Single-Cell Genomics-Based Molecular Algorithm for Early Cancer Detection

Abstract

As one of the prime applications of liquid biopsy, the detection of tumor-derived whole cells and molecular markers is enabled in a noninvasive means before symptoms or hints from imaging procedures used for cancer screening. However, liquid biopsy is not a diagnostic test of malignant diseases per se because it fails to establish a definitive cancer diagnosis. Although single-cell genomics provides a genome-wide genetic alternation landscape, it is technologically challenging to confirm cell malignancy of a suspicious cell in body fluids due to unknown technical noise of single-cell sequencing and genomic variation among cancer cells, especially when tumor tissues are unavailable for sequencing as the reference. To address this challenge, we report a molecular algorithm, named scCancerDx, for confirming cell malignancy based on single-cell copy number alternation profiles of suspicious cells from body fluids, leading to a definitive cancer diagnosis. The scCancerDx algorithm has been trained with normal cells and cancer cell lines and validated with single tumor cells disassociated from clinical samples. The established scCancerDx algorithm then validates hexokinase 2 (HK2) as an efficient metabolic function-associated marker of identifying disseminated tumor cells in different body fluids across many cancer types. The HK2-based test, together with scCancerDx, has been investigated for the early detection of bladder cancer (BC) at a preclinical phase by detecting high glycolytic HK2high tumor cells in urine. Early BC detection improves patient prognosis and avoids radical resection for enhancing life quality.

Detection and surveillance of circulating tumor cells in osteosarcoma for predicting therapy response and prognosis

“…Third, high HK2 expression was also found in OS cell lines but was rarely observed in leukocytes from the peripheral blood (Figure 1F and Supplementary Figure S3). Meanwhile, HK2 staining colocalized with mitochondrial staining (Figure 1G), in agreement with literature reports 11,12,15,16 .…”

“…In our previous studies, we developed a hexokinase 2 (HK2)based test for detecting rare tumor cells in multiple body fluids (e.g., pleural effusion, urine, blood, and cerebrospinal fluid) and cancers [13][14][15][16] . HK2 is associated with metabolic reprogramming, a hallmark of cancer 17,18 .…”

“…High expression of HK2 in tumor tissues is critical for the proliferation, migration, and chemoresistance of tumor cells [20][21][22] . This functional marker enables the detection of CTCs with epithelial traits and EMT, particularly cytokeratin negative CTCs, on the basis of our recent studies [13][14][15][16] . Because OS is metabolically driven by aerobic glycolysis 23,24 , HK2 may be a suitable CTC marker for OS.…”

Technology and Future of Multi-Cancer Early Detection

“…In parallel with approaches that look for cell-free DNA using NGS, capture and analysis of single-cell genomes through circulating tumor cells can greatly enhance the interpretation of potential cancer signatures [18]. The challenge of this approach is the capture of the cells for which continued development has pointed to several high-quality signatures that are agnostic to tumor type [19]. Once captured, a single cell that represents a malignant population can be analyzed across all oncogenic markers as a system to produce a definitive diagnosis and potential treatment.…”

Artificial intelligence assists precision medicine in cancer treatment

“…In addition, Wang et al. developed a molecular algorithm for early cancer detection, which is used to confirm malignant cellular tumors according to the spectrum of changes in single-cell copy numbers based on doubtful cells in humoral, resulting in a well-defined cancer diagnosis ( 115 ). Furthermore, Olivier B et al.…”