Understanding Immune Systems

Increasing experimental power, accelerating novel insights


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Immune systems are a complex collection of specialised cells differentiated by phenotype and function.

Understanding cellular heterogeneity is fundamental to gaining deep biological insights but immune diversity and dynamic plasticity makes it difficult to do this.

The video below illustrates how higher experimental power through flow cytometry, novel single cell seq-based technologies and high dimensional analysis could help.


 

Webinars

Episode 1 : FlowJo™ high dimension analytics is your game changer

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In this launch webinar of Series 1, Frank and Serena demonstrate how you could gain far deeper biological insights by leveraging an alternative easy-to-apply approach to higher dimension data analysis.

Frank starts by highlighting the common challenges and limitations of conventional 2D sequential gating, which is a widely adopted approach to analysing flow data.

Serena then presents a simple 4 step FlowJoTM workflow [based on a selection of easily available plugins] that allows you to 1) perform a quality assessment and control (QC) of your data, 2) collectively visualize all the cells simultaneously, 3) identify the presence of any novel sub-populations present within your study sample and finally 4) conduct a detailed characterization of those specific subsets of interest to you.

Using Tregs as a representative study population, you will see how FlowJo™ goes beyond the conventional approach of limiting your analysis to the classic core phenotyping markers of the population: CD3+ CD4+ CD25+ CD127-. Instead, supplementary markers within a larger panel are leveraged to reveal 10 unique and discrete sub-clusters of Tregs. And we show how each of these sub-populations can then be interrogated to reveal its unique phenotype thereby enabling further focussed characterisation experiments.

This powerful analytical approach can be easily applied to further study your own cellular populations of interest. You can contact all our speakers directly for further details or support.




Frank Heuts, PhD - Flow Cytometry Applications Consultant - Northern Europe - [email protected]


Frank holds a PhD in immunology and is the specialist for high end flow cytometry applications in the UK, Ireland, Benelux and Nordics where he provides extensive technical, panel design and data analysis support on high end flow cytometry analysers and sorters. Prior to joining BD, Frank was a Senior Scientist at biotech Plasticell Ltd focussing on stem cell differentiation. During his academic career Frank used high parameter flow cytometry and in vivo imaging to investigate the role of a various of human and mouse immune cells in transplantation and autoimmune diseases.  

Serena Di Cecilia, PhD - Senior European Application Scientist, FlowJo, Informatics - [email protected]

Serena holds a PhD in Molecular Oncology and a postdoc in translational medicine. With significant experience in multi-parameter flow cytometry-based biomarker discovery, analysis of haematological and cancer diseases, and Next Generation Sequencing Serena‘s expertise now centers on supporting higher dimensional flow data analytics. Prior to joining BD and the FlowJo team, Serena was a Flow Cytometry data analyst in a Contract Research Organization focusing on clinical trials data analysis for big Pharma companies.

Episode 2 : Single cell multiomics driving deeper biological insights

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In this second episode we'll focus on gaining a deeper understanding of the underlying biology of the cells that most interest you by simultaneously leveraging broader protein and mRNA profiles through unbiased exploratory approaches.

Carrie starts by addressing a few common challenges with flow cytometry that you too may already be experiencing. Hasi then presents an overview of several novel methods to drive new biomarker discovery through the power of single cell multiomics (scM) technologies. Carrie then presents a brief review of the data analysis workflow (from the point of generating your scM sequencing data through to analysis with SeqGeq™ software) illustrating the simplicity and accessibility of this powerful approach. The presentation concludes with a review of a recent publication (from the journal Cell) to help illustrate the benefits of scM and its potential to drive your own longer-term research strategies.

Remember, You can contact all our speakers directly for further details or support.



Carrie Maynard - European Single-Cell Applications Scientist 

Carrie focused on working together with our biotech, pharmaceutical and translational lab key accounts to get their single-cell assays up and running. This included both flow cytometry and single cell multiomics. Prior to joining BD, Carrie was a scientist developing immunotherapies for cancer in a successful start up biotech Tusk Therapeutics which was acquired by Roche in 2018. In her academic career, Carrie focused on using imaging, flow cytometry and single cell mRNA sequencing to map the immune response to therapy in cancer.

