Chen, Tianmeng
(2021)
Immune Response to Trauma: A Roadmap from Single-Cell Transcriptome and Epigenome to Patient Classifications.
Doctoral Dissertation, University of Pittsburgh.
(Unpublished)
Abstract
Immune dysfunction is an important factor driving mortality and adverse outcomes after trauma but remains poorly understood, especially at cellular level. In this dissertation, we applied both single-cell RNA sequencing (scRNA-seq) and single-cell assay for transposase-accessible chromatin using sequencing (scATAC-seq) to deconvolute the trauma-induced immune response.
First, we describe our work to apply scRNA-seq to circulating and bone marrow mononuclear cells in injured mice and peripheral blood mononuclear cells (PBMCs) in trauma patients. These are the first reported studies to characterize the mammalian response to systemic injury using scRNA-seq. In mice, the greatest changes in gene expression were seen in monocytes across both compartments. After systemic injury, the gene expression pattern of monocytes markedly deviated from steady state with corresponding changes in critical transcription factors (TFs), which can be traced back to myeloid progenitors. These changes involved up-regulation of inflammation and suppression of steady-state features, which were largely recapitulated in the human single-cell analysis. We generalized the major changes in human CD14+ monocytes into six signatures, which further defined two transcriptional subtypes (Signature Group: SG1 vs. SG2) identified in the whole-blood leukocyte transcriptome of trauma patients in the initial 12h after injury. Compared with SG2, SG1 patients exhibited delayed recovery, more severe organ dysfunction and a higher incidence of infection and non-infectious complications.
Next, we performed scATAC-seq on PBMCs isolated from a subset of trauma patients subjected to scRNA-seq, to determine if trauma-induced immune dysfunction was associated with epigenomic changes. While corroborating previous transcriptomic changes, we uncovered global epigenetic alterations reflecting de-repression of polycomb targets, across multiple immune cell types. These included developmental loci, not normally expressed in hematopoietic lineages. Using whole-blood leukocyte transcriptomes of trauma patients, we validated the newly identified pathologic epigenomic signature in an independent dataset and defined the Epigenetic Groups (EG subtypes) associated with differential prognosis and distinct from SG subtypes.
Patient classifications based on either SG or EG subtypes including the independent prognostic value for each classification model were also recapitulated in burn and sepsis patients. These studies provide evidence for the broad impact of our analyses in the research field of critical illness.
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Details
| Item Type: |
University of Pittsburgh ETD
|
| Status: |
Unpublished |
| Creators/Authors: |
|
| ETD Committee: |
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| Date: |
8 September 2021 |
| Date Type: |
Publication |
| Defense Date: |
6 July 2021 |
| Approval Date: |
8 September 2021 |
| Submission Date: |
7 August 2021 |
| Access Restriction: |
2 year -- Restrict access to University of Pittsburgh for a period of 2 years. |
| Number of Pages: |
171 |
| Institution: |
University of Pittsburgh |
| Schools and Programs: |
School of Medicine > Cellular and Molecular Pathology |
| Degree: |
PhD - Doctor of Philosophy |
| Thesis Type: |
Doctoral Dissertation |
| Refereed: |
Yes |
| Uncontrolled Keywords: |
Trauma, single-cell RNA-sequencing, single-cell ATAC sequencing, immune response, patient classification, subtype |
| Date Deposited: |
08 Sep 2021 18:48 |
| Last Modified: |
08 Sep 2023 05:15 |
| URI: |
http://d-scholarship.pitt.edu/id/eprint/41614 |
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