Few Thoughts about Noncoding RNAs in Cancer

The discovery

An unknown molecular structure with significant functional role in the biology of the cell was discovered more than 30 years ago, becoming one of the most promising discoveries in the transcriptomics regulation of gene expression (1,2). MicroRNAs (a type of non-coding RNA) were initially described as short RNA sequences that seemed not to code for any protein. Calin et al. were the first to identify a significant link between dysregulated microRNAs and cancer and to show that patients with B cell chronic lymphocytic leukaemia, which has an increased survival rate, commonly have miR-15a and miR-16a deleted and/or down-regulated at 13q14(3). Later, noncoding RNAs (ncRNAs) in cancer have become a cornerstone of molecular oncology after being shown to have a significant role in gene transformation into proteins. Initially dismissed as transcriptional noise, these molecules have emerged as pivotal regulators of gene expression, tumor progression, and therapeutic resistance. Due to their short sequence, 19-25 nucleotides for microRNA and about 200 nucleotides for lncRNAs, ncRNAs target several genes, up to hundreds of genes in multiple cancers, with an impressive regulation activity that can limit the translation into proteins of defect transcripts or limit whether activity. Initially called dark matter, or “junk”, the discovery of these structures was granted the 2024 Nobel Prize in medicine for Ambros and Ruvkun. It has attracted high interest from the scientific and industrial community over the last 30 years, with an increasing number of studies at fundamental and translational levels.

The long path from their discovery to their capacity to become future biomarkers and therapeutics for precision oncology reflects a profound shift in our understanding of the genome.

Cancer Invasion, Metastasis, and Tumor Heterogeneity

Cancer is a collection of genomic alterations that validate the capacity of the tumor cells to invade surrounding tissues and develop their immune support through different immune cell populations, and metastasis through angiogenesis or lymphatic dissemination. All these steps are hallmarks of malignancy, representing the spread of cancer cells from the primary tumour to distant organs, transforming cancer into a highly-aggressive disease if not diagnosed in the early stages (4,5). This complex process involves the degradation of extracellular matrices, epithelial-mesenchymal transition (EMT), and intravasation into blood or lymphatic vessels. Noncoding RNAs (ncRNA)play critical roles in regulating these mechanisms. RNAs play critical roles in regulating these mechanisms. For instance, miRNAs like miR-10b promote metastasis by targeting tumor suppressor genes, while lncRNAs such as HOTAIR modulate chromatin remodeling to enable invasive behavior. Tumor heterogeneity, one of the most threatening characteristics in limiting cancer treatment, arises from genetic, epigenetic, and phenotypic diversity within the tumor microenvironment. This diversity makes treatment difficult and generates resistance to several therapies. ncRNAs contribute to tumor heterogeneity by regulating cell signaling pathways and epigenetic scenes, emphasising their role in cancer progression and therapy resistance. ncRNA were shown to have an impactful role in the mechanisms of coding genes in cancer evolution, with the number of studies worldwide being over hundreds of thousands today.

The advance of ncRNAs

Noncoding RNAs are RNA molecules that regulate cellular processes without encoding proteins. Little is known about their potential capacity to encode some peptide groups, but this has to be demonstrated and shown only in some specific studies. The discovery of tRNA and rRNA in the mid-20th century highlighted their roles in protein synthesis. Still, it was only in the late 1990s and the beginning of the XXI century that small RNAs like microRNAs (miRNAs) and long noncoding RNAs (lncRNAs) were identified as regulators of gene expression (6, 7). In 1993, Victor Ambros and colleagues identified lin-4, a small RNA that regulates developmental timing in Caenorhabditis elegans (1). This discovery marked the beginning of the miRNA era. By the early 2000s, researchers had established connections between miRNA dysregulation and human cancers, heralding a new era in cancer biology (6, 8). NcRNAs complexly regulate gene expression, maintaining cellular balance. MicroRNAs, for example, bind to the 3’ untranslated regions (UTRs) of target mRNAs, leading to translational repression or degradation (9,10). Dysregulated microRNAs can alter the expression of tumor suppressors or oncogenes. The miRNA can show behaviors such as “oncomirs” or tumor-suppressor miRs, promoting or inhibiting cell proliferation and, accordingly, impacting survival in various cancers (5,6,11,12).

