Cambridge Healthtech Institute's 5th Annual

The Liquid Biopsy Summit

Defining Circulating Biomarkers and Refining Translational Technologies

June 15 - 17, 2020

Monday, June 15

9:30 am Short Course Registration and Morning Coffee

10:00 Pre-Conference Lunch Short Course

SC1: Pre-Analytical Variables in Liquid Biopsy Testing - Recognizing, Planning and Mitigating Impacts on Your Test

1:00 pm Lunch for Short Course Participants

1:30 Pre-Conference Lunch Short Course

SC2: Liquid Biopsy from Bench to Bedside

4:00 Main Conference Registration

4:45 Welcome by Conference Organizer

Mary Ann Brown, Executive Director, Conferences, Cambridge Healthtech Institute

4:50 Chairperson's Remarks

Christina Lockwood, PhD, DABCC, DABMGG, Associate Professor, Laboratory Medicine; Director, Genetics and Solid Tumors Laboratory; Medical Director, Brotman Baty Institute for Precision Medicine, University of Washington

4:55 KEYNOTE PRESENTATION: Current and Future Clinical Uses for Liquid Biopsies

Walter Koch, PhD, Vice President & Head, Global Research, Roche Molecular Diagnostics

Today, the analysis of circulating DNA in the bloodstream provides results for prenatal diagnosis, organ transplant rejection, and molecular pathology in solid tumors that can identify the best therapeutic options. Future diagnostic applications in development include monitoring therapy responses/resistance, prognosis prediction, and screening for early detection of cancer in non-symptomatic individuals. Technological advances and an expanding number of analytes are supporting important roles for liquid biopsies in precision pathology and medicine.

5:40 FIRESIDE CHAT: Enhancing the Science and Clinical Utility of Liquid Biopsies

Walter Koch, PhD, Vice President & Head, Global Research, Roche Molecular Diagnostics

Christina Lockwood, PhD, DABCC, DABMGG, Associate Professor, Laboratory Medicine; Director, Genetics & Solid Tumors Laboratory; Medical Director, Brotman Baty Institute for Precision Medicine, University of Washington

6:10 Welcome Reception in the Exhibit Hall with Poster Viewing

7:15 Close of Day

Tuesday, June 16

8:00 am Morning Coffee

ISOLATING & ANALYZING CTCs

8:15 Chairperson's Remarks

Nithya Ramnath, Professor, Internal Medicine Hematology & Oncology, University of Michigan

Sunitha Nagrath, PhD, Associate Professor, Chemical Engineering; Co-Director, Single Cell Analysis Core, Rogel Cancer Center BioInterfaces Institute, University of Michigan

Circulating tumor cells (CTCs) are shed from the primary tumor into the peripheral blood. CTCs are emerging as important biomarkers with high clinical relevance. Enumeration of CTCs may have several clinical uses, including determination of prognosis in patients with established malignancy, or even detection of previously undiagnosed cancer.  However, due to the limitation of sensitivity and specificity of current technologies for CTC isolation, the full potential of CTCs has yet to be realized. Furthermore, emerging research show that a small number of cells have stem cell-like nature in various cancers and those are called cancer stem cells (CSC) which may arise from differentiated cancer cells through EMT and have the potential to self-renew and are pluripotent. Emerging microfluidic technologies are promising for isolating both CTCs and CSCs with a high yield and specificity. We present novel integrated nano microfluidic technologies that enable both functional and genomic assays beyond enumeration. The molecular and genetic profiling of CTCs is a viable alternative to painful, costly, and invasive biopsies. We demonstrate liquid biopsy using CTCs as a resource to identify genomic alterations in cancer and present the opportunities for diagnosis, therapy and surveillance.

9:05 Liquid Biopsy Using the Nanotube-CTC-Chip

Balaji Panchapakesan, PhD, Professor & Director, Small Systems Laboratory, Mechanical Engineering, Worcester Polytechnic Institute

We report the development of the nanotube-CTC-chip for isolation of tumor-derived epithelial cells (circulating tumor cells, CTCs) from peripheral blood, with high purity, by exploiting the physical mechanisms of preferential adherence of CTCs on a nanotube surface. The nanotube-CTC-chip is a new 76-element microarray technology that combines carbon nanotube surfaces with microarray batch manufacturing techniques for the capture and isolation of tumor-derived epithelial cells. Using a combination of red blood cell (RBC) lysis and preferential adherence, we demonstrate the capture and enrichment of CTCs with a 5-log reduction of contaminating WBCs.  The nanotube-CTC-chip successfully captured CTCs in the peripheral blood of breast cancer patients (stage 1-4) with a range of 4-238 CTCs per 8.5 ml blood or 0.5-28 CTCs per ml. CTCs (based on CK8/18, Her2, EGFR) were successfully identified. Ongoing work in breast and lung cancer will be presented and discussed. CTC enumeration, based on multiple markers in multiple different cancer types using the nanotube-CTC-chip, enables dynamic views of metastatic progression. It could potentially have predictive capabilities for diagnosis and treatment response.

