What is aberrant splicing? Addressing the molecular foundations

Molecular biology is the scientific discipline committed to comprehend the diverse molecular structures and chemical processes that constitute the basis of cell interaction. Conceptually located right in between of genomics and biochemistry, this field has undergone game-changing transformation over the past decades, highlighting the discovery of DNA structure — Watson and Crick proposed their well-known double-helix conformation in a Nature publication back in 1953[1], setting the theoretical and experimental foundations for what was yet to come regarding further understanding of DNA nature and its molecular behaviour.

Among the countless number of processes that occur in cells at the molecular level, alternative splicing is one of a kind. First observed in 1977, it permits the obtention of different proteins — i.e., splice variants — from a single protein-coding gene[2]. That is possible because the minimal coding units of genes, known as exons, can either be skipped or included in the mature messenger RNA (mRNA) that will end up being converted to proteins in the cytoplasm. This alternance in the final structure of the mRNA, which eventually depends on both random and foreseeable factors, confers to alternative splicing its stochastic nature. Alternative splicing is a complex mechanism involving multiple steps until obtaining specific protein isoforms. It must be understood not only as a paramount biological process that contributes to protein diversity within the organism, but also as a natural source of diseases-causing errors in gene expression. For example, intronic splice site mutations of tumour suppressor genes often lead to exon-skipping events, thus truncating proteins similar to standard nonsense mutations[3]. Health problems stemming from this behaviour are often referred as aberrant alternative splicing (or simply aberrant splicing) events.

RNA Diseases — Wide spectrum of malignant outcomes

Transcription is the molecular process through which DNA is copied into messenger RNA (mRNA). Before being translated — that is, converted into proteins in the cytoplasm — there are multiple post-transcriptional processes that may take place, encompassing editing, modification, degradation, and splicing. We have addressed the latter, but it is important to understand that these defects or malfunctions can happen not only in splicing but also in any of the above-mentioned phenomena. Within this framework, human diseases caused by these events have been recently referred as “RNA diseases”[4], and we will follow this terminology.

RNA diseases compress neurological, muscular, cardiac, and cancer-related disorders. Some examples are included in the following table:

In literature, plenty of examples can be found regarding what are the exact genes whose misregulation triggers unwanted biochemical responses within cells, leading to some of the mentioned diseases. NUMB is an example of these genes and the main target for TAONas-LUAD, specifically its exon 9. Very briefly, NUMB gene encodes a protein — protein numb homolog — which is known to play a pivotal role in the determination of cell fates during development. In particular, it is key in asymmetrical cell division during neurogenesis (the process by which the nervous system creates new neurons), allowing for differential cell fate specification in the central and peripheral nervous systems[9]. Among the different exon that constitute NUMB, the one to watch for TAONas-LUAD researchers is exon 9. It has been shown how the inclusion of this exon in the mature mRNA is highly correlated with increased cell proliferation and consequent malignant outcomes in lung tissue[10], eventually leading to lung adenocarcinoma (i.e., LUAD).

And the list is not limited to NUMB: BRCA1 misregulation is associated with hereditary breast cancer, RB1 with retinoblastoma, KRAS with colorectal cancer, etc. Furthermore, cancer is only the tip of the iceberg, since many more disorders find their outset in gene misregulation.

TAONas-LUAD role — Committed to achieve clinical relevance

In TAONas-LUAD, this is our exact therapeutic focus:

“We try to disentangle the underlying molecular mechanisms behind aberrant splicing, and, with this know-how, we design tailor-made antisense oligonucleotides (AONs) aimed to revert the malignant biochemical cascades that lead to RNA diseases”

Designing AONs that effectively deliver therapeutic impact demands thorough understanding of the whole splicing process, as well as a well-thought, clinically-proven methodology encompassing optimal administration route, formulation, and dose. In TAONas-LUAD we have the privilege of working with many distinguished and experienced professionals in the field, ensuring that the correct steps are taken in this hard journey towards finding the right solution for aberrant splicing. The main focus of the project leaders as of now is placed is NUMB exon 9, but we slowly plan to broaden our scope and develop a full AON-based platform targeting aberrant splicing across numerous RNA diseases. Make sure you accompany us in this insightful adventure!

