(3fa) Biochemical and Cellular Libraries Reveal Cancer-Associated Histone Mutations That Perturb Nucleosome Structure and Inhibit Cell Differentiation

Recent whole genome sequencing data mining efforts have revealed thousands of mutations in histones, the DNA-packaging proteins in eukaryotic genomes, across a wide range of cancer types (Figure 1). These occur in all four core histones in both the unstructured tail and folded globular domains and remain largely uncharacterized. Here we used two high-throughput approaches, a DNA-barcoded mononucleosome library and a humanized yeast library, to profile the biochemical and cellular effects of these mutations. We identified cancer-associated mutations in the histone globular domains that enhance fundamental chromatin remodeling processes, nucleosome sliding and histone exchange, and are lethal in yeast. In mammalian cells these mutations promote cancer phenotypes, upregulating cancer-associated gene pathways and inhibiting cellular differentiation by altering expression of lineage-specific transcription factors. This work represents the first comprehensive functional analysis of the histone mutational landscape in human cancers, and leads to a model in which histone mutations that perturb nucleosome remodeling can contribute to the development of cancer phenotypes.

Research Interests

I am interested in utilizing techniques in protein chemistry and engineering to build new experimental tools and platforms for biological discovery. In my doctoral research with Prof. David Tirrell at Caltech, I developed methods for studying protein synthesis in cellular systems. The work utilized combined approaches in mass spectrometry-based proteomics, chemical biology, and molecular biology to measure proteome-wide changes in protein synthesis at highly precise time scales. In doing this work it was impressed on me the exciting capability of new analytical methods to explore previously inaccessible biological questions — I believe that scientific advances of this kind are crucial in addressing challenging problems in biology and public health.

In my postdoctoral studies I joined Prof. Tom Muir’s lab with two goals in mind: first, to expand my skillset in synthetic organic chemistry for studying protein function, and second, to study the field of chromatin biology, a fascinating and complex area that interfaces genetics, biochemistry, and biophysics in understanding the epigenetic regulation of gene expression in eukaryotic cells. During my postdoc I played a central role in a collaborative research platform that identified and defined the landscape of cancer-associated mutations found in the histone packaging proteins in chromatin. To rapidly characterize these mutations, I built a DNA-barcoded nucleosome library, which allows thousands of biochemical measurements to be performed in a single-pot using next generation sequencing technologies. Overall, this work performed the first biochemical characterization of the newly identified histone mutational landscape, and led to a new model in which mutations that disrupt the core nucleosome structure can lead to genetic dysregulation.

In all of my work, tool development has played a key role in developing new insights into biological systems. I want to develop a research program that integrates efforts in tool development with biochemical investigations to understand the mechanisms of epigenetic regulation in humans. Central to this effort will be the use of protein engineering techniques to design and build protein-based biological probes, which will include methods that utilize protein evolution, protein splicing (inteins), and non-canonical (synthetic) amino acids. In particular, tools for characterizing the complex interactome of key epigenetic components, including chromatin remodelers, transcription factors, as well as the large number of chemical modifications on histone and chromatin-associated proteins, are greatly needed in the chromatin field. I will also develop tools to characterize the relatively new area of chromatin biology highlighted by my postdoctoral work, namely the mutations and post-translational modifications in histones that disrupt the core structure of the nucleosome. There are currently no methods to probe this kind of destabilizing effect in cells, and techniques to access this information will be crucial for understanding how nucleosome core stability affects gene regulatory programs. In parallel with this effort I will perform biochemical investigations of chromatin utilizing ‘designer chromatin,’ in which synthetic chromatin building-blocks can be synthesized with chemical precision, allowing the precise characterization of native chromatin substrates.

Teaching Interests

Central to my research themes are the development of new tools to better understand biology, which was an outlook that was fundamentally shaped by my chemical engineering background. I believe that chemical engineers are ideally suited for the highly interdisciplinary research landscape in modern academics and industry. This is particularly true in the biological sciences, where our quantitative background provides a solid foundation for understanding the underlying kinetics and physics of biological systems, while our training in chemistry and biochemistry offers practical skills for controlling and probing these systems. Furthermore, -omics experiments that generate ‘big data’ are becoming increasingly routine in the biological sciences, but getting the most out of these experiments necessitates quantitative and bioinformatic skills that usually requires some background in coding. Essentially, I believe that the chemical engineering skillset poises students to be the true ‘jack of all trades’ in the biological sciences, and I want to contribute to and develop educational programs to help realize this goal. In particular, I think engineers on a biological track would greatly benefit from learning material in chemical biology, protein chemistry, and bioinformatics. These are areas of rapid development in the biological sciences that will greatly benefit from the rigorous, quantitative, and structured approaches that are central to chemical engineering programs.