Hasi Patel - Senior Single Cell Solution Architect - [email protected]

Hasi has extensive business experience in client facing roles in academia and pharma covering various sequencing and single cell applications and supports customers across UKI, Nordics and Benelux establish total single cell solution workflows. Prior to joining BD, Hasi held a European commercial role in a private company providing high performance computing services to scientists, enabling optimized and secure clinical bioinformatics data processing.

Episode 3 : Bridge the gap from multiomics to higher parameter flow

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ILC White Paper


Edyta and Vadir continue the journey of understanding immune systems by looking a little closer at how single cell multiomics (scM) -  via the SeqGeqTM data analysis platform - can help advance your flow cytometry research strategies.

We illustrate this by examining a specific population of immune cells (the Innate Lymphoid cells - ILCs) typically studied with a small number of conventional phenotyping surface markers. 

This representative immune population serves to demonstrate how the application of scM can surpass approaches limited to examining a limited number of conventional phenotyping population identifiers. Instead, we share an unbiased exploratory approach of a specific immune population through the analysis of broader protein and mRNA expression profiles. Complementary datasets (protein and mRNA) of ILCs were collected simultaneously and fed into the analytics platform SeqGeqTM  (that is very similar in format and usabliity to FlowJoTM) revealing discrete subsets of ILCs within the parent ILC population.

Importantly, unique novel markers expressed by ILCs were defined and subsequently used to design higher parameter flow cytometry panels which when coupled with high dimension analytics with FlowJo™ plugins (see Episode 1) supports a deeper understanding of the biology of the individual subsets within the target population and potentially their association to disease.

The overall analytical approach that is presented can be easily applied to further study your own cellular populations of interest.

Remember, You can contact all our speakers directly for further details or support.



Edyta Kowalczyk - Bioinformatics Support Engineer - [email protected]

Edyta is trained in Python/R programming and NGS data analysis and has significant experience in large‐scale, high throughput data and scRNAseq omics data analysis methods. Much of her expertise comes from having previously worked on the development of bioinformatics solutions in the area of precision medicine and cancer immunotherapy. Edyta is currently responsible for analysis of scRNA sequencing data and supporting customers over Europe in bioinformatics related queries.

Vadir Lopez-Salmeron - Single Cell MultiOmix Application Support - [email protected]

Vadir Holds a PhD in Molecular Biology and a Postdoc in developmental biology and is currently the Team Leader of Multi-Omics support at BD in Europe. Bringing a wealth of expertise in Single Cell genomics, Vadir support partnerships with customers that require a smooth transition towards the application of novel technologies that enable the analysis of thousands of cellular parameters at a single cell level.

Episode 4 : Go beyond the comfort zone - master higher parameter flow

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Episode 1 of this series set out to share the benefits of higher parameter flow cytometry to gain deeper biological insights to support your pursuit of understanding immune systems. Episodes 2 and 3 (addressing single cell multiomics) support the transition towards higher parameter flow by presenting approaches to identify novel and interesting cellular markers.

Once you’ve identified and selected those interesting new markers you’re likely to begin to rebuild and advance your existing flow panel. This next step - higher parameter panel design - can actually be quite easy as long as you have the right support to navigate through spill-over and spread. Join our experts Vesna and Jens in this episode for a demo of the very latest tools and tips on panel design.

You should leave this meeting confident that great panel design is easily achievable if you bear in mind the biology of your samples and some basic dye properties. This seminar will serve as a good refresher for those already experienced in panel design.

Remember, You can contact all our speakers directly for further details or support.



Vesna Melkebeek - European Scientific & Training Support Specialist - [email protected]

Vesna holds a PhD in Veterinary Immunology and used flow cytometry, cell sorting and imaging through her academic career to study the impact of different vaccination strategies and adjuvants on the intestinal mucosal immune system in animals. As a highly experienced member of the European Scientific and Training Support team, Vesna now focuses primarily on high parameter panel design and supports researchers with diverse needs ranging from instrument setup through to data analysis. In addition to this, Vesna also provides multicolor and cell sorting user training.

