Identification of predictive biomarkers of treatment free remission in patients with chronic myeloid leukaemia

Nosratzadeh, Isla (2026) Identification of predictive biomarkers of treatment free remission in patients with chronic myeloid leukaemia. PhD thesis, University of Glasgow.

Abstract

Chronic myeloid leukaemia (CML) is a haematological malignancy that occurs because of a translocation between chromosomes 9 and 22 to produce the BCR∷AB1 fusion oncogene on the so-called Philadelphia (Ph) chromosome. The subsequent BCR∷ABL1 protein is a constitutively active tyrosine kinase which results in overactive downstream signalling pathways resulting in uncontrolled proliferation and expansion of myeloid cells, which if left untreated can be fatal.

Targeted tyrosine kinase inhibitors (TKIs) for patients with CML elicit an excellent response and patients can have close to normal life expectancy. However, patients will remain on treatment for the rest of their lives risking side effects which will dramatically effect their quality of life. To avert this many patients who achieve a deep molecular response (DMR)/MR4 (BCR::ABL1 to ABL<0.01% on international scale) are able to stop taking their TKI but remain in remission, this gives them all the benefits of being in remission without any negative side effects, this is called treatment free remission (TFR). While this is an excellent and attractive option for many patients, only about 50% of patients that attempt TFR are able to maintain it. In order to examine the difference between patients that maintain TFR and those that relapse the De- Escalation and Stopping Treatment of Imatinib, Nilotinib or sprYcel in Chronic Myeloid Leukaemia (DESTINY) clinical trial was carried out (NCT01804985). During this trial bone marrow (BM) samples were taken from 160 patients looking to achieve TFR. Patients in MMR response (MR3; BCR::ABL1<0.1%) and DMR were recruited, these patients had an initial de-escalation period where they reduced their TKI dose to half for 12 months, if TFR was maintained they then went on to total TKI cessation for a further 24 months. At the trial endpoint 72% of MR4 and 36% of MR3 patients maintained TFR. BM samples from both relapse (R_E) and TFR (TFR_E) patients at trial entry, point of relapse (R_X) and end point of trial (TFR_X) were obtained. These were used to characterise the bone marrow microenvironment (BMM) between the two outcome groups and importantly identify predictive biomarkers of TFR.

The BMM is a complex, multi-cellular niche in the BM with its primary purpose being to maintain and protect haematopoietic stem cells (HSCs) and allow for haematopoiesis to occur in response to the body’s needs. The intricate network of cells and proteins within the BMM are dependent on a delicate balance of these parts working together to prevent haematological disease. In patients with CML there are several changes that occur to the BMM which allow for the survival and protection of leukaemic stem cells (LSCs) and disease progression.

To better understand the changes to the BMM and LSCs in CML patients that maintain TFR a three-pronged approach was taken.

The supportive stroma of the BMM comprising mesenchymal stem cells (MSCs) is essential to the BMM; MSCs are responsible for tissue repair, immunomodulation, HSC maintenance and produce several cell types of the BMM (multipotency). MSCs extracted from DESTINY samples were found to have increased senescence in R_E compared to TFR_E. Using RNAseq the same comparison found increased CXCL12 expression, known for maintaining quiescence in LSCs and HSCs. Additionally, RNAseq analysis of MSCs found increased expression of PTK7, known to be part of senescence associated secretory phenotype (SASP), in R_E patients vs TFR_E. The HLA-B gene, which is a part of the MHC and is involved in presenting to cytotoxic CD8+ T lymphocytes, was found to be downregulated within the same comparison. This indicates MSCs of patients at the start of trial who go on to relapse have an increased senescent profile which is producing a pro-inflammatory response within the BMM, additionally these MSCs have increased immunosuppressive activity. These factors could contribute to producing BMM that is unable to support remission after TKI cessation.

The stem and progenitor populations of CML are essential in the treatment and understanding of the disease, CML begins and is maintained by LSCs, and this results in the aberrant expansion of the progenitor cells. To first distinguish between TFR and relapse patients, cell surface markers that had previously been established as potential markers of LSCs were used to generate LSC panels. While none of the markers selected were viable predictive biomarkers of TFR, CD44 marker was found to be increased in all DESTINY samples compared to CML patients at diagnosis, apparently indicating an increased expression in LSCs after TKI use, but this could be due to increased quiescence of LSCs in patients. Additionally, colony forming assays of these samples also showed increased number of colonies produced by progenitors at end point of trial compared to start of trial within TFR patients indicating increased cell proliferation is occurring in TFR patients after TKI cessation however this is part of normal haematopoiesis as this is not leading to relapse.

Finally, to gain a high-throughput, detailed, unbiased examination of the changes within the BMM proteomic analysis was used, in the form of liquid chromatography mass spectrometry (LC-MS). This provided a comprehensive examination of the proteomic profile of patients that relapse and those that maintain TFR. From this, gene set enrichment analysis (GSEA) was carried out which found negative enrichment of ‘humoral immune response’, ‘complement activation’, ‘complement activation, classical pathway’ and ‘humoral immune response mediated by circulating immunoglobulin’ pathways in R_E compared to TFR_E. This suggests a decreased immune function in CML patients that go on to relapse.

Overall, we can say the supportive stroma of relapse patients is more senescent and appears to have increased pro-inflammatory markers than patients that are able to maintain TFR. Additionally, patients who relapse have a dysregulated immune response which could be contributing to relapse. The changes seen identify significant differences between the two outcomes and provide potential predictive markers for the prediction of TFR that would need to be further elucidated.

• Item Type: Thesis (PhD)
• Qualification Level: Doctoral
• Additional Information: Due to copyright issues this thesis is not available for viewing.
• Subjects: R Medicine > RC Internal medicine > RC0254 Neoplasms. Tumors. Oncology (including Cancer)
• Colleges/Schools: College of Medical Veterinary and Life Sciences > School of Cancer Sciences
• Supervisor's Name: Jorgensen, Dr. Heather, Wheadon, Professor Helen, Copland, Professor Mhairi and von Kriegsheim, Dr. Alex
• Date of Award: 2026
• Depositing User: Theses Team
• Unique ID: glathesis:2026-86055
• Copyright: Copyright of this thesis is held by the author.
• Date Deposited: 23 Jun 2026 14:11
• Last Modified: 23 Jun 2026 14:16
• Thesis DOI: 10.5525/gla.thesis.86055
• URI: https://theses.gla.ac.uk/id/eprint/86055