High-throughput RNA sequencing technology for comprehensive transcriptome profiling and biomarker identification in inflammatory breast cancer

The technology utilizes TGIRT-seq, a high-throughput RNA sequencing method, to identify potential biomarkers for inflammatory breast cancer by profiling coding and non-coding RNAs in tumor and blood samples, aiding in diagnosis and disease monitoring.

Background

Inflammatory breast cancer (IBC) is recognized as the most aggressive form of breast cancer, characterized by rapid progression and a high likelihood of metastasis. Despite its severity, IBC accounts for only a small percentage of breast cancer cases, yet it is responsible for a disproportionate number of breast cancer-related deaths. The unique clinical presentation of IBC, which often lacks a distinct tumor mass, complicates early detection and diagnosis. This underscores the critical need for reliable biomarkers that can facilitate early diagnosis and monitor disease progression.

Current treatment regimens have improved survival rates, but the absence of FDA-approved targeted therapies specific to IBC highlights the necessity for advancements in molecular diagnostics to guide treatment and improve patient outcomes. Current approaches to identifying biomarkers for IBC predominantly focus on polyadenylated mRNAs or mature miRNAs, which may overlook a significant portion of the transcriptome, including long non-coding RNAs, small non-coding RNAs, and intron RNAs. These approaches often rely on retroviral reverse transcriptases, which have limitations in fidelity and processivity, potentially leading to incomplete or inaccurate transcriptome profiles. Additionally, the rarity of IBC and the challenge of obtaining high-quality tissue samples due to the dispersed nature of the tumors further complicate biomarker discovery.

Blood-based biomarkers offer a minimally invasive alternative, but the instability of RNA in blood and the complexity of the plasma RNA landscape pose significant challenges. These limitations necessitate the development of more comprehensive and accurate RNA sequencing methods to uncover novel biomarkers that can enhance the diagnosis and management of IBC.

Technology description

The described technology utilizes TGIRT-seq, a high-throughput RNA sequencing method, to identify potential biomarkers for inflammatory breast cancer (IBC). This method profiles both coding and non-coding RNAs from tumor tissues, peripheral blood mononuclear cells (PBMCs), and plasma samples.

The study highlights numerous overexpressed RNAs in IBC, including those with high intron-exon depth ratios, indicating an imbalance in transcription and RNA splicing. Notably, potential biomarkers in plasma, such as T-cell receptor pre-mRNA fragments, intron RNA fragments, and retroelement RNAs, were found to be globally up-regulated in IBC. The comprehensive transcriptome profiles provided by TGIRT-seq can aid in the diagnosis and monitoring of IBC progression.

TGIRT-seq differentiates itself by its ability to comprehensively profile both coding and non-coding RNAs, including intron and retroelement RNAs, which are often overlooked in traditional RNA sequencing methods focused on polyadenylated mRNAs. The technology's high fidelity and processivity allow for accurate detection of full-length RNA sequences, making it possible to identify novel biomarkers that reflect molecular aberrations and immune responses in IBC. This capability is particularly significant for minimally invasive blood-based assays, enabling real-time monitoring of disease progression and response to treatment.

The identification of intron RNA fragments and retroelement RNAs as potential biomarkers underscores TGIRT-seq’s unique advantage in capturing a broader spectrum of RNA biotypes, providing new insights into the molecular underpinnings of IBC.

Benefits

Comprehensive profiling of coding and non-coding RNAs in IBC tumors, PBMCs, and plasma
Identification of numerous overexpressed RNAs in IBC, including those with high intron-exon depth ratios
Potential biomarkers in plasma include T-cell receptor pre-mRNA fragments, intron RNA fragments, and retroelement RNAs
Utility of TGIRT-seq in providing comprehensive transcriptome profiles
Identification of novel biomarkers for IBC, aiding in diagnosis and monitoring of disease progression
Detection of intron RNAs as potential plasma biomarkers for IBC
Identification of TRBJ1 RNA fragments as strong candidates for IBC-specific plasma RNA biomarkers
Potential for TGIRT-seq to identify hypertranscription in aggressive cancers
Identification of LINE and other retroelements as potential plasma biomarkers for IBC
Non-invasive liquid biopsy potential for differentiating IBC from non-IBC and monitoring disease progression