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Gene & Protein in Disease BCL11A targets and chromatin binding patterns

immunostaining of B-pDCs. Similar to BCL11A, AXL is kindly provided the CAL-1 cell line. Library preparation
7
upregulated by type I interferon to enhance its functional and Illumina ChIP- and RNA-seq were performed at the
activity. 37 NGS core of the MD Anderson Cancer Center.
We are confident that our data support the limited Funding
conclusions drawn. However, one experimental control
remains missing, which is formal proof that the peaks Support for this work was provided by the Lymphoma
observed in Figure 1B are exclusively dependent on Research Foundation Fellowship 300463 (to J.D.D.),
BCL11A. To address this, we plan to generate clustered the NIH Grant R01CA31534, the Cancer Prevention
regularly interspaced short palindromic repeats knockout Research Institute of Texas (CPRIT) Grants RP120348
cell lines expressing critical BCL11A target genes and and RP120459, and the Marie Betzner Morrow Centennial
test whether the ChIP signal is eliminated on BCL11A Endowment (to H.O.T.).
knockout. Conflict of interest
While this approach will require several months to
execute properly, it is central to extending this work to The authors declare no conflicts of interest.
bona fide human leukemic targets. Future efforts will focus Author contributions
on functional analyses of B-pDCs to better understand
their role in immune response and cancer progression. Conceptualization: Joseph D. Dekker, Haley O. Tucker
Investigation: All authors
Another strategy involves reanalyzing our data using
model-based analysis of ChIP-seq to identify additional Methodology: All authors
Writing – original draft: All authors
mouse leukemic BCL11A target genes and overlapping
binding sites within those genes. Despite potential Writing – review & editing: All authors
limitations in quantitative accuracy, we remain confident Ethics approval and consent to participate
that the major peaks identified were sufficient to support
our conclusions. These findings, along with previously Not applicable.
published data from others, form the foundation for the Consent for publication
model presented in Figure 2.
Finally, further analyses into the specific transcriptional Not applicable.
mechanisms downstream of these and additional Availability of data
target genes are required. This will help distinguish the
implications of target cell-dependent differences in their GSE105827 (RNA-seq), GSE99019 (ChIP-seq), and
regulation. GSE52868 (pre-B RNA-seq) are the accession numbers
to previously published datasets. Other data will be made
5. Conclusion available on request to the corresponding author.
In our previous research and in this manuscript, we References
demonstrated that BCL11A not only regulates the
development of classical pDCs and B-pDCs in mice, 1. Harman BC, Miller JP, Nikbakht N, Gerstein R, Allman D.
but that its overexpression also regulates murine B-cell Mouse plasmacytoid dendritic cells derive exclusively
leukemias in humans. Using ChIP-seq analyses, we showed from estrogen-resistant myeloid progenitors. Blood.
that BCL11A exerts this regulatory effect through direct 2006;108(3):878-885.
binding to the promoters and enhancers of genes critical doi: 10.1182/blood-2005-11-4545
to leukemia development. Further investigation into the 2. Adams NM, Das A, Yun TJ, Reizis B. Ontogeny and function
specific transcriptional mechanisms downstream of these of plasmacytoid dendritic cells. Annu Rev Immunol.
and other target genes is needed to clarify the impact of 2024;42(1):347-373.
target cell-dependent differences in their regulation.
doi: 10.1146/annurev-immunol-090122-041105
Acknowledgments 3. Reizis B, Bunin A, Ghosh HS, Lewis KL, Sisirak V.
Plasmacytoid dendritic cells: Recent progress and open
We thank June V. Harriss for expert assistance in the questions. Annu Rev Immunol. 2011;29:163-183.
generation of Bcl11a conditional knockout mice and
Chhaya Das and Maya Ghosh for help in ChIP experiments doi: 10.1146/annurev-immunol-031210-101345
and cell culture. Dr. Takahiro Maeda and Dr. Boris Reizis 4. Shigematsu H, Reizis B, Iwasaki H, et al. Plasmacytoid

Volume 4 Issue 2 (2025) 5 doi: 10.36922/gpd.8131