| Description | Abstract:
Next-Generation Sequencing of bulk samples, revolutionized our understanding of LifeScience research and the ability to discover biomarkers and understand cancer biology at a completely new level (e.g., TCGA dBase). Single-cell sequencing, however, pointed out the extreme weaknesses of bulk-sequencing approaches, for both understanding sample heterogeneity and rare-cell populations. Single-cell sequencing (sc-Seq) approaches, while great at discovering new cell-classes and rare cells, suffers from the extreme limitation of requiring tissues to be dissociated, so that you never know how these (newly discovered) cell-types are organized in space, or function in the context of tissue architecture. To solve this problem, NanoString has developed a next generation of optical barcodes that enables spatially resolved, unlimited multiplexing of proteins and mRNA (in situ) from very difficult tissue types (e.g., formalin-fixed paraffin embedded, FFPE). The assay utilizes affinity reagents (antibodies or in-situ hybridization probes) coupled to oligonucleotide tags which are either: 1) released from discrete regions of the tissue using focused UV (~ 385nm) exposure and then digitally counted at unlimited multiplex (ex-situ via GeoMx) or 2) imaged directly in space (in 3D) at single-cell and subcellular resolution by the CosMx Spatial Molecular Imaging (SMI). Data will be presented highlighting the utilization of GeoMx Whole Transcriptome Atlas (up to 22,000 in-situ probes for protein-coding genes) to understand healthy and diseased Tissue and Cancer Biology (GeoMx now published in over 100 peer-reviewed manuscripts including Nature Medicine, Nature, Cell, Clinical Cancer Research). Data for CosMx will be presented, describing the largest single-cell FFPE study ever put into the public domain (over 800,000 single cells, over 260 Million transcripts) examining non-small-cell lung-cancer . The CosMx SMI platform will be commercially released H2 2022, and represents the highest-plex, highest sensitivity method of multi-omic subcellularly resolved detection in FFPE tissues. Also in H2 2022, NanoString launches a Spatial Biology Cloud-Based Portal, that allows both GeoMx and CosMx (big-)data to be analyzed in a integrated multi-user collaborative manner, absolutely essential for modern spatial biology studies. Large public-domain data sets using both GeoMx (The Spatial Organ Atlas) and CosMx SMI can be found at www.nanostring.com. Together, the GeoMx and CosMx spatial biology platforms have the potential to transform the study and understanding of all areas of LifeScience research (Discovery, Translational, and Clinical). Bio:
Joe Beechem joined NanoString in 2012 as the Senior Vice President of Research and Development and is now also the company’s Chief Scientific Officer. He is co‐inventor of both the GeoMx® Digital Spatial Profiler (DSP), which affords whole transcriptomic quantitative profiling of RNA and 100’s of plex protein from tissue sections as well as the next‐generation CosMx® Spatial Molecular Imager platform (H2 2022 launch) with highest‐plex multi‐omic imaging with single‐cell and sub‐cellular capability. Dr. Beechem leads a multidisciplinary team at NanoString based in Seattle, WA where he and his colleagues develop innovative technology platforms and assays based on the company’s nucleic‐acid based optical and photo‐active barcodes for multiplexed quantification of biomolecules. Joe’s R&D Team now focus 100% on technology development for unlimited‐plex multi‐omic spatial biology applications. Dr. Beechem is an author on over 150 peer‐reviewed papers in diverse fields: biomathematics, physics, chemistry, physiology, spectroscopy, diagnostics, medicine and biology. He received a doctorate in Biophysics from The Johns Hopkins University, Post‐Doc in Physics (UIUC) and started his career (11 years) as a tenured faculty member at Vanderbilt University Medical Center, along with a decade‐long career at Life Technologies as CSO and building Next‐Generation Sequencers. This seminar is part of BioE’s 10-week departmental Spring Seminar Series and BIOEN 509 course for enrolled students. |
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