Hochedlinger Lab

2024 Krantz Awards Recipient

2024 Spark Award: Leveraging Histone Mutants to Uncover Epigenetic Vulnerabilities in Cancer
Konrad Hochedlinger, PhD

Learn about the Krantz Awards

Research Summary

The Hochedlinger laboratory explores the fundamental question of how cells maintain their identity. We hypothesize that factors that reinforce specific cell states, such as pluripotency and differentiation, continue to play functional roles in other cellular contexts including development, tissue homeostasis and cancer. Using stem cell models and reprogramming systems as discovery tools ex vivo, our laboratory has elucidated novel mechanisms that maintain cell identity and function upstream of cell type specific transcription and chromatin factors. Specifically, work from our lab over the past five years revealed that common cellular processes such as protein sumoylation, chromatin assembly, alternative mRNA polyadenylation and P-body homeostasis play key roles in the maintenance of cell identity across distinct lineages. We now aim to probe the functional conservation of these mechanisms across physiological cell fate transitions in vivo using animal models and cell transplantation. As our strategy is not confined to one particular cell type or tissue, we are in a position to uncover shared regulatory principles crucial for the maintenance of cell identity across different developmental contexts.

Research Projects

While development and cellular differentiation were long thought to be irreversible processes, our ability to reprogram differentiated cells to an embryonic-like state revealed that mechanisms that safeguard cell identity and thus restrict developmental plasticity can be overcome through experimental manipulation. Indeed, seminal somatic cell nuclear transfer (SCNT) experiments proved that the nuclei of terminally differentiated cells and even certain cancer cells retain full developmental potential. While SCNT is a powerful assay to test the developmental potential of a given genome, it does not allow one to study how differentiated cell states are established and maintained. By contrast, transcription factor-induced reprogramming of somatic cells into induced pluripotent stem cells (iPSCs) is a molecularly defined and tractable system to dissect fundamental questions of cell state. Our lab initially used this approach to provide crucial insight into the basic mechanisms by which transcription factors and chromatin signaling establish and maintain identity in either pluripotent or differentiated cells, and we began to probe the conservation of these principles in other cellular contexts. For example, we discovered that the transcription factor Sox2, which is essential for the establishment and maintenance of pluripotent stem cells, is re-expressed in adult gastric stem cells where it maintains tissue identity by suppressing an alternative intestinal cell program and tumorigenesis. Similarly, we demonstrated that the manipulation of safeguard mechanisms previously identified during iPSC reprogramming in other cellular contexts facilitate the derivation of selfrenewing muscle stem-like cells, which have been notoriously difficult to capture using conventional strategies. More recently, our lab uncovered two post-transcriptional processes, alternative polyadenylation (APA) and Processing body (P-body) turnover, as novel safeguard mechanisms using unbiased screens. While APA and P-bodies are thought to control different aspects of gene regulation in the nucleus (APA) and cytoplasm (P-bodies), a key commonality that emerged from our work is that both processes regulate the protein homeostasis of hundreds of fate- instructive genes. Together, these examples underscore the power of our approach to gain insights into tissue identity through the study of pluripotency and cellular reprogramming.

Considering that several of the safeguard mechanisms we previously identified in reprogramming converge on chromatin regulators, we have recently developed versatile histone-mutant transgenic tools to directly probe the physiological role of chromatin modifications in cell fate change. These lysine-to-methionine (K-to-M) mutants, which dominantly block methylation at specific sites, have allowed us to uncover previously unappreciated functions of H3K4, H3K9, H3K27 and H3K36 methylation in the regulation of pluripotency, reprogramming, tissue homeostasis and aging, which is the basis for ongoing work in the lab. We are also using these tools to identify epigenetic vulnerabilities in cancer.

Thus, by pursuing our hypothesis that different physiological as well as experimentally induced cell fate transitions utilize common mechanisms, our lab has uncovered novel epigenetic, transcriptional and post-transcriptional regulators of cell identity. As we pursue a deeper understanding of how these underexplored regulators and processes guide cell fate transitions in vivo, we are poised to discover shared principles by which they safeguard cell identity during development and tissue homeostasis and how this knowledge may be exploited in a therapeutic setting to alter cell fate.