[1] Watson, J. D. & Crick, F. H. C. Molecular structure of nucleic acids: A structure for deoxyribose nucleic acid. Nature 171, 737–738 (1953).

[2] Chow, L. T., Gelinas, R. E., Broker, T. R. & Roberts, R. J. An amazing sequence arrangement at the 5′ ends of adenovirus 2 messenger RNA. Cell 12, 1–8 (1977).

[3] Venables, J. P. Aberrant and alternative splicing in cancer. Cancer Research 64, 7647–7654 (2004).

[4] Kataoka, N., Mayeda, A. & Ohno, K. Editorial: RNA Diseases in Humans—From Fundamental Research to Therapeutic Applications. Frontiers in Molecular Biosciences 6, 53 (2019).

[5] Nussbacher, J. K., Tabet, R., Yeo, G. W. & Lagier-Tourenne, C. Disruption of RNA metabolism in neurological diseases and emerging therapeutic interventions. Neuron 102, 294–320 (2019).

[6] Zavileyskiy, L. G. & Pervouchine, D. D. Post-transcriptional regulation of gene expression via unproductive splicing. Acta Naturae 16, 4–13 (2024).

[7] Shi, D.-L. RNA-Binding proteins in cardiomyopathies. Journal of Cardiovascular Development and Disease 11, 88 (2024).

[8] Carmo-Fonseca, M. & Valcárcel, J. The unfolding landscape of RNA and disease. RNA 31, 273–276 (2025).

[9] Pece, S., Confalonieri, S., Romano, P. R. & Di Fiore, P. P. NUMB-ing down cancer by more than just a NOTCH. Biochimica Et Biophysica Acta (BBA) – Reviews on Cancer 1815, 26–43 (2010).

[10] Bechara, E. G., Sebestyén, E., Bernardis, I., Eyras, E. & Valcárcel, J. RBM5, 6, and 10 differentially regulate NUMB alternative splicing to control cancer cell proliferation. Molecular Cell 52, 720–733 (2013).

Lung cancer is still one the most challenging oncological diseases, with approximately 2.2 million new cases diagnosed globally each year. This alarming figure has contributed to intensify the pharmaceutical industry investment in looking for effective treatments, resulting in groundbreaking deals that demonstrate both the commercial potential and therapeutic necessity of such drugs. These strategic transactions reflect the industry’s commitment to addressing lung cancer while aligning companies for significant market opportunities:

• Bristol Myers Squibb’s Acquisition of Mirati Therapeutics (2023) — This acquisition strengthened BMS’s position in targeted lung cancer therapies, particularly through adagrasib, a KRASG12C inhibitor targeting mutations found in approximately 13% of Non-Small Cell Lung Cancer (NSCLC) patients. The deal was revolutionary because KRAS was historically considered “undruggable,” making this breakthrough significant for treatment-resistant cases[1].
• Merck’s Acquisition of Harpoon Therapeutics (2024) — This represented one of the most strategically significant lung cancer deals of 2024. Announced in January and completed in March 2024, Merck acquired the clinical-stage immunotherapy company for $680 million ($23.00 per share in cash). The centrepiece of this acquisition was HPN328 (now MK-6070), a T-cell engager targeting delta-like ligand 3 (DLL3), an inhibitory canonical Notch ligand expressed at high levels in Small-Cell Lung Cancer (SCLC) and neuroendocrine tumours[2].
• GSK’s B7-H3 ADC Program – GSK’227 (2023) — GSK achieved a major regulatory milestone in August 2024 when the FDA granted Breakthrough Therapy Designation for GSK’227, its investigational B7-H3-targeted antibody-drug conjugate for extensive-stage SCLC. This designation was based on promising early clinical evidence from the ARTEMIS-001 Phase 1 trial conducted by Hansoh Pharma[3].
• Novartis’s Strategic Acquisitions in Lung Cancer (2024) — In 2024, Novartis strengthened its lung cancer portfolio with two key deals. It acquired Mariana Oncology for $1 billion upfront, gaining radioligand therapies like MC-339 for SCLC. This expanded Novartis’s precision radioligand platform beyond existing therapies[4]. Additionally, Novartis secured global rights to Legend’s CAR-T therapy LB2102, targeting DLL3, with a $100 million upfront payment and up to $1.01 billion in milestones. LB2102 received FDA orphan drug status and is in Phase I trials[5]^.

