Development of CRISPR-based barcoding tools for single cell genomics in cancer
Abstract/Contents
- Abstract
- A thorough investigation of the evolution of specialized cellular functions is critical to fully understand how tumors evolve. The genetic alterations that drive cancer growth have been well characterized through large scale genome sequencing projects and have led to significant therapeutic advances like targeted small molecule inhibitors. However, the genetic alterations that drive cancer growth are not predictive of the underlying transient gene expression or transcriptional states that occur within a tumor or population of cancer cells. These states are critical to the adaptation of tumors to therapeutic interventions and to tumor microenvironmental changes. With the advent of high-throughput single-cell RNA-sequencing technologies, thorough characterization of the heterogeneity of cell states within a tumor is now possible. However, the extent to which these cell states are inherited cannot be understood with single snapshot measurements of transcript abundance levels. This work first harnesses the Type V CRISPR/Cas12a system to engineer compact barcode sequences with optimized capacity to enable tracking of ~700 subclonal populations within a single clone. With this added resolution, we integrated the technology with single-cell RNA-sequencing to investigate the heritability of gene expression, or transcriptional memory, in melanoma cells. We initially identified EZH2, a member of the polycomb repressive complex 2 (PRC2), as a putative regulator of transcriptional memory. This work has implications for identifying the epigenetic regulators of gene expression programs that may control therapeutically relevant phenotypes like drug resistance and metastasis.
Description
| Type of resource | text |
|---|---|
| Form | electronic resource; remote; computer; online resource |
| Extent | 1 online resource. |
| Place | California |
| Place | [Stanford, California] |
| Publisher | [Stanford University] |
| Copyright date | 2022; ©2022 |
| Publication date | 2022; 2022 |
| Issuance | monographic |
| Language | English |
Creators/Contributors
| Author | Hughes, Nicholas William |
|---|---|
| Degree supervisor | Cong, Le |
| Degree supervisor | Winslow, Monte |
| Thesis advisor | Cong, Le |
| Thesis advisor | Winslow, Monte |
| Thesis advisor | Fire, Andrew Zachary |
| Degree committee member | Fire, Andrew Zachary |
| Associated with | Stanford University, Department of Genetics |
Subjects
| Genre | Theses |
|---|---|
| Genre | Text |
Bibliographic information
| Statement of responsibility | Nicholas William Hughes. |
|---|---|
| Note | Submitted to the Department of Genetics. |
| Thesis | Thesis Ph.D. Stanford University 2022. |
| Location | https://purl.stanford.edu/bv484fz4364 |
Access conditions
- Copyright
- © 2022 by Nicholas William Hughes
- License
- This work is licensed under a Creative Commons Attribution Non Commercial 3.0 Unported license (CC BY-NC).
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