Shopping Cart (0)
My Account

Shopping Cart
SELECTBIO Conferences Single Cell Analysis Summit 2019

Single Cell Analysis Summit 2019 Agenda

Co-Located Conference Agendas

Lab-on-a-Chip & Microfluidics 2019: Companies, Emerging Technologies & Commercialization Track "B" | Lab-on-a-Chip & Microfluidics 2019: Emerging Themes, Technologies and Applications Track "A" | Single Cell Analysis Summit 2019 | Point-of-Care Diagnostics, Global Health & Biosensors 2019 | Microfluidics & Flow Chemistry 2019 | 

Print Agenda

Wednesday, 9 October 2019


Morning Coffee, Pastries and Networking in the Exhibit Hall

Session Title: Emerging Trends in Single Cell Analysis (SCA), circa 2019

Venue: Coronado Ballroom 4 & 5


Precision Medicine Using Liquid Biopsies: A New Paradigm for Managing Cancer Diseases
Steve Soper, Foundation Distinguished Professor, Director, Center of BioModular Multi-scale System for Precision Medicine, The University of Kansas, United States of America

Precision medicine seeks to match patients to appropriate therapies that optimize clinical outcome from molecular signatures of their disease. These molecular signatures can be secured from circulating markers found in blood (i.e., liquid biopsies). The marker types include circulating tumor cells (CTCs), cell-free DNA (cfDNA), and extracellular vesicles (EVs). Unfortunately, many disease-associated blood markers are a vast minority in a mixed population making them difficult to analyze due to deficiencies in current technologies used for their isolation. To address this deficiency, we are generating innovative microfluidic tools for selecting circulating markers from whole blood and determining the presence/absence of disease-specific molecular signatures secured from the liquid biopsy markers to guide therapy for a patient. The microfluidics can process whole blood (=1 mL) and search for CTCs, cfDNA, or EVs and make them available for downstream molecular processing. The microfluidics are made in plastics via injection molding, making them particularly attractive for clinical implementation, which demands low-cost disposables. In this keynote address, I will discuss our microfluidic platform for cfDNA and EV isolation. The chip consists of 1.4 million pillars that provides a high surface area for generating high loads of the target material. The chip is made from a plastic via injection molding. For the EV isolation, the pillars contain surface-immobilized antibodies directed against antigens from cancer cells that are epithelial based (EpCAM) and those with a mesenchymal phenotype (fibroblast activation protein alpha, FAPa). I will talk extensively about our EV isolation chip, and its use in several clinical examples and securing molecular information from the affinity-selected exosomes, for example mRNA expression profiling using droplet digital PCR.


Yu-Hwa LoKeynote Presentation

Single Cell Phenotype Analysis and Isolation based on Image-Guided Cell Sorting
Yu-Hwa Lo, Professor, University of California San Diego, United States of America

We present unique technologies that bridge single cell genomics and single cell phenotype analysis.  Tissue samples can contain millions of cells.  Even with high throughout sequencing, the NGS technologies and analysis tools may handle 1000 to 10,000 single cells for each sample due to cost and throughput considerations.  This corresponds to a very low (~0.1%) sampling ratio and increases the risk of missing important rare cells in the sample.  Currently people use cell sorting according to biomarkers to avoid the under sampling problem.  However, recent studies have shown that there exist far more cell types and degrees of heterogeneity, especially in tumorous tissues, than we have assumed before. The limited number of biomarkers and specificity of these markers have compromised our abilities to classify and sample cells in order to produce complete, unbiased understanding of the most interesting and significant cells in the population.  

To address this bottleneck, we developed high throughput flow cytometer cell sorting systems that can analyze and isolate single cells based on their phenotypic characteristics such as cell volume, shape, morphology, nuclear features, organelle distribution, speckle counts, etc.  The systems can detect both fluorescent and label-free (scattering) geometric features.  Coupled with machine learning and neural network, the systems offer capabilities to select and isolate single cells of different cell types and cell states, and to normalize the population (i.e. to select equal number of cells of the same type) to remove bias in the downstream genetic analysis.


