{
  "abstract": "Background Renal clear cell carcinoma (ccRCC) is a deadly cancer treated with immune checkpoint blockade (ICB). 1 Despite large ccRCC trials, no predictive biomarkers for ICB success have been identified.1 Although 14q- is present in up to 40% of ccRCC cases, its immunologic and molecular impact has not been investigated.2 Given that TRAF3 and NFKBIA, key regulators of nf-kb signaling, are located on chromosome 14q, we hypothesize that 14q- in ccRCC is associated with increased inflammation and improved ICB response via aberrant NF-κB signaling.Methods We collected data from 2,490 ccRCC patients from publicly available sources , our own independent retrospective study, and the Oncology Research Exchange Network. These data include bulk and single cell RNAseq (scRNAseq), 3–7whole exome sequencing (WES), and reverse phase protein array. We also performed multiplex immunofluorescence (mIF) for spatial analysis of T cells on 20 patient slides with paired WES and ICB response. Finally, we utilized AI methodology to predict immunotherapy response based on 14q- and T regulatory cell (Treg) interactions. All data were analyzed with R8–15 and nf-core pipelines.16 All results were statistically significant with false-discovery-rate-adjusted p-values of <0.05.Results In our data,14q- co-occurs with 3p deletion (3p-/14q-). Our analysis shows that 3p-/14q- status is associated with increased NF-κB-target transcription and NF-κB protein p65 phosphorylation. Expression of lymphotactic protein and NF- κB target CCL20 was increased in scRNAseq of tumor cells (figure 1A).17 18 Simultaneously, 3p-/14q- immune microenvironments in single cell and bulk RNAseq reveals increased effector CD8+ T cell infiltration compared with controls (3p-/14qWT, 3pWT/14qWT) (figure 1B-C). mIF images from 3p-/14q- tumors show Tregs significantly aggregate with tumor cells in ICB responders compared to non-responders (figure 2A). Cell-cell communication analysis on Tregs and tumor cells from 3p-/14q- scRNA sequencing of two patients (an ICB responder and non-responder) revealed FLT3LG (expressed by tumor cells) is uniquely interacting with FLT3 on responder Tregs. We found 14q- and increased FLT3 expression resulted in significantly improved progression-free survival in the CheckMate19 ICB trials in ccRCC (figure 2B).Conclusions These results are the first to show 14q- is associated with an anti-tumor inflammatory phenotype in ccRCC and suggest aberrant NF-κB activation in 3p-/14q- tumors is the underlying mechanism of inflammation. Further, our study is the first to propose 14q- coupled with FTL3 can positively predict ICB response in ccRCC.References Matthew Kyle L, Jason Z, Rajan G, Shannon M, Jennifer J, Eric FK, et al. Characterization of tumor mutation burden, PD-L1 and DNA repair genes to assess relationship to immune checkpoint inhibitors response in metastatic renal cell carcinoma. Journal for immunotherapy of cancer. 2020;8(1):e000319.Yoshimoto T, Matsuura K, Karnan S, Tagawa H, Nakada C, Tanigawa M, et al. High-resolution analysis of DNA copy number alterations and gene expression in renal clear cell carcinoma. The Journal of Pathology. 2007;213(4):392–401.Su C, Lv Y, Lu W, Yu Z, Ye Y, Guo B, et al. Single-cell RNA sequencing in multiple pathologic types of renal cell carcinoma revealed novel potential tumor-specific markers. (2234-943X (Print)).Yu ZA-O, Lv YA-O, Su CA-O, Lu WA-O, Zhang RA-OX, Li JA-O, et al. Integrative single-cell analysis reveals transcriptional and epigenetic regulatory features of clear cell renal cell carcinoma. (1538–7445 (Electronic)).Bi K, He MX, Bakouny Z, Kanodia A, Napolitano S, Wu J, et al. Tumor and immune reprogramming during immunotherapy in advanced renal cell carcinoma. (1878–3686 (Electronic)).Krishna C, DiNatale RG, Kuo F, Srivastava RM, Vuong L, Chowell D, et al. Single-cell sequencing links multiregional immune landscapes and tissue-resident T cells in ccRCC to tumor topology and therapy efficacy. (1878–3686 (Electronic)).Li R, Ferdinand JR, Loudon KW, Bowyer GS, Laidlaw S, Muyas F, et al. Mapping single-cell transcriptomes in the intra-tumoral and associated territories of kidney cancer. (1878–3686 (Electronic)).Friedman J, Hastie T, Tibshirani R, Narasimhan B, Tay K, Simon N, et al. glmnet: lasso and elastic-net regularized generalized linear models. cran2023.Chen T, Guestrin C, editors. Xgboost: A scalable tree boosting system. Proceedings of the 22nd acm sigkdd international conference on knowledge discovery and data mining; 2016.Therneau TM, Lumley T, Elizabeth A, Cynthia C. survival: Survival Analysis. cran2023.Hao Y, Hao S, Andersen-Nissen E, Mauck WM, 3rd, Zheng S, Butler A, et al. Integrated analysis of multimodal single-cell data. Cell. 2021;184(13):3573–87.e29.Stuart T, Butler A, Hoffman P, Hafemeister C, Papalexi E, Mauck WM, 3rd, et al. Comprehensive integration of single-cell data. Cell. 2019;177(7):1888–902.e21.Butler A, Hoffman P, Smibert P, Papalexi E, Satija R. Integrating single-cell transcriptomic data across different conditions, technologies, and species. Nature Biotechnology. 2018;36(5):411–20.Satija R, Farrell JA, Gennert D, Schier AF, Regev A. Spatial reconstruction of single-cell gene expression data. Nature Biotechnology. 2015;33(5):495–502.Wilk AJ, Shalek AK, Holmes S, Blish CA. Comparative analysis of cell-cell communication at single-cell resolution. Nature Biotechnology. 2024;42(3):470–83.Schapiro D, Sokolov A, Yapp C, Chen Y-A, Muhlich JL, Hess J, et al. MCMICRO: a scalable, modular image-processing pipeline for multiplexed tissue imaging. Nature Methods. 2022;19(3):311–5.Guo Q, Jin Y, Chen X, Ye X, Shen X, Lin M, et al. NF-κB in biology and targeted therapy: new insights and translational implications. Signal Transduction and Targeted Therapy. 2024;9(1):53.Miao H, Zhang Y Fau - Lu Z, Lu Z Fau - Yu L, Yu L Fau - Gan L, Gan L. FOXO1 increases CCL20 to promote NF-κB-dependent lymphocyte chemotaxis. (1944-9917 (Electronic)).Braun DA-O, Hou Y, Bakouny ZA-O, Ficial MA-O, Sant’ Angelo M, Forman J, et al. Interplay of somatic alterations and immune infiltration modulates response to PD-1 blockade in advanced clear cell renal cell carcinoma. (1546-170X (Electronic)).Abstract 1229 Figure 1NF-κB signaling is associated with increased CCL20 (A) and increased anti-tumor lymphocytes (specifically effector CD8+ T cells) (B, C) in 3p-/14q- tumorsAbstract 1229 Figure 2mIF of 3p-/14q- responders (R) and non-responders (NR) revealed Treg/tumor cell aggregates (A). The primary interaction between these cells was FLT3LG and FLT3. High FLT3 and 14q- status confers improved progression-free survival when treated with ICB",
  "authors": [
    {
      "affiliations": [
        "The Ohio State University, Columbus, OH, USA"
      ],
      "name": "Raven Vella"
    },
    {
      "affiliations": [
        "Georgetown University, Washington, DC, USA"
      ],
      "name": "Emily L Hoskins"
    },
    {
      "affiliations": [
        "The Ohio State University, Columbus, OH, USA"
      ],
      "name": "Michele R Wing"
    },
    {
      "affiliations": [
        "The Ohio State University, Columbus, OH, USA"
      ],
      "name": "Julie R Reeser"
    },
    {
      "affiliations": [
        "The Ohio State University, Columbus, OH, USA"
      ],
      "name": "Eric Samorodnitsky"
    },
    {
      "affiliations": [
        "The Ohio State University, Columbus, OH, USA"
      ],
      "name": "Sayan M Chowdhury"
    },
    {
      "affiliations": [
        "The Ohio State University, Columbus, OH, USA"
      ],
      "name": "Yuanquan Yang"
    },
    {
      "affiliations": [
        "The Ohio State University, Columbus, OH, USA"
      ],
      "name": "Sameek Roychowdhury"
    }
  ],
  "title": "1229 14q deletion in renal clear cell carcinoma is associated with increased anti-tumor immunity and improved response to PD-1 checkpoint blockade potentially driven by NF-κB signaling",
  "uid": "72e34c9c-ac65-5141-b651-47a0e6bb5ea7"
}