Pan-Cancer DNA Methylation Analysis and Tumor Origin Identification of Carcinoma of Unknown Primary Site Based on Multi-Omics

Abstract

The metastatic cancer of unknown primary (CUP) sites remains a leading cause of cancer death with few therapeutic options. The aberrant DNA methylation (DNAm) is the most important risk factor for cancer, which has certain tissue specificity. However, how DNAm alterations in tumors differ among the regulatory network of multi-omics remains largely unexplored. Therefore, there is room for improvement in our accuracy in the prediction of tumor origin sites and a need for better understanding of the underlying mechanisms. In our study, an integrative analysis based on multi-omics data and molecular regulatory network uncovered genome-wide methylation mechanism and identified 23 epi-driver genes. Apart from the promoter region, we also found that the aberrant methylation within the gene body or intergenic region was significantly associated with gene expression. Significant enrichment analysis of the epi-driver genes indicated that these genes were highly related to cellular mechanisms of tumorigenesis, including T-cell differentiation, cell proliferation, and signal transduction. Based on the ensemble algorithm, six CpG sites located in five epi-driver genes were selected to construct a tissue-specific classifier with a better accuracy (>95%) using TCGA datasets. In the independent datasets and the metastatic cancer datasets from GEO, the accuracy of distinguishing tumor subtypes or original sites was more than 90%, showing better robustness and stability. In summary, the integration analysis of large-scale omics data revealed complex regulation of DNAm across various cancer types and identified the epi-driver genes participating in tumorigenesis. Based on the aberrant methylation status located in epi-driver genes, a classifier that provided the highest accuracy in tracing back to the primary sites of metastatic cancer was established. Our study provides a comprehensive and multi-omics view of DNAm-associated changes across cancer types and has potential for clinical application.

Analytical and clinical validation of a circulating tumor DNA-based assay for multi-cancer early detection

“…Metastatic tumors display methylation signatures different from primary early-stage tumors and may not be detected by our algorithms which learned those signatures from samples with rigor selection criteria for non-metastatic cancer (stage I-II and IIIA) in our training dataset ( 26 ). Moreover, 30% - 60% of patients with metastatic cancer have cancer of unknown primary sites which may be out of the scope of the SPOT-MAS test ( 27 ). Moreover, we performed TF analysis by ichorCNA analysis for the 7 false negative cases and none of them displayed TF above the overall LOD of our test for detecting 5 cancer types ( Table S6 and Figure S2 ).…”

“…Metastatic tumors display methylation signatures different from primary early-stage tumors and may not be detected by our algorithms which learned those signatures from samples with rigor selection criteria for non-metastatic cancer (stage I-II and IIIA) in our training dataset (26). Moreover, 30% -60% of patients with metastatic cancer have cancer of unknown primary sites which may be out of the scope of the SPOT-MAS test (27).…”

CUP-Syndrom – Diagnostik aus Sicht der Pathologie

“…Ein von Forschern entwickelter diagnostischer Assay, EPICUP, sagte in 87 % von 216 Fällen die Lokalisation des primären Tumors voraus. Diese Vorhersagen wurden durch verschiedene Tests, einschließlich Immunhistochemie, verifiziert [ 20 ]. Mit dem Einsatz von künstlicher Intelligenz (KI) und maschinellem Lernen auf DNA- und RNA-Sequenzierungsdaten wurde kürzlich gezeigt, dass in rund 71,7 % von CUP-Fällen eine akkurate Vorhersage über den Primärtumor gemacht werden konnte, woraufhin in 41,3 % der Fälle die Diagnose von Pathologen und Pathologinnen angepasst wurde [ 1 ].…”

Accurate Identification of Primary Site in Tumors of Unknown Origin (TUO) Using DNA Methylation

“…Tumor of unknown origin (TUO) is a heterogenous group of tumors characterized by the presence of metastatic disease without an identified site of primary tumor at presentation. They account for 3-6% of all metastatic cancer diagnoses and represent a significant unmet clinical burden 1,2 . Patients with TUO typically have a poor prognosis, with a median survival time of less than one year 1,3 .…”