Morning Coffee Break and Networking in the Exhibit Hall


Lydia SohnKeynote Presentation

Linking Physical Phenotype to Drug Resistance: Single-Cell Mechanical Measurements of Acute Promyelocytic Leukemia
Lydia Sohn, Almy C. Maynard and Agnes Offield Maynard Chair in Mechanical Engineering, University of California-Berkeley, United States of America

We have developed an efficient, label-free method of screening cells for their phenotypic profile, which we call Node-Pore Sensing (NPS).  NPS involves measuring the modulated current pulse caused by a cell transiting a microfluidic channel that has been segmented by a series of inserted nodes.  By simply inserting between two nodes a “contraction” channel through which cells can squeeze, we can use NPS to measure simultaneously physical properties of cells, including size, resistance to deformation, transverse deformation, and ability to recover from deformation.  “Mechano-NPS”, as we now call our method, can distinguish malignant from non-malignant epithelial cells and discriminate between sub-lineages and, chronological age groups of primary human mammary epithelial cells.  As I will discuss, we have recently been using mechano-NPS to study acute promyelocytic leukemia (APL) cells, showing that mechanical phenotyping is predictive of the leukemia’s response to retinoic acid (RA), a first-line chemotherapeutic for APL. By measuring cell recovery, mechano-NPS provides information on a cell’s viscoelastic behavior.  While this confers the advantage of making more in-depth biophysical analyses of single cells, it also potentially provides new information to be included in a diagnostic classification.


CellenionCellenONE: An Open Platform For Single Cell Applications
Joshua Cantlon, Product Development Manager, Cellenion

The cellenONE is a versatile tool for single cell experimentation. We will be sharing new data on miniaturization for sequencing, mass-spec, and cloning applications. Also, we will share images from our fluorescent image based single cell isolation (FIBSCI) technology used on multiple particle types including nuclei, plant cells, and bacteria.


Molecular Machines and Industries (MMI)The Good, the Bad and the Ugly: Selective Single Cell Isolation
David Hitrys, Commercial Leader, Single-Cell Isolation, Molecular Machines and Industries (MMI)

Isolation of single cells is an essential pre-requisite for many research projects in pathology, oncology or forensics. Discussed is the development of the novel “Shake Mode” feature of the robotic-capillary system called CellEctor from MMI enabling efficient and gentle uptake of living adherent cells for many kinds of downstream analysis as well as for further cultivation.


Klaus PantelKeynote Presentation

Clinical Applications of Liquid Biopsies
Klaus Pantel, Chairman, Department of Tumor Biology, University Medical Center Hamburg-Eppendorf, Germany

The analysis of circulating tumor cells (CTCs) and tumor cell products (DNA,RNA, extracellular vesicles) released into the blood may provide clinically relevant information as “liquid biopsy” and provide new insights into tumor biology (Pantel & Alix-Panabieres, Nature Rev Clin. Oncol. 2019). Various technologies have been developed over the past 10 years which include label-dependent assays based on the expression of tumor-associated cell surface antigens and label-independent assays based on physical properties of tumors cells distinct from the surrounding leukocytes (Pantel & Alix-Panabieres, Nature Rev Clin. Oncol. 2019). After detection CTCs can be further analyzed at the DNA, RNA and protein level to obtain global information on tumor biology and targets relevant to cancer therapy (Pantel & Alix-Panabieres, Nature Rev. Clin. Oncol. 2019). In particular, microRNAs control various genes and pathways that impact the biology of tumor cells (Anfossi, Bababayan, Pantel, Calin, Nature Rev. Clin. Oncol. 2018).