9:35 Circulating Tumor Cell Characterization in Non-Small Cell Lung Cancer Patients and Xenograft Models

Jussuf Kaifi, MD, PhD, FACS, Chief, Division for Cardiothoracic Surgery, Ellis Fischel Cancer Center, University of Missouri Columbia

Analysis of circulating tumor cells (CTCs) in non-small cell lung cancer (NSCLC) patients has high potential for precision medicine. To characterize rare CTC populations, highly innovative human tissue- and CTC-derived xenograft (PDX/CDX) models from early-stage NSCLC patients were developed in immunodeficient mice. Comparative analyses of genomic and transcriptomic features using these models will lead to better understanding of CTC tumor biology and identify molecular targets associated with metastasis-initiating CTCs.

9:55 Sponsored Presentation (Opportunity Available)

10:25 Coffee Break in the Exhibit Hall with Poster Viewing

11:00 Detection of Residual Disease and Emerging Drug Resistance in Hematologic Malignancies by Ultra Sensitive Duplex Sequencing

Jesse Salk, MD, PhD, CEO & CSO, TwinStrand Biosciences

Cancer is driven by clonal evolution. The ability to sensitively and specifically detect tumor-associated mutations that mark low-level residual disease after treatment or the early emergence of impending drug resistance is clinically actionable, yet is technically very challenging. Duplex Sequencing is an ultra-accurate NGS method that reduces sequencing errors below one-in-ten-million. Here we demonstrate its application for informing precision medicine efforts in hematologic malignancies.

11:30 The Application of CTC Technology to Cytopathology

Alarice Lowe, MD, Associate Professor, Pathology; Director, Circulating Tumor Cell Lab, Stanford University

Circulating Tumor Cell (CTC) technologies are ideally suited to evaluation of cytopathology specimens and can provide rapid comprehensive evaluation of liquid specimens while maximizing the diagnostic, prognostic, and predictive information obtained from minimal samples.

12:00 pm CTC Clusters: Significance in Non-Small Cell Lung Cancer

Nithya Ramnath, Professor, Internal Medicine Hematology & Oncology, University of Michigan

Using a high-throughput (2.5 mL/min), label-free, inertial microfluidic device, Labyrinth, we isolated CTC clusters from 15/17 metastatic lung cancer patients. Presence of these clusters corresponded to poorer progression-free survival. Work is underway to understand specific targeting of these mostly EpCAM-CTC clusters to reduce incidence of metastasis and improve survival in patients with locally advanced non-small cell lung cancer (NSCLC). 

12:30 Session Break

1:15 Session Break

ISOLATING & EVALUATING cfNAs

1:55 Chairperson's Remarks

Varsha Rao, PhD, Director, Clinical R&D, Claret Bioscience

2:00 Novel Photopolymer Gel Blood Collection Tubes to Standardize the Recovery of Tumor Circulating Cell-Free Nucleic Acids

Pamela Ward, PhD, Associate Professor, Clinical Pathology, University of Southern California

Novel photopolymer gels have been developed to function as separators in blood collection tubes. Centrifugation separates the plasma and cellular phases and UV curing of the Photogel generates a solid barrier that permanently separates these constitute parts. The plasma can be decanted and used for ccfDNA isolation in the absence of contaminating genomic DNA. Under different centrifugation conditions, platelet enriched plasma can be isolated for recovery of educated platelets, which offer rich reserves of cancer associated RNA biomarkers. While much advancement is being made in the detection of cancer associated biomarkers in liquid biopsies, less attention is being placed on sample integrity, which plays a critical role in the accuracy and reliability of a test. This presentation will showcase the robustness of this novel Photogel blood collection tube that improves and standardizes the isolation of plasma for the downstream recovery of ccfDNA and tumor educated platelets.

