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4583 Immune Escape after Allogeneic Hematopoietic Cell Transplantation in Pediatric Patients with Acute Myeloid Leukemia

Program: Oral and Poster Abstracts
Session: 701. Experimental Transplantation: Basic and Translational: Poster III
Hematology Disease Topics & Pathways:
Research, Acute Myeloid Malignancies, AML, Biological therapies, Translational Research, genomics, pediatric, Diseases, immune mechanism, Therapies, Myeloid Malignancies, Biological Processes, Study Population, Human, Transplantation
Monday, December 12, 2022, 6:00 PM-8:00 PM

Sanam Shahid, MD1, Nicholas Ceglia2*, Jean-Benoit Le Luduec3*, Andrew McPherson2*, Barbara Spitzer, MD1, Viktoria Bojilova2*, M. Kazim Panjwani3*, Mikhail Roshal, MD4, Sohrab Shah2*, Omar Abdel-Wahab, MD5, Benjamin Greenbaum2* and Katharine C. Hsu, MD, PhD5

1Department of Pediatrics, Memorial Sloan Kettering Cancer Center, New York, NY
2Department of Epidemiology and Biostatistics, Memorial Sloan Kettering Cancer Center, New York, NY
3Memorial Sloan Kettering Cancer Center, New York, NY
4Department of Pathology and Laboratory Medicine, Hematopathology Service, Memorial Sloan Kettering Cancer Center, New York, NY
5Department of Medicine, Memorial Sloan Kettering Cancer Center, New York, NY

Introduction: Although allogeneic hematopoietic cell transplantation (allo-HCT) is curative for high-risk pediatric acute myeloid leukemia (AML), post-transplantation relapse occurs in 20-50% of patients and comprises the primary cause of treatment failure and mortality. To explore the effects of immune-mediated selective pressures imposed by allo-HCT on tumor evolution in relapsed pediatric AML, we performed exploratory analysis at single-cell resolution using a multimodal proteogenomic approach.

Methods: We evaluated bone marrow aspirate (BMA) samples obtained at diagnosis and at post-transplant relapse for four pediatric AML patients at Memorial Sloan Kettering Cancer Center (MSKCC). Using single-cell RNA-seq, T cell receptor (TCR)-seq, and cellular indexing of transcriptomes and epitopes (CITE)-seq, we identified several epigenetic and phenotypic alterations that may permit pediatric AML cells to escape the graft-versus-leukemia effect.

Results: A total of 79,334 single-cell transcriptomes were profiled from nine BMA samples obtained from four pediatric AML patients at diagnosis (n = 45,345) and post-transplant relapse (n = 15,412) and from one healthy 20-year-old female donor (n = 18,577). We identified several significantly downregulated immune-related processes in AML blasts at disease relapse following allo-HCT compared to initial disease diagnosis, including antigen processing and presentation, cytokine-mediated signaling, and IFN-γ mediated signaling. We observed a global downregulation of MHC class II (MHC-II) genes HLA-DR, -DP, -DQ, -DM, -DO and MHC-II regulators CIITA and CD74 when comparing mean expression at diagnosis with post-transplant relapse.

Given the significant intratumoral heterogeneity present in pediatric AML, we further evaluated the downregulation of MHC-II at relapse within subpopulations of AML blasts. AML blast cells were stratified into six subtypes along the myeloid differentiation axis: hematopoietic stem cell (HSC)-like, progenitor-like, granulocyte-monocyte progenitor (GMP)-like, promonocyte-like, monocyte-like, or cDC-like. Downregulation of MHC-II expression observed at post-transplant relapse was most profound in progenitor-like blasts and was accompanied by correlative changes in upstream MHC-II transcriptional regulation.

To elucidate the immune pressures leading to the MHC-II changes in AML blasts, detailed profiling of the leukemia-associated immune compartment was performed, including single-cell CITE-seq and TCR-seq. When compared to BMA samples obtained at diagnosis, post-transplant relapse samples exhibited clonal expansion of exhausted CD8+ T cells, suggesting recruitment of cytotoxic T cells to the bone marrow environment and lower effector functionality at the time of post-transplant relapse. In comparison to diagnosis samples, post-transplant relapse samples revealed an over-representation of regulatory T cells with a relative decrease in naïve CD4+ T cells, indicative of an immunosuppressive tumor microenvironment. Pathway enrichment validated an overall dysfunctional pattern in T cells and NK cells at post-transplant relapse with lower observed response to IFN-γ, TNF-α signaling via NF-κB, and IL-2/STAT5 signaling.

Conclusions: We observed an overall downregulation of MHC-II genes at post-transplant relapse not previously reported in pediatric AML. A dampened CD4+ T cell response, suggested by the reduced conventional CD4+ T cell population and diminished IFN-γ, TNF-α, and IL-2 response signature in NK and CD8+ T cells, could be a possible mechanism for post-transplant relapse driven by downregulation of AML MHC-II expression. We further propose that progenitor-like AML blasts may be critical to this phenomenon based on the relative expansion of progenitor-like AML clones at post-transplant relapse and further suppression of MHC-II relative to other subpopulations. The novel computational methods utilized here serve as a strong foundation to guide future single-cell studies to define the functions and mechanisms of immunomodulatory AML populations, to evaluate their relationship to the bone marrow microenvironment, and to modify their activities for therapeutic benefit.

Disclosures: Panjwani: US provisional patent: Patents & Royalties. Roshal: NGM: Other: Funding; Roche: Other: Funding; Auron Therapeutics: Other: Ownership / Equity interests; Provision of services; Beat AML: Other: Funding; Physicians' Education Resource: Other: Provision of services; Celgene: Other: Provision of services. Shah: Imagia Canexia Inc: Other: personal fees. Abdel-Wahab: Envisagenics Inc., AIChemy, Harmonic Discovery Inc., and Pfizer Boulder: Membership on an entity's Board of Directors or advisory committees; H3B Biomedicine, LOXO Oncology, and Nurix Therapeutics: Research Funding; H3B Biomedicine, Foundation Medicine Inc, Merck, Prelude Therapeutics, and Janssen: Consultancy. Greenbaum: Merck, Bristol-Meyers Squibb, Chugai Pharmaceuticals: Honoraria; Bristol-Meyers Squibb: Research Funding; PMV Pharma and Rome Therapeutics: Consultancy. Hsu: WuGen: Membership on an entity's Board of Directors or advisory committees.

*signifies non-member of ASH