Revisiting AML single-cell datasets in BBrowser to learn how monocytic AML survives Venetoclax - BioTuring's Blog
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Revisiting AML single-cell datasets in BBrowser to learn how monocytic AML survives Venetoclax

Acute myeloid leukemia (AML) happens when the myeloid precursor cells in the bone marrow grow abnormally (making up  myeloblasts). A common treatment for AML is Venetoclax. This drug inhibits BCL2, an oncoprotein that prevents cell death and is often overexpressed in the majority of blasts from AML patients (Bensi et al, 1994). However, more than 50% of patients still relapse after Venetoclax treatment (Maiti A et al.2018). Why?

Venetoclax treatment for AML

Fig.1: Venetoclax inhibits BCL2 expression to induce cell death in AML cells

In an attempt to answer this question, we revisited currently available AML single-cell transcriptomics datasets. Out of 200 datasets in BBrowser, we picked 2 AML works from Pei et al. (2020) and van Galen et al (2019). The first study profiled cells in pre-Venetoclax treatment and relapse; the second looked at different stages of Venetoclax treatment (and also other treatments like chemotherapy and Ara-C consolidation (HIDAC)).

We combined these two data sets to gain a broader view of gene expression dynamics along the timeline of Venetoclax treatment: from day 0 to relapse. Here we summarized some insights from our reanalysis using BBrowser.

Fig.2. (A)  t-SNE of AML cells from Pei et al (2020) indexed in BBrowser, colored by Diagnosis and Relapse (left) and by cell types (right) (B) t-SNE of cells from a Venetoclax-treated patient in van Galen et al (2019) colored by timepoints (left) and cell types (right)

1. Does monocytic AML rely on BCL2 to survive? 

Let’s first revisit Pei et al (2020). The study found that BCL2 had very low expression (nearly 0) in monocytic AML cells (CD14+) before Venetoclax and in relapse. In contrast, hematopoietic stem cells (CD34+ primitive AML) express this gene abundantly. Thus, Venetoclax targets the CD34+ primitive AML populations and may not affect the monocytic AML population.

We queried BCL2 in these 2 cell types in the data set from Pei et al., and confirmed the low expression of this gene in monocytic AML at the diagnosis and relapse stage (Fig.3A and B).

We then asked if BCL2 expression in AML monocytes stayed modest like this throughout the entire treatment timeline.

As Pei and colleagues did not profile BCL2 during treatment, the work of van Galen et al. might help to clarify that! We looked it up in the monocyte population of Patient AML328, who was treated with Venetoclax-based therapy.

We saw that BCL2 barely expressed across the timeline of Venetoclax treatment from pretreatment to Day 171 in van Galen and colleagues’ work  (Fig.3C). This reinforces Pei and colleagues’ finding of low BCL2 expression in AML monocytes, suggesting that blocking BCL2 only in monocytes is not enough.

Fig.3.  BCL2 expression in (A) hematopoietic stem cells and in (B) monocytes in Diagnosis and Relapse (Pei et al., 2020) . (C) BCL2 expression in patient AML328’s monocytes from pre-treatment (Day 0) to later stages of Venetoclax treatment (Day171) from the data of  van Galen et al. (2019).

2. MCL1 expression is up-regulated in relapse while remaining relatively stable during Venetoclax treatment

In fact, the survivor kit of a cell does not just include BCL2.  MCL1 was also an anti-apoptotic factor in the intrinsic pathway to protect cancer cells from cell death. They will inhibit effectors like BAX, BAK and BOK in the mitochondria of cells to avoid cell death.

Pei and colleagues discovered that MCL1 is upregulated in relapsed monocytic AML, compared with diagnosis, suggesting that monocytic AML may rely more on MCL1 than BCL2 for cell survival in Venetoclax-based treatment. This means MCL1 co-performs with BCL2 the function of keeping cells survive, suggesting MCL1 as an additional target for treatment.

We confirmed this in our differential expression analysis (Fig.4).

However, we questioned if the upregulation of MCL1 is a product of the treatment or is a biomarker for identifying relapse.

Looking at van Galen and colleagues’ data set, we queried MCL1 expression across monocytes in different Venetoclax treatment time points. The expression of MCL1 seems to stay unchanged over the course of treatment (Fig.4C). Therefore, MCL1 upregulation may likely be a biomarker for relapse and not a result of Venetoclax treatment.

Fig.4 MCL1 expression in (A) hematopoietic stem cells and (B) monocytes in Diagnosis and Relapse (Pei et al., 2020); (C) MCL1 expression in patient AML328’s monocytes from pre-treatment (Day 0) to later stages of Venetoclax treatment (Day171) 

Above are some insights from our re-exploration of the 2 AML single-cell datasets. Keep in mind that we don’t have the response group to really compare if MCL1 upregulation only happens in relapse. Additional data are required to answer the question.

For detailed instructions on how to reproduce the analysis, check out our video below:


Maiti A, DiNardo CD, Cortes JE, et al: Interim analysis of phase II study of venetoclax with 10-day decitabine (DEC10-VEN) in acute myeloid leukemia and myelodysplastic syndrome. (Presented December 2, 2018) ASH Annual Meeting & Exposition.

Juárez-Salcedo LM, Desai V, Dalia S. Venetoclax: evidence to date and clinical potential. (2019) Drugs Context. 2019;8:212574. doi:10.7573/dic.212574

Shanshan Pei, Daniel A. Pollyea, et al. Monocytic Subclones Confer Resistance to Venetoclax-Based Therapy in Acute Myeloid Leukemia Patients. (2020) Cancer Discov. Published January 23 2020 DOI: 10.1158/2159-8290.CD-19-0710

Bensi, L & Longo, R & Vecchi, A & Messora, C & Garagnani, Lorella & Bernardi, S & Tamassia, M. & Sacchi, S. BCL-2 oncoprotein expression in acute myeloid leukemia.(1994) Haematologica. 80. 98-102.

Van Galen P, Hovestadt V, Wadsworth Ii MH, et al. Single-Cell RNA-Seq Reveals AML Hierarchies Relevant to Disease Progression and Immunity.(2019) Cell ;176(6):1265-1281.e24. doi:10.1016/j.cell.2019.01.031


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