De novo sequencing of circulating miRNAs identifies novel markers predicting clinical outcome of locally advanced breast cancer

Abstract

BackgroundMicroRNAs (miRNAs) have been recently detected in the circulation of cancer patients, where they are associated with clinical parameters. Discovery profiling of circulating small RNAs has not been reported in breast cancer (BC), and was carried out in this study to identify blood-based small RNA markers of BC clinical outcome.MethodsThe pre-treatment sera of 42 stage II-III locally advanced and inflammatory BC patients who received neoadjuvant chemotherapy (NCT) followed by surgical tumor resection were analyzed for marker identification by deep sequencing all circulating small RNAs. An independent validation cohort of 26 stage II-III BC patients was used to assess the power of identified miRNA markers.ResultsMore than 800 miRNA species were detected in the circulation, and observed patterns showed association with histopathological profiles of BC. Groups of circulating miRNAs differentially associated with ER/PR/HER2 status and inflammatory BC were identified. The relative levels of selected miRNAs measured by PCR showed consistency with their abundance determined by deep sequencing. Two circulating miRNAs, miR-375 and miR-122, exhibited strong correlations with clinical outcomes, including NCT response and relapse with metastatic disease. In the validation cohort, higher levels of circulating miR-122 specifically predicted metastatic recurrence in stage II-III BC patients.ConclusionsOur study indicates that certain miRNAs can serve as potential blood-based biomarkers for NCT response, and that miR-122 prevalence in the circulation predicts BC metastasis in early-stage patients. These results may allow optimized chemotherapy treatments and preventive anti-metastasis interventions in future clinical applications.

Epigenetic Mechanisms in Stroke and Epilepsy

“…As an example, recent studies have identified specific microRNAs that are upregulated in the blood within hours after a heart attack and are currently investigating the use of these microRNAs as potential biomarkers for myocardial infarction (Salic and De Windt, 2012). microRNAs are widely used in several types of cancer, with one study identifying microRNAs that correlate with the clinical outcome of breast cancer patients (Wu et al, 2012). Currently, microRNAs are undergoing evaluation for possible clinical use as biomarkers for neurological diseases (de Planell-Saguer and Rodicio, 2011).…”

Cross-kingdom inhibition of breast cancer growth by plant miR159

“…We have previously profiled small RNAs in the sera of 42 stage II-III BC patients by Solexa deep sequencing [7]. By systemically aligning the detected sequences to the miRNAome of Arabidopsis thaliana and soybean (Glycine max), multiple plant miRNAs were identified but only with sparse counts (Supplementary information, Table S1), possibly due to the 2'-O-methylation on the 3'-terminal ribose in plant-derived miRNAs that causes reduced ligation efficiency of adaptor oligonucleotides [37].…”

“…Supplementary information, Table S1 indicating the plant miRNA alignment result is derived from our previously published serum smRNA-seq data set that includes 42 female stage II-III BC patients participating in neoadjuvant chemotherapy clinical trials at City of Hope [7]. All serum samples were collected at diagnosis before any treatment.…”

“…They play an important role in human diseases, and notably dysregulation of miRNAs has been found in many cancers including breast cancer (BC) [3,4]. In addition to their intracellular presence, miRNAs are also detected in nearly all biofluids, including serum and plasma, and circulating miRNAs have emerged as potential biomarkers for cancer diagnosis and prognosis [5][6][7][8]. miRNAs can be secreted through extracellular vesicles (EVs), such as exosomes, shedding vesicles, and apoptotic bodies, or in complexes with protein or lipid-based carriers [9,10].…”

NDAMDA: Network distance analysis for MiRNA‐disease association prediction

“…With the rapid development of high‐throughput sequencing technologies, researchers have identified plenty of miRNAs associated with breast cancer. For example, higher levels of circulating miR‐122 specifically predicted metastatic recurrence in patients with stage II‐III breast cancer 37. Besides, miR‐155 was up‐regulated greater than twofold in breast cancer compared with normal adjacent tissue (NAT),38 while a decreased level of serum miR‐155 was found after surgery and 4 cycles of chemotherapy 39.…”