ESPACE Industry-Academia Webinar: Building a Human Cell Atlas of the Pancreas

ESPACE Industry-Academia Webinar: Building a Human Cell Atlas of the Pancreas
Event23 March 2022

Based on methods and standards for sample procurement, single cell profiling, spatial proteomics, and computational pipelines, the ESPACE consortium is building a first version of the Human Cell Atlas of the Pancreas. To demonstrate the achievements of the project to date and to foster knowledge exchange and cooperation between industry and academia, ESPACE hosts the webinar “Building a Human Cell Atlas of the Pancreas”. This event will consist of two main parts: an introduction of state-of-the-art single-cell technologies by industry partners as well as presentations of ESPACE findings by members of the consortium.

Date and time: May 31st, 2022, 14h-18h CEST.

Registration: Sign up here (free of charge)

The webinar is open for everyone who is interested in learning about ESPACE findings and wishes to expand their knowledge of single cell technologies. It is, however, especially tailored for industry representatives and members of the science community.

Agenda

2 pm      Welcome and Introduction by Christian Lawerenz (Steinbeis)

2.10 pm Part1: Building the Human Cell Atlas of the Pancreas: Recent developments in single-cell technologies and ESPACE findings

  • Every Cell Matters: Molecular Cartography™ for atlassing of healthy and diseased tissues by Benedikt Nilges (Resolve BioSciences)
  • Integrative analysis of single cell genomics of the healthy pancreas by Timo Trefzer (Charité)
  • Sharing histological findings in the pancreas tissue samples by Felix Schicktanz and Katja Steiger (Technical University of Munich)
  • Using single cell sequencing during process optimization of an iPSC-derived islet-like cluster cell therapy product by Matthias Austen (evotec)

3.50 pm Coffee Break

4.10 pm Part2: Building the Human Cell Atlas of the Pancreas: Recent developments in single-cell technologies and ESPACE findings

  • Single-Cell Spatial Phenotyping: Setting the pace of Discovery Biology by Virginie Goubert (akoyabio)
  • Sharing spatial proteomics to illuminate cell type heterogeneity in pancreas by Anna Martinez-Casals (KTH Royal Institute of Technology)
  • Accelerating Genomics Data Processing with Persistent Memory and Big Memory Software by Michael McManus (Intel)
  • ESPACE data in the cloud derived from raw data and images will be presented by Sven Twardziok (Charité)

5.40 pm Discussion

6.00 pm End of the Webinar

 Presentations

1) Every Cell Matters: Molecular Cartography™ for atlassing of healthy and diseased tissues by Benedikt Nilges (Resolve BioSciences)

Single-cell profiling technologies like scRNAseq have had a big impact on inferring the function of these cells from transcriptomic composition but are of limited utility without information on the spatial organization of these cells in the microenvironments of the intact tissue.
Benedikt Nilges will show how Molecular Cartography (MC) can be used to generate high-resolution, quantitative information on gene expression in intact tissue slices. MC is based on a hybridization approach that enables digital quantification of single mRNA molecules at 300 nm resolution in three-dimensions within a 10 µm thick tissue section

2) Integrative analysis of single cell genomics of the healthy pancreas by Timo Trefzer (Charité)

The presentation of the transcriptomics and ATAC sequencing efforts by the ESPACE consortium will highlight cell annotations, different gene expression patterns and epigenetics. Thereby, the different cohorts of healthy adult tissue and islet populations are analysed in greater detail with almost 1M cells in total, especially in the context of common micropathologies and type-2-diabetes. Christian Conrad and Timo Trefzer envision to provide this updated integrated Human Cell Atlas of the Pancreas to the scientific community with more biological questions to be answered. In ESPACE

3) Sharing histological findings in the pancreas tissue samples by Felix Schicktanz and Katja Steiger (Technical University of Munich)

One main contribution of TUM to the ESPACE project was the classification of the collected pancreas tissue samples in order to detect pathological changes that might influence the downstream procedures. Since the ESPACE project aims to investigate the physiological intact pancreas, the sample donors should be free of diseases that might change the histomorphological appearance of the pancreas and disturb the physiological function of the pancreas. Nevertheless, we could detect in one case a major pathological finding, while other samples showed minor pathological changes as fibrosis or beginning development of neoplastic changes, which raises the question where the line is to be drawn between physiological variance and the beginning of pathological development.

