Andrew Burden

All Publications

• A Patient-Derived Screen Identifies HDAC Inhibitors as Enhancers of Phagocytosis and Potent Immunotherapy Partners. Cancer immunology research Khalaj, M., Burden, A. T., Gutierrez, M. L., Hoonsbeen, S. C., Nejad, P., Raveh, T., Young, J. S., Fattahi, F., Weissman, I. L. 2026

  Abstract

  Glioblastoma multiforme (GBM) is a lethal brain tumor with limited treatment options. Tumor-associated macrophages and microglia (TAMs) drive immune suppression and tumor progression, making them a key therapeutic target for GBM. Enhancing TAM phagocytosis in GBM has shown promise, particularly with innate checkpoint inhibitors, such as CD47-blocking antibodies. However, small molecule approaches, which offer tunable and potentially synergistic mechanisms, remain underexplored in this context. In this study, we conducted a large-scale small molecule screen on primary TAMs isolated directly from GBM patient tumors, testing 1,365 compounds to identify drugs that enhance TAM phagocytosis. This screen revealed enrichment for histone deacetylase (HDAC)-targeting drugs among the top hits. HDAC inhibitors enhanced phagocytosis of cancer cells across multiple primary human TAM-GBM combinations, and synergized with CD47 blockade ex vivo. In a xenograft GBM model, Pracinostat suppressed tumor growth and extended survival, with additive benefit when combined with CD47 antibodies. RNA-sequencing and H3K27Ac CUT&Tag profiling of Pracinostat-treated TAMs in vivo revealed a two-tier mechanism: transcriptional reprogramming toward a pro-inflammatory state via NF-κB activation, and epigenetic priming of FcγR-mediated phagocytic machinery, providing a mechanistic basis for the observed synergy with CD47 blockade. Our findings establish a patient-first functional screening platform for identifying TAM-reprogramming therapeutics in GBM, validate HDAC inhibitors as a lead class that potentiates innate checkpoint immunotherapy, and provide additional candidate compounds for clinical investigation.

  View details for DOI 10.1158/2326-6066.CIR-25-0506

  View details for PubMedID 42446904

• Lineage tracing of both quiescent G0 and active Hoxb5+ LT-HSCs that actively contribute to homeostatic mouse hematopoiesis. Proceedings of the National Academy of Sciences of the United States of America Xiang, J., Almeida, L., Pasillas, J., Sun, C. T., Wang, Y., Koren, E., Hanson, E. C., Brakebill, A., Wang, C., Burden, A. T., Weissman, I. L. 2025; 122 (49): e2513724122

  Abstract

  Studying the lineage commitment and differentiation potential of long-term hematopoietic stem cells (LT-HSCs) is important to understand the dynamics of hematopoiesis. A central question concerns which hematopoietic stem and progenitor cell populations are responsible for sustaining steady-state hematopoiesis in vivo without conditioning. Noninvasive HSC fate-mapping strategies to address this question require specific labeling of LT-HSCs only. In this study, we selectively labeled a subset of Hoxb5+ LT-HSCs-excluding short-term HSCs (ST-HSCs) and multipotent progenitors (MPPs)-to track the progeny of these cells. Hoxb5+ LT-HSCs comprise ~1 in 100,000 bone marrow cells. MPPs were not labeled until several months post-induction, indicating their derivation from LT-HSCs. At no time were MPPs labeled and LT-HSCs not, consistent with the origin and maintenance of MPPs from LT-HSCs. Hoxb5+ LT-HSCs are the principal contributors to steady-state in situ hematopoiesis, but only a fraction of LT-HSCs were labeled by the Cre/LoxP conversion to a lineage-tracing color. We tested whether quiescent HSCs could have incised the DNA at loxp sites, but did not finish the rearrangement. Analysis of phosphorylated H2AX (γ-H2AX) revealed that quiescent LT-HSCs retain Cre/LoxP-induced DNA incisions, which are repaired upon cell cycle entry, leading to the appearance of newly labeled LT-HSCs at later time points, mainly of the myeloid-biased HSC. Moreover, most LT-HSCs exhibit marked expansion in response to hematopoietic stress. With the age-related shift of blood formation from balanced to myeloid biased, the myeloid-biased HSCs expand preferentially after 6 mo of tracking.

  View details for DOI 10.1073/pnas.2513724122

  View details for PubMedID 41325518

• Macrophages release neuraminidase and cleaved calreticulin for programmed cell removal. Proceedings of the National Academy of Sciences of the United States of America Banuelos, A., Baez, M., Zhang, A., Yılmaz, L., Kasberg, W., Volk, R., Georgeos, N., Koren-Sedova, E., Le, U., Burden, A. T., Marjon, K. D., Lippincott-Schwartz, J., Zaro, B. W., Weissman, I. L. 2025; 122 (21): e2426644122

  Abstract

  Calreticulin (CALR) is primarily an endoplasmic reticulum chaperone protein that also plays a key role in facilitating programmed cell removal (PrCR) by acting as an "eat-me" signal for macrophages, directing their recognition and engulfment of dying, diseased, or unwanted cells. Recent findings have demonstrated that macrophages can transfer their own CALR onto exposed asialoglycans on target cells, marking them for PrCR. Despite the critical role CALR plays in this process, the molecular mechanisms behind its secretion by macrophages and the formation of binding sites on target cells remain unclear. Our findings show that CALR undergoes C-terminal cleavage upon secretion, producing a truncated form that functions as the active eat-me signal detectable on target cells. We identify cathepsins as potential proteases involved in this cleavage process. Furthermore, we demonstrate that macrophages release neuraminidases, which modify the surface of target cells and facilitate CALR binding. These insights reveal a coordinated mechanism through which lipopolysaccharide (LPS)-activated macrophages regulate CALR cleavage and neuraminidase activity to mark target cells for PrCR. How they recognize the cells to be targeted remains unknown.

  View details for DOI 10.1073/pnas.2426644122

  View details for PubMedID 40397678