Tumor Heterogeneity in Leukemia and Lymphoma: Insights from Single-Cell Analyses

Authors

  • Pang Hou Wen Department of Life Sciences, Faculty of Science, University of Malaya, Federal Territory of Kuala Lumpur, Malaysia Author

DOI:

https://doi.org/10.64229/fxex4a63

Keywords:

Tumor Heterogeneity, Single-Cell Rna Sequencing, Leukemia, Lymphoma, Clonal Evolution, Tumor Microenvironment, Therapy Resistance, Minimal Residual Disease

Abstract

Tumor heterogeneity is a fundamental property of leukemia and lymphoma that drives disease progression, relapse, and therapy resistance. For decades, bulk genomic and transcriptomic analyses have provided a foundational understanding of these malignancies but have obscured the cellular diversity within the tumor ecosystem. The advent of high-throughput single-cell technologies, particularly single-cell RNA sequencing (scRNA-seq), has revolutionized our capacity to deconvolute this complexity. This review synthesizes how single-cell analyses are reshaping our understanding of tumor heterogeneity in hematological cancers. We explore the role of intra-clonal genetic diversity in Acute Myeloid Leukemia (AML) and B-cell Acute Lymphoblastic Leukemia (B-ALL), the functional and transcriptional plasticity of subpopulations, and the dynamic interplay between malignant cells and the immune microenvironment in both leukemia and lymphoma. We further highlight how the tumor microenvironment in lymphomas fosters heterogeneity and immune evasion. Furthermore, the integration of single-cell data with spatial transcriptomics and computational models is beginning to predict evolutionary trajectories, offering a window into future clinical behaviors. Critically, we discuss how single-cell approaches have identified pre-existing or emergent resistant subclones under therapeutic pressure, providing a mechanistic basis for treatment failure. The clinical implications are profound, paving the way for single-cell diagnostics for minimal residual disease (MRD) monitoring and the identification of novel therapeutic targets. We conclude that single-cell multi-omics is an indispensable tool for unraveling the multifaceted nature of tumor heterogeneity, with the potential to propel the field toward more precise and effective therapeutic strategies.

References

[1]Greaves, M., & Maley, C. C. (2012). Clonal evolution in cancer. Nature, 481(7381), 306–313. https://doi.org/10.1038/nature10762

[2]Stuart, T., & Satija, R. (2019). Integrative single-cell analysis. Nature Reviews Genetics, 20(5), 257–272. https://doi.org/10.1038/s41576-019-0093-7

[3]Trapnell, C., Cacchiarelli, D., Grimsby, J., Pokharel, P., Li, S., Morse, M., Lennon, N. J., Livak, K. J., Mikkelsen, T. S., & Rinn, J. L. (2014). The dynamics and regulators of cell fate decisions are revealed by pseudotemporal ordering of single cells. Nature Biotechnology, 32(4), 381–386. https://doi.org/10.1038/nbt.2859

[4]van Galen, P., Hovestadt, V., Wadsworth II, M. H., Hughes, T. K., Griffin, G. K., Battaglia, S., Verga, J. A., Stephansky, J., Pastika, T. J., Lombardi Story, J., Pinkus, G. S., Pozdnyakova, O., Galinsky, I., Stone, R. M., Graubert, T. A., Shalek, A. K., Aster, J. C., Lane, A. A., & Bernstein, B. E. (2019). Single-cell RNA-seq reveals AML hierarchies relevant to disease progression and immunity. Cell, 176(6), 1265-1281.e24. https://doi.org/10.1016/j.cell.2019.01.031

[5]Ng, S. W. K., Mitchell, A., Kennedy, J. A., Chen, W. C., McLeod, J., Ibrahimova, N., Arruda, A., Popescu, A., Gupta, V., Schimmer, A. D., Schuh, A. C., Yee, K. W., Bullinger, L., Herold, T., Görlich, D., Büchner, T., Hiddemann, W., Berdel, W. E., Wörmann, B., … Dick, J. E. (2016). A 17-gene stemness score for rapid determination of risk in acute leukaemia. Nature, 540(7633), 433–437. https://doi.org/10.1038/nature20598

[6]Good, Z., Sarno, J., Jager, A., Samusik, N., Aghaeepour, N., Simonds, E. F., White, L., Lacayo, N. J., Fantl, W. J., Fazio, G., Gaipa, G., Biondi, A., Tibshirani, R., Bendall, S. C., Nolan, G. P., & Davis, K. L. (2018). Single-cell developmental classification of B cell precursor acute lymphoblastic leukemia at diagnosis reveals predictors of relapse. Nature Medicine, 24(4), 474–483. https://doi.org/10.1038/nm.4505

[7]Petti, A. A., Williams, S. R., Miller, C. A., Fiddes, I. T., Srivatsan, S. N., Chen, D. Y., Fronick, C. C., Fulton, R. S., Church, D. M., & Ley, T. J. (2019). A general approach for detecting expressed mutations in AML cells using single cell RNA-sequencing. Nature Communications, 10(1), 3660. https://doi.org/10.1038/s41467-019-11591-1