These transactions demonstrate how companies are diversifying therapeutic approaches, addressing lung cancer’s heterogeneity. There is particular focus on historically difficult-to-treat populations, especially SCLC, which has traditionally shown only 3% five-year survival rates. The convergence of innovative mechanisms, substantial financial investment, and global commercial expertise positions these therapies to potentially transform lung cancer treatment. These deals reflect not just commercial opportunity but genuine commitment to addressing one of oncology’s most challenging diseases.

[1] James, D. (2024, February 22). BristOL Myers Squibb completes acquisition of Mirati to bolster oncology pipeline. PharmExec. https://www.pharmexec.com/view/bristol-myers-squibb-completes-acquisition-of-mirati-to-bolster-oncology-pipeline

[2] Merck to acquire Harpoon Therapeutics, further diversifying oncology pipeline – Merck.com. (2025, July 13). Merck.com. https://www.merck.com/news/merck-to-acquire-harpoon-therapeutics-further-diversifying-oncology-pipeline/

[3] GSK receives US FDA Breakthrough Therapy Designation for its B7-H3-targeted antibody-drug conjugate in relapsed or refractory extensive-stage small-cell lung cancer  | GSK. (2024, August 20). https://www.gsk.com/en-gb/media/press-releases/gsk-receives-us-fda-breakthrough-therapy-designation/

[4] Husni, D. G. (2024, May 3). Novartis agrees to acquire Mariana Oncology for $1 billion, gains small lung cancer candidate. BioPharm International. https://www.biopharminternational.com/view/novartis-agrees-to-acquire-mariana-oncology-for-1-billion-gains-small-lung-cancer-candidate

[5] Jirehl. (2023, November 20). jirehl. https://thehealthcaretechnologyreport.com/novartis-secures-exclusive-global-rights-for-treatment-targeting-small-cell-lung-cancer/

Introduction: what are therapeutic oligonucleotides?

The fight against cancer is entering a new era, fuelled by a wave of innovation in precision and personalized medicine. Therapeutic oligonucleotides are to highlight in this regard: short, synthetic strands of nucleic acids that can modulate gene expression with unparalleled specificity. As science deepens our understanding of cancer at the molecular level, oligonucleotides are emerging as a powerful tool to target previously “undruggable” pathways. Several type of therapeutic oligonucleotides can be defined in this sense:

• Antisense oligonucleotides (AONs): Bind to mRNA to prevent translation or promote degradation.
• Small interfering RNAs (siRNAs): Harness the RNA interference pathway to silence specific genes.
• Aptamers: Structured oligonucleotides that bind proteins with high affinity, acting similarly to antibodies.
• miRNA mimics/inhibitors: Modulate endogenous microRNA pathways involved in cancer progression.

These molecules are designed to interfere directly with gene expression, allowing unprecedented precision in addressing genetic drivers of cancer. Their relevance in oncology is precisely driven by the fact that cancer often find its inception in genetic mutations, overexpression, or silencing of specific genes^[1]. By employing therapeutic oligonucleotides, we are able to:

• Targeting non-coding RNAs and intracellular targets not accessible to small molecules or antibodies.
• The ability to modulate gene expression at the RNA level, before disease-driving proteins are even produced.
• Potential for tissue-specific delivery, especially using lipid nanoparticles or ligand-based targeting.

Therapeutic oligonucleotides can be engineered to be tumour-specific, reduce systemic toxicity, and minimize off-target effects — a vital need in oncology.

How are they fitting in the market?

