RNA technologies

Developing RNA-based compounds to the stage of clinical use

RNA for targeted therapies

Um die molekularen Signalwege in gesunden und kranken Herzen besser zu verstehen, analysieren Forschende nicht-codierende Mikro-RNAs mithilfe der Real-time-PCR. Mikro-RNAs, die im Zusammenhang mit der Krankheit stehen, wie  etwa die Mikro-RNA-132, können somit identifiziert werden.
© Fraunhofer ITEM, Ralf Mohr
In order to better understand the molecular signaling pathways in healthy and diseased hearts, researchers analyze non-coding microRNA molecules by real-time PCR.
© Fraunhofer ITEM, Ralf Mohr
Process development and GMP production of mRNA therapeutics for early-phase clinical trials can take place directly at Fraunhofer ITEM.

RNA-based therapeutics are a drug class with huge potential for medicine — and scientists have barely scratched the surface of their possible use. Fraunhofer ITEM researchers develop novel drugs and methods for RNA-based therapeutic concepts.

The targeted use of RNA compounds based on coding or non-coding RNA sequences enables a tailored response of the respective target cells under certain pathological conditions. Fraunhofer researchers use a wide range of RNA-based compounds, such as small interfering RNA (siRNA), nucleoside-modified messenger RNA (modRNA), or RNA blockers – from target discovery through to clinical use. Bioinformatic models play a key role when it comes to selecting disease-associated RNAs, studying their interaction with other genes, and optimizing drug design.

Special viral and non-viral administration technologies, both at the molecular and equipment level, are being developed for the targeted use of RNA compounds. Local delivery via the airways is a promising solution in particular for RNA therapeutics used to combat lung diseases, as this enables the therapeutic agent to reach the site of action directly, thus minimizing systemic drug exposure.

Safety and efficacy testing of RNA compounds

For safety and efficacy testing of therapeutics, Fraunhofer ITEM researchers use existing and develop new model systems that are based on human cells and tissues. They can also test RNA-based therapeutics in early-phase clinical trials.

Process development and GMP production of RNA-based drugs

Fraunhofer ITEM researchers develop bioprocessing methods and production technologies for modular and automated manufacturing of RNA molecules and RNA nanocarriers, and these can be scaled right up to industry level.

Rapid, safe and reliable production technologies for the manufacture of RNA-based vaccines and drugs are a fundamental requirement for successful translation into marketable products.

To support this, process development and GMP production of mRNA therapeutics for early-phase clinical trials take place directly at Fraunhofer ITEM. The early-phase clinical trials can also be conducted in-house.

RNA molecules as biomarkers

Various RNA molecules are attracting increasing interest for diagnostic purposes as well. The expression profiles of RNA molecules are altered in many pathologies, such as cardiopulmonary diseases and cancer. RNA can be obtained from various liquid biopsies, such as blood, urine, or cerebrospinal fluid. Taking a liquid biopsy is much less invasive for patients than a tissue biopsy. Next generation sequencing technologies allow the RNA composition of a sample to be determined.

RNA expression profiles can thus be used as biomarkers to characterize diseases, predict the response to a specific therapy, and monitor treatment success. Fraunhofer ITEM researchers have developed technologies that enable the analysis of even very small quantities of RNA, making it possible to determine the expression profiles of single cells or cell-free, circulating RNA (cfRNA).

RNA molecules as biomarkers
© Fraunhofer ITEM, Ralf Mohr
So far, mainly mRNA and miRNA expression profiles have been used as biomarkers, although circular RNA (circRNA) is also emerging more and more as a biomarker with great potential.

Our technologies and methods

Identification of target structures

© Fraunhofer ITEM, Ralf Mohr

Computer-based models can provide clues to molecular RNA targets in different human organ pathologies.

Based on these structures, RNA drug candidates can be synthesized and subsequently validated in translational model systems.

