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SELECTBIO Conferences Single Cell Analysis Summit 2018

Single Cell Analysis Summit 2018 Agenda



Co-Located Conference Agendas

Single Cell Analysis Summit 2018 | 

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Tuesday, 2 October 2018

08:00

Conference Registration, Materials Pick-Up, Morning Coffee, and Breakfast Pastries


Session Title: Emerging Trends in Single Cell Analysis, circa 2018

09:00

John NolanKeynote Presentation

Single Vesicle Analysis: Making Sense of Exosome Diversity
John Nolan, Professor, The Scintillon Institute, United States of America

Extracellular vesicles (EVs) are released by all cells and carry molecular cargo that can be delivered to nearby and distant cells to affect their function. Biofluids such as plasma contain EVs from many different cell types, and thus represent a rich source of potential biomarkers for liquid biopsy and other applications. However, progress towards this potential is slowed by the small size and heterogeneous nature of EVs found in various biofluids. We have been developing high resolution analysis methods to measure and characterize individual EV and classes of UVs to better understand their cellular source, molecular cargo, and potential destinations and functional effects. These methods includes optimized dye formulations, antibodies, and calibrators and standards needed for inter-lab comparisons. In this presentation I will highlight the potential roles of EV in biology, the challenges for their measurement, and new insights into the diversity of EVs revealed by new high resolution analysis methods.

09:30

Lydia SohnKeynote Presentation

A Platform for Detecting Tumor-Derived Exosomes
Lydia Sohn, Professor, Department of Mechanical Engineering, University of California, Berkeley, United States of America

Late-stage lung-cancer diagnosis is the major contributor to the poor survival of lung cancer patients. The lack of symptoms specific to early-stage lung cancer and the low sensitivity and high cost of current screening methods, are current barriers to early diagnosis. To address this challenge and enable rapid, cost-effective lung cancer screening, we are developing a microfluidic platform to detect tumor-derived exosomes in saliva. Our detection method utilizes resistive-pulse sensing to measure the size change of a micron-sized antibody-coated colloid when tumor-derived exosomes bind to it. Microscale in size, our platform can easily be manufactured using standard lithographic techniques. In this talk, I will describe our platform and the results we have achieved thus far to demonstrate its utility toward detecting tumor-derived exosomes for earl-stage detection of lung cancer.

10:00

Cancer Relapse Pathways Revealed by Single-cell Molecular Analysis
Jiang Zhong, Assistant Professor, University of Southern California, United States of America

I will discuss our study on single-cell molecular analysis of cancer relapse pathways.

10:30

Coffee and Networking in the Exhibit Hall

11:15

Mass Spectrometry Analysis of Live Single Cancer Stem Cells
Zhibo Yang, Assistant Professor, University of Oklahoma Health Sciences Center, United States of America

Mass spectrometry (MS) is a rapidly developing area for sensitive detection and accurate identification of broad ranges of biomolecules. We have developed a miniaturized multifunctional device, the Single-probe, that can be coupled to MS to analyze live single cells. One of the ongoing projects is to study cancer stem cells (CSCs). CSCs are vital for tumor development, relapse, and metastasis. However, current research in CSC biology is largely limited by the difficulty of obtaining sufficient CSCs. Thus, using MS method to study CSCs is a promising approach. We conducted a series of metabolomic analysis of live colorectal (HCT-116) CSCs, and compared the results with HCT-116 non-stem cancer cells (NSCCs). Our results show metabolomic features of CSCs are distinctly different from NSCCs at single cell level. Particularly, CSCs have significantly higher levels of unsaturated lipids compared to NSCCs. We demonstrated two enzymes, NF-?B and ALDH1A1, regulate the lipid desaturation in CSCs. In addition, our studies indicate that metabolites involved in TCA (tricarboxylic acid) cycle are more abundant in CSCs than those in NSCCs, indicating that their major energy production pathways are drastically different. Our studies suggest that lipid desaturation and tricarboxylic acid (TCA) cycle could be potential targets for CSC-targeted treatment.

11:45

Correlation of Single Cell RNA-Seq Data with Chemotherapy Response in Ovarian Cancer
Timothy K. Starr, Assistant Professor, University of Minnesota, United States of America

Our research focuses on understanding the genetic complexity of high grade serous ovarian cancer with the goal of using this knowledge to guide therapy. We have analyzed gene expression levels from primary ovarian cancer epithelial tissue using single cell sequencing technology. We will present our findings as well as our ongoing efforts to correlate single cell data with patient outcomes.