Publications

View a list of publications by researchers at the Hochedlinger Laboratory

Selected Publications

Gorelov R, Weiner A, Huebner A, Yagi M, Haghani A, Brooke R, Horvath S, Hochedlinger K. Dissecting the impact of differentiation stage, replicative history and cell type composition on epigenetic clocks. Stem Cell Reports (in press).

Hoetker, M. S., M. Yagi, B. Di Stefano, J. Langerman, S. Cristea, L. P. Wong, A. J. Huebner, J. Charlton, W. Deng, C. Haggerty, R. I. Sadreyev, A. Meissner, F. Michor, K. Plath, and K. Hochedlinger. H3k36 Methylation Maintains Cell Identity by Regulating Opposing Lineage Programmes. Nat Cell Biol 2023 (in press)

Huebner, A. J., R. A. Gorelov, R. Deviatiiarov, S. Demharter, T. Kull, R. M. Walsh, M. S. Taylor, S. Steiger, J. T. Mullen, P. V. Kharchenko, and K. Hochedlinger. Dissection of Gastric Homeostasis in Vivo Facilitates Permanent Capture of Isthmus-Like Stem Cells in Vitro. Nat Cell Biol 2023 (25), no. 3 (Mar): 390-403.

Yagi M, Ji F, Charlton J, Cristea S, Messemer K,…Goldhamer DJ, Wagers AJ, Michor F, Meissner A, Sadreyev RI, Hochedlinger K. Dissecting dual roles of MyoD during lineage conversion to mature myocytes and myogenic stem cells. Genes Dev. 2021 Sep 1;35(17- 18):1209-1228.

Brumbaugh J, Kim IS, Ji F, Huebner AJ, Di Stefano B, Schwarz BA, Charlton J, Coffey A, Choi J, Walsh RM, Schindler JW, Anselmo A, Meissner A, Sadreyev RI, Bernstein BE, Hock H, Hochedlinger K. Inducible histone K-to-M mutations are dynamic tools to probe the physiological role of site-specific histone methylation in vitro and in vivo. Nat Cell Biol. 2019 Nov;21(11):1449-1461.

Di Stefano B, Luo EC, Haggerty C, Aigner S, Charlton J, Brumbaugh J, Ji F, Rabano Jiménez I, Clowers KJ, Huebner AJ, Clement K, Lipchina I, de Kort MAC, Anselmo A, Pulice J, Gerli MFM, Gu H, Gygi SP, Sadreyev RI, Meissner A, Yeo GW, Hochedlinger K. The RNA Helicase DDX6 Controls Cellular Plasticity by Modulating P-Body Homeostasis. Cell Stem Cell. 2019 Nov 7;25(5):622-638.e13.

Brumbaugh J, Di Stefano B, Wang X, Borkent M1, Forouzmand E, Clowers KJ, Ji F4, Schwarz BA, Kalocsay M, Elledge SJ, Chen Y, Sadreyev RI, Gygi SP, Hu G, Shi Y, Hochedlinger K. Nudt21 Controls Cell Fate by Connecting Alternative Polyadenylation to Chromatin Signaling. Cell. 2018 Jan 11;172(1- 2):106-120.e21.

Research Image

(A) Comparison of proliferation rates (%EdU incorporation) between p63+ basal stem cells isolated from diverse epithelia reveals tissue-specific differences. (B) Basal stem cells with higher proliferation rates exhibit higher DNA methylation age relative to basal stem cells with lower proliferation rates based on the Mouse PanTissue Clock (shown here), as well as the Universal Clock-2 and -3. These results indicate that the epigenetic age of adult tissues is in part driven by the proliferative history of resident cells, such as basal stem cells (See: Gorelov et al., Stem Cell Reports, 2024). Image: Rebecca Gorelov, PhD.

Our Researchers

Konrad Hochedlinger, PhD

Group Members

• Andres Binker Cosen**
• Julie Finn*
• Rebecca Gorelov**
• Joy Horng**
• Pamela Kleck
• Nikolaos Tsopoulidis, PhD
• Aaron Weiner, PhD
• Masaki Yagi, PhD

* Administrative Assistant
** Graduate Student