New single-cell analysis technique has identified mutation combinations linked to the transformation of chronic blood cancers into acute leukaemia.
Genetic combinations that may drive the transformation of chronic myeloproliferative neoplasms into aggressive acute leukaemia have been identified by Australian researchers, potentially opening a path towards earlier detection and treatment of high-risk disease.
Myeloproliferative neoplasms (MPNs) are rare blood cancers caused by acquired mutations in blood-forming stem and progenitor cells. The mutations cause overproduction of one or more types of blood cells and can lead to chronic disease that persists for years.
However, additional genetic changes can accumulate within the abnormal cells, causing MPNs to progress to myelofibrosis or transform into post-MPN acute myeloid leukaemia (AML).
Around one in three people with an MPN will eventually progress to a more severe form of disease, according to QIMR Berghofer researchers, but it’s difficult to predict which patients are at greatest risk.
Post-MPN AML is particularly aggressive, with a median survival of six months or less and limited response to treatment.
Researchers from QIMR Berghofer’s Leukaemia Research Laboratory have now developed a single-cell sequencing approach called LOTR-Seq to investigate how individual genetic mutations affect the behaviour of MPN stem cells and contribute to leukemic transformation.
The technique combines single-cell RNA sequencing with long-read genetic analysis, allowing researchers to examine the genetic makeup and activity of individual blood-forming stem cells at the same time.
The team analysed more than 50,000 individual blood-forming stem cells from people with chronic MPN and post-MPN AML, focussing on the most common MPN driver mutation JAK2 V617F. Using the technique, they identified nine additional mutated loci across six genes: JAK2, IDH1, IDH2, TP53, SRSF2, and U2AF1.
The different mutations were associated with distinct cellular behaviours that could favour cancer progression. These included increased aggressiveness and proliferation, as well as persistence in an immature, stem-cell-like state.
The researchers also found that the cellular diversity seen in chronic-phase MPN was substantially altered after transformation to AML, with the transcriptional profile of the stem-cell compartment becoming more uniform and appearing to be shaped by the combination of additional mutations.
Professor Steven Lane, who leads QIMR Berghofer’s Leukaemia Research Laboratory and is a clinical haematologist at the Royal Brisbane and Women’s Hospital, said the findings could eventually change how MPNs are managed.
“At the moment we can only treat disease symptoms. Our findings raise the possibility, for the first time, that we might be able to identify precursors of the genetic combinations that lead to leukaemia,” said Professor Lane.
“That would give us the opportunity to act at that early stage to prevent the development of life-threatening disease.”
The researchers said the findings were particularly important because additional mutations are common in chronic-phase MPN. More than 40% of patients with chronic-phase MPN harbour mutations relevant to myeloid malignancies in addition to their original MPN driver mutation, while post-MPN AML typically carries multiple genetic abnormalities.
Dr Jasmin Straube, a Cancer Council Queensland Next Generation Cancer research fellow and co-author of the study, said the uncertainty around disease progression could be a substantial burden for patients.
“It is a significant mental burden for many MPN patients knowing that at any time they could progress to a severe disease with a dismal prognosis. It’s a massive driving factor for me to increase understanding so we can predict those at high risk and prevent their chronic disease progressing to leukaemia,” she said.
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Dr Megan Bywater, co-laboratory head of the QIMR Berghofer Leukaemia Research Group, said the genetic complexity of MPNs had made them difficult to study.
“Our goal is to understand the complex biology so we can improve outcomes for patients. It’s really exciting to have built this experimental method which is helping us solve this problem for the MPN community,” Dr Bywater said.
The researchers are now planning to build on the findings through almost $3 million in funding from the Federal Government’s Medical Research Future Fund Stem Cell Therapies Program.
The next phase of the work will involve identifying additional high-risk combinations of mutations in people with MPN and investigating whether treatment can target the abnormal stem cells before they progress to AML.
The team plans to conduct a clinical trial testing interferon alpha, a treatment that their laboratory has previously found can target MPN stem cells. Participants will be monitored for two years to assess the treatment’s effects and determine whether it can eliminate abnormal blood-forming stem cells.
The trial will combine LOTR-Seq with spatial tissue analysis technologies, which can show where disease-driving cells are located within the bone marrow and how they interact with surrounding cells.
“Spatial technology allows us to map the location and behaviour of the disease-driving stem cells hiding in the bone marrow and see how they’re interacting with neighbouring cells,” Dr Straube said.
“We know these stem cells don’t act in isolation, so potentially we can target these interactions as well as the cancer-causing stem cells to really drive them out of the bone marrow.”
The researchers will collaborate with MPN patient groups including MPN Alliance Australia as they develop the clinical research program.
