Abstract LB350: True live single circulating tumor cell capture with no leukocytecontaminant assay for multiomics in large cancer patient population
Authors: Jayant Khandare, Atul Bharde, Ganesh Khutale, Saloni Andhari, Himanshi Bathani, Neha Mohare, Ajay Pandita, Sankar Mohan, Mohan Uttarwar, Gowhar Shafi
Journal: Cancer Research (2025)

Abstract Background: Capture and release of true live single circulating tumor cells (sCTCs) with no other blood cell contaminants including leucocytes is extremely challenging. Comprehensive genome wide profiling could be complementary with tissue and ctDNA. Omics of sCTC DNA, protein overexpression, and RNA, in several cancers, are unknown. We evaluated sCTC technology with sensitivity, specificity, positive predictive value (PPV), negative predictive value (NPV), false positivity, and stability in a Pan-Cancer large population. We show comparative comprehensive genome-wide profiles of sCTCs when assessed individually to blood ctDNA in NSCLC patients. Methods: In a breakthrough study, 1368 cancer patients of 25 cancer types were investigated retrospectively for CGPs using sCTCs OncoIndx Ikon platform. It consists of conjugated ligands, anti-epithelial cell adhesion molecule (EpCAM) antibody, and transferrin on 2 mm glass beads for selective capture, live imaging, and release of live CTCs. Sensitivity, specificity, positive prediction value (PPV), negative prediction value (NPV), and accuracy were evaluated based on the number of blood-spiked MCF-7 cells. Post-blood-draw, the stability of CTCs was assessed over 7 days. The stability of the kit was evaluated, 0-6 days, 1, 3, 6 months, and 1 year. False positive assessments were performed using blood samples from healthy individuals (n = 40; aged 18-51 years, 20 males and 20 females) and glass beads without ligands. Further, sCTC DNA was amplified, and a comprehensive 1080 gene OncoIndx panel was used to evaluate the mutational outcome with paired patient samples with CtDNA in 70 NSCLC cancer patients. Result: From the cohort of 1368 cancer patients' blood (NSCLC, breast, CRC, prostrate, HCC, etc with early and advanced stage cancers), a total of 2395 CTCs (2,008 single CTCs and 387 clusters) were isolated using the OncoIndx Ikon platform. CTCs were detected in 82.24% (1,125) of the blood samples. Analytical validation demonstrated a high cell capture efficiency (99 %) when assayed for varying numbers of spiked MCF-7 cells. Sensitivity and specificity values were 97% and 98%, respectively, while the positive prediction value (PPV) was 99%, the negative prediction value (NPV) was 93.5% and an overall accuracy of 99%. The assay showed stability for 1 year. No CTCs were detected in 48 healthy volunteer samples as well when the kit was without targeting ligands. CGP outcome showed at least 1 pathogenic or actionable mutation (100% positivity). A broader mutational profile with SNVs, Indels, NS, FS, StrV, and SpIV was compared. Interestingly, we observed early detection of resistance genes compared to the bulk sequencing in over 60 paired NSCLC patients when 25% of patients had no mutations detectable (NMDs) by CtDNA. Further, we analyzed the expression of surface protein markers on sCTC, including PDL-1, HER2, and EGFR. Overall survival was evaluated, in NSCLC patients who underwent SOC. Conclusions: Single live CTCs showed a comparative genome-wide profile when paired with CtDNA in NSCLC patients. The omics outcome of sCTC holds immense potential in targeted and antibody-drug conjugates (ADCs) therapies with equivalent or better OMICS outcome over to tissue and CtDNA. Especially when tissue is an issue and in patient recruitment in early-phase clinical trials. Citation Format: Jayant Khandare, Atul Bharde, Ganesh Khutale, Saloni Andhari, Himanshi Bathani, Neha Mohare, Ajay Pandita, Sankar Mohan, Mohan Uttarwar, Gowhar Shafi. True live single circulating tumor cell capture with no leukocytecontaminant assay for multiomics in large cancer patient population [abstract]. In: Proceedings of the American Association for Cancer Research Annual Meeting 2025; Part 2 (Late-Breaking, Clinical Trial, and Invited Abstracts); 2025 Apr 25-30; Chicago, IL. Philadelphia (PA): AACR; Cancer Res 2025;85(8_Suppl_2):Abstract nr LB350.