Virtual <br>MACS® Genomics Day

Virtual 
MACS® Genomics Day

September 23, 2021

Achieve new heights in your genomic analysis 

Genomic analysis, such as single-cell gene expression, represents an invaluable tool to decipher many biological questions, and is often applied at several stages of the drug discovery and development process to identify and validate druggable targets. In the Virtual MACS Genomics Day our panel of speakers presented how they applied different types of single-cell genomic analyses to uncover insights in oncology, neuroscience, immunology, and gene therapy, as well as introduced latest technology innovations for single-cell genomic analysis.

Did you miss the event? No problem! Now available as on-demand recording you still have the chance to achieve new heights in your genomic analysis. So tune in and get inspired!

Video

Virtual MACS® Genomics Day

Watch the trailer and get a sneek peek of this interactive, virtual live event bringing together the genomics community.

Recorded talks | Part 1

Speakers
 

Using single-cell genomics to understand tissue immunology

Speaker: Prof. Dr. Michael Delacher
Research Center for Immunotherapy (FZI), Institute for Immunology, University Medical Center Mainz, Germany

Abstract
Advances in tissue processing, cell sorting, single-cell processing, and next-generation sequencing technologies allow the investigation of immune cells at an unprecedented level. We used these technologies to understand a novel function of immune cells: to promote homeostasis and regeneration of tissues. In this context, regulatory T cells have been studied in detail. The utilization of single-cell T-cell receptor sequencing allowed clonal evolution tracking, while single-cell RNA sequencing comparisons were used to delineate developmental trajectories of T cells in blood and tissues. More recently, single-cell chromatin accessibility studies enabled us to identify programs shared between mouse and human, thereby identifying a subtype of human regulatory T cell with tissue repair capacity. These findings lead to a new understand of tissue T cell immunology.

About Prof. Dr. Michael Delacher
Michael Delacher has recently been appointed W2 Professor for Systems Biology and established his lab within the Department of Immunology at the University Medical Center Mainz, Germany. His lab investigates how the immune system contributes to healthy tissue homeostasis and how it fosters regeneration upon tissue damage, e.g., caused by infections or cancer. To do so, he uses complex tissue processing, high parameter flow cytometry, single-cell sequencing methods, and genetic mouse model systems. As undergraduate student, Prof. Delacher studied Biotechnology and Molecular Medicine. As Ph.D. student, he worked in the Department of Tumor Immunology of the German Cancer Research Center in Heidelberg and the Department of Immunology of the Weizmann Institute of Science in Israel.

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Epigenomic priming of immune genes implicates oligodendroglia in multiple sclerosis susceptibility

Speaker: Mandy Meijer
Karolinska Institute, Solna, Sweden

Abstract
Multiple sclerosis (MS) is characterized by a targeted attack on oligodendroglia (OLG) and associated myelin by immune cells, which are thought to be the main drivers of MS susceptibility. Assessing chromatin accessibility at the single-cell level, we found that immune genes exhibit a primed chromatin state in mouse and human OLG in a non-disease context, compatible with rapid transitions to immune-competent states in MS. A subset of immune genes present bivalency of H3K4me3/H3K27me3 in oligodendrocyte precursor cells (OPCs), with Polycomb inhibition leading to their increased activation upon interferon-gamma (IFNg) treatment. Some MS susceptibility single-nucleotide polymorphisms (SNPs) overlap with these primed regulatory regions in mouse and human OLG, and treatment of mouse OPCs with IFNg leads to chromatin architecture remodeling at these loci and altered expression of interacting genes. Our data indicates that susceptibility for MS may involve OLG, which therefore constitute novel targets for immunological-based therapies for MS.