12:15

Networking Lunch in the Exhibit Hall Plus Poster Viewing


Session Title: Technologies for Single Cell Analysis

14:00

Direct Assessment of Combination Drug Efficacy in Individual Patients Using a New Sensitive Single Cell Imaging Screening Platform
Tania Vu, Associate Professor, Oregon Health and Science University, United States of America

I describe a new single cell imaging platform that enables validation and value for identifying the effectiveness of single agent/drug combinations in individual cancer patient samples. I will show the value of this functional cytometry platform for identifying drug target effectiveness, and overall drug efficacy and resistance in individuals.

14:30

Molecular Machines & Industries (MMI)Advancements in Single Cell Isolation Technology
Dan Lucking, Director of Sales, US, Molecular Machines & Industries (MMI)

Technology is making it easier and faster for researchers to identify single cells or other areas of interest from live cell cultures, tissue sections, and other types of samples and cell populations. We’ll walk through an introduction of two of these technologies, laser microdissection and an automated capillary based method. You’ll see how a researcher can get very particular about what cells he/she wants for downstream analysis and how to capture them with the click of a mouse. You’ll have the opportunity to see videos made using actual customer samples (tissue on slides and live cells in plates) to get a real sense of how individual cells of interest were collected and organized.

15:00

High-Resolution Lineage Mapping of Myogenesis in vivo
Ermelinda Porpiglia, Life Science Research Associate, Stanford University School of Medicine, United States of America

Muscle regeneration is a dynamic process during which the state and identity of the cells involved changes over time. Adult muscle stem cells are the driving force in skeletal muscle repair and regeneration. Mostly quiescent in healthy individuals, they become activated in response to muscle injury. While the phenotypic identity of muscle stem cells has been previously established, muscle progenitor cells, which are at a stage in between the stem cell and the mature functional myogenic cell, have not yet been identified in vivo. Progenitor cells hold enormous potential as a platform to study the cellular behavior and molecular control of stem cell fate, to identify novel therapeutic targets for muscle diseases, and to develop cell therapy applications for regenerative medicine. However, a major roadblock in their identification has been a lack of tools to resolve cellular heterogeneity in skeletal muscle, underscoring the importance of single-cell studies. We have capitalized on single-cell mass cytometry (CyTOF), a transformative technology that allows the discovery of novel subsets within a complex cell population, to capture stem cell fate decisions in vivo. We discovered novel cell surface markers that define a myogenic progression in vivo, by combining a high-throughput flow cytometry screen with CyTOF analysis of skeletal muscle. Importantly, using new marker sets we identified stem cells and previously unrecognized progenitor cell populations. We showed by lineage tracing experiments that these progenitor populations originate from muscle stem cells and exhibit distinct regenerative potential in vivo. Moreover, high dimensional CyTOF analysis in response to acute injury revealed the cellular and molecular dynamics of muscle regeneration at a level of resolution not previously possible.

15:30

Coffee Break and Networking in the Exhibit Hall

16:00

Towards Single-cell DNA Digital Sequencing
Larry Xi, CEO and CSO, Digenomix Corp, United States of America

Single-cell DNA sequencing has been shown to gain greater insights into the clonal structures of heterogeneous cancer tissues that bulk DNA sequencing has never been able to resolve.  However, biased whole genome amplifications from single-cell DNA reduce the resolution and the potential of this approach.   We proposed a scheme, BIG (Barcoding-In-Genome), that could increase the resolution by turning the analog mode of DNA sequencing into digital mode.  This digital mode will give exact, absolute copy number for every gene and can only be achieved on single-cell platforms.

16:30

Yu-Hwa LoKeynote Presentation

Assays for High Throughput Quantitative Studies of Single Cell Secretions and Physiology
Yu-Hwa Lo, Professor, University of California San Diego, United States of America

17:00

Holger SchmidtKeynote Presentation

Chip-Scale Integration of Optical and Electrical Single Molecule Analysis
Holger Schmidt, Narinder Kapany Professor of Electrical Engineering, University of California-Santa Cruz, United States of America

Lab-on-chip devices have long held the promise of providing a convenient and rapid way to analyze small amounts of biological samples. However, when pushed to the ultimate limit of single molecule sensitivity, the detection mechanism is often based on off-chip elements. I will discuss a chip-scale platform that offers both integrated optical and electrical single molecule analysis. Optical integration is achieved by using liquid-core waveguides interfaced with traditional photonic elements to implement advanced functionalities. Examples include multiplex detection of single viruses, simultaneous detection of proteins and nucleic acid biomarkers, and front-to-back sample handling and single DNA detection on a single chip. Electrical single molecule analysis is achieved by integration of solid-state nanopores. Novel nanopore detection capabilities such as feedback-controlled delivery of single molecules to a fluidic channel are demonstrated. The combination of both optical and electrical detection modalities results in a novel, high throughput platform for single molecule analysis.

