to perform cell lysis and individual mRNA and cell barcoding, allowing measurement of ~400 immune-related mRNAs and 30 proteins at the single cell level. We were able to de-multiplex the pooled samples with high specificity after sequencing. The targeted mRNA and AbSeq panel provided robust clustering of immune cell types and showed that genes related to critical immune responses, including inflammation and lymphocyte activation, are differentially regulated in specific immune-cell subsets in obese mouse. Using this multiomic analysis of genes differentially regulated in immune cells from different tissues, we propose a model to explain the immuno-phenotype we observed in obese mouse. 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.

While flow cytometry continues to be a critical tool for immunologists, one of the more difficult aspects of this practice is panel design. Fully resolving dim populations of interest can be challenging. Low antigen density, fluorescence spillover, available fluorochromes and limited catalog offerings are just a few of the factors that make panel design difficult often leading to sub-optimal resolution. Previously, we have shown that following a basic set of principles can reduce the number of iterations needed to maximize the resolution for populations of interest. Here we show how recent developments, including the BD Horizon™ Guided Panel Solution (GPS) and BD OptiBuild™ reagents, help simplify panel design even further. The BD GPS was designed with the best practices of panel design at its core. By guiding the user through critical steps in this process and flagging potential problem areas in a proposed panel, the GPS minimizes the need for early panel iteration. BD OptiBuild reagents vastly improves the catalog offering of fluorochrome/specificity combinations, thus reducing the need for panel redesign due to limited reagent availability. To demonstrate the utility of these new tools, we walk through panel design for an 8 color assay on both 3 laser (8 parameter) and 5 laser (18 parameter) systems. The analysis of these panels shows that by using these tools, the chances of obtaining a successful panel increase. Additionally, panel design can be made easier and population resolution improved when utilizing a 5 laser system where impacts of spillover and spread can be minimized. Together, using these tools and approaches the goal is to minimize the number of iterations required to develop panels that meet the needs of the investigator.

Flow cytometry has long been a critical tool for immunologists. As the number of parameters used in flow cytometry continues to increase, one of the more difficult aspects of this practice is panel design. Fully resolving dim populations of interest can be challenging. Low antigen density, fluorescence spillover, available fluorochromes and limited catalog offerings are just a few of the factors that make panel design difficult and lead to sub-optimal resolution. Here, we present a basic set of principles that can help simplify panel design. Following these principles helps reduce the number of iterations needed to maximize the resolution for populations of interest. Additionally, we present a basic methodology that can be used to characterize your flow cytometer and generate a matrix showing the relative impact of fluorochrome combinations on population resolution. Using this Resolution Impact Matrix [RIM], low complexity, no/low compensation panels can be more easily created. Similarly, when performing higher order multicolor experiments, this characterization is critical to help design the optimum panel for that instrument. When used together, these two methods can help simplify the panel design process and lead to higher quality data.

The anaphylatoxin C5a is an especially potent mediator of both local and systemic inflammation. However, C5a also plays an essential role in mucosal host defense against bacterial, viral, and fungal infection. We have developed a response-selective agonist of human C5a, termed EP67, which retains the immunoenhancing activity of C5a at the expense of its inflammatory, anaphylagenic properties. EP67 insufflation results in the rapid induction of pulmonary cytokines and chemokines. This is followed by an influx of innate immune effector cells, including neutrophils, NK cells, and dendritic cells. EP67 exhibits both prophylactic and therapeutic protection when tested in a murine model of influenza A infection. Mice treated with EP67 within a twenty-four hour window of non-lethal infection were significantly protected from influenza-induced weight loss. Furthermore, EP67 delivered twenty-four hours after lethal infection completely blocked influenza-induced mortality (0% vs. 100% survival). Since protection based on innate immune induction is not restricted to any specific pathogen, EP67 may well prove equally efficacious against a wide variety of possible viral, bacterial, and fungal pathogens. Such a strategy could be used to stop the worldwide spread of emergent respiratory diseases, including but not limited to novel strains of influenza.

While UV lasers have been available for many years, their utility has been mainly restricted to DNA/RNA binding fluorochromes (e.g. DAPI, Hoescht 33342) for studying cell cycle or stem cell side populations. The low fluorescence intensity of standard fluorescent dyes, such as AlexaFluor™ 350 or AMCA, have made them impractical for routine immunological flow analyses. Here we report the development of a novel class of highly fluorescent polymeric reporters which are excitable by a UV (355nm) laser. The introduction of these dyes has the potential to dramatically extend the functionality of the UV laser adding up to 6 totally new colors for multi-color cytometric flow studies. The first Brilliant UltraViolet (BUV) polymer has an excitation maximum near 355nm with emission below 405nm. Cross laser excitation is minimal requiring very little compensation into the Brilliant Violet 421 channel. Furthermore these polymers can serve as the basis for developing a wide range of bright, ultraviolet excitable tandem reagents, which span the entire spectrum from UV to the near IR. Data will be presented to demonstrate how the superior staining performance and unique excitation / emission profiles of these new dyes offer a broader pallet of colors for those designing multi-parameter flow panels. Comparative flow performance will be presented as will multicolor staining panels which highlight their compatibility with conventional flow reagents.