Genetic Insights into Advanced Chronic Myeloid Leukemia
Study reveals genetic changes that may lead to better treatment for advanced CML.
Zafar Iqbal, N. Alanazi, A. AlGarni, S. Almukhaylid, M. AlMajed, S. Alanazi, M. Khan, M. Sabar, A. Jameel, A. Hussian, D. Almaghlouth, A. Alsuwaidani, G. Alsalem, N. AlMutairi, H. Almasoudi, B. AlShehab, S. Alfayez, M. Butwyibah, B. Alnajad, F. Alali, A. Al-Rasasi, K. Adeel, S. Al Hakeem, T. Karar, F. Alsaab, Y. Taleb, S. Shahbaz, S. Malik, A. Mahmood, S. Basit, M. Anharullah, A. Aleem, I. F. Zafar, R. Naeem, M. Shamas
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Table of Contents
Chronic Myeloid Leukemia (CML) is a type of cancer that affects the blood and bone marrow. It is caused by the uncontrolled growth of certain blood cells, specifically a type called granulocytes. In CML, a genetic change known as the Philadelphia chromosome plays a key role. This change occurs when pieces of two chromosomes swap places, creating a new gene that drives the cancer's growth.
CML is relatively rare, affecting 1 to 2 people per 100,000 adults worldwide. It accounts for about 15% of all new cases of leukemia in adults.
Stages of CML
CML progresses in three stages:
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Chronic Phase (CP): Initially, CML often presents as a chronic phase, where patients may not feel sick and can live normal lives for years. During this phase, there is a high number of immature blood cells, but patients generally have a good survival rate.
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Accelerated Phase (AP): Some patients may move to an accelerated phase, where the disease becomes more aggressive. In this stage, patients may experience more symptoms and may not respond well to treatment.
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Blast Crisis (BC): This is the most severe phase of CML and is marked by a rapid increase in immature cells. Patients in this phase often have a very poor prognosis and may only survive for a few months.
Symptoms of CML
Many people with CML may not notice symptoms early on. However, as the disease progresses, symptoms may include:
- Fatigue
- Weight loss
- Night sweats
- Fever
- Anemia (low red blood cell count)
- High white blood cell count
- Enlargement of the spleen (splenomegaly)
Treatment Options
CML has transformed over the years due to advancements in treatment. The mainstay of treatment for CML is a group of drugs known as tyrosine kinase inhibitors (TKIs).
- Imatinib: This was the first TKI approved for CML and has significantly changed the outlook for patients.
- Nilotinib and Dasatinib: These are other TKIs that are used in cases where Imatinib is ineffective.
Despite these advances, some patients may not respond to TKIs or may develop resistance to them, especially in the later stages of the disease.
Study Focus
This study examined patients with advanced CML, specifically those in the accelerated phase and blast crisis. Researchers aimed to identify genetic changes in these patients that could point to new treatment options.
They gathered information from 141 CML patients over several years. Some patients had been treated with Imatinib, while others were switched to alternative treatments due to resistance. The study also looked at how different genetic mutations affected the patients' responses to treatment.
Patient Criteria
The researchers included patients from a medical center, focusing on those with diagnosed CML. They categorized patients into three groups based on their disease stage:
- Chronic Phase (CP)
- Accelerated Phase (AP)
- Blast Crisis (BC)
The study sought to find common patterns in the genes of patients that may point to effective treatments.
Testing Methods
Blood samples from patients were taken to analyze the genetic material (DNA). The researchers used advanced techniques to look for mutations in the genes associated with CML, as well as those linked to other types of leukemia.
They focused on known genes that had mutations in other leukemias, including Acute Myeloid Leukemia (AML) and Acute Lymphoma Leukemia (ALL). The goal was to find druggable mutations that could be targeted with existing therapies.
Findings
The researchers identified numerous genetic variants in the DNA of patients, particularly in those with advanced disease. Some of these mutations were already known to be linked to responses to treatment in other types of leukemia.
- Genes like RPTOR, BRCA1/BRCA2, and others showed notable mutation rates in patients with blast crisis.
- The study highlighted notable increases in mutations from the accelerated phase to the blast crisis phase, suggesting that these mutations could be vital in understanding and treating advanced CML.
Druggable Mutations
The researchers identified several mutations that could potentially be targeted by existing medications. This is essential because finding new uses for already approved drugs can save time and resources, allowing for quicker treatment options.
These drugs include:
- Arsenic Trioxide
- Venetoclax
- Doxorubicin
- Azacitidine
These medications have been shown to be effective in treating other types of leukemia and may offer new hope for CML patients, especially those who do not respond to standard TKIs.
Treatment Outcomes
The study also noted how different patients responded to treatment. While many did well with initial therapies, patients in the blast crisis phase showed much poorer outcomes.
- Nearly 75% of patients in this phase did not respond well to treatment.
- In comparison, survival rates were significantly better for patients in the chronic phase.
These findings underline the urgent need for better approaches to treat patients with advanced CML.
Conclusion
In summary, this study sheds light on the genetic landscape of CML, particularly in advanced stages. It highlights the importance of understanding the specific mutations occurring in patients, as these may provide critical clues for developing new treatment strategies.
By identifying these druggable mutations, the hope is to repurpose existing medications to create more effective treatment plans for patients suffering from CML, especially those who find themselves in the most challenging stages of the disease.
