(6jg) Multi-Dimensional Single Cell Analysis with a Chemistry, Materials, and Nanotechnology Toolset

The single cell is the unit cell of biology, and modern single cell analysis can now reveal the heterogeneity of biology. However, just as single cell resolution unveils heterogeneity invisible to bulk assays, multidimensional analysis illuminates the dark spaces in biological networks – the interplay between proteins, transcripts, and other biomolecules that is invisible to any single measurement method. Capturing this level of resolution in single cells requires effective coordination in nanoliter volumes across a panel of chemistry, molecular biology, and nanotechnology tools. My research interests are to develop nanomaterials and molecular probes to isolate single cells, and sieve and strain them for multi-dimensional single cell analysis. In particular, my research vision is to use my expertise in cell perturbation to add the aspect of intracellular delivery to single cell analysis: to deliver constructs into cells that can process and output information and add more dimensions to cell analysis.

Postdoctoral work: “Integrated measurements of transcripts and proteins in single cells”; “Microfluidic platforms for multi-dimensional single cell analysis”

James Heath, California Institute of Technology and now Institute for Systems Biology.

Graduate dissertation: “Engineering cell access using nanostraws”

Nicholas Melosh, Stanford University

Research Interests:

I’ve focused on two facets of nanobiotechnology in my career, cell manipulation and cell analysis. As a postdoc in the Heath lab, I created a platform to analyze proteins and transcripts in the same cell to be published shortly. The guiding principle of the project is to maximize the leverage of established techniques: we used bead-based single cell transcriptomics and barcoded protein immunoassays on the same single cells, and we encoded the position of each cell into DNA barcodes to reconstruct a spatial transcriptomic map of cells to match the proteomics. This project was instrumental for me to both confront the challenges of single cell measurements including proteomics and transcriptomics, and also to witness the impact of single cell analysis through the Heath lab’s translational projects at UCLA’s medical school and consortia like the Parker Institute for Cancer Immunotherapy.

In graduate school, I developed a nanoscale platform for intracellular delivery with Nick Melosh. We used high aspect ratio nanostructures – nanostraws – to create fluidic conduits to cells, toeing the fine line between effective intracellular delivery and cell disruption. The project itself required a balance of nanomaterials engineering, cell and molecular biology, and surface science, and I gained an appreciation for the biophysical barriers to cell access and the nanoscale levers to pull to manipulate cells. We used the nanostraws to deliver time-resolved signals, cell-impermeable probes, and more importantly, to assist collaborators in studying biology. It is this intersection – intracellular delivery as applied to multi-dimensional analysis – where I see my research group making the most impact, by delivering probes of cellular information into cells to couple with transcriptome sequencing.

In the future, I’m interested in coupling single cell transcriptomics to other single cell observations. As with my integrated proteomics-transcriptomics postdoc work, the primary tool will be to use DNA barcodes. My research program revolves around developing new methods to selectively deliver barcodes, or attach logic to barcodes to couple their sequencing to biological parameters. This includes materials level approaches using nanoparticles or microfluidics, biological assays such as competitive binding probes and DNA base-pairing logic, and computation-level strategies, especially to add information into DNA barcodes. With tools capable of linking transcriptomics to other measurements such as protein levels or fluorescent intensity, I can turn my focus to biological questions for heterogeneous systems, especially in my background field of cancer.

Both my postdoc and graduate work have been well funded. My current Ruth Kirschstein postdoc fellowship (NIH F32) received a first percentile 12.0 impact score, and my PhD was funded by both NSF and NDSEG graduate fellowships. Outside of my primary research projects, I’ve had numerous formative research experiences, from surface deposition at Argonne National Labs, to DNA information storage in Irene Chen’s lab at Harvard, to my twin undergraduate research positions at MIT, in phosphoproteomics and biologically template materials, with Forest White and Angela Belcher respectively.

Teaching Interests:

In addition to being a teaching assistant in graduate school (MATSCI 380 – Nanobiotechnology, 2013 and 2015), I’ve been focused on mentorship and I’m looking forward to a teaching program for postdocs that I’ve enrolled in for the winter (STEP at University of Washington). I benefited from excellent mentors as an undergrad, and since then I’ve mentored 6 undergraduates, as well as other graduate students. I’ve published or submitted papers with all but one of the undergraduates, and one of them submitted a first author publication under my guidance. I would be happy to teach courses of almost any flavor, as my own undergraduate coursework at MIT spanned my two majors of mathematics and materials science, as well as two minors of biomedical engineering and chemistry. I’m most excited to teach courses similar to the nanobiotechnology course that I TA’ed, literature based survey courses that reconstruct a sense of history behind a field through the progression of papers published.

Selected Publications:

Google scholar: 5 first author papers, h-index: 12

1. Alexander M Xu, Sally A Kim, Derek S Wang, Amin Aalipour, Nicholas A Melosh. Temporally resolved direct delivery of second messengers into cells using nanostraws. Lab on a Chip, 2016.
2. 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, 2014.
3. Jules J VanDersarl*, Alexander M Xu*, Nicholas A Melosh. Nanostraws for direct fluidic intracellular access. Nano Letters, 2011.
4. Alexander M Xu, Paul H Huang. Receptor tyrosine kinase coactivation networks in cancer. Cancer Research, 2010.
5. Alexander M Xu, Qianhe Liu, Kaitlyn L. Takata, Sarah Jeoung, Yapeng Su, Igor Antoshechkin, Sisi Chen, Matthew Thomson, James R Heath. Integrated measurement of cytosolic proteins and transcripts in single cells. In peer review.