Multi-omics studies of Zika virus infection in nervous system cells to investigate novel oncolytic virotherapy for childhood cancer

Abstract

Paediatric nervous system tumours account for a third of all childhood cancer cases, and survival is disproportionately poor. Aggressive treatment regimens significantly impair quality of life and subject survivors to socio-economic challenges. Novel immunotherapies, such as oncolytic viruses (OVs), that harness the patient’s immune system to eradicate the tumour with minimal adverse effects are desperately needed. Zika virus (ZIKV) is efficacious against paediatric nervous system tumours in vitro and in vivo; however, how this efficacy is achieved and the molecular mechanisms involved are virtually unknown. To address this, I generate an array of large data and omics datasets of ZIKV-infected nervous system cells to investigate infection across the host cell transcriptome, global proteome, immunopeptidome and secretome. I integrate these datasets with publicly available resources to enhance the scope of my research by yielding additional molecular and functional insights, which also help validate my findings. I primarily analyse ZIKV infection of paediatric neuroblastoma and brain tumour cells. However, I also investigate infection of neural precursor cells (NPCs) derived from congenital Zika syndrome (CZS)-affected patients to further our understanding of ZIKV neuropathology. In my thesis, I first present a comprehensive re-analysis of publicly available datasets and literature concerning ZIKV-infected neuroblastoma cells. This led to the cancer cell ZIKV life cycle being mapped out for the first time, creating an instrumental reference tool for future research. I identify a conserved TNF and cytokine response of ZIKV-infected nervous system tumour cells at the transcriptome level. Following these observations, I demonstrate that TNF-alpha is implicated in brain tumour cell oncolysis and highlight it as a potential prognostic marker for oncolytic ZIKV (oZIKV) therapy. A highly relevant finding is that I demonstrate ZIKV infection to induce a clinically relevant and diverse pro-inflammatory brain tumour cell secretome. Through modelling responses of the medulloblastoma tumour microenvironment (TME) and the immune system to this secretome in silico, I shed significant insight into the anti-tumoural immune response evoked by oZIKV infection. I present evidence that ZIKV infection of brain tumour cells engages the HLA class I pathway and I document brain tumour cell surface presented ZIKV epitopes for the first time. I identify the ZIKV non-structural (NS) protein 3 helicase as a rich source of immunogenic peptides, highlighting its potential utility as an immunotherapy or vaccine candidate. Collectively, my thesis describes multiple host mechanisms and pathways involved in neuropathogenic and oncolytic ZIKV infection of nervous system cells, and my work delivers a unique collection of multi-omics datasets to the research community. My research significantly contributes to the growing body of evidence supporting the progression of oZIKV therapy towards clinical trials.

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Identifiers

ORCID for Matthew Lewis Sherwood: orcid.org/0000-0002-1912-9758

ORCID for Rob Ewing: orcid.org/0000-0001-6510-4001

ORCID for Paul Skipp: orcid.org/0000-0002-2995-2959

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