Abstract PR015: Epigenetic Dysfunction Promotes Dependence on the NF-I/A Transcription Factor in Kidney Cancer

Abstract Background: clear cell Renal Cell Carcinoma (ccRCC), the predominant form of adult kidney cancer, is typically treated using Tyrosine Kinase Inhibitors (TKIs), Immune Checkpoint inhibitors (ICIs), and (recently) HIF2α blockade. Unfortunately, these therapies ultimately fail to cure advanced ccRCC in many patients. New targets that complement these therapies are thus urgently required. The Nuclear Factor IA (NF-I/A) transcription factor (TF) represents one such HIF-independent target in ccRCC. Methods: VHL loss globally alters the tumor epigenome. Using ChIP-Seq, we measured the changes in H3K27 acetylation (H3K27ac), a histone mark associated with gene activation. We custom-generated a CRISPR/Cas9 library targeting the top 400 genes marked by increased H3K27ac and higher gene expression (measured by RNA-Seq) in VHL-deficient cells. CRISPR/Cas9 dropout screens were performed in vitro and in vivo (6 biological replicates) and top candidates were identified using the STARS algorithm. Validation studies were done in a panel of ccRCC lines using in vitro assays (e.g., Cut-&-Run, qPCR, western blots, and proliferation) and in ccRCC mouse models in vivo. Triplicate data was analyzed and compared statistically using ANOVA or Student’s t-test, corrected for multiple testing (as needed); p<0.05 considered significant. NF-I/A’s interactome and post-translational modifications (PTMs) were analyzed using label-free quantitative Mass Spectrometry. Clinical validations were performed using publicly available TCGA datasets and additionally using the ccRCC patient cohorts at MSKCC and at the Yale School of Medicine. Results: Our in vitro and in vivo CRISPR/Cas9 screens identified the Nuclear Factor IA (NF-I/A) transcription factor (TF) as an oncogenic dependency in ccRCC. NF-I/A loss led to fitness defects in vitro and diminished tumor growth in vivo, both in localized and metastatic tumors. These effects were rescued with wild-type NF-I/A but not a TF activity dead mutant. Molecular analysis in cells and validations in human tumor datasets suggest that: (1) NF-I/A regulates adipogenic programs in lipid-rich ccRCCs; (2) Higher NF-I/A expression is associated with dysregulated angiogenic signatures and lower immune infiltration in human tumors; and (3) Lower NF-I/A expression was associated with better ICI response. Binding studies and drug screening approaches have identified NF-I/A PTMs and transcriptional complexes that might be amenable to future targeting. Conclusions: We discovered NF-I/A as a novel, HIF-independent, oncogenic dependency in kidney cancer. NF-I/A has been studied in metabolic disorders, but its cancer relevance is relatively unknown. We address this conceptual gap and demonstrate that NF-I/A’s adipogenic function governs tumor metabolism and alters the production of lipid-derived chemo-attractants (e.g., leukotrienes). Thus, NF-l/A functions as both a cell-intrinsic oncogene and a host immune modulator. Altogether, these findings establish the foundations for future drug discovery efforts to target NF-I/A’s oncogenic function. Citation Format: Carleigh Salem, Jason Scovell, Shannon Zayas, Cerise Tang, Anasuya Dighe, Treg Grubb, Neil Ruthen, Suza Mohammad Nur, Belinda Willard, Sakari Vanharanta, Fengshen Kuo, A Ari Hakimi, David Braun, Ed Reznik, Abhishek A. Chakraborty. Epigenetic Dysfunction Promotes Dependence on the NF-I/A Transcription Factor in Kidney Cancer [abstract]. In: Proceedings of the AACR Special Conference in Cancer Research: Innovations in Kidney Cancer Research: From Molecular Insights to Therapeutic Breakthroughs; 2026 Mar 13-16; Philadelphia, PA. Philadelphia (PA): AACR; Cancer Res 2026;86(5_Suppl_2):Abstract nr PR015.