Tuesday, 2 October 201808:00 | Conference Registration, Materials Pick-Up, Morning Coffee, and Breakfast Pastries | |
Session Title: Emerging Trends in Single Cell Analysis, circa 2018 |
| | 09:00 |  | Keynote Presentation Single Vesicle Analysis: Making Sense of Exosome Diversity
John Nolan, CEO, Cellarcus Biosciences, Inc., 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 |  | Keynote Presentation A Platform for Detecting Tumor-Derived Exosomes
Lydia Sohn, Almy C. Maynard and Agnes Offield Maynard Chair in 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 |  Isolating Adherent Single Cells – The Taming of The Shrew
Chris Wetzel, Director of Sales and Marketing, MMI Microscope-based Single Cell Isolation
• Applications: Why analyze single cells
• Tools: How to precisely isolate a single cell
• Case study: Isolating adherent single cells selectively
| 15:00 |  From Raw Data to Pathways - Single Cell RNA-Seq Analysis with Partek Flow
Paul Fullerton, Field Application Scientist, Partek, Inc.
A major bottleneck in scRNA-Seq experiments is bioinformatic analysis of data sets with thousands of cells. But it does not have to be. In this live demonstration, we will show you how the intuitive graphical user interface and interactive tools of Partek Flow data analysis software can simplify your scRNA-Seq data processing, with the same power, speed, and flexibility of command-line tools. We will also demonstrate how Partek Flow can empower your analysis of multi-sample and multi-condition scRNA-Seq experiments such as cancer immunotherapy studies.
| 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 |  cellenONE® X1 – The Next Generation Platform for Single Cell Isolation and NGS Library Prep
Joshua Cantlon, Technical Sales and Applications Engineer, Scienion US
The cellenONE® X1 Redefines Single-cell Genomics. Enabled by its core technology, a piezo-acoustic, picoliter-volume dispenser, it offers unmatched accuracy and flexibility for dispensing bulk reagents and single cells with micron precision in any labware. The cellenONE® X1 platform breaks away from the limitations of current technologies based on finely tuned emulsions or large volume plate based approaches. Emulsion based platforms do not offer multiple interventions, while plate based platforms have limited scalability. The cellenONE® X1 is opening a big door into the small world of single-cell analysis by combining the low volumes found only in emulsions with the flexibility of a liquid handler to enable scalable nanoliter volume library prep of single cells. The cellenONE® X1 also offers a new paradigm for rare samples allowing up to 95% recovery from samples containing as little as 100 cells, making it ideal for clinical sample processing. The patented deterministic approach and real-time feedback allow true single cell isolation while offering the precision and confidence required by the growing single-cell sequencing and cloning communities. The cellenONE® X1 drives the single-cell genomics revolution into the next era. We will present data for applications including single-cell 3' RNAseq, WGA, and a never before seen COMPLETE RNAseq workflow.
| 17:00 |  | Keynote 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 |  Biology 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 | 19:30 | HP Free Workshop Entitled "Deep Dive -- HP Inkjet Chips for New Research Applications" | 21:00 | Close of Day's Programming |
Wednesday, 3 October 201808:00 | Morning Coffee Networking in the Exhibit Hall | 09:00 |  | Keynote 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 |  | Keynote 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 |  | Keynote 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
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| 10:30 | Coffee Break and Networking in the Exhibit Hall | 11:00 | Single Cell-ICP-MS Methods Development for Rapid Tracking of Nanoparticles and Algaecide Uptakes by Yeast and Cyanobacteria
Honglan Shi, Research Professor, Lab Director of Center for Single Nanoparticle, Single Cell, and Single Molecule Monitoring, Missouri University of Science and Technology, United States of America
High-throughput single cell-ICP-MS methods were developed. Newly developed methods were applied to evaluate the efficiencies of copper-based algaecide for treatment of harmful algae and cytotoxicity of silver nanoparticles to yeast cells. | 11:30 | 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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