RNA Fusion: Advances and Impact on Health

RNA fusion events play a critical role in both normal cellular function and disease. These hybrid RNA molecules arise from genetic rearrangements or transcriptional errors, sometimes leading to abnormal protein production. Their significance extends beyond basic biology, serving as key biomarkers and therapeutic targets, particularly in cancer.

Advancements in sequencing technologies have improved detection and analysis, enhancing diagnostic precision and therapeutic development. Understanding their origins, regulatory impact, and clinical relevance is essential for targeted treatment strategies.

How Fusion Transcripts Arise

Fusion transcripts result from structural genomic alterations or RNA processing errors, forming hybrid RNA molecules. These events often stem from chromosomal rearrangements such as translocations, inversions, and deletions, which bring together previously separate gene segments. The well-documented BCR-ABL1 fusion in chronic myeloid leukemia, for example, results from a translocation between chromosomes 9 and 22, generating an aberrant tyrosine kinase that drives uncontrolled cell proliferation.

Beyond large-scale genomic changes, transcriptional read-through events can also produce fusion transcripts when RNA polymerase bypasses normal termination signals, generating chimeric transcripts spanning adjacent genes. Errors in RNA splicing further contribute, with alternative splicing sometimes leading to exon shuffling between different genes, creating novel fusion products. This phenomenon is particularly relevant in cancer, where splicing dysregulation can generate oncogenic fusion proteins. A Nature Communications (2021) study identified recurrent fusion transcripts in glioblastoma arising from aberrant exon-exon junctions, highlighting the role of splicing defects in tumor biology.

Repetitive DNA elements also facilitate fusion transcript formation. Alu elements, a type of short interspersed nuclear element (SINE), mediate genomic rearrangements through non-allelic homologous recombination. Misalignment during DNA replication or repair can induce deletions or duplications that link previously unconnected gene segments. Research in Genome Research (2022) found that Alu-mediated recombination events contribute to fusion transcripts in prostate cancer, emphasizing their role in transcriptome diversity.

Mechanisms That Drive Dysregulation

RNA fusion dysregulation arises from multiple molecular processes that disrupt normal gene expression and transcript stability. Chromosomal instability, a hallmark of many cancers, increases the likelihood of structural rearrangements that generate fusion transcripts. Tumors with high genomic instability, such as ovarian and lung cancers, frequently exhibit interchromosomal translocations. A Nature Genetics (2023) study found that chromothripsis—chromosomal shattering and reassembly—creates complex fusion transcripts in glioblastoma and sarcomas, disrupting regulatory elements and leading to unchecked oncogenic expression.

Epigenetic modifications also influence RNA fusion dysregulation by altering chromatin accessibility and transcriptional activity. DNA methylation and histone modifications can activate or suppress genomic regions, affecting fusion transcript formation. Research published in Cell Reports (2022) showed that hypomethylation at translocation breakpoints in acute lymphoblastic leukemia facilitates fusion gene expression by reducing repression of normally silenced regions. Histone modifications such as H3K27 acetylation have been linked to increased transcriptional read-through events, further promoting fusion formation.

RNA processing defects, particularly splicing factor mutations, play a significant role in fusion transcript dysregulation. Mutations in genes such as SF3B1, U2AF1, and SRSF2, frequently observed in myelodysplastic syndromes and chronic lymphocytic leukemia, disrupt splice site recognition and exon inclusion. A Cancer Discovery (2021) study found that SF3B1 mutations activate cryptic splice sites, generating aberrant exon-exon junctions with oncogenic potential. These mutations not only create novel fusions but also enhance transcript stability, prolonging their impact on cellular function and driving tumorigenesis.

Common Fusion Events In Disease

RNA fusion events are implicated in multiple diseases, most notably cancer. Some fusion transcripts act as oncogenic drivers, altering signaling pathways and promoting uncontrolled proliferation. One well-characterized example is the EWSR1-FLI1 fusion in Ewing sarcoma, a rare but aggressive bone and soft tissue cancer. This fusion results from a translocation between chromosomes 11 and 22, producing an aberrant transcription factor that disrupts gene expression, enhancing cell cycle progression while repressing differentiation pathways. Its persistence correlates with poor prognosis, making it a valuable therapeutic target.

