Biology subjects

E Silva, B.

Publications and source records attributed to E Silva, B..

3 recordsLinked to original sources

bioRxiv2026

Biases introduced by Ficoll-based isolation in acute myeloid leukemia sample analyses support the use of hemolysis

Acute myeloid leukemia (AML) is a heterogeneous malignancy whose characterization relies on immunophenotyping and molecular profiling. While hemolysis is recommended for leukocyte isolation in clinical diagnostics, Ficoll-based density gradient centrifugation is widely used in research and biobanking. Here, we evaluated the impact of Ficoll isolation on commonly performed analyses of AML samples. Ficoll altered flow cytometry-based characterization by systematically enriching lymphocytes and AML blasts while depleting granulocytes. The increased T-cell content impaired AML engraftment in NSG mice, as T cells mediated terminal graft-versus-host disease. Although Ficoll had minimal impact on ex vivo AML blast expansion or chemotherapy response, RNA sequencing identified 1,136 differentially expressed genes compared with hemolysis, with Ficoll-processed samples notably leading to an overestimation of leukemic stem cell gene set expression. Immunogenomic deconvolution highlighted that Ficoll leads to an overestimation of CD8+ T-cell and monocyte abundances in sequenced samples. Mutation calling from RNA-seq data revealed substantial discrepancies between methods, including failure to detect a clinically relevant DNMT3A R882 mutation in a Ficoll-processed sample. Together, these findings support the systematic use of hemolysis to preserve cellular diversity and avoid unpredictable biases introduced by Ficoll-based isolation.

cell biology↗

bioRxiv2024

Use of human AML cells to study graft-versus-leukemia immunity in xenogeneic mouse models of GVHD

Allogeneic hematopoietic cell transplantation (allo-HCT) is the main therapeutic approach for patients with high-risk acute myeloid leukemia (AML), but the rate of relapse remains high and is associated with poor outcomes. Discovering new approaches to maximize the graft-versus-leukemia (GVL) effects while mitigating graft-versus-host disease (GVHD) should therefore be pursued. Because of the difficulties in modeling AML in mice, patient-derived xenotransplantations (PDX) in immunodeficient NSG mice are preferred to study the GVL effects. In PDX, AML is typically induced through the intravenous injection of cell lines or leukemic blasts obtained from patients. GVHD and GVL effects are induced by (co)-injecting human T cells or peripheral blood mononuclear cells (PBMCs). While this approach enables the induction of systemic leukemia, notably developing in the spleen and bone marrow of the animals, it can also be associated with difficulties in monitoring the disease, notably by flow cytometry. This can be circumvented by using luciferase-expressing AML cells or transplanting the leukemic cells in Matrigel to generate solid tumors that are easier to monitor. Here, we provide detailed instructions on how to prepare human PBMCs and leukemic cells, transplant them, and monitor the disease in NSG mice.

immunology↗

bioRxiv2022

Autophagy degrades immunogenic endogenous retroelements induced by 5-azacytidine in acute myeloid leukemia

The hypomethylating agent 5-azacytidine (AZA) is the first-line therapy for acute myeloid leukemia (AML) patients unfit for intensive chemotherapy. Evidence suggests that the anti-tumor effect of AZA results partly from T-cell cytotoxic responses against MHC-I-associated peptides (MAPs) whose expression is induced by hypomethylation. Through a proteogenomic approach, we analyzed the impact of AZA on the transcriptome and MAP repertoire of four AML cell lines and validated salient findings in the transcriptome of 437 primary AML samples. We demonstrate that AZA caused pleiotropic changes in AML cells via perturbation of transcription, translation, and protein degradation. Overall, 1,364 MAPs were upregulated in AZA-treated cells, including several cancer-testis antigens. Increased MAP abundance was due to the upregulation of corresponding transcripts in a minority of cases and post-translational events in most cases. Furthermore, AZA-induced hypomethylation increased the abundance of numerous transcripts, of which 38% were endogenous retroelements (EREs). Upregulated ERE transcripts triggered innate immune responses but were degraded by autophagy and not processed into MAPs. Autophagy resulted from the formation of protein aggregates caused by AZA-dependent inhibition of DNMT2, a tRNA-methyl transferase enzyme. We found that autophagy inhibition had a synergistic effect with AZA on AML cell proliferation and survival, increased ERE levels and triggered pro-inflammatory responses. Finally, autophagy gene signatures were associated with a lower abundance of CD8+ T-cell markers in AML patients expressing high levels of EREs. Altogether, this work demonstrates that the impact of AZA is regulated at several levels and suggests that inhibiting autophagy could improve the immune recognition of AML blasts in patients.

immunology↗