{
  "abstract": "Background Findings from a pilot transcriptomic study of sentinel lymph nodes (SLN) led us to hypothesize that dendritic cells (DC) and T helper 2 (Th2) cells play an early critical role in modulating and directing the antitumor immune response. Here we report our expanded transcriptomic analysis of tumors and SLN from triple negative breast cancer (TNBC) patients. We analyzed only tumor-negative SLN to remove confounding tumor contributions and allow scrutiny of early nodal immune signatures, and their relationship to outcome.Methods In this IRB-approved study, RNA was isolated from FFPE tissue blocks of 65 node-negative patients treated at our center from 2008-2022. Bulk RNA sequencing was performed on primary TNBC and corresponding SLN in a cohort with 3.5 years median follow up, 30 recurrences, 62 years median age, 70% white/30% Black, 58% Stage II/42% Stage I. Processing, quality control, and data analysis used field-standard methodologies, including DESeq2 for gene-level and Gene Set Enrichment Analysis (GSEA) for pathway-level association with recurrence.Results When supervised by recurrence, 13 differentially expressed genes were identified in SLN (padj<0.05); 80% were members of the dark genome. The pseudogenes HNRNPA3P2, MT-CO3P12 and RN7sKP78, which regulate gene expression, exhibited higher expression in SLN from recurrent patients. Protein-encoding genes NDP (Norrin protein) and HOXA13 (homeobox) also had significantly higher expression, while PIGR (polymeric immunoglobulin receptor) had lower expression. GSEA of SLN supervised by recurrence detected 36 significantly different immune signature gene sets (out of 208 gene sets), including DC and Th signatures, with normalized enrichment scores (NES) ranging from -3.5 to +2.4 (padj<0.05) ( figure 1). Six of these gene sets that significantly associated with outcome were unique to SLN and not tumor, including the centroblastic B cell signature which positively associated with recurrence (NES +1.700). Negatively associated signatures included CD8 T cell (NES -2.154), plasmacytoid dendritic cell (NES -1.661), immune landscape/would healing (NES -1.605), activated lung neutrophil (NES -1.498), and activated blood neutrophil (NES -1.485). As shown in the enrichment map (figure 2), the 36 SLN immune signatures associated with outcome were predominately T cell and adaptive immune response pathways that included an overlap of genes also involved with NK and innate immune response pathways.Conclusions Tumor-negative SLN in TNBC express distinct genes and immune signature gene sets, including those significantly associated with outcome. Certain SLN immune gene sets that significantly associated with outcome were unique to SLN and not tumor, supporting further examination of this site of the early immune response.Ethics Approval This study obtained approval for human subjects research from the University and Medical Center IRB (UMCIRB 22-002439). Informed consent was not required for this retrospective study.Acknowledgements Authors acknowledge funding to East Carolina University from an American Cancer Society Research Scholar Grant.Abstract 1269 Figure 1GSEA of SLN finds 36 immune signature gene sets significantly associated with recurrence. Gene sets in red were only significantly associated with outcome in SLN, not tumorAbstract 1269 Figure 2Cytoscape enrichment map of SLN immune signatures significantly associated with outcome",
  "authors": [
    {
      "affiliations": [
        "East Carolina University, Greenville, NC, USA"
      ],
      "name": "Nasreen A Vohra"
    },
    {
      "affiliations": [
        "East Carolina University, Greenville, NC, USA"
      ],
      "name": "Debjani A Ghosh"
    },
    {
      "affiliations": [
        "UNC Chapel Hill, Chapel Hill, NC, USA"
      ],
      "name": "Siyao Liu"
    },
    {
      "affiliations": [
        "UNC Chapel Hill, Chapel Hill, NC, USA"
      ],
      "name": "David Corcoran"
    },
    {
      "affiliations": [
        "East Carolina University, Greenville, NC, USA"
      ],
      "name": "Kathryn M Verbanac"
    }
  ],
  "title": "1269 Transcriptomic analysis of tumor and sentinel lymph node in triple negative breast cancer and association with outcome",
  "uid": "3110e472-1acc-5a44-83b9-d4729cf57314"
}