Plasma cell-free RNA profiling distinguishes cancers from pre-malignant conditions in solid and hematologic malignancies

Abstract

Cell-free RNA (cfRNA) in plasma reflects phenotypic alterations of both localized sites of cancer and the systemic host response. Here we report that cfRNA sequencing enables the discovery of messenger RNA (mRNA) biomarkers in plasma with the tissue of origin-specific to cancer types and precancerous conditions in both solid and hematologic malignancies. To explore the diagnostic potential of total cfRNA from blood, we sequenced plasma samples of eight hepatocellular carcinoma (HCC) and ten multiple myeloma (MM) patients, 12 patients of their respective precancerous conditions, and 20 non-cancer (NC) donors. We identified distinct gene sets and built classification models using Random Forest and linear discriminant analysis algorithms that could distinguish cancer patients from premalignant conditions and NC individuals with high accuracy. Plasma cfRNA biomarkers of HCC are liver-specific genes and biomarkers of MM are highly expressed in the bone marrow compared to other tissues and are related to cell cycle processes. The cfRNA level of these biomarkers displayed a gradual transition from noncancerous states through precancerous conditions and cancer. Sequencing data were cross-validated by quantitative reverse transcription PCR and cfRNA biomarkers were validated in an independent sample set (20 HCC, 9 MM, and 10 NC) with AUC greater than 0.86. cfRNA results observed in precancerous conditions require further validation. This work demonstrates a proof of principle for using mRNA transcripts in plasma with a small panel of genes to distinguish between cancers, noncancerous states, and precancerous conditions.

Liquid biopsy by analysis of circulating myeloma cells and cell-free nucleic acids: a novel noninvasive approach of disease evaluation in multiple myeloma

“…reported that the CMMC level at baseline was a good predictor of disease progression of MM, corresponding to M protein, BMPCs, and the serum free light chain (sFLC) ratio [39]. By analyzing the cell-free messenger RNA (cf-mRNA) using RNA sequencing (RNA-seq), a selected cf-mRNA panel recapitulated the transition from MGUS to MM and distinguished normal controls and patients with MGUS from those with MM [81].…”

Diagnostic and Therapeutic Potential of Circulating-Free DNA and Cell-Free RNA in Cancer Management

“…Various studies have advocated for the presence of mutations and different genetic information in the cf RNA of cancer patients when compared to healthy patients. Hieter et al performed plasma cf RNA-sequencing to use cf RNA as a biomarker for hepatocellular carcinoma and multiple myeloma, showing that cf RNA has different expressions throughout the cancer progression stages; therefore, it is possible to identify the precancerous and cancerous conditions of patients through the cf RNA-based analysis [ 66 ]. The diagnosis of cancer through cf RNA can also be conducted by using a urine analysis; Kim et al reported that the urine of bladder cancer patients has higher levels of cf RNA compared to healthy persons.…”

“…In addition, it can distinguish among cancer stages and types. In a recent study, Hieter et al distinguished the cancers from their premalignant conditions using cf RNA profiles and predicted the occurrence of cancer [ 66 ]. Raez et al analyzed and measured cf RNA expression to monitor the clinical responses of patients with non-small cell lung cancer and reported that cf RNA can be used as a predictive tool for cancer onset and progression.…”

Current Insights into miRNA and lncRNA Dysregulation in Diabetes: Signal Transduction, Clinical Trials and Biomarker Discovery

“…We have previously elucidated the ncRNA interactome in cancer chemoprevention [ 7 , 14 , 15 ], mesothelioma [ 8 ], prostate cancer [ 16 ] and neuropathic pain [ 17 ], and also delineated miRNA-lncRNA interactions [ 18 ]. Cell-free RNAs, also called extracellular RNAs [ 19 ], are released into the circulatory system as a result of cell necrosis or apoptosis [ 20 , 21 ]. Cell-free ncRNAs have been observed to be dysregulated in peripheral blood samples of T2D patients.…”