2:30 SRSLY: A Single-Stranded Approach for Improved cfDNA Fragmentomics

Varsha Rao, PhD, Director, Clinical R&D, Claret Bioscience

Nucleosome and DNA-binding factor positioning inferred from cfDNA fragmentation patterns (as revealed by NGS) can be used to predict biological state and identify tissue-of-origin. SRSLYTM - an efficient library preparation facilitates improved cfDNA fragmentomics by retaining full sequence information, including native termini and by recovering a substantial fraction of short DNA fragments. These improvements can consequently enhance the performance of liquid biopsy-based diagnostic tools.

3:00 Sponsored Presentation (Opportunity Available)

3:30 Refreshment Break in Exhibit Hall with Poster Viewing

4:00 Methods for Genome and Nucleosome Profiling of Cell-Free DNA in Advanced Cancer

Gavin Ha, PhD, Assistant Member, Computational Biology & Public Health Sciences, Fred Hutchinson Cancer Research Center

Circulating tumor DNA (ctDNA) from liquid biopsies provides a non-invasive route to profile genomic alterations and transcriptional regulation in cancer. I will describe computational algorithms that we are developing to detect transcriptional patterns using nucleosome profiling. We apply our methods to identify genomic and transcriptomic signatures in ctDNA from advanced prostate cancer patients and highlight its applications for monitoring disease burden and tumor plasticity.

4:30 Miniaturized Sensors and Future of Liquid Biopsy for Detection of Circulating Tumor Markers

Reza Mohamadi, PhD, Faculty of Pharmacy, University of Toronto

Miniaturized sensors will shape the future of liquid biopsy. Early sings of cancer can be detected in blood without the need of taking a blood sample. In this presentation an overview of recent advances in using miniaturized sensors for detection of circulating tumor markers, including circulating tumor cells (CTCs), circulating nucleic acids (cNAs), and extracellular vesicles (EVs) will be provided.

5:00 A Novel Method for Enrichment of Short DNA Fragments for NIPT and Oncology Applications

David Ge, PhD, CEO and Co-Founder, Apostle, Inc.

The fragment sizes of circulating free DNA show subtle variability from different origins, for example, fetal vs. maternal, cancer vs. normal. The current liquid biopsy technologies offer little resolution in differentiating and enriching for this small but important difference, resulting in sample rejections, test inaccuracies, and limited clinical utility of liquid biopsies. Here we present a novel method, termed Apostle MiniEnrich, to address this challenge and efficiently capture this subtle variability, with data showing significant enrichment of target cfDNA fragments (Average Fetal Fraction/FF before enrichment = 12.96%; Average FF after enrichment = 19.92%; Average Delta FF = 6.97%, P = 0.001).  This method may have the potential to rescue rejected or non-reportable clinical samples and improve test accuracy, and may enable a much broader utility of liquid biopsies.

5:30 Close of Day

Wednesday, June 17

7:30 am Breakfast Breakout Discussion Groups

EXPLORING EXTRACELLULAR VESICLES

8:30 Chairperson's Remarks

Nola Klemfuss, Administrative Director, Brotman Baty Institute for Precision Medicine

Daniel Chiu, PhD, A. Bruce Montgomery Professor of Chemistry; Endowed Professor in Analytical Chemistry; Professor of Bioengineering, University of Washington

This presentation will describe two flow-based technologies we developed for the analysis of single rare cells and individual extracellular vesicles. I will outline the workings of these new tools, describe their performance, and discuss the clinical questions we are addressing with  these next-generation technologies.

9:20 Non-Coding RNAs as Liquid Biopsy Biomarkers in Gastrointestinal Cancer

Ajay Goel, PhD, Professor and Chair, Molecular Diagnostics and Experimental Therapeutics, Beckman Research Institute, City of Hope Comprehensive Cancer Center

Non-coding RNAs (ncRNAs) are emerging as important regulators of gene expression in cancer. Overexpression of specific non-coding RNAs (including microRNAs, SnoRNAs, piRNAs and circular RNAs) have been linked to the stepwise disease progression in colorectal cancer (CRC). Given their cancer-specific pattern of expression, remarkable stability, and presence in blood and other body fluids, ncRNAs are considered to be highly promising cancer biomarkers. Accumulating evidence firmly supports the existence of unique 'ncRNA signatures' that can not only facilitate earlier detection of the tumor, but can also assist in predicting disease recurrence and therapeutic outcome to current treatment regimens.

