Abstract 6805: DKC1 promotes colorectal cancer progression and therapy resistance by dysregulating sphingolipid biosynthesis
Authors: Umar Khalid Khan, Ayush Goel, Shivansh Nigam, Nazia Chaudhary, Anjali Bajpai, Ayush Praveen, Akshay Shendre, Shannon Carskadon, Abhimanyu Kapoor, Anjali Tewari, Abhijit Chandra, Sorab N. Dalal, Nallasivam Palanisamy, Bushra Ateeq
Journal: Cancer Research (2025)

Abstract Colorectal cancer (CRC) is the second most frequent lethal malignancy globally. It has been associated with limited treatment effectiveness in most cases, leading to modest clinical outcomes with first-line therapies. Despite the recent advancements in the treatment modalities, most patients fail to respond by switching to alternative bypass mechanisms and acquiring drug resistance. This emphasizes an urgent need to discover the underlying mechanistic circuitry in CRC pathogenesis and explore alternative robust drug targets to overcome the lack of treatment response thereby improving the patient's survival. In addition, molecular heterogeneity associated with tumor profiles also influences treatment outcomes, prompting a fundamental need for molecular characterization of colorectal tumors to design targeted therapies. Here, we used a bottom-up approach to delineate the clinical significance of Dyskerin pseudouridine synthase 1 (DKC1) in CRC patients. We observed elevated DKC1 levels in tumor specimens compared to adjacent normal tissue, associated with aggressive disease and poor recurrence-free survival. Moreover, patients acquiring resistance against standard treatment regimen (FOLFOX/FOFIRI) showed increased expression of DKC1. Importantly, loss-of-function studies suggest high DKC1 imparts oncogenicity by promoting cell cycle progression, suppressing cell death, and conferring stem cell-like phenotype. Notably, gene signature profile from DKC1-high patient tumors exhibit similarity to Consensus Molecular Subtype 2 (CMS2) of CRC. We deciphered a positive feedback loop operating between canonical WNT signaling and DKC1, responsible for orchestrating DKC1 expression and its associated tumorigenicity. Comprehensive lipidomic and transcriptomic analyses reveal perturbed sphingolipid metabolism and an abundance of very-long-chain fatty acid ceramides, particularly Cer(d18:2/23:0) and Cer(d18:1/24:0) in DKC1-positive CRC. Mechanistically, Co-IP and ChIP-PCR results confirmed that DKC1 and SOX2 together drive the expression of SGPP2, modulating sphingolipid biosynthesis and targeting SGPP2 in DKC1-positive CRC alleviates oncogenic properties. Taken together, we demonstrate that elevated DKC1 expression imparts chemoresistance, and pharmacological inhibition of DKC1 and WNT signaling effectively attenuates the growth of therapy-resistant patient-derived organoids as well as CRC cells in a synergistic manner. Conclusively, we propose the DKC1/WNT axis as a promising therapeutic target for chemotherapy non-responding CRC patients. The study also highlights the utility of complex sphingolipids as a plasma-based biomarker providing a new paradigm for the non-invasive diagnosis of advanced-stage CRC patients. Citation Format: Umar Khalid Khan, Ayush Goel, Shivansh Nigam, Nazia Chaudhary, Anjali Bajpai, Ayush Praveen, Akshay Shendre, Shannon Carskadon, Abhimanyu Kapoor, Anjali Tewari, Abhijit Chandra, Sorab N. Dalal, Nallasivam Palanisamy, Bushra Ateeq. DKC1 promotes colorectal cancer progression and therapy resistance by dysregulating sphingolipid biosynthesis [abstract]. In: Proceedings of the American Association for Cancer Research Annual Meeting 2025; Part 1 (Regular Abstracts); 2025 Apr 25-30; Chicago, IL. Philadelphia (PA): AACR; Cancer Res 2025;85(8_Suppl_1):Abstract nr 6805.