17:30

10x GenomicsBiology at True Resolution with the 10x Genomics Product Portfolio
Jason Kim, Technical Sales Specialist, 10x Genomics

A deep dive into 10x Genomics single cell assays and their applications in research.

18:00

Networking Cocktail Reception with Beer and Wine in the Exhibit Hall. Engage with Colleagues and Visit the Exhibitors

19:00

Close of Day 1 of the Conference.

Wednesday, 3 October 2018

08:00

Morning Coffee Networking in the Exhibit Hall

09:00

Sheng ZhongKeynote Presentation

Rainbow-Seq: Combining Cell Lineage Tracking with Single-Cell RNA Sequencing in Preimplantation Embryos
Sheng Zhong, Professor of Bioengineering, University of California-San Diego, United States of America

Single-cell RNA-seq experiments cannot record cell division history and therefore cannot directly connect intercellular differences at a later developmental stage to their progenitor cells. We developed Rainbow-seq to combine cell division lineage tracing with single-cell RNA-seq. With distinct fluorescent protein genes as lineage markers, Rainbow-seq enables each single-cell RNA-seq experiment to simultaneously read single-cell transcriptomes and decode the lineage marker genes. We traced the lineages deriving from each blastomere in two-cell mouse embryos and observed inequivalent contributions to the embryonic and abembryonic poles in 72% of the blastocysts evaluated. Rainbow-seq on four- and eight-cell embryos with lineage tracing triggered at two-cell stage exhibited remarkable transcriptome-wide differences between the two cell lineages at both stages, including genes involved in negative regulation of transcription and signaling. These data provide critical insights on cell fate choices in cleavage embryos. Rainbow-seq bridged a critical gap between cellular division history and single-cell RNA-seq assays.

09:30

Paul BohnKeynote Presentation

Zero-Mode Waveguide Spectroelectrochemistry of Single Oxidoreductase Enzyme Molecules
Paul Bohn, Arthur J. Schmitt Professor of Chemical and Biomolecular Engineering and Professor of Chemistry and Biochemistry, University of Notre Dame, United States of America

Single electron transfer events in both immobilized and freely diffusing redox-active enzymes can be imaged with facility using electrochemical zero-mode waveguide (E-ZMW) arrays. These bimodal nanoelectrochemical-nanophotonic nanopore arrays are composed of high density zeptoliter-volume recessed dual-ring electrode nanopores. Thus, they provide a link between single electron-transfer events and light emission in fluorigenic redox reactions, such as those involving flavin-containing enzymes, i.e. flavoenzymes. The bimodal optical-electrochemical functionality of the E-ZMW makes it possible to perform single molecule spectroelectrochemical measurements under conditions where the enzyme is potential controlled and optically-coupled, while the enzyme substrate is generated in situ electrochemically at a nearby second working electrode.   Thus, the E-ZMW makes it possible to study single enzyme turnover events in an environment where both confinement and molecular crowding may be controlled.  The ability to combine electrochemical and spectroscopic measurements at the single molecule level is a new tool for the characterization of reaction dynamics.

10:00

Identifying a Predictive Signature of Neuronal Reactivity in Single Hippocampal Nuclei
Sara Linker, Staff Scientist, Lab of Fred H. Gage, Laboratory of Genetics, The Salk Institute for Biological Studies, United States of America

Activity-induced remodeling of neuronal circuits is critical for memory formation. This process relies in part on transcription, but neither the rate of activity nor baseline transcription is equal across neuronal cell types. In this study, we isolated mouse hippocampal populations with different activity levels and used single nucleus RNA-seq to compare their transcriptional responses to activation. We found that 1 hr after novel environment exposure sparsely active dentate granule (DG) neurons had a much stronger transcriptional response compared to more highly active CA1 pyramidal cells and vasoactive intestinal polypeptide (VIP) interneurons. Activity continued to impact transcription in DG neurons up to 5 hr, with increased heterogeneity. By re-exposing the mice to the same environment, we identified a unique transcriptional signature that selects DG neurons for reactivation upon re-exposure to the same environment. These results link transcriptional heterogeneity to functional heterogeneity and identify a transcriptional correlate of memory encoding in individual DG neurons.


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