Jens Fleischer - Flow Cytometry Application Consultant - [email protected]

Jens holds a PhD in Immunology and Cell Biology. Based at our European Center for Single Cell Solutions in Heidelberg, Jens specialises in our high-end instrumentation portfolio including including consultation on the design of bespoke instrument configurations to meet specific user and experimental requirements. The support he provides extends to higher parameter panel design on standard and custom-made systems alongside high dimensional data analysis with FACSDivaTM and FlowJoTM. Additionally, his expertise extends to include sorting and consultation on associated biosafety requirements.

Episode 5 : Visualizing higher dimension data with FlowJo™ Plugins

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Date: coming soon - sign up for alerts


FlowJoTM offers over 30 independent and easily accessible plugins (see FlowJo Exchange at flowjo.com) to slice, dice and process your flow cytometry data in numerous different ways. But which ones should you use, what do they really do, and where do you start?

Join us for a 30 min exploration of our favourites and we’ll help guide you through some of the best options only a mouse click away.
Bottom line: no more coding in R to visualize your data, we’ve got you covered.
Just click and collect novel insights!

Remember, You can contact all our speakers directly for further details or support.

Serena Di Cecilia, PhD - Senior European Application Scientist, FlowJo, Informatics - [email protected]

Serena holds a PhD in Molecular Oncology and a postdoc in translational medicine. With significant experience in multi-parameter flow cytometry-based biomarker discovery, analysis of haematological and cancer diseases, and Next Generation Sequencing Serena‘s expertise now centers on supporting higher dimensional flow data analytics. Prior to joining BD and the FlowJo team, Serena was a Flow Cytometry data analyst in a Contract Research Organization focusing on clinical trials data analysis for big Pharma companies.

Ioannis Panetas - European Application Scientist, FlowJo, Informatics - [email protected]

Ioannis focuses on flow data analysis using high dimensional workflows in FlowJo™, with extensive experience in Multiparameter Flow Cytometry. He is currently responsible for trainings and supporting customers around Europe in analysis related queries. Prior to joining the FlowJo team, during his PhD, Ioannis specialized in Flow Cytometry and Imaging of Innate Immune cell populations of homeostatic and diseased tissues.

Episode 6 : A deep cell sorting detour, with Hyperfinder

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Date: coming soon - sign up for alerts


You may have discovered an interesting and novel population of cells through high dimensional flow cytometry analysis.
And you may now want to obtain a purified population of those cells to study them further – perhaps functional competence, phenotype plasticity or genome.

Challenge: Cell sorters cannot use the dimensionality reduction algorithms in real time on events captured during sample acquisition.
This makes it impossible to sort populations visualized with tSNE or UMAP.

Solution: Hyperfinder! A powerful FlowJo™ plugin that automatically finds the shortest gating strategy (in 2D plots) to your specific clusters of interest identified in the high dimensional data space.

Remember, You can contact all our speakers directly for further details or support.

Jens Fleischer - Flow Cytometry Application Consultant - [email protected]

Jens holds a PhD in Immunology and Cell Biology. Based at our European Center for Single Cell Solutions in Heidelberg, Jens specialises in our high-end instrumentation portfolio including including consultation on the design of bespoke instrument configurations to meet specific user and experimental requirements. The support he provides extends to higher parameter panel design on standard and custom-made systems alongside high dimensional data analysis with FACSDivaTM and FlowJoTM. Additionally, his expertise extends to include sorting and consultation on associated biosafety requirements.

Serena Di Cecilia, PhD - Senior European Application Scientist, FlowJo, Informatics - [email protected]

Serena holds a PhD in Molecular Oncology and a postdoc in translational medicine. With significant experience in multi-parameter flow cytometry-based biomarker discovery, analysis of haematological and cancer diseases, and Next Generation Sequencing Serena‘s expertise now centers on supporting higher dimensional flow data analytics. Prior to joining BD and the FlowJo team, Serena was a Flow Cytometry data analyst in a Contract Research Organization focusing on clinical trials data analysis for big Pharma companies.

A series of lab coat badges are being released to help build a community that seeks to gain deeper immune insights


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(as well as alerts about upcoming webinars and badges)


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