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Single-Cell Analysis of Normal and Perturbed Early T-Cell Developmental Processes


Zhou, Wen (2021) Single-Cell Analysis of Normal and Perturbed Early T-Cell Developmental Processes. Dissertation (Ph.D.), California Institute of Technology. doi:10.7907/733t-mg82.


Early T-cell development converts multipotent precursors to committed pro-T cells, silencing progenitor genes while inducing T-cell genes. However, both the underlying steps of developmental progression and the regulations involved have remained obscure. Although some of the expressions of important regulators in early T-cell development have been studied in bulk populations, the nature of heterogeneity in this constantly refreshed developmental continuum makes it difficult to understand the developmental trajectories that the cells have undergone using bulk analysis, both in natural conditions and under gene perturbations.

Combining droplet-based single cell RNA sequencing (scRNA-seq), deep-sequenced whole-transcript scRNA-seq, and seqFISH for key regulatory genes, we established regulatory phenotypes of sequential ETP subsets; confirmed initial co-expression of progenitor- with T-cell specification genes; defined stage-specific relationships between cell-cycle and differentiation; and generated a pseudotime model from ETP to T-lineage commitment, supported by RNA velocity and transcription factor perturbations. This model was validated by developmental kinetics of ETP subsets at population and clonal levels. The results imply that multilineage priming is integral to T-cell specification in natural developing pro-T cells in the thymus.

Moreover, we examined the functional implications of some of the transcription factors (TFs) through bone marrow (BM) derived ex-vivo differentiation systems. Using scRNA-seq, Cell Hashing, and a pool-based CRISPR/Cas9 perturbation system, we established the normal and perturbed developmental trajectories before and after the T-lineage commitment stages. Our analysis revealed that, without the essential lineage commitment TF, Bcl11b, the developing early T cells immediately realized the lack of the essential regulator around the proliferating late DN2a stage. But instead of pushing the developmental path backwards to resemble the earlier stage of uncommitted cells, cells lacking Bcl11b underwent a diverging route of accumulation of 'non-T' genes that are not naturally expressed in earlier stages, potentially leading to the eventual loss of Notch responses. Our results also revealed the complex regulations by TFs that set up the earliest T-lineage progression and commitment conditions. The SCENIC analysis suggested that Gata3 and Tcf7, despite both being important regulatory factors for T-lineage progression, have very different regulatory roles in controlling proliferation and suppressing myeloid lineages. Furthermore, pseudotime analysis also showed that some of the stem and progenitor genes and 'multilineage' associated genes expressed by early pro-T cells potentially hold back the T-lineage differentiation speed. In summary, our study leveraged both in vivo thymic pro-T cells' developmental trajectory obtained through single-cell analysis and ex-vivo derived T cells for internal-controlled perturbations, and revealed some profound roles of TFs in regulating early T-cell differentiation processes.

Item Type:Thesis (Dissertation (Ph.D.))
Subject Keywords:Single-cell analysis, early T-cell development, transcriptome profiling, scRNA-seq
Degree Grantor:California Institute of Technology
Division:Chemistry and Chemical Engineering
Major Option:Biochemistry and Molecular Biophysics
Thesis Availability:Public (worldwide access)
Research Advisor(s):
  • Rothenberg, Ellen V.
Thesis Committee:
  • Wold, Barbara J. (chair)
  • Bronner, Marianne E.
  • Cai, Long
  • Rothenberg, Ellen V.
Defense Date:19 January 2021
Non-Caltech Author Email:wenzhou.caltech (AT)
Record Number:CaltechTHESIS:01292021-130102777
Persistent URL:
Related URLs:
URLURL TypeDescription associated with Chapter 2.
Zhou, Wen0000-0003-0357-2744
Default Usage Policy:No commercial reproduction, distribution, display or performance rights in this work are provided.
ID Code:14062
Deposited By: Wen Zhou
Deposited On:12 Feb 2021 16:48
Last Modified:01 Nov 2021 23:56

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[img] MS Excel (Supplementary Table S1) - Supplemental Material
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