About Mandy Meijer
Mandy Meijer is Ph.D. student in Molecular Neurobiology at the Karolinska Institutet, Stockholm, Sweden. Her research focuses on investigating the role of peptidylarginine deiminases in oligodendrocyte development, as well as characterizing distinct chromatin states within the oligodendrocyte lineage with single-cell assay for transposase-accessible chromatin using sequencing (scATAC-seq) in both development and disease. She obtained her master’s degree in Molecular Neuroscience at the University of Amsterdam, the Netherlands, where she also finished her bachelor studies in Psychobiology.

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Chromium X: The new era of single cell is here 

Speaker: Luca Mazzitelli , Ph.D.
Science and Technical Advisor, 10x Genomics

Abstract
Our latest single-cell instrument, Chromium X, was designed and built to help you achieve your research goals, now and in the future. For every stage of your single-cell journey, Chromium X has the power to make it happen and the flexibility to match the scale of your research needs. When you're ready to take the next step to expand your single-cell profiling or increase your sample sizes, you will already be prepared – with a complete single-cell system right at your bench. Meet the new Chromium X, learn about its capabilities, and see the breadth of its applications. 

About Luca Mazzitelli, Ph.D.
Luca Mazzitelli is Science and Technical Advisor for 10x Genomics supporting distributors in EMEA area. Luca studied Plant Biotechnology at the University of Napoli “Federico II”, and finished his Ph.D. at the University of Dundee and Scottish Crop Research Institute studying in the field of Plant Sciences. Upon completing his Ph.D., Luca joined Qiagen as PCR Array Sales Specialist covering Italy and EMEA commercial partners. Over the past four years, Luca developed Qiagen's NGS franchise as a Customer Solution Manager - Genomics, which is a background he now lends to 10x Genomics. 

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Recorded talks | Part 2

Speakers
 

Optimization and validation of dissociation pipeline for producing 10x single-cell RNA-seq data from solid ovarian carcinoma tissue

Speaker: Thomas Parry
University of Edinburgh, Scotland

Abstract
Single-cell RNA sequencing (scRNA-seq) is a powerful technology that involves the assaying of the RNA-expression profile (transcriptome) of individual cells. High-throughput microfluidic platforms for scRNA-seq enable the profiling of 100’s to 10,000’s of single cells simultaneously with the possibility of multiplexing the libraries from multiple experiments. Sequencing cells from perturbed states; such as solid cancer tissue, present the opportunity to interrogate features not resolved from sequencing the bulk extracted RNA.Generating high quality scRNA-seq datasets from cancer tissue is no trivial task. From the moment the tissue is excised from the patient to loading the dissociated single cell mixture into the microfluidic system to capture the transcripts. There are many parameters that can impact the sequenced product and downstream analysis. 

About Thomas Parry
Thomas Parry is Ph.D. candidate at the University of Edinburgh, Scotland, with an extensive experience using Seurat (v3-v4) and suite of Bioconductor packages for analysis and visualization of single-cell RNAseq datasets. He obtained his M.Sc. in Clinical Pharmacology at the University of Glasgow and completed his Bachelor studies in Biomedical Sciences at the Nottingham Trent University.

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Illumina’s latest technology and portfolio advancements

Speaker: Pawel Zajac, Ph.D.
Staff Segment Marketing Manager EMEA, Cell Biology, Illumina

Abstract
Illumina sequencing is an integral part of single-cell and spatial sequencing workflows. We invite you to join this presentation to learn about the latest news, see how to match a sequencing solution to your project, and ask your questions to Illumina sequencing experts.

About Pawel Zajac, Ph.D.
Pawel Zajac, Ph.D., is Cell and Molecular Biology Marketing Manager for Europe, Middle East, and Africa at Illumina. He focuses on enabling researchers with single-cell and spatial sequencing technologies in several areas. Pawel has a Ph.D. from the Royal Institute of Technology (KTH) in Stockholm, Sweden, and worked as postdoc at the Karolinska Institute in Stockholm. His research focused on method development in single-cell RNA sequencing and multiplex amplification. Pawel is the author of >10 peer-reviewed articles in journals including Nature Methods and Genome Biology.