LncRNAs, with structures around 200 nucleotides, modulate gene expression through diverse mechanisms. Among the well-characterised lncRNAs, HOTAIR MALAT, GAS5, and H19 are known to behave differently in several cancer types and subtypes. They can be overexpressed at different levels in breast, colorectal, lung, bladder, renal, and gastric cancers and recruit different complexes to silence tumour suppressor genes, facilitating metastasis (13). Similarly, MALAT1 enhances splicing and epigenetic modifications, contributing to tumor progression (10). ncRNAs’ stability, tissue-specific expression, and presence in biofluids make them excellent biomarkers.For example, microRNA-21 (miR-21) is a non-coding RNA that is overexpressed in breast, colorectal, and pancreatic cancers, and has been proposed as a biomarker for these cancers (14, 15). Likewise, miR-155 is involved in resistance to chemotherapy, potentially involved in the reconversion of drug resistance, considering it a significant threat for patients with cancer, especially in advanced stages, where resistance increases cancer mortality. (16). Also, lncRNAs are gaining traction as biomarkers. The PCA3 test, based on the prostate cancer-associated lncRNA PCA3, offers a non-invasive diagnostic tool (17). Elevated plasma levels of lncRNA HULC correlate with hepatocellular carcinoma, showcasing its diagnostic potential (18). The structure of lncRNAs can be used to specify higher-order organisation in RNP complexes and chromatin states by serving as modular scaffolds. These modes of regulation are increasingly important as long RNAs are recognised as crucial for gene control across all cellular types (19).

The therapeutic application of ncRNAs is expanding rapidly. miRNA mimics restore tumor-suppressive miRNAs, while inhibitors (anti-miRs) target oncogenic miRNAs (20). A notable example is miR-34a, a tumor-suppressive miRNA often downregulated in cancers. MRX34, a liposome-based miR-34a mimic, was investigated in clinical trials for liver cancer, though safety concerns halted its progression (21). Similarly, anti-miR-122 therapies targeting liver-specific miR-122 have shown promise in preclinical models (22). As stated earlier, miRNAs can be involved in immune system regulation of the tumor cells contributing to tumor growth and invasion of tumor cells representing on one side a potential target for cancer treatments but also a limitation when it comes to drug resistance (23). LncRNAs are also emerging as therapeutic targets. Silencing MALAT1 using antisense oligonucleotides (ASOs) reduces metastasis in lung cancer models (24). Targeting HOTAIR with RNA interference (RNAi) strategies has succeeded in preclinical studies, highlighting the potential of lncRNA-based therapies (25).

Challenges and future directions

Despite their promise, challenges remain. Off-target effects and delivery hurdles complicate the clinical translation of ncRNA-based therapies. Advances in delivery systems, such as lipid nanoparticles and exosomes, may overcome these barriers. Emerging technologies like single-cell RNA sequencing and advanced bioinformatics promise to uncover novel ncRNAs and their specific roles in cancer. These tools could identify ncRNA signatures unique to cancer subtypes, enabling personalized therapies.

Resources

The following resources offer valuable tools and databases for studying noncoding RNAs (ncRNAs) in cancer research. They can be used to investigate ncRNA roles in gene regulation, tumor biology, and therapy development, identify novel biomarkers, and explore therapeutic targets.

Table 1. Resources to investigate ncRNAs, their structure, role and functionality.

Conclusion

The discovery of noncoding RNA (ncRNA) and understanding its structure, role, and functionality illuminated essential aspects of gene regulation and transcriptomics profiling of many cancers. Due to extended tumor heterogeneity and immune system involvement in malignancy development, we still face significant limitations in using ncRNAs as novel biomarkers. Still, they have revolutionized our understanding of gene regulation and opened a new path for future therapeutics. In the coming years, integrating ncRNAs into clinical practice will revolutionise cancer diagnostics and treatment, leading to improved outcomes and advancements in precision medicine.

References

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