Lead optimization

© Fraunhofer ITEM, Ralf Mohr

Analytical methods are essential for the optimization of RNA-modulating agents. Oligonucleotide-based binding assays are used to validate the structure of the active ingredient in advance and adjust it accordingly.

The ensuing efficacy testing and pharmacokinetics studies are also performed with the help of bioanalytical methods. Microscale thermophoresis (MST) and HPLC platforms are available as well.

 

Efficacy testing in human model systems and RNA-based analytical methods (PK/PD studies)

© Fraunhofer ITEM, Ralf Mohr

Human and animal tissue culture models

Heart

  • Cell cultures
  • Cardiac tissue slices
  • 3D organoid models

Lung

  • Cell cultures
  • Isolated perfused lung
  • Precision-cut lung slices (PCLS)
  • 3D organoid models

Liver

  • Cell cultures
  • Precision-cut liver slices(PCLiS)

Toxicology (in vitro/in vivo)

  • Preclinical testing in vivo
  • Preclinical tests using different in-vitro and ex-vivo lung and heart models
  • Safety pharmacology
  • Toxicological risk assessment
    • Identification and use of predictive biomarkers for toxicological endpoints
    • Generation of mechanistic data to support next generation risk assessment
    • Assessment of genotoxic impurities according to ICH M7, including review of literature, QSAR analysis, and PDE derivation

 

© Fraunhofer ITEM, Ralf Mohr

mRNA manufacture

© Fraunhofer ITEM, Ralf Mohr
  • Plasmid production and purification up to 400 L fermentation scale; Fraunhofer ITEM holds an EU GMP manufacturing authorization
  • Enzymatic in-vitro transcription, functionalization, and purification of mRNA as active pharmaceutical ingredient (up to gram scale)
  • Microfluidic formulation of mRNA LNPs as formulated bulk
  • Automated or manual aseptic filling of mRNA LNPs as medicinal products in up to 7000 10R vials (grade A (EU) / class 100 (US) in grade-B clean-room environment, validated media fill). Other filling formats are available on request.
  • QC analyses for IPC and release testing of medicinal products in-house or, when necessary, by qualified external service providers
  • In-house QP available, mRNA therapeutics can be released and supplied as IMP for clinical use

RNA targeted delivery

Different technologies and cardiopulmonary 2D and 3D model systems are used to develop the targeted, organ-specific delivery of RNA therapeutics.

  • Bioanalytics for therapeutic RNA interaction with the target sequence
  • Manufacturing and validation of nanoparticles as carriers of RNA therapeutics
  • Biological validation of RNA-nanoparticle complexes
  • Development of cell-specific nanoparticles
  • Nebulization of RNA-nanoparticle complexes
© Fraunhofer ITEM, Ralf Mohr

Clinical trials phases I/II

Proband wird von Studienarzt untersucht und informiert
© Fraunhofer ITEM, Ralf Mohr
  • Phase-I unit and infrastructure for clinical research
  • Broad range of diagnostic methods for safety and efficacy assessment
    • MRI to visualize lung ventilation and blood flow
    • ECG, echocardiography, and telemetry
  • Controlled aerosol inhalation
  • Broad range of challenge models for early proof of concept

RNA research: recent projects and highlights

 

RNA therapeutic for treatment of heart failure and organ fibroses

Prof. Thomas Thum, Institute Director of Fraunhofer ITEM, has developed a RNA therapy for treating heart failure, which has already been successfully tested in patients in a phase 1b clinical trial.

 

Project RNAuto

Fraunhofer develops automated production technologies for mRNA-based drugs.

RNA drug against cardiac fibrosis

The EU is funding this research project with around 2.5 million euros.

Development pipeline for RNA-based drugs

Rapid therapeutic approaches for viral diseases: A research team from Fraunhofer ITEM and Hannover Medical School has been successful in a Europe-wide SPRIND challenge.

 

Project Cell Painting

Fraunhofer researchers have established a promising tool for next generation risk assessment.