4) Using single cell sequencing during process optimization of an iPSC-derived islet-like cluster cell therapy product by Matthias Austen (evotec)

As part of its program for the development of novel iPSC-based cell therapy products, Evotec is currently developing iPSC-derived islet-like clusters as therapy for insulin dependent diabetes. As an essential part of process optimization for this and other projects, we are using single cell sequencing of intermediate and end stage cell material obtained during directed differentiation from pluripotent to final product stage. Single cell sequencing provides an unbiased and highly detailed view on cell populations, and allows, for example, the detection of unexpected cell populations, the tracking of differentiation trajectories and characterization of cell maturation and functional states. Evotec bioinformatics has developed an interactive analysis platform which allows project scientists to interrogate single cell data sets, and to build testable hypotheses for process optimization.

5) Single-Cell Spatial Phenotyping: Setting the pace of Discovery Biology by Virginie Goubert (akoyabio)

In her presentation, Virgine Goubert will describe a comprehensive spatial phenotyping framework that captures the continuum of needs across discovery, translational and clinical research. Key applications in biomarker discovery such as identifying cells in-situ, discovering novel or rare-cell phenotypes, and mapping cellular neighbourhoods (distinct tissue substructures) will be presented and new technologies that enable rapid whole-slide imaging to drive unbiased discovery will be introduced.

6) Sharing spatial proteomics to illuminate cell type heterogeneity in pancreas by Anna Martinez-Casals (KTH Royal Institute of Technology)

Spatial proteomics is a powerful tool to investigate the cellular architecture as well as localization of specific proteins within the healthy pancreas of adult individuals, thus adding spatial knowledge to complement the other rich molecular technologies in the framework of the Pancreatic Human Cell Atlas. To enable deep phenotyping of cells through simultaneous detection of many proteins, we have used the CODEX technology that allows highly multiplexed immunostaining based on DNA-barcoded antibodies. The team created a 27-plex panel of in-house conjugated antibodies. This will be used to study the cellular architecture and microenvironmental niches in 9 different TMA sections including a total of 198 tissue samples from 17 different donors each sampled from 4 different regions from adult healthy pancreas. The analysis of this data provides a great opportunity to explore cell-cell heterogeneity between neighbouring cells and to describe the inter- and intraindividual variations.

7) Accelerating Genomics Data Processing with Persistent Memory and Big Memory Software by Michael McManus (Dell)

As the size and complexity of single-cell datasets expands and the rapidity with which they need to be processed increases, organizations are facing the challenge of having to optimize their infrastructure to handle a simultaneous growth in both volume and velocity. This presentation by Michael McManus will cover the recent technology developments that aim to address these challenges and provides a best practice example of memory optimization for the purposes of single-cell genomics data processing. A brief overview from work with The Translational Genomics Research Institute (TGen), an affiliate of City of Hope, will be provided.

8) ESPACE data in the cloud derived from raw data and images will be presented by Sven Twardziok (Charité)

Building a first version of the Human Cell Atlas of the pancreas requires to combine different methods and standards for sample procurement, single cell profiling and spatial proteomics. To provide a technological infrastructure for collaboration, Sven Twardziok and his team have built a cloud solution for gathering, sharing, integration of data as well as sharing of code and analysis pipelines. In this talk, Sven presents the ESPACE solution for providing a cloud infrastructure that is used by the ESPACE consortium for sharing, integration and analysis of research data. This infrastructure can be easily adapted and rolled out to other research projects in the single cell community.

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