[8]Baryawno, N., Przybylski, D., Kowalczyk, M. S., Kfoury, Y., Severe, N., Gustafsson, K., Kokkaliaris, K. D., Mercier, F., Tabaka, M., Hofree, M., Dionne, D., Papazian, A., Lee, D., Ashenberg, O., Subramanian, A., Vaishnav, E. D., Rozenblatt-Rosen, O., Regev, A., & Scadden, D. T. (2019). A cellular taxonomy of the bone marrow stroma in homeostasis and leukemia. Cell, 177(7), 1915-1932.e16. https://doi.org/10.1016/j.cell.2019.04.040

[9]Roider, T., Seufert, J., Uvarovskii, A., Frauhammer, F., Bordas, M., Abedpour, N., Stolarczyk, M., Mallm, J. P., Herbst, S. A., Bruch, P. M., Gundert, L., Wiest, T., Schäfer, H., Kubsch, T., Huang, Y., Schreck, C., Wagner, L., Riegel, D., Follo, M., … Brors, B. (2020). Dissecting intratumour heterogeneity of nodal B-cell lymphomas at the transcriptional, genetic and drug-response levels. Nature Cell Biology, 22(7), 896–906. https://doi.org/10.1038/s41556-020-0532-x

[10]Potter, N., Jones, L., Blair, H., Strehl, S., Harrison, C. J., Greaves, M., & Wiemels, J. L. (2018). Single-cell analysis of clonal architecture in acute myeloid leukaemia. Leukemia, 33(5), 1113–1123. https://doi.org/10.1038/s41375-018-0319-2

[11]Sharma, S. V., Lee, D. Y., Li, B., Quinlan, M. P., Takahashi, F., Maheswaran, S., McDermott, U., Azizian, N., Zou, L., Fischbach, M. A., Wong, K. K., Brandstetter, K., Wittner, B., Ramaswamy, S., Classon, M., & Settleman, J. (2010). A chromatin-mediated reversible drug-tolerant state in cancer cell subpopulations. Cell, 141(1), 69–80. https://doi.org/10.1016/j.cell.2010.02.027

[12]Giustacchini, A., Thongjuea, S., Barkas, N., Woll, P. S., Povinelli, B. J., Booth, C. A. G., Sopp, P., Norfo, R., Rodriguez-Meira, A., Ashley, N., Jamieson, L., Vyas, P., & Jacobsen, S. E. W. (2017). Single-cell transcriptomics uncovers distinct molecular signatures of stem cells in chronic myeloid leukemia. Nature Medicine, 23(6), 692–702. https://doi.org/10.1038/nm.4336

[13]Miles, L. A., Bowman, R. L., Merlinsky, T. R., Csete, I. S., Ooi, A. T., Durruthy-Durruthy, R., Bowman, M., Famulare, C., Patel, M. A., Mendez, P., Ainali, C., Tsirigos, A., Buisson, R., Nakitandwe, J., Grieb, B., Mose, L. E., Hadjadj, D., Sun, Q., Trowbridge, J. J., … Papapetrou, E. P. (2020). Single-cell mutation analysis of clonal evolution in myeloid malignancies. Nature, 587(7834), 477–482. https://doi.org/10.1038/s41586-020-2864-x

[14]Velten, L., Story, B. A., Hernández-Malmierca, P., Raffel, S., Leonce, D. R., Milbank, J. H., Paulsen, M., Demir, A., Szu-Tu, C., Frömel, R., Buchholz, F., Lutz, C., Nowak, D., Jann, J. C., Pabst, C., Boch, T., Hofmann, W. K., Müller-Tidow, C., Trumpp, A., … Haas, S. (2021). Identification of leukemic and pre-leukemic stem cells by clonal tracking from single-cell transcriptomics. Nature Communications, 12(1), 1366. https://doi.org/10.1038/s41467-021-21650-1

[15]Wang, L., Fan, J., Francis, J. M., Georghiou, G., Hergert, S., Li, S., Gambe, R., Zhou, C. W., Yang, C., Xiao, S., Cin, P. D., Bowden, M., Kotliar, D., Shukla, S. A., Brown, J. R., Neuberg, D., Chabner, M., & Livak, K. J. (2017). Integrated single-cell genetic and transcriptional analysis suggests novel drivers of chronic lymphocytic leukemia. Genome Research, 27(8), 1300–1311. https://doi.org/10.1101/gr.217331.116

Downloads

Published

2025-11-21

Issue

Section

Articles

How to Cite

Pang Hou Wen. (2025). Tumor Heterogeneity in Leukemia and Lymphoma: Insights from Single-Cell Analyses. Hematological Disorders in the Single-Cell Era, 1(2), 14-20. https://doi.org/10.64229/fxex4a63