Hematologic malignancies frequently harbor fusion transcripts that drive leukemogenesis. The PML-RARA fusion in acute promyelocytic leukemia (APL), arising from a translocation between chromosomes 15 and 17, disrupts retinoic acid signaling, blocking myeloid differentiation and leading to an accumulation of immature leukemic blasts. Targeted therapy with all-trans retinoic acid (ATRA) has transformed APL from a highly fatal disease to one with cure rates exceeding 80%, underscoring the importance of identifying and targeting fusion-driven mechanisms. Similarly, the NUP98 fusion family, seen in various acute leukemias, disrupts nuclear pore complex function and transcriptional regulation, contributing to aggressive disease progression.

Solid tumors also exhibit recurrent fusion events with clinical significance. The TMPRSS2-ERG fusion, present in approximately 50% of prostate cancers, results from an interstitial deletion that links the androgen-regulated TMPRSS2 promoter with the ERG oncogene, driving overexpression of ERG and enhancing invasive potential. This fusion helps define molecular subtypes of prostate cancer, influencing treatment decisions. Similarly, the KIF5B-RET fusion in non-small cell lung cancer (NSCLC) leads to constitutive activation of the RET kinase, promoting tumor growth. Patients harboring this fusion have shown significant responses to RET inhibitors such as selpercatinib, highlighting the therapeutic relevance of fusion transcript identification in precision oncology.

Targeted RNA Sequencing Approaches

Detecting fusion transcripts with high sensitivity and specificity requires advanced sequencing techniques tailored to capture these hybrid RNA molecules. Targeted RNA sequencing enhances detection by focusing on specific gene regions, improving both cost efficiency and data interpretability.

Amplicon-Based

Amplicon-based RNA sequencing uses reverse transcription followed by PCR amplification of target regions, making it highly sensitive for detecting known fusion transcripts. This approach relies on gene-specific primers to selectively amplify fusion junctions, allowing deep sequencing coverage and detection of low-abundance transcripts. Commercial assays like the Archer FusionPlex system use anchored multiplex PCR (AMP) to detect fusions without prior knowledge of breakpoints, increasing the likelihood of identifying novel events. However, this method has limitations, including potential amplification bias and reduced ability to detect fusions involving unknown partners.

Hybrid Capture

Hybrid capture-based sequencing employs biotinylated probes to enrich fusion transcripts before sequencing, providing broader coverage than amplicon-based methods. By capturing entire gene regions rather than specific junctions, hybrid capture enables detection of both known and novel fusions, as well as alternative splicing events. This approach is particularly useful for degraded RNA samples, such as those from formalin-fixed, paraffin-embedded (FFPE) tissues. However, it requires greater sequencing depth and longer processing times. While it reduces amplification bias, extremely low-abundance fusion transcripts may still be challenging to detect.

Multiplex Panels

Multiplex RNA sequencing panels integrate multiple target genes into a single assay, enabling simultaneous detection of a broad range of fusion events. These panels are valuable for precision oncology, covering clinically relevant fusion genes across various cancers. Platforms such as the Illumina TruSight RNA Fusion Panel and Thermo Fisher’s Oncomine Comprehensive Assay use a combination of amplicon and hybrid capture strategies to maximize sensitivity and specificity. Multiplex panels streamline fusion detection in clinical settings, reducing the need for multiple separate tests. However, they may have limited flexibility for detecting rare or novel fusions outside the predefined gene set and can be costly for routine diagnostics.

Interpreting Results In Clinical Context

The detection of fusion transcripts provides critical insights into disease pathology, but accurate interpretation is complex. The clinical significance of a fusion event depends on factors such as its oncogenic potential, expression levels, and association with specific disease subtypes. Some fusions, like BCR-ABL1 in chronic myeloid leukemia, are well-established drivers with direct therapeutic implications, while others may be incidental findings with no clear pathological role. Distinguishing between pathogenic and passenger fusions requires integrating sequencing results with clinical presentation, histopathology, and additional molecular markers. Bioinformatics tools such as FusionCatcher and STAR-Fusion help filter artifacts and prioritize clinically relevant fusions, but expert review remains necessary, particularly for rare or novel events.

Transcript abundance and structural complexity also inform treatment decisions. High expression levels of oncogenic fusions often correlate with aggressive disease, influencing prognosis and therapeutic selection. Some fusion transcripts may lack functional protein-coding capacity, rendering them biologically irrelevant despite their presence in sequencing data. Functional validation through proteomic analysis or in vitro assays provides additional evidence for clinical actionability. As sequencing technologies advance, integrating RNA fusion data with whole-genome and epigenomic profiling will further refine diagnostics and expand therapeutic opportunities.