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2992 Unveiling the Tumor Microenvironment in Extranodal NK/T-Cell Lymphoma (ENKTCL) Patients with in Situ Spatial Transcriptomics

Program: Oral and Poster Abstracts
Session: 622. Lymphomas: Translational – Non-Genetic: Poster II
Hematology Disease Topics & Pathways:
Research, Translational Research
Sunday, December 8, 2024, 6:00 PM-8:00 PM

Dimitra Karagkouni, PhD1,2,3*, Maria J. J. Fernandez Turizo, MD4, Nikolaos Kalavros1,2,3,5*, Sean M McCabe, BS6*, Alexandra W Lenart, BA7*, Shivani Nanda1,2,3*, Athanasios Ploumakis1,2,3,5*, Antonella Amaral2,5*, Anna B Rider, BSc8*, Aliyah R. Sohani, MD3,6*, Mwanasha H. Merrill, MD9, Eric D. Jacobsen, MD10, Maria Elena Cabrera, MD11*, Pablo Villegas12*, Ioannis S Vlachos, PhD1,2,3,5* and Salvia Jain, MD2,3,6

1Department of Pathology, Beth Israel Deaconess Medical Center, Boston, MA
2Broad Institute of Harvard and MIT, Cambridge, MA
3Harvard Medical School, Boston, MA
4Department of Medicine, Beth Israel Deaconess Medical Center, Harvard Medical School, Brookline, MA
5Spatial Technologies Unit, Harvard Medical School Initiative for RNA Medicine, Beth Israel Deaconess Medical Center, Boston, MA
6Division of Hematology and Oncology, Department of Medicine, Massachusetts General Hospital Cancer Center, Boston, MA
7Department of Medicine, Massachusetts General Hospital, Boston, MA
8Department of Pathology, Massachusetts General Hospital, Boston, MA
9Department of Medical Oncology, Dana Farber Cancer Institute, Boston, MA
10Dana Farber Cancer Institute, Boston, MA
11Hematology Department, Hospital del Salvador, Santiago, Chile
12Pathology Department, Hospital del Salvador, Santiago, Chile

Background: ENKTCL is characterized by heterogeneity in genomic mutations, EBV-encoded gene expression, and host HLA-variants conferring differing susceptibility to viral genes. However, the cellular architecture of the ENKTCL tumor microenvironment (TME) and its potential association with sensitivity to chemotherapy across diverse racial and ethnic groups globally remain poorly understood.

Aim: We sought to decipher the heterogeneous landscape of ENKTCL TME in diagnostic patient samples at the cellular level and in situ to identify key cell populations, their spatial distribution within the TME, and cell-to-cell interactions that correlated with chemotherapy response.

Methods: We conducted high-resolution, in situ spatial transcriptomic profiling using the 10x Genomics Xenium platform on 12 formalin-fixed, paraffin-embedded (FFPE) ENKTCL tumor samples. We designed a custom ENKTCL-specific 480 target gene panel through systematic analyses of publicly available clinical, genomic, and transcriptomic data. Specific probes for ~20 genes related to EBV infection and viral replication were also incorporated to capture viral dynamics and effects on the TME. Importantly, the cohort incorporated patients from distinct ethnic backgrounds across the United States (n=7) and South America (n=5) to enable a more heterogeneous representation of this disease. Within the cohort, 5 cases were male and 7 female, and the median age of diagnosis was 52 (range, 25-71). The median Ann Arbor stage at diagnosis was I (range, I-IV). Of the 12 cases, 11 had nasal, and 1 case had cutaneous involvement as the primary site of disease. Overall, 6 patients had advanced stage, and 6 patients had localized disease. Based on the PINK score, patients were identified as low risk (n=3), intermediate risk (n=2), and high risk (n=7). The cohort received distinct but heterogeneous frontline treatments that included SMILE (n=4), CHOEP (n=1), DeVIC (n=3), MTX/Asp/Dex (n=1), cisplatinum with radiotherapy (n=2), and palliative radiation therapy (n=1). After frontline treatment, patients exhibited CR (n=5), PR (n=4), or PD (n=3). Following frontline therapy, 1 patient underwent allogeneic stem cell transplant. The median time for relapse was 5 m (range, 4-6). Overall, 3 patients underwent second-line treatment, with GemOx (n=1), Brentuximab Vedotin (n=1), and SMILE (n=1), achieving PR (n=2) and PD (n=1). Third and fourth-line treatments included romidepsin (n=1), palliative chemotherapy (n=1), cytotoxic T-lymphocytes on a clinical trial (n=1) and pralatrexate (n=1).

Results: In situ transcriptomics enabled an in-depth, unbiased interrogation of the cellular and transcriptional landscape of the ENKTCL TME. After quality control, we identified a total of 2,122,592 cells from all samples in the cohort, spanning 9 major lineages, including tumor-infiltrating lymphocytes such as NK, T, B, plasma, and myeloid cells, as well as fibroblasts, endothelial, epithelial, and mast cells, characterized based on canonical marker expression. Intensive lymphocyte infiltration was observed, with over 700,000 T and NK cells and approximately 650,000 myeloid cells composing the largest compartments. More than 100,000 cells were identified as EBV-infected, including macrophages, NK, NKT, and transformed B cells. Notably, EBV-infected NK, B, and mast cells were more abundant in CR patients, while changes were also observed in macrophages, with higher abundances in the PD and relapsed patient groups. Only the PR group presented significantly elevated abundances of EBV-infected NKT cells, while CD8+ T cells were less prevalent in CR patients. We uncovered numerous differences between groups at the organizational, spatial, cellular, and molecular levels, pointing to specific ENKTCL TME endophenotypes associated with outcomes.

Conclusion: This study represents the first use of spatial transcriptomics to interrogate the ENKTCL TME in situ. The extensive insights gained from cell co-localization and cell-cell communication signals will prioritize novel biomarkers that underlie responsiveness to chemotherapy. Correlative multi-omic analyses with genomic alterations and HLA specificity in a first-of-its-kind multiregional and highly multiplexed cohort are underway and will be reported at the meeting.

Disclosures: Jacobsen: Takeda: Consultancy; Novartis: Consultancy; F. Hoffman-LaRoche: Consultancy; Pharmacyclics: Consultancy; Merck: Consultancy; AstraZeneca: Consultancy; Ascerta: Consultancy. Vlachos: NIDDK: Research Funding; NHLBI: Research Funding; NCI: Research Funding; Guidepoint Global: Consultancy; Mosaic: Consultancy; Harvard Stem Cell Institute: Research Funding. Jain: Acrotech: Membership on an entity's Board of Directors or advisory committees, Research Funding; Kyowakirin: Research Funding; Crispr therapeutics: Membership on an entity's Board of Directors or advisory committees; Abcuro Inc: Consultancy, Membership on an entity's Board of Directors or advisory committees, Research Funding; Daiichi Sankyo: Membership on an entity's Board of Directors or advisory committees, Research Funding; Myeloid Therapeutics: Consultancy, Membership on an entity's Board of Directors or advisory committees; SecuraBio: Membership on an entity's Board of Directors or advisory committees, Research Funding; SIRPant Immunotherapeutics: Consultancy, Membership on an entity's Board of Directors or advisory committees, Research Funding; Mersana Therapeutics: Consultancy, Membership on an entity's Board of Directors or advisory committees.

*signifies non-member of ASH