Targeting long non-coding RNAs for novel treatment strategies in vascular diseases

Project Information

LongTx

Grant agreement ID: 101088370

DOI

10.3030/101088370

EC signature date 4 May 2023

Start date 1 September 2023

End date 31 August 2028

Funded under

• European Research Council (ERC)

Total cost

€ 1 999 495,00

EU contribution

€ 1 999 495,00

Coordinated by

KLINIKUM DER TECHNISCHEN UNIVERSITÄT MÜNCHEN (TUM KLINIKUM)
Germany

Periodic Reporting for period 1 - LongTx (Targeting long non-coding RNAs for novel treatment strategies in vascular diseases)

Reporting period: 2023-09-01 to 2026-02-28

Summary of the context and overall objectives of the project

The rapid discovery of new RNA classes has introduced exciting therapeutic opportunities that either mimic or inhibit RNA function. Unlike traditional protein-targeting drugs—which are limited because only about 10–15% of the approximately 20,000 human proteins are involved in disease, and many of these are considered “undruggable” due to the absence of suitable binding sites—RNA-based therapies offer alternative strategies to modulate disease pathways. In recent years, RNA-based drugs, particularly those employing RNA interference and nucleic acid analogues, have demonstrated significant clinical benefits in treating previously untreatable diseases. These therapies exploit complementary base-pairing mechanisms to regulate endogenous RNA processes. However, major challenges remain, including the instability of RNA in biological fluids due to rapid degradation by RNases, difficulties in delivering negatively charged RNA molecules across hydrophobic cell membranes, and the potential for off-target effects, especially in tissues with limited uptake. To overcome these limitations, local delivery systems such as drug-eluting stents and balloons have been developed to enhance targeted RNA delivery in vascular tissues. The author’s current research proposal focuses on applying these local RNA-based therapeutic approaches in large preclinical animal models of cardiovascular diseases, such as stroke and abdominal aortic aneurysm, to improve treatment efficacy and precision.
LongTx tries to overcome the fact that no current treatments can slow aneurysm progression or reduce carotid plaque rupture risk. RNA-targeting therapies hold major promise but require accurate target identification from human tissue and appropriate in vitro and in vivo models. Effective delivery methods are also crucial. LongTx is pursuing this by focusing on long non-coding RNA targets using antisense oligonucleotide-based strategies, which may lead to new treatments for carotid artery disease, stroke, and abdominal aortic aneurysms—conditions that often co-occur and greatly impact aging populations.

Work performed from the beginning of the project to the end of the period covered by the report and main results achieved so far

In the first 24 months of LongTx, my ERC funded team and me have investigated the role long non-coding RNAs (lncRNAs) play in vascular smooth muscle cell (VSMC) plasticity in the context of vascular disease, mainly carotid artery disease and stroke, as well as abdominal aortic aneurysms. We have identified two extremely crucial lncRNAs beyond the ones mentioned as preliminary data in our proposal. We have been thoroughly investigating DLX6-AS1, a lncRNA with variants exclusive to carotid arteries, as a novel therapeutic target in carotid artery disease. DLX6-AS1 is exclusively expressed in a VSMC substate we termed ‘Modulated VSMCs’. In these Modulated SMCs a switch seems to be happening, where VSMCs turn to become either more detrimental to disease progression, switching VSMCs into a more inflammatory, foamy cell substate – or to a more matrix-producing VSMC substate (fibroblast-like) that has plaque stabilizing effects in carotid artery disease.
In human tissue specimens and experimental models of abdominal aortic aneurysm disease, we were able to identify LINC-PINT (p53-induced transcript) as a critical gatekeeper of VSMC contractility. Similar to our work on DLX6-AS1 in carotid artery disease, we were capable to establish this phenotype already in extensive in vitro investigations (aims 1&2/milestones 1&2) of my LongTx proposal. We have now entered the next aims of LongTx, in which we want to test how modulation of these two lncRNAs affects vascular disease progression using the described in vivo models. Initial results are very promising that inhibition of the two lncRNAs now in focus, DLX6-AS1 and LINC-PINT, using antisense oligonucleotides will achieve a very disease-specific rescue affect. In addition to the work described above, we have studied and tested how therapeutic modulation of lncRNA NUDT6 affects both, carotid artery disease and AAA disease.

As this is a 24-month Interim report, I am listing three major achievements of the first part of LongTx:
1) Optimization of artery-on-chip based ex vivo drug testing systems as highlighted in the publication below:
Paloschi V, Pauli J, Winski G, Wu Z, Li Z, Botti L, Meucci S, Conti P, Rogowitz F, Glukha N, Hummel N, Busch A, Chernogubova E, Jin H, Sachs N, Eckstein HH, Dueck A, Boon RA, Bausch AR, Maegdefessel L. Utilization of an Artery-on-a-Chip to Unravel Novel Regulators and Therapeutic Targets in Vascular Diseases. Adv Healthc Mater. 2024; 13(6):e2302907. doi: 10.1002/adhm.202302907.
2) Being awarded the Russel Ross Award and Lecture of the American Heart Association (AHA) at the Scientific Sessions 2023 for my work on non-coding RNAs in vascular diseases. Title of the lecture was: Targeting non-coding RNAs in vascular disease. The lecture was accompanied by the following publication: Maegdefessel L, Fasolo F. Long Non-Coding RNA Function in Smooth Muscle Cell Plasticity and Atherosclerosis. Arterioscler Thromb Vasc Biol. 2025 Feb;45(2):172-185. doi: 10.1161/ATVBAHA.124.320393.
3) Development of a delivery matrix specifically for RNA-based therapies (antisense oligonucleotides, ASOs) that we will test in the second half of LongTx in large animal models (LDLR-depleted) Yucatan mini-pigs. These matrices, using lipid nanoparticle encoding of ASOs, will be patented and form the basis of a prototype for RNA-delivery balloons and stents to treat affected patients with vascular diseases locally.

Progress beyond the state of the art and expected potential impact (including the socio-economic impact and the wider societal implications of the project so far)

We have pushed towards the advancement of atherosclerotic plaque-on-chip models, which allow us to perform ex vivo cultures of human plaques for the purpose of testing lncRNA-based treatment strategies for atherosclerotic diseases. We have initiated collaborations with Prof. Petra Mela at TUM Bioengineering on how to utilize bioreactors to keep plaque tissue intact and under physiological flow. These systems will in the near future provide a clinical-trial-in-a-dish setting to implement lncRNA-ASO drug testing. Interestingly, the FDA has recently approved human organs-on-chips and organoids as preclinical drug testing devices, partly replacing the need to perform animal studies. In addition to the work on ex vivo/plaque-on-chip models, we have initiated a collaboration with the Fraunhofer Institute for Device Development and Product Design in Berlin, enabling us to build prototypes for drug-eluting balloons and stents for local RNA deployment. Together with researchers at Fraunhofer, we believe to optimize delivery matrices for RNA-based therapies on balloons and stents. This will be tested in the last Aim (5) of our LongTx proposal (in 2026-2028).
Our work using multi-omics on human diseased vascular tissue specimens has further been recognized by other researchers building an integrated cell atlas of human atherosclerosis based on single cell sequencing, to which we contributed with our ERC funded ressearch:

Traeuble K, Munz M, Pauli J, Sachs N, Vafadarnejad E, Carrillo-Roa T, Maegdefessel L, Kastner P, Heinig M. Integrated single-cell atlas of human atherosclerotic plaques. Nat Commun. 2025 Sep 10;16(1):8255. doi: 10.1038/s41467-025-63202-x