Therapeutical oligonucleotides are not only attractive for oncology purposes from a theoretical perspective, but are also gradually finding their place in the market through both KOLs acceptance and regulatory clearance:

• Accelerated approvals: FDA and EMA have already approved oligonucleotide-based drugs for rare genetic diseases, and oncology is now in focus.
• Big Pharma interest: Companies like AstraZeneca, Ionis Pharmaceuticals, and Alnylam are investing heavily in oligo-RNA platforms^[2].
• Clinical pipeline growth: Dozens of oligonucleotide therapeutics are in oncology clinical trials, targeting solid tumours and haematological malignancies^[3].
• AI & bioinformatics are increasingly used to design safer and more efficient oligos, with better off-target prediction and immunogenicity control^[4].
• Delivery breakthroughs: Nanoparticles, exosomes, and antibody-oligo conjugates are enabling targeted delivery to tumour tissues^[5].

Furthermore, this targeted market is extremely appealing in terms of size with $15 billion figure being achieved by 2030, with oncology as a key driver. Aligned with this, investment in RNA-based therapies hit record highs in the past three years, signalling strong confidence in the modality’s future.

Conclusion

As our understanding of cancer deepens at the molecular and transcriptomic levels, therapeutic oligonucleotides are emerging as a powerful tool to transform this knowledge into highly targeted treatments. These molecules hold significant promise for tackling cancers that have proven resistant to traditional therapies — and may well shape the future of oncology. @TAONAS LUAD is at the forefront of this trend, advancing innovation in the field.

Author: Marc Domínguez
Date: June, 2025

Fonts

[1] Bonnal SC, et al. Nat Rev Clin Oncol 17:457-474 (2020)

[2] https://oligofastx.com/innovation-on-the-horizon-how-big-pharma-investment-is-driving-the-development-of-oligonucleotide-based-medicines/

[3] Xiong, H., Veedu, R. N., & Diermeier, S. D. (2021). Recent advances in oligonucleotide therapeutics in oncology. International Journal of Molecular Sciences, 22(7), 3295.

[3] Amol D. Gholap, Abdelwahab Omri, Advances in artificial intelligence-envisioned technologies for protein and nucleic acid research, Drug Discovery Today, Volume 30, Issue 5, 2025,104362, ISSN 1359-6446, https://doi.org/10.1016/j.drudis.2025.104362.

[5] Roberts, T. C., Langer, R., & Wood, M. J. (2020). Advances in oligonucleotide drug delivery. Nature reviews Drug discovery, 19(10), 673-694.

Last month, the TAONas-LUAD consortium reunited in Barcelona for its third Annual Meeting, an important milestone as the project enters its final year. The meeting, held on May 5–6, brought together partners from all participating institutions, alongside our advisory teams, for two days of exchange, reflection, and planning.

The gathering provided a great opportunity for face-to-face discussions, with active participation from Antonio Maraver (INSERM), the Valcárcel Lab and TBDO teams from CRG, Jérémie Parot (SINTEF), and several members of the Inveniam Group team. The Asphalion team also joined to support the regulatory pathway and coordinate interactions with regulatory agencies.

As in previous years, we welcomed our Scientific Advisory Board members, Dr. Roy van der Meel and Dr. Adrian Krainer, whose valuable discussions and insights continue to guide the scientific and strategic direction of the project. Their presence, together with that of Biotech Advisor José Luis Cabero, added great value to the discussions and planning.

The first day of the meeting focused on the business development dimension of TAONas-LUAD. Discussions covered the roadmap for a potential spin-off, envisioned as the vehicle to bring our therapeutic solution closer to clinical application. Maria Buxadé, who recently joined the team, will be leading the spin-off incorporation and fundraising strategy, working hand in hand with Inveniam.

The second day shifted the focus to scientific and technical progress. It opened with the first of two working sessions with the Scientific Advisory Board, followed by a series of presentations covering the latest advances across the consortium. From preclinical development to formulation, team members shared progress and openly discussed the challenges encountered over recent months. These sessions helped set the course for the months ahead.

The meeting concluded with strategic decisions on the next steps around testing the lead candidate in PDX models, exploring combinatory approaches with existing therapies, and our current position towards regulatory studies and GMP-compliant production.

As the TAONas-LUAD project approaches its final phase, the meeting in Barcelona marked a moment of alignment and renewed focus on the work ahead.