Using cfRNA as a tool to evaluate clinical treatment outcomes in patients with metastatic lung cancers and other tumors

Abstract

Aim: We report an exploratory analysis of cfRNA as a biomarker to monitor clinical responses in non-small cell lung cancer (NSCLC), breast cancer, and colorectal cancer (CRC). An analysis of cfRNA as a method for measuring PD-L1 expression with comparison to clinical responses was also performed in the NSCLC cohort. Methods: Blood samples were collected from 127 patients with metastatic disease that were undergoing therapy, 52 with NSCLC, 50 with breast cancer, and 25 with CRC. cfRNA was purified from fractionated plasma, and following reverse transcription (RT), total cfRNA and gene expression of PD-L1were analyzed by real-time polymerase chain reaction (qPCR) using beta-actin expression as a surrogate for relative amounts of cfDNA and cfRNA. For the concordance study of liquid biopsies and tissue biopsies, the isolated RNA was analyzed by RNAseq for the expressions of 13 genes. We had to close the study early due to a lack of follow-up during the Covid-19 pandemic. Results: We collected a total of 373 blood samples. Mean cfRNA PCR signals after RT were about 50-fold higher than those of cfDNA. cfRNA was detected in all patients, while cfDNA was detected in 88% of them. A high concordance was found for the expression levels of 13 genes between blood and solid tumor tissue. Changes in cfRNA levels followed over the course of treatments were associated with response to therapy, increasing in progressive disease (PD) and falling when a partial response (PR) occurred. The expression of PD-L1 over time in patients treated with immunotherapy decreased with PR but increased with PD. Pre-treatment levels of PD-L1 were predictive of response in patients treated with immunotherapy. Conclusion: Changes in cfRNA correlate with clinical response to the therapy. Total cfRNA may be useful in predicting clinical outcomes. PD-L1 gene expression may provide a biomarker to predict response to PD-L1 inhibition.

Cell-free circulating tumor RNAs in plasma as the potential prognostic biomarkers in colorectal cancer

“…ctDNA profiling is now being routinely applied clinically for both companion diagnosis and screening for minimal residual disease (MRD) among cancer patients. However, the detection of ctDNA for MRD is challenging as only a minute amount of ctDNA are present in blood at earlier cancer stages, especially in post-surgical setting ( 7 , 10 , 50 ). The cfDNA concentration may fall below the detection limit of the NGS-based ctDNA test, resulting in a very low or even zero mutation allele frequency (MAF) for the mutations ( 51 ).…”

“…The cfDNA concentration may fall below the detection limit of the NGS-based ctDNA test, resulting in a very low or even zero mutation allele frequency (MAF) for the mutations ( 51 ). More importantly, it is difficult to determine the tumor tissue of origin (TOO) in cancer patients and differentiate informative cfDNA mutations from benign variants such as clonal hematopoiesis ( 7 ). Therefore through the amplification of tumor-derived RNA signal, we have shown that the detection of the expressed cfRNA in blood is technically feasible and may help circumvent the existing limitation in ctDNA detection, which will increase cancer detection sensitivity ( 7 , 10 ).…”

“…More importantly, it is difficult to determine the tumor tissue of origin (TOO) in cancer patients and differentiate informative cfDNA mutations from benign variants such as clonal hematopoiesis ( 7 ). Therefore through the amplification of tumor-derived RNA signal, we have shown that the detection of the expressed cfRNA in blood is technically feasible and may help circumvent the existing limitation in ctDNA detection, which will increase cancer detection sensitivity ( 7 , 10 ). To our knowledge, this is the first study that compared the plasma transcriptomes derived both pre-operatively and post-operatively.…”

“…Genomic alterations associated with oncogenic drivers have traditionally been detected with invasive tissue biopsy, which is highly dependent on the amount of tumor tissue recovered in the biopsy and the initial analysis of the tissue for diagnosis ( 7 ). Liquid biopsy, through the use of circulating tumor molecules isolated from blood, has shown to be a promising minimally-invasive approach to detect, monitor, and evaluate the genetic profile of cancer patients ( 8 ).…”

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

“…In the 1990s, the Human Genome Project demonstrated that cf DNA has tumor-specific mutations. Most of the cancer research was focused on cf DNA as compared to cf RNA because of its stability and detectability; however, numerous studies have speculated that cf RNA may have more potential compared to cf DNA [ 6 , 7 , 8 ].…”