Beyond Genetics: Exploring the Role of Epigenetic Modification in Chronic Lymphocytic Leukemia

While cancer has long been understood as a genetic disease, recent evidence has begun to shed light on the role of epigenetic changes in cancer pathogenesis.1 Epigenetics refers to DNA  modifications that do not alter the DNA sequence but affect gene expression, such as methylation and histone modification.2 In chronic lymphocytic leukemia (CLL), research has shown that epigenetic changes are a major determinant of the different biological features of the disease.1

So far, the role of epigenetic modification in CLL has primarily been examined through the study of TCL1A, an oncogene abnormally expressed in CLL. Higher levels of TCL1A expression are more common in CLL patients with adverse features, such as high-risk (cyto)genetics, faster tumor cell proliferation, and poorer responses to treatment. Mice that have been genetically engineered to express high levels of TCL1A develop a disease that resembles CLL, including changes in the methylome. In previous research, TCL1A was found to interact with the DNA methyltransferase 3A (DNMT3A) enzyme, reducing the enzymatic activity of DNMT3A, and thereby contributing to epigenetic reprogramming in CLL.1

However, beyond this finding, epigenetic regulation has not been well-studied in CLL. In partixular, Histone-modifying enzymes (HME) have not been investigated in detail, despite the fact that histone modification is known to play a vital role in the pathogenesis of CLL.1

To explore this further, a research team explored the interaction between TCL1A and KDM1A, a lysine-specific histone demethylase whose upregulation has been linked to poor clinical outcomes in multiple cancers, including leukemias.

The role of KDM1A in CLL

The researchers, led by Marco Herling of the University of Leipzig, Germany, carried out a series of experiments using patient data and samples, animal models, and in vitro studies. First, they used mass spectrometry to study patient and control samples, establishing that TCL1A interacts with KDM1A to enhance its activity in B cells, indicating that this could be a mechanism through which increased TCL1A levels in CLL alter the epigenetic signature of B cells. They then compared KDM1A expression levels in data from a prospective clinical trial of two anti-cancer therapies in CLL to explore the enzyme’s relationship with disease outcomes. These results demonstrated that high KDM1A expression was associated with more aggressive disease features and worse clinical outcomes in the group of 337 patients.1

Digging deeper

To further explore the relevance of KDM1A, the researchers studied the effects of Kdm1a knockdown in the CLL mouse model. This showed that the knockdown of Kdm1a resulted in significantly longer overall survival (67 days vs. 39-41 days), more stable white blood cell counts, and decreased leukemic cell counts. Studying the spleens of the animals revealed that this was due to an increased rate of CLL-cell apoptosis coupled with a reduced rate of proliferation. Interestingly, the team showed that the knockdown of Kdm1a did not only have a direct impact on B cells but also helped reshape the tumor microenvironment, impairing features that help support tumor cell proliferation and survival. This potential role for KDM1A in modulating the tumor microenvironment has also been suggested in breast cancer studies.1

Additionally, the team compared RNA expression between the two models, discovering that of 1013 differentially expressed genes between the two genotypes, 81% were upregulated in cells from the knockdown model. The team believes this suggests that Kdm1a suppresses global transcriptional activity in murine CLL. In particular, the expression of programmed-cell-death genes was overrepresented in cells from the knockdown model, providing further support for the pro-apoptotic role of KDM1A.1

Finally, to confirm KDM1A as a potential therapeutic target in CLL, the team explored the effect of anti-KDM1A compounds on leukemic cells, revealing that pharmacologic KDM1A inhibition increased histone methylation and induced CLL cell apoptosis. They also demonstrated a synergistic effect between KDM1A inhibitors and the existing therapies - venetoclax and idasanutlin - suggesting anti-KDM1A agents could potentially be used as combination therapies.1

The future of KDM1A inhibition in CLL

The researchers say that this is the first report on the role of KDM1A in CLL, establishing its pathogenic role and potential as a therapeutic target. It is hoped that targeting HMEs is a strategy that may help to overcome therapy resistance - a major challenge in CLL that often leads to disease relapse - by exploiting synergisms between KDM1A inhibition and currently targeted molecular pathways. However, the team states that further research will be needed to optimize these combinations for use in relapsed/refractory CLL.1

A powerful analytical assistant

In this study, the researchers employed TissueGnostics´ StrataQuest image cytometry software to compute and analyze murine spleen sections, helping to reveal the impact of KDM1A on B cell proliferation and apoptosis.

Using StrataQuest’s automated analysis workflow, the researchers defined the percentage of KDM1A+ cells in murine spleen in Eμ-TCL1A mice overexpressing TCL1A with CLL-like syndroms and Kdm1a knock-down Eμ-TCL1A mice. They further quantified B220 expressing cells (murine B cells) and identified KDM1A+B220+ cells. For all of these markers, there were less marker-positive cells in Kdm1a knock-down Eμ-TCL1A mice. The number of Ki-67+B220+ proliferating B cells was as well reduced. 1

To further characterize the tumor microenvironment in mice with CLL symptoms, the team utilized StrataQuest to define the percentage of T cells, KDM1A+ T cells, and Ki-67+ T cells, all of which were reduced in Kdm1a knock-down Eμ-TCL1A mice. Additionally, the group assessed how many murine F4/80+ macrophages also express KDM1A in this model.1

The contextual image analysis software StrataQuest is a powerful tool for researchers who want to study the molecular and cellular basis of a disease. StrataQuest can automatically detect and quantify cells and biomarkers in tissue sections. It can also detect a wide variety of biomarkers in tissues of any origin, helping to streamline and automate the analytical process. Offering statistical analysis, integration with other bioinformatics tools, and a user-friendly interface, StrataQuest is an invaluable tool for researchers who want to gain a deeper understanding of the biology of cancer. Contact our team today to get more information about using StrataQuest in your research.

References and Further Reading

  1. Jian Q, Stachelscheid J, Bloehdorn J, et al. Oncogenic role and target properties of the lysine-specific demethylase KDM1A in chronic lymphocytic leukemia. Blood. 2023; doi: 10.1182/blood.2022017230. [online ahead of print]
  2. National Cancer Institute (NCI) Dictionary of Cancer Terms. Available at: Accessed May 2023.

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