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Recorded talks | Part 3

Speakers
 

scAAVengr, a transcriptome-based pipeline for quantitative ranking of engineered AAVs with single-cell resolution

Speaker: Bilge Esin Ozturk, Ph.D.
Department of Ophthalmology, University of Pittsburgh, Pittsburgh, USA

Abstract
Adeno-associated virus (AAV)-mediated gene therapies are rapidly advancing to the clinic. However, quantitative comparison of AAVs, especially in large animals, remains challenging. Here, we developed an efficient single-cell AAV engineering pipeline (scAAVengr) for rapid, quantitative in vivo comparison of transgene expression from newly engineered AAV capsid variants across all different cell types in a tissue in parallel, and in the same animals. The scAAVengr pipeline allowed us to quantitatively evaluate the clinical potential of multiple lead candidates across all retinal cell types, in the foveal and peripheral retina, in a large animal model with eyes similar to humans. Our results validate scAAVengr as a powerful method for identification and development of AAV vectors for clinical translation. 

About Bilge Esin Ozturk, Ph.D.
Bilge Esin Ozturk, Ph.D., is Postdoctoral Associate in the Byrne Lab at the University of Pittsburgh, Department of Ophthalmology, specializing in AAV vector development, since 2017. She received her B.Sc. in Molecular Biology and Genetics and obtained her M.Sc. in Molecular Mechanisms of Disease. During her Ph.D. in Biotechnology she focused on studying mechanisms involved in cell cycle regulation in cancer cells. Her training in vision science started in the Blindness Genetics Group at Radboud University Nijmegen during her Master’s program, searching for candidate genes for inherited retinal dystrophies, and continued in gene therapy for retinal diseases in Flannery lab at UC Berkeley. In her current position in Byrne lab, she is working on projects addressing the most critical issues in the field of gene therapy; to efficiently target cells for specific gene delivery, enhance tropism for important cell types, and to improve the carrying capacity of AAVs.

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Immuno-profiling of murine preclinical tumor models in the multi-omic era. A way to improve translational prediction for immune-based therapeutics

Speaker: Hervé Luche, Ph.D.
Centre d'immunophénomique (Phenomin-CIPHE), Marseille, France

Abstract
The identification of the major cellular players involved in the progression of a type of cancer is a key step for the success of new immunotherapies for effective personalized medicine. It is however a daunting challenge because complex relationships exist between tumor cells and immune system cells. To characterize the impact of a gene involved in the anti-tumor response, cellular phenotyping of leukocytes infiltrating a tumor (TILs) is necessary. We study TILs at the single-cell level in mice grafted with MC38 tumors treated or not by an immuno-oncological agent. For explorational studies, scGen approaches such as CITEseq have been integrated in the immune-profiling pipeline. Through this presentation, I will show the route we followed to build this capability at CIPHE both in terms of application as well as analysis. Application on preclinical characterization of therapeutic treatment will be presented. 

About Hervé Luche, Ph.D.
Hervé Luche, Ph.D., studied developmental immunology in the lab of Hans-Joerg Fehling After obtaining his Ph.D., he worked as postdoc in the lab of Bernard and Marie Malissen where he engineered knock-in mouse strains to address lineage commitment issues. He combined detection of fluorescent proteins, multiparametric flow cytometry as well as microarray analysis to understand the pattern of genes that were involved in lineage decisions at the molecular level. In 2012, Hervé Luche  joined the Centre for ImmunoPHEnomics (CIPHE) in Marseille-Luminy, France, to lead a team of engineers of the immuno-phenotyping module. Being in charge of the CIPHE immunophenotyping service, a multidisciplinary team of specialists, he guides the development of standardized methodologies, functional assays, and high-content cytometry panels of leukocytes to establish a status of the immune system at basal, inflammatory, oncology, or infectious conditions in preclinical mouse models. Hervé Luche is an early adopter of mass cytometry as well as scGenomic effort towards functional phenotyping.

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