Research Background and Interests
Research Focus 1: Telomeres and Telomerase
A fundamental challenge in cancer and aging research is the lack of appropriate model systems that recapitulate the small physiological changes that compound over the human lifespan to lead to pathologies. A particularly fascinating subject is the tenuous balance inherent in the telomere maintenance pathway: slight aberrant activation is strongly linked to cancer while a relatively small deficiency results in premature stem cell aging and tissue failure. Our research focuses on developing genetically accurate human model systems that can recapitulate these pathologic defects in the telomerase pathway as well as the tools to gain a mechanistic understanding of the molecular changes that drive them. Moreover, we apply the insights and technologies developed during our studies of telomere biology towards the broader and often synergistic goal of investigating aspects of human stem cell biology, tissue physiology and pathology that are specific to humans and difficult to model with conventional model organisms.
Our goal is to shed light on the key functions of telomeres and telomerase in tissue homeostasis, tumorigenesis and aging. Telomeres are the repetitive DNA sequences at the end of linear eukaryotic chromosomes that allow a cell to distinguish the natural chromosome end from aberrant DNA breaks. Telomeric DNA repeats can be generated de novo by the enzyme telomerase thereby providing a compensatory mechanism that counteracts terminal sequence loss caused by the end replication problem. As a result, telomeres and telomerase are essential to genomic integrity and their disruption is associated with cancer and aging. The use of genetic mouse models has been a powerful way to gain insight into the fundamental mechanisms of how the telomere evades recognition by the DNA-damage machinery, the consequences of telomerase loss, and how the single stranded telomeric overhang is established. However, telomere shortening naturally occurs only in human somatic cells, but not in mouse cells. This telomere shortening, which functions as a tumor suppressor mechanism by limiting the replicative potential of human cells, is the result of selective silencing of telomerase expression in human cells upon their differentiation. Notably, this process is reversed and telomerase reactivated in about 90% of all human tumors after which telomerase expression becomes essential for their proliferation.
1. Genetic and molecular identification of three human TPP1 functions in telomerase action: recruitment, activation, and homeostasis set point regulation. Sexton A.N., Regalado S.G., Lai C.S., Cost G.J., O'Neil C.M., Urnov F.D., Gregory P.D., Jaenisch R., Collins K., and Hockemeyer D. Genes and Development. 2014.
Commentary: Genes Dev. 2014. Modern genome editing meets telomeres: the many functions of TPP1. Karlseder J.
2. Cancer-associated TERT promoter mutations abrogate telomerase silencing. Chiba K, Johnson JZ, Vogan JM, Wagner T, Boyle JM, and Hockemeyer D. Elife. 2015
3. Control of telomerase action at human telomeres. Hockemeyer D. and Collins K. Nature Structure and Molecular Biology. 2015
4. Mutations in the promoter of the telomerase gene TERT contribute to tumorigenesis by a two-step mechanism. Chiba K. &, Lorbeer F.K., Shain A.H., McSwiggen D.T., Schruf E., Oh A., Ryu J., Darzacq X., Bastian B.C., and Hockemeyer D. Science. 2017
Commentary: New insights into melanoma development. Shay JW. Science. 2017.
Research Focus 2: Developing Tools to Study Cell Biology in Primary Human Organoids
The advent of 3D tissue differentiation with modern genome engineering
While mouse models of cancer have provided important insights into basic mechanisms, key differences in tumor biology between mice and humans have impeded the translation of these findings into successful therapeutics. For example, mice and humans differ in their tumor spectra: while common laboratory mouse strains develop cancers primarily in mesenchymal tissues such as lymphomas and sarcomas, most human tumors develop from epithelial cells and lead to carcinomas. Such fundamental differences between mice and humans are not restricted to cancer biology but can be identified in almost all aspects of biology, like neural development and degeneration, (more examples). Over the last few years, my lab has developed robust protocols to edit and differentiate hPSCs into a variety of human cell types and tissue organoids. Together with our collaborators, we leverage these cell systems to enable studies that address questions about human cell biology and diseases that require a human primary cell system. Our overall goal is to develop better cell model systems that can be used to uncover the mechanisms of human disease and to identify points of vulnerability for novel therapeutics.
1. Human intestinal tissue with adult stem cell properties derived from pluripotent stem cells. Forster R., Chiba K., Schaeffer L., Regalado S.G., Lai C.S., Gao Q., Kiani S., Farin H.F., Clevers H., Cost G.J., Chan A., Rebar E.J., Urnov F.D., Gregory P.D., Pachter L., Jaenisch R., and Hockemeyer D. Stem Cell Reports. 2014.
2. 4D cell biology: big data image analytics and lattice light-sheet imaging reveal dynamics of clathrin-mediated endocytosis in stem cell-derived intestinal organoids. Schöneberg J., Dambournet D., Liu TL, Forster R., Hockemeyer D., Betzig E., and Drubin D.G. Molecular Biology of the Cell. 2018.
3. Genetically engineered human cortical spheroid models of tuberous sclerosis. Blair J.D., Hockemeyer D., and Bateup H.S. Nature Medicine. 2018.
4. Genome-edited human stem cells expressing fluorescently labeled endocytic markers allow quantitative analysis of clathrin-mediated endocytosis during differentiation. Dambournet D., Sochacki K.A., Cheng A.T., Akamatsu M., Taraska J.W., Hockemeyer D., and Drubin D.G. Journal of Cell Biology. 2018.
5. Observing the cell in its native state: Imaging subcellular dynamics in multicellular organisms. Liu T.L., Upadhyayula S., Milkie D.E., Singh V., Wang K., Swinburne I.A., Mosaliganti K.R., Collins Z.M., Hiscock T.W., Shea J., Kohrman A.Q., Medwig T.N., Dambournet D., Forster R., Cunniff B., Ruan Y., Yashiro H., Scholpp S., Meyerowitz E.M., Hockemeyer D., Drubin D.G., Martin B.L., Matus D.Q., Koyama M., Megason S.G., Kirchhausen T., and Betzig E.. Science. 2018.
Research Focus 3: Studying Human Diseases using Functional Genomics in Primary Stem Cell Models
The rapid development of next-generation sequencing technologies has greatly expanded our knowledge of the organization of the human genome. Thousands of disease-associated mutations have been identified by large-scale human sequencing efforts and a myriad of novel genomic elements have been predicted by bioinformatics. However, the majority of these newly proposed features await experimental validation in a cell-type and disease-specific context.
Towards the goal of experimental-validated functional annotation of the entire human genome, we will use CRISPR-guided mutagenesis to establish a collection of human pluripotent stem cells (hPSCs) harboring deletions and point mutations on both annotated and less-annotated genomic regions relevant for human disease. This will serve as a versatile platform to systemically assess functions of genomic features on gene regulation, cell fate control, disease ontology, etc, in multiple human cell lineages and differentiation states in authentic human genetic background.
1. Induced Pluripotent Stem Cells Meet Genome Editing. Hockemeyer D, Jaenisch R. Cell Stem Cell. 2016.
2. Widespread Translational Remodeling during Human Neuronal Differentiation. Blair J.D., Hockemeyer D., Doudna J.A., Bateup H.S., Floor S.N. Cell Reports. 2017.