Understanding treatment resistance and disease progression in hypodiploid ALL

Primary supervisor: Bela Wrench, Queen Mary University of London

Secondary supervisor: Simone Zaccaria, UCL

Project

The focus of this PhD is to understand treatment resistance and mechanisms of disease progression in a poor risk subset of ALL termed hypodiploid ALL and to propose novel therapeutic targets.

Hypodiploid ALL inclusive of high hypodiploidy (40-45 chromosomes), Low hypodiploidy (HoL; 33- 39) and near haploidy (23-29 chromosomes) are among the poorest prognosis leukaemias in both children and adults with < 25% overall survival and uncertainty around the role of immunotherapy. The mechanisms that accelerate chemo-resistance associated with hypodiploidy ALL are poorly understood. Furthermore, the selection processes that drive hypodiploid relapse are not well characterised as few hypodiploid tumours have undergone longitudinal analysis at high resolution. An emerging theme is whether this specific aneuploidy is associated with chromosomal instability (CIN) and how CIN might impact upon prognosis and treatment resistance. Whole genome sequencing (WGS) of paired pre-treatment and recurrent hypodiploid ALL tumours performed by our group demonstrates that chromosomal patterns can change over the disease course suggesting a possible link between increased karyotype heterogeneity and CIN-linked resistance to therapy in these tumours. To further establish if CIN is an important player in hypodiploid ALL evolution and to establish if it might be specifically targeted, we will:

(i) Analyse existing WGS datasets of low hypodiploidy ALL tumours accessible via the Wrench laboratory (adults) and National Genomics Research Library (paediatric plus adult tumours) using computational algorithms developed by the Zaccaria group to determine the karyotype/copy number heterogeneity at baseline as a measure of the level of endogenous CIN (Zaccaria & Raphael, Nat. Comms., 2020). This analysis will be complemented by high resolution single-cell WGS studies (scWGS) of rare cohorts of matched pre-treatment and recurrent hypodiploid tumours to further understand how CIN-linked events relate to relapse evolution whilst also determining the dynamics of karyotype selection more generally (Zaccaria & Raphael, Nat. Biotech., 2021).

(ii) In addition to profiling terminally advanced primary tumours, we will additionally evaluate the role of CIN in the dynamic process of resistance. To do this, we will model clinical scenarios of drug tolerant persistor populations (DTPs or minimal residual disease, Heydt et al., Nat. Comms 2021) through to relapse using in vitro chemotherapy schedules generated from four hypodiploidy cell lines that accurately recapitulate primary tumour genetics (Holmfeldt et al., Nat. Genetics 2021). Sequential stages of pre-treatment through to DTP and subsequent regrowth/relapse stages will be assayed for CIN rates and mechanisms using tools established in the McClelland laboratory (Tamura et al. , Cancer Research 2020) alongside scWGS to monitor the timing and temporal development of CIN phenotypes under therapy. Should we detect CIN, we will antagonise with CIN inhibitors to formally test if increased CIN determines cancer treatment responses in vitro.

(iii) Finally we will identify which distinct signalling pathways underpin treatment resistance of hypodiploid ALL using in vitro models. Given the global gene dosage effects arising from multiple chromosomal loss and the link between hypodiploidy and disruptions to cell signalling we will apply LC-MS/MS phosphoproteomic signalling and KSEA scoring to identify the distinct signalling networks associated with emergence of DTP in hypodiploidy vs non hypodiploidy tumour controls. Candidate cell signalling pathways revealed through these profiling studies will be further validated by kinase inhibitor compounds to test if their modulation specifically interferes with hypodiploid-linked resistance thus providing a basis for future initiatives that seek to limit such events. Such efforts are important as targeting the specific chemo-resistance of hypodiploid ALL has proven elusive and fundamental insights into this process to define new therapeutic perspectives are urgently required in both paediatric and adult disease.

Candidate background

This project would suit candidates with a background in haematological malignancies, an interest in leukaemia molecular genetics, and an interest to develop and apply cancer bioinformatics skills to analyse cancer evolution from DNA sequencing data.

Potential Research Placements

1. Sarah McClelland, Bart’s Cancer Institute, Queen Mary University of London
2. Simone Zaccaria, UCL Cancer Institute
3. Pedro Cutillas, Bart’s Cancer Institute, Queen Mary University of London

References

1. Tamura, N., et al. Specific Mechanisms of Chromosomal Instability Indicate Therapeutic Sensitivities in High-Grade Serous Ovarian Carcinoma. Cancer research 80, 4946-4959 (2020).
2. Heydt, Q., et al. Adipocytes disrupt the translational programme of acute lymphoblastic leukaemia to favour tumour survival and persistence. Nat. Comm. 12, 5507 (2021).
3. Holmfeldt, L., et al. The genomic landscape of hypodiploid acute lymphoblastic leukemia. Nat. Genet. 45, 242-252 (2013).
4. Zaccaria, S. & Raphael, B.J. Characterizing allele- and haplotype-specific copy numbers in single cells with CHISEL. Nat. Biotech. 39, 207-214 (2021).
5. Zaccaria, S. & Raphael, B.J. Accurate quantification of copy-number aberrations and whole- genome duplications in multi-sample tumor sequencing data. Nat. Comm. 11, 4301 (2020).