10:05 Coffee Break in the Exhibit Hall with Poster Viewing

10:30 Nano-Plasmonic Technology for Molecular Analysis of Cancer Exosomes

Hyungsoon Im, PhD, Assistant Professor, Center for Systems Biology, Massachusetts General Hospital, Harvard Medical School

Exosomes have emerged as promising circulating biomarkers easily accessible by liquid biopsy for the diagnosis and prognosis of cancers. This presentation will discuss the recent progress of nano-plasmonic exosome technology and their applications for sensitive detection and molecular profiling of circulating exosomes.

11:00 Extracellular Vesicle-Based Liquid Biopsy via Lipid-Based Nanoprobes

Hongzhang Simon He, PhD, CEO, Captis Diagnostics

Extracellular vesicles (EVs) can mediate intercellular communication by transferring cargo proteins and nucleic acids between cells. The pathophysiological roles and clinical value of EVs are under intense investigation, yet most studies are limited by technical challenges in the isolation of nanoscale EVs (nEVs). Here, we will discuss a lipid-nanoprobe system that enables spontaneous labelling of nEVs for subsequent magnetic enrichment in 15 minutes, with isolation efficiency and cargo composition similar to what can be achieved by the much slower and bulkier method of ultracentrifugation. We also show that this approach allows for downstream analyses of nucleic acids and proteins, enabling the identification of EGFR and KRAS mutations following nEV isolation from the blood plasma of non-small-cell lung-cancer patients. The efficiency and versatility of the lipid-nanoprobe approach opens up opportunities in point-of-care cancer diagnostics.

11:30 Tumor-Derived Exosomes Emerge as Key Components of Precision Oncology

Theresa Whiteside, PhD, Professor, Pathology, Immunology & Otolaryngology, University of Pittsburgh

In cancer, extracellular vesicles (EVs) and their small subset of 30-150nm exosomes, emerge as potential biomarkers of disease progression and response to therapy. Specifically, tumor derived exosomes (TEX), which mimic tumor cells in content, can serve as noninvasive tumor biopsy surrogates. Immunocapture from body fluids of TEX allows for their molecular profiling and correlations of TEX signatures with each patient's clinicopathologic endpoints. Exosome-based monitoring of cancer progression is a potentially transformative approach to precision oncology.

12:00 pm Session Break

12:30 Luncheon Presentation (Sponsorship Opportunity Available) or Enjoy Lunch on Your Own

1:00 Session Break

EXPLORING OTHER APPLICATIONS, BIOFLUIDS, & BIOMARKERS

1:45 Chairperson's Remarks

Alex Greninger, MD, PhD, MS, MPhil, Assistant Professor, Lab Medicine, University of Washington

Niaz Banaei, MD, Professor, Pathology and Medicine; Medical Director, Stanford Health Care Clinical Microbiology Laboratory; Director, Stanford Clinical Microbiology Fellowship; Associate Program Director, Stanford Clinical Pathology Residency Training, Stanford University School of Medicine

2:35 Cell-Free DNA for Monitoring Allograft Rejection

Nik Krumm, MD, PhD, Department of Laboratory Medicine, University of Washington

Donor-derived cell-free DNA (dd-cfDNA) is a sensitive, non-invasive marker of acute allograft rejection for heart and kidney transplants. We have developed a clinically applicable method for estimating dd-cfDNA fraction using ultra-low pass sequencing and low-density genotype information. We have tested our method using samples obtained from cardiac transplant patients at the University of Washington and describe early validation and results.

3:05 Liquid Biopsy Platform for Neuro-Degenerative Diseases

Milana Frenkel-Morgenstern, PhD, Senior Lecturer & Director, Bioinformatics, Cancer Genomics & Biocomputing of Complex Diseases lab, Bar Ilan University

We developed a unique liquid biopsy platform that uses circulating cell-free DNA in the blood plasma of Alzheimer's and Parkinson's patients. We identified novel biomarkers circulating in the blood at the early stages of the diseases. The most recent findings will be discussed.

3:35 Cell-Free Nucleic Acid for Pathogen Detection

Alex Greninger, MD, PhD, MS, MPhil, Assistant Professor, Lab Medicine, University of Washington

Cell-free nucleic acids are an attractive biomarker for detection of a variety of pathogens.  This talk will cover recent studies and new data on plasma cfDNA sequencing for detecting and quantifying viruses, bacteria, fungi, and eukaryotic parasites along with its clinical impact.

4:05 Conference Wrap Up

4:15 Close of Conference

* The program is subject to change without notice, due to unforeseen reason.

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