Translational regulation in aggressive B-cell lymphomas

The Germinal Centre (GC) reaction is a dynamic process where B-cells undergo recombination and somatic hypermutation of immunoglobulin genes in response to antigen stimulation. This essential component of the adaptive immune system is associated with cycles of intensive proliferation and selection, which carries a risk of malignant transformation. Aggressive lymphomas arising from the GC stage of B-cell development are the most common haematological malignancies with heterogeneous molecular mechanisms and clinical presentation. Although the last decade witnessed considerable advances in the biology of GC reaction and related tumours, the studies focused predominantly on the network of transcription factors. The advances in Next Generation Sequencing technologies have opened new possibilities to explore mechanisms of regulation beyond the level of transcription. Ribo-Seq is a technique combining ribosome footprinting with deep sequencing of mRNA fragments that allows to map the position of translating ribosomes with single nucleotide precision. Here I investigate the mechanisms of translational regulation contributing to lymphoma development. Firstly, I introduce RiboStream, an automated bioinformatic pipeline designed to streamline processing of Ribo-Seq datasets while maintaining transparency and reproducibility of the computational workflow. Then, I provide an overview and benchmarking of current methods for identifying translationally regulated genes. Based on these I select a strategy to reveal that overexpression of two B-cell oncogenes, BCL6 or MYC, is followed by preferential translational of selected transcripts. Next, I show that loss-of-function mutations in RNA-helicase (DDX3X) promote early development of MYC-driven lymphoma by buffering the effects of MYC on translation of ribosomal proteins and the rate of global protein synthesis. Finally, I explore a genome-wide distribution of translating ribosomes to study the scope of non-canonical translation in lymphoid cells. Taking advantage of a large dataset of 79 Ribo-Seq libraries I reveal pervasive translation of ostensibly non-coding regions, and design a knock-down CRISPR screen library to identify those important for B-cell survival.

Name dc:type.qualificationname

Doctor of Philosophy (PhD)

Level dc:type.qualificationlevel

Doctoral

Grantor dc:publisher.institution

University of Cambridge

Year dc:date.issued

2021

Author dc:creator

• Krupka, Joanna Alicja

Advisors dc:contributor.advisor

• Hodson, Daniel James
• Samarajiwa, Shamith

• lymphoma
• translation
• genomics
• B-cell
• haematology

Licence

• https://www.rioxx.net/licenses/all-rights-reserved/

Language dc:language

eng

DOI dc:identifier.doi

https://doi.org/10.17863/CAM.85702

OAI identifier oai:identifier

oai:www.repository.cam.ac.uk:1810/338292