Biology ETDs

Publication Date

Summer 7-31-2023

Abstract

ABSTRACT αβ and γδ T cells play an essential role in the adaptive immune response and are present in the majority of jawed vertebrates. The T cell receptor (TCR) structure and genetic organization have been generally stable throughout 400 million years of gnathostome evolution. However, the TCRδ chain has displayed degrees of plasticity unseen in other TCR isoforms. One such form appears to be a chimera of a TCR chain with an antibody-like binding domain, known as VHδ and has been found a wide array of vertebrates including cartilaginous fish, coelacanths, amphibians, tuataras, birds, crocodilians, and monotreme mammals. Another, more extreme form found in mammals, in the form of TCRμ, and cartilaginous fish, in the form of NAR-TCR, is a variant with a three extracellular domains structure and is a chimera of TCR and immunoglobulin (Ig) domains. The plasticity of TCRδ has resulted in two extremes in vertebrates with regards to the γδ T cell lineage. At one end of the extremes is an ancient and complete loss of γδ T cells. My research vi unveils the deletion of the genes which encode the TCRδ and TCRγ chains in a highly successful vertebrate lineage, the squamate reptiles (Chapter 2 of this dissertation). At the other extreme is the gain of a third T cell lineage, the mammalian γμ T cell, that appears to have evolved from γδ T cells. Using a model marsupial, Monodelphis domestica, I confirmed that the novel TCRμ chain, found only in marsupials and monotremes, pairs with the conventional TCRγ, defining the γμ T cell (Dissertation Chapter 3). My analysis of a single cell deep coverage transcriptome also contributed to determining the crystal structure of the γμTCR, confirming that three extracellular domain structure with an unpaired variable (V) domain (Dissertation Chapter 3). As part of my dissertation research, I investigated the evolution and genomic organization of the genes encoding the TCRμ chain in marsupials and monotremes (Dissertation Chaper 4). The TCRμ chain is encoded by genes, the TRM locus, that is organized as a cluster (Vμ-Vμj-Cμ) rather than the canonical transclocon arrangement in the genome. I confirmed that there are three classes of TRM clusters based on sequence identity and investigated the conservation of this organization in a distantly related marsupial, the Tasmanian devil, Sarcophilus harrisii. I found remarkable similar organization in the opossum and devil, differing primarily in duplication events that gave rise to the tandem arrays extant today (Dissertation Chapter 4). I also examined the TRM locus in a monotreme, the platypus, and identified a translocon/cluster hybrid arrangement. Utilizing publicly available platypus TCRμ transcripts, I confirmed that each transcript is encoded by genes also located within a cluster (Dissertation Chapter 4). With further analysis of the single cell dataset, I determined that γμT cells make up 10% of total splenocytes and 37% of splenic T cells. A majority have a CD8αα+ phenotype, whereas none were CD4+. I also found that γμ T cells are not present in adult peripheral blood (Dissertation vii Chapater 3). Given the possibility that γμ T cells are tissue resident, I investigated their presence of in opossum tissues. My research discovered that they localize to the intestinal tract and associated tissues like the liver and spleen. In other words, they are located in the tissues associated with portal circulation (Dissertation Chaper 5). Lastly, I followed up on an unexpected result that the TCRμ chains found in opossum peripheral tissues are primarily encoded by only one of three classes of genes, class III. I investigated characteristics in a devil transcriptome and found TCRμ transcripts also encoded by class III genes in the liver and spleen. In my dissertation I present possible explanations for this unexpected result (Dissertation Chapter 5). In conclusion, the results presented in my dissertation provide insight into both the gain and loss of TCR genes during vertebrate evolution and contribute knowledge into the biological relevance of novel T cell types across vertebrate lineages.

Keywords

T cell receptor, Marsupial, Monotreme

Document Type

Dissertation

Degree Name

Biology

Level of Degree

Doctoral

Department Name

UNM Biology Department

First Committee Member (Chair)

Robert Miller

Second Committee Member

Irene Salinas

Third Committee Member

Christopher Johnston

Fourth Committee Member

Christopher Amemiya

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