Thesis Benoit Nicolet
On 3 September 2020 Benoit Nicolet defended his PhD thesis 'You only live twice: Gene expression regulation in hematopoiesis and T cells' at the University of Amsterdam.
Promotores: Prof R.A.W. van Lier MD PhD and M.C. Wolkers PhD
Venue: Agnietenkapel, University of Amsterdam (invitation only) and online
Summary
In the first part of this thesis, we developed several methods to identify and study the effector function of T cells. We used transcriptome and proteome analysis to uncover CD29 (b1 integrin; ITGB1), a cellular marker which identify CD8+ T cells that preferentially produce cytotoxic molecules, such as interferon-g. The expression of CD29+ T cell gene signature in melanoma patients associated with better overall survival, especially in patients with high CD8+ infiltrates. We also studied how these effector function of CD8+ T cells are regulated by developing Flow-FISH a method allowing the simultaneous measurement of mRNA and protein of individual gene products at a single-cell level in a high throughput manner. There we found that mRNA protein measurements are key to understand T cell effector function regulation. This led us to investigate the global relationship between mRNA and protein expression in human CD8+ T cells during differentiation and upon activation, using deep transcriptome sequencing and mass-spectrometry. Together we show that T cell gene expression regulation is key to understand the function, and its implication for T-cells immune-therapies and vaccines.
The second part of this thesis focused on circular RNA (circRNA), a novel kind of non-coding RNA. We investigated the circRNA expression in the hematopoietic system, thus far unknown, and found a cell-type specific, abundant, circRNA expression throughout hematopoiesis. Red blood cells and platelets expressed the highest levels circRNA levels and the highest diversity. We further characterized the functionality of circRNA in terminal hematopoiesis using a multi-omics approach.
Chapters
Chapter one
General introduction
PART ONE
Chapter two
CD29 identifies IFN-y–producing human CD8+ T cells with an increased cytotoxic potential Abstract
Chapter three
Combined single-cell measurement of cytokine mRNA and protein identifies T cells with persistent effector function Abstract
Chapter four
Limited but gene-class specific correlation of mRNA and protein expression in human CD8+ T cells
PART TWO
Chapter five
Circular RNA expression in human hematopoietic cells is widespread and cell-type specific Abstract
Chapter six
Circular RNAs are abundant in terminal erythropoiesis and megakaryopoiesis but show scarce evidence of translation-regulation or translation
Chapter seven
General discussion
Addendum
Bringing circular economy to the lab
Download
Download thesis (university repository)
