(6ar) Multidimensional Single Cell Analysis: Devices and Technology for Cancer Biology

My research lab will develop new methods to study single cells in multiple dimensions, to better understand cell heterogeneity and cancer biology. We will focus on combining transcriptomics with phenotypic and phenomenological measurements to generate insights and hypotheses beyond the central dogma. In the field of cancer biology, we will target questions such as cell invasiveness, metabolism, and adhesion, that are largely invisible to the primary –omics methods (genomics, transcriptomics, proteomics), but have great clinical significance.

Single cell analysis has revolutionized biology, and it is perched at the nexus of biology, chemistry, and materials science. Recent advances in microfluidics, DNA preparation, and high-throughput processing have made single cell transcriptomics a benchtop tool. Yet, single cell transcriptomics has provided more exciting questions than satisfying answers to this point, largely because cell function is not clearly derived from knowledge of the transcriptome. To push our understanding deeper, my lab will combine high throughput single cell transcriptomics with the practical tools and workhorses of biology.

Tools like fluorescence microscopy and pulse-chase labeling can effectively describe the phenomenology of biology. When combined with the transcriptome, the functional phenomenology of the cell, i.e. subcellular localization of fluorescent proteins, can be correlated to gene regulatory networks and the control systems of the cell. In order to make multiple orthogonal measurements in a single cell (fluorescence microscopy + transcriptomics for instance), we will develop new devices and materials, chemistries, and bioengineering strategies. My lab will use systems biology and computational approaches to process these novel data sets, and study the heterogeneity of cancer phenomena.

Research Experience:

Postdoctoral: Multi-omic single cell measurements (Jim Heath, Caltech and the Institute for Systems Biology)

During my postdoc I developed new strategies to measure proteins and transcripts from the same single cells. Contrary to current technologies that convert protein to RNA signals, I created DNA mappings between transcriptomes and protein measurements by encoding the location of cells as DNA. This forms the basis for bridging transcriptomics with other measurement tools. The strategy of encoding physical parameters as DNA (location, time) was combined with microfluidic devices to make unorthodox multi-omic measurements in the same single cells, in this case bead-based transcriptomics and fluorescence sandwich immunoassays. This leads to new opportunities in systems biology to study cross-biomolecular species interactions. I also worked on projects in single cell analysis for immunotherapy and cell transitions over time.

Doctoral: Intracellular delivery strategies (Nick Melosh, Stanford University)

During graduate school, I created a new platform for intracellular delivery called nanostraws. Using microfabrication and deposition techniques from materials science, I created nanoscale conduits to cells to deliver different molecular species ranging from ions to small molecules to DNA plasmids. The nanostraws had unique characteristics like temporal control of delivery, and were adapted to platforms for oral ingestion and immune cell studies. This project required a unique perspective on the mechanics and mechanobiology of cells, and the nanobiointerfaces needed to control single cells precisely.

Other: DNA nanotechnology (Irene Chen, Harvard); Virus biotemplating (Angela Belcher, MIT); Cancer phosphoproteomics (Forest White, MIT); Atomic layer deposition of transparent conducting oxides (Jeff Elam, Argonne National Lab)

Awards: F32 Postdoctoral Fellowship, NSF Graduate Fellowship, NDSEG Graduate Fellowship

Teaching Interests:

My teaching interests include nanotechnology, nano-interfaces in biology, biomaterials, surface science, and systems biology. My teaching and learning experience has been highly interdisciplinary, with undergraduate degrees in Materials Science and Math, graduate studies in Materials Science, and a postdoc in a Chemistry and Chemical Engineering department and a Systems Biology institute. This has prepared me to teach courses in thermodynamics, polymers, and biochemistry as topics relevant to Chemical Engineering students. I am most excited to teach a course on nanobiotechnology, where the difference between biotic and abiotic systems becomes blurred. I TA’d a similar course as a graduate student for two quarters. Many nanobiotechnology courses tend to focus on the field of drug delivery, but I would focus on modern biological technologies enabled by nanoscience, to prepare students not just for academia but also for relevant jobs in modern biotech. Primary topics include high-throughput biology, next generation sequencing and DNA nanotechnology, neuroscience, and chemical biology. I am also excited to blend my new experience at the Institute for Systems Biology into my teaching by focusing on the computational aspects of high-throughput chemistry and biology, and how biological insights can be extracted from big data.

My teaching style will be drawn from my interdisciplinary background. In terms of training chemical engineers for their future careers, I can appreciate and build on the strong analytical skills that most chemical engineers possess while exposing them to new topics in the many research topics I have been involved in. Design projects are an effective way to allow students to branch out from coursework, think across disciplines, and be creative, and my courses will encourage that diversity. My own analytical background is strong, and I have placed a heavy emphasis on mentorship, with one of my students publishing a first author manuscript.

Selected Publications:

6 first authors, h-index=14

1. AM Xu, Qianhe Liu, Kaitlyn Takata, Sarah Jeoung, Yapeng Su, Igor Antoshechkin, Sisi Chen, Matthew Thomson, James R Heath. Integrated Measurement of Cytosolic Proteins and Transcripts in Single Cells. Lab on a Chip, 21, 3251-3262. (2018)

• Front cover

2. Alexander M Xu, Derek S Wang, Peyton Shieh, Yuhong Cao, Nicholas A Melosh. Direct Intracellular Delivery of Cell-Impermeable Probes of Protein Glycosylation by Using Nanostraws. ChemBioChem, 18, 623-628. (2017)
3. Alexander M Xu, Amin Aalipour, Sergio Leal-Ortiz, Armen H Mekhdjian, Xi Xie, Alexander R Dunn, Craig C Garner, Nicholas A Melosh. Quantification of Nanowire Penetration into Living Cells. Nature Communications, 5, 3613. (2014)
4. Alexander M Xu*, Jules J VanDersarl*, Nicholas A Melosh. Nanostraws for Direct Fluidic Intracellular Access. Nano Letters, 12, 3881-3886. (2011)

• Front cover

5. Alexander M Xu and Paul H Huang. Receptor Tyrosine Kinase Coactivation Networks in Cancer. Cancer Research, 70, 3587-3590. (2010)

Co-authored papers appearing in: Immunity, Science Signaling, Cancer Research, ACS Nano, Molecular Biosystems, Nano Letters