Liquid biopsy analyses with validated platforms provides reliable information on early detection of cancer, identification of cancer patients at risk to develop relapse (prognosis), and it may serve to monitor tumor evolution, identify therapeutic targets or mechanisms of resistance on metastatic cells. Metastatic cells might have unique characteristics that can differ from the bulk of cancer cells in the primary tumor currently used for stratification of patients to systemic therapy. Moreover, monitoring of blood samples before, during and after systemic therapy (e.g., chemotherapy, targeted therapy or immunotherapy (Hofman et al., Ann. Oncol. 2019)) might provide unique information for the future clinical management of the individual cancer patient and might serve as surrogate marker for response to therapy.

In conclusion, the liquid biopsy analysis can be used to improve the management of individual cancer patients and contribute to personalized medicine. CTCs are complementary to other liquid biopsy biomarkers (Alix-Panabieres & Pantel, Cancer Discovery, 2016; Bardelli & Pantel, Cancer Cell 2017). Validation of liquid biopsy assays is essential and currently performed by the EU/IMI consortium CANCER-ID (


Networking Lunch in the Exhibit Hall, Exhibits and Poster Viewing


Single Vesicle Analysis to Understand Intercellular Communication
John Nolan, CEO, Cellarcus Biosciences, Inc., United States of America

Extracellular vesicles are released from cells carrying molecular cargo that can be transferred to other cells to affect their function. Understanding the diversity of EV released from cells is important for understanding their roles in basic biology and well as to develop EV-based biomarkers and therapeutics. A particular challenge in the field is methods to sensitively detect EVs and measure their cargo, as the small size and heterogeneity of EVs limit the usefulness of conventional biochemical analysis. Single vesicle analysis offers the possibility to understand the heterogeneity of EVs released from cells, and we have developed flow cytometry (FC)-based methods to detect and size EVs as small as ~75 nm and measure cargo to ~30 molecules per vesicle. We are using these tools to measure the number, size, and cargo of EVs released from cells and to study the roles of EVs in cell-cell communication.


Single Cell Sequencing For Predicting Chemotherapy Response in Ovarian Cancer
Timothy K. Starr, Assistant Professor, University of Minnesota, United States of America

Women with ovarian cancer suffer from high rates of recurrence and chemotherapy resistance leading to mortality. We have implemented a prospective study that incorporates single cell RNA sequencing, along with other genomic and transcriptomic analyses, to identify cellular biomarkers that predict response to chemotherapy. The ability to predict response to front-line chemotherapy would enable earlier implementation of alternative therapies when treating women with ovarian cancer.


Catherine Alix-PanabieresKeynote Presentation

Liquid Biopsy in Cancer Patients: A focus on Metastasis-Initiator Circulating Tumor Cells
Catherine Alix-Panabieres, Associate Professor, University Medical Center of Montpellier, France

Circulating tumor cells (CTCs) in blood are promising new biomarkers potentially useful for prognostic prediction and monitoring of therapies in patients with solid tumors including colon cancer. Moreover, CTC research opens a new avenue for understanding the biology of metastasis in cancer patients. However, an in-depth investigation of CTCs is hampered by the very low number of these cells, especially in the blood of colorectal cancer patients. Thus, the establishment of cell cultures and permanent cell lines from CTCs has become the most challenging task over the past year.

We described, for the first time, the establishment of cell cultures and a permanent cell line from CTCs of one colon cancer patient (Cayrefourcq et al.Cancer Res. 2015). The cell line designated CTC-MCC-41 is in culture for more than three years and has been characterized at the genome, transcriptome, proteome and secretome levels. This thorough analysis showed that CTC-MCC-41 cells resemble characteristics of the original tumor cells in the colon cancer patient and display a stable phenotype characterized by an intermediate epithelial/mesenchymal phenotype, stem-cell like properties and an osteomimetic signature indicating a bone marrow origin. Functional studies showed that CTC-MCC-41 cells induced rapidly in vitroendothelial cell tube formation and in vivotumors after xenografting in immunodeficient mice. In 2017, we defined the molecular portrait of these metastasis-competent CTCs (Alix-Panabières et al. Clin Chem. 2017). These results highlight that CTC-MCC-41 line display a very specific transcription program completely different than those of the primary and metastatic colon cancer cell lines.More recently, we characterized 8 additional CTC lines using blood samples from the same metastatic cancer: a unique biological material collected before and after chemotherapy and targeted therapy, and during cancer progression (Soler et al. Sci. Rep. 2018).

