Genetic and molecular basis of myeloid neoplasms at single cell resolution

Myeloproliferative neoplasms (MPN) originate in a single human haematopoietic stem cell which acquires a somatic mutation and undergoes clonal expansion. This initial clone usually accumulates further genetic lesions during disease progression, giving rise to a genetically heterogeneous population of tumour cells, which are also molecularly and functionally distinct. This makes it challenging to effectively target all cancer cells in a particular patient, and as a consequence, currently available drug therapies fail to completely eliminate clonal haematopoiesis.
Therefore, there is an urgent need to develop new therapies specifically targeting the mutant clone. To do so, it is essential to characterize clonal diversity in MPN at the genetic and molecular level. Single cell genomic techniques are ideally placed to resolve such heterogeneity. However, the lack of technologies integrating genetic and transcriptional readouts from the same single cell has limited their application to study intratumoral heterogeneity.
To overcome such limitation, I first developed TARGET-seq, a single cell multi-omic method for the high-sensitivity detection of mutations within single cells in parallel with whole transcriptome analysis and cell surface proteomics.
Following extensive validation in cell lines, I applied TARGET-seq to study haematopoietic stem and progenitor cells (HSPCs) from patients with myeloproliferative neoplasms. TARGET-seq analysis revealed a high degree of genetic heterogeneity, identifying both linear and branching patterns of clonal evolution. Different genetic subclones had distinct transcriptional signatures, with subclones carrying poor prognosis collaborating mutations showing increased transcriptional diversity as compared to clones carrying exclusively mutations in JAK2. Wild-type cells from MPN patients were enriched in inflammatory signatures as compared to cells from normal donors, suggesting a cell-extrinsic effect disrupting gene expression in non- mutant cells. This could underly therapy resistance or influence the development of secondary haematological malignancies. Moreover, TARGET-seq analysis identified putative biomarkers of JAK2-mutant cells, which could be used for disease monitoring and are potential targets for immunotherapy.
I then analysed HSPCs from MPN patients undergoing disease transformation to secondary Acute Myeloid Leukaemia (sAML), a poor prognosis complication affecting up to 20 % of MPN patients. TARGET-seq analysis identified leukemic subclones emerging from haematopoietic stem cells rather than more mature progenitors, in contrast to findings in de novo AML. The acquisition of TP53 mutations, associated with disease transformation, led to chromosomal aberrations and highly-complex patterns of clonal evolution. This supports a model in which acquisition of TP53 mutations drive leukemogenesis by promoting increased genetic instability and molecular heterogeneity in HSPCs.
In summary, single-cell multi-omic analysis allowed me to identify distinct and biologically relevant molecular signatures of different genetic subclones in HSPCs from patients with myeloid neoplasms. Ultimately, this analysis could potentially guide the development of new therapeutic approaches to specifically target disease propagating cells.

Keywords: TARGET-seq
stem cell
haematopoiesis
single cell
scRNA-seq
cancer
NGS
leukaemia
single-cell
sequencing
Advisor: Mead, A
Jacobsen, S