The need for continued research in this area is vital as it promises to improve outcomes for those affected by chronic myeloid leukemia.
Original Source
Title: Investigations on druggable gene mutations related to AML/ALL lineage genes in Advanced Phases of CML: Implications in patient-tailored therapy of blast crisis CML in TKI era
Abstract: Background: Chronic Myeloid Leukemia (CML) is a myeloproliferative stem cell malignancy. Chronic Phase CML (CP-CML) is treatable with overall survival equivalent to the general population. Nevertheless, a proportion of CP-CML progresses to the accelerated phase (AP-CML) and ultimately blast crisis (BC-CML), with the latter having an overall survival (OS) of 3-23 months, making it almost a fatal manifestation. Therefore, the treatment of BC-CML is one of the biggest challenges in modern cancer medicine. Moreover, the OS of BC-CML is very variable indicating its heterogeneity. Although BC-CML is a different clinical entity than acute leukemias, it resembles AML (as myeloid BC-CML) or ALL (lymphoid BC-CML). Therefore, this study was designed to find out AML-/ALL lineage gene mutations in BC-CML using very sensitive next-generation sequencing. Patients & Methods: The study included 141 CML patients (123 CP-CML as control groups; 6 AP-CML and 12 BC-CML as experimental groups). Most of the patients received imatinib mesylate (IM) as first-line treatment. All response criteria were per European LeukemiaNet (ELN) guidelines 2020. Whole exome sequencing (WES) was carried out to find out druggable gene mutations and the druggability of the mutated genes was determined using the online Artificial intelligence (AI) tool www.pandrugs.com. SAS/STAT software version 9.4 was used for data analysis (SAS Institute Inc., Cary, NC, USA). For statistical computing, the R package was employed (Vienna, Austria). The study was approved by the ethical committee of KAIMRC and carried out per the guidelines of the Helsinki Declaration Results: Overall male-to-female ratio was 1.6:1 and the mean age was 36.4 (range: 9 -67) years. Eighteen (12.8%) patients progressed to AP-CML while 12 (8.5%) to BC-CML finally. BC-ML patients had overall poorer response to TKIs and higher mortality rate (75%) that prompted to look for additional gene mutations. WES showed overall 64 AML-/ALL- associated gene mutated in advanced phase CML patients. Overall WES coverage was about 110X. AP-CML had 1644 variants, whereas BC-CML had 2531 variants, with a 54% gain in mutations from AP-CML to BC-CML (P< 0.000001). Among AML-/ALL- related mutated genes were NPM1 (%1.98), DNMT3A (%1.86), PML (%1.82), AKT1 (%1.62), CBL (%1.30), JAK2 (%0.71), TET2 (%0.59), IDH1 (%0.32), and BCL2. These mutations can be targeted by some drugs already approved by FDA to treat different blood cancers and include that included Venetoclax, Ivosidenib, Azacitidine, Decitabine, Doxorubicin, Vincristine, Quizartinib, Pacritinib, Vandetanib and Bortezomib. Conclusions: Our studies highlighted the role of myeloid-/lymphoid-lineage genetic abnormalities in CML blast crisis transformation and TKI-resistance. Whole-exome sequencing (WES)-based mutational analysis of BC-CML as experimental group and CP-CML as well as healthy subjects as controls found that genes exclusively mutated in BC-CML samples, in addition to BCR-ABL1, were RPTOR, BRCA1/2, STAB1, NF1, ACIN1, EGFR, NDRG2, ERG, MYH11, NPM1, DNMT3A, PML, AKT, CBL, JAK2, FLT-3, TET2, IDH1/2 and BCL2. Bioinformatics-based drug discovery (pandrugs2) analysis of WES data revealed various FDA-approved drugs targeting these blood cancer-related gene mutations detected in our BC-CM. It is important to mention that many of these drugs are already in clinical trials for BC-CML. . Hence we conclude that pan-cancer genetic analysis of BC-CML subjects by employing sensitive NGS assays coupled with AI-based drug discovery tools can detect druggable gene mutations in these patients that can provide rich sources of drug repurposing for personalized therapy of this fatal BC-CML. Keywords: Blast crisis Chronic Myeloid Leukemia; druggable mutations; pa-tient-tailored treatment; AML lineage genes; ALL lineage genes.
Authors: Zafar Iqbal, N. Alanazi, A. AlGarni, S. Almukhaylid, M. AlMajed, S. Alanazi, M. Khan, M. Sabar, A. Jameel, A. Hussian, D. Almaghlouth, A. Alsuwaidani, G. Alsalem, N. AlMutairi, H. Almasoudi, B. AlShehab, S. Alfayez, M. Butwyibah, B. Alnajad, F. Alali, A. Al-Rasasi, K. Adeel, S. Al Hakeem, T. Karar, F. Alsaab, Y. Taleb, S. Shahbaz, S. Malik, A. Mahmood, S. Basit, M. Anharullah, A. Aleem, I. F. Zafar, R. Naeem, M. Shamas
Last Update: 2024-12-22 00:00:00
Language: English
Source URL: https://www.medrxiv.org/content/10.1101/2024.09.08.24313260
Source PDF: https://www.medrxiv.org/content/10.1101/2024.09.08.24313260.full.pdf
Licence: https://creativecommons.org/licenses/by/4.0/
Changes: This summary was created with assistance from AI and may have inaccuracies. For accurate information, please refer to the original source documents linked here.
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