Such data may supply insights for the discovery of new biomarkers to identify the most aggressive CTC sub-populations and for the development of new drugs to inhibit metastasis-initiator CTCs in colon cancer.


Cancer-Associated Subclones Among Mesenchymal Stem Cells Revealed by Single-Cell Transcriptome Analyses
Jiang Zhong, Assistant Professor, University of Southern California, United States of America

Despite the clinical benefits, detrimental effects of mesenchymal stem cells (MSCs) in clinical reports have been reported, in some cases fomenting tumorigenicity. Some of MSC subpopulations may be responsible for variation in the efficacy of bone marrow transplantation (BMT) and MSC-based therapy as well as tumorigenicity. Such heterogeneity of MSCs was not fully addressed until the arrival of the single-cell transcriptome technology. Recently, we report three discrete stages of osteogenesis based on a single-cell transcriptome analysis of individual MSCs during osteocyte differentiation. We identified a subpopulation of osteogenesis-resistant MSCs that have cancer stem cell characteristics. Further analysis indicated that the YAP1, ß-Catenin and Cadherin4/6 pathways involved in osteogenesis-resistance. Clinical surveys using 51 clinical databases across 6,965 patients revealed a correlation between YAP1/ ß-Catenin/Cadherin4/6 over-expression and cancer progression. This study suggested that a differentiation-resistant population of MSC with cancer stem cell characteristics is responsible for the tumorigenicity of MSC. Therefore, intervention of the YAP1, ß-Catenin and Cadherin4/6 pathway could potentially prevent tumorgenicity in MSC therapies by addressing the preexisting subpopulation of MSCs namely those differentiation-resistant populations associated with active YAP1-Cadherin pathway. Biologically active molecules targeting YAP1/ ß-Catenin/Cadherin could improve MSC therapy for a defined subset of patients by minimizing the tumorgenicity of MSCs.


Afternoon Coffee Break


Click Chip Enables Non-Invasive mRNA Analysis in Circulating Tumor Cells
Yazhen Zhu, Assistant Professor, David Geffen School of Medicine at UCLA, United States of America

Recent research focus in the field of circulating tumor cells (CTCs) has moved beyond the simple capture or enumeration of CTCs and gravitated towards approaches that allow for in-depth molecular analysis. CTCs house intact mRNA, providing more reliable gene signatures in tumors non-invasively. Exploring the use of CTC-derived mRNA offers a non-invasive diagnostic solution for understanding underlying tumor biology, guiding treatment intervention, and monitoring disease progression. Recently, we demonstrated a new covalent chemistry-enabled CTC capture/release platform – “Click Chip”. This platform is designed by integrating bioorthogonal ligation-mediated CTC capture (sensitive and rapid) and disulfide cleavage-driven CTC release (mild, specific, and rapid) on nanostructured substrates to enable efficient purification of CTCs with high-quality CTC-derived mRNA. The CTC-derived mRNA was subjected to RT-droplet digital PCR (RT-ddPCR) or Nanostring nCounter platform. In our proof of concept study, ALK/ROS1 rearrangements were quantified using CTC-mRNA recovered by Click Chips and matched with those identified in biopsy specimen in late-stage ALK/ROS1 positive NSCLC patients. Further, CTC-mRNA recovered from HCC patients by Click Chips can be used for HCC-specific mRNA profiling for predicting HCC prognosis. This streamlined workflow is optimum for non-invasive gene expression profiling based on high-quality CTC-derived mRNA.

Add to Calendar ▼2019-10-09 00:00:002019-10-09 00:00:00Europe/LondonSingle Cell Analysis Summit 2019Single Cell Analysis Summit 2019 in Coronado Island, CaliforniaCoronado Island,