 

Project ZET-O-MAP

Researchers from Fraunhofer ITEM have succeeded in developing an analysis pipeline to identify biomarkers for developmental toxicity. 

Types of RNA

There are many different types of RNA. The most widely known is messenger RNA (mRNA). It carries the genetic information needed to produce proteins, such as for the SARS-CoV-2 spike protein in coronavirus vaccines. But in addition to mRNA, a large number of other RNA molecules are present in the organism. These are referred to as non-coding RNAs, including, for example, microRNA (miRNA), long non-coding RNA (lncRNA), and circular RNA (circRNA), and they play essential regulatory roles inside cells. Their dysregulation can result in a broad range of diseases, which is why they are crucial therapeutic targets.

Messenger RNA

 

Messenger-RNA (mRNA) is a single-stranded ribonucleic acid that carries and transmits genetic information for building a certain protein inside a cell.

mRNA-based drugs introduce the blueprint for a particular protein into cells and the cells will then synthesize this protein. In the case of mRNA vaccines, the synthesized protein serves as antigen, triggering an immune response to build protection.

MicroRNA

 

MicroRNA is a class of highly conserved, short, non-coding RNAs that play a crucial role in the complex network of gene regulation.

The various miRNA molecules regulate gene expression with a high degree of specificity at the post-transcriptional level and can thus serve as therapeutic targets.

Small interfering RNA

 

The term small interfering RNA (siRNA) refers to synthetically produced RNA molecules that are used in research, but also as therapeutic agents. siRNA molecules with any desired sequence can be produced by chemical synthesis. 

To introduce siRNA into cells, a method known as liposomal transfection or lipofection is mainly used. It couples RNA with liposomes that fuse with the target cell membrane, thereby delivering the siRNA into the cell.

Circular RNA

 

Circular RNA (circRNA)  is a type of single-stranded ribonucleic acid which, unlike linear RNA, forms a covalently closed continuous loop. Because circular RNA does not have 5' or 3' ends, it is resistant to exonuclease-mediated degradation and is presumably more stable than most linear RNA in cells.

circRNA is involved in gene regulation and has been linked to some diseases such as cancer. The biological function of most circRNA molecules is as yet unclear.

IncRNA

 

Long non-coding RNAs (lncRNA) are generally defined as transcripts with more than 200 nucleotides that are not translated into protein.

They are involved in gene regulation at the transcriptional, post-transcriptional and epigenetic levels and have an impact on DNA replication timing and chromosome stability.

modRNA

 

Nucleoside-modified messenger RNA (modRNA) is a synthetic, chemically modified mRNA, in which some nucleosides have been replaced by other naturally modified nucleosides or by synthetic nucleoside analogues.

Such RNA molecules are used in experimental or therapeutic contexts to induce the production of a desired protein in certain cells.

Publications

  • Foinquinos A, Batkai S, Genschel C, Viereck J, Rump S, Gyöngyösi M, Traxler D, Riesenhuber M, Spannbauer A, Lukovic D, Weber N, Zlabinger K, Hašimbegović E, Winkler J, Fiedler J, Dangwal S, Fischer M, de la Roche J, Wojciechowski D, Kraft T, Garamvölgyi R, Neitzel S, Chatterjee S, Yin X, Bär C, Mayr M, Xiao K, Thum T. Preclinical development of a miR-132 inhibitor for heart failure treatment. Nature Commun. 2020;11:633. https://www.nature.com/articles/s41467-020-14349-2
  • Gupta SK, Garg A, Bar C, Chatterjee S, Foinquinos A, Milting H, Streckfuss-Bomeke K, Fiedler J, Thum T. Quaking Inhibits Doxorubicin-Mediated Cardiotoxicity Through Regulation of Cardiac Circular RNA Expression. Circ Res. 2018;122:246-254. https://www.ahajournals.org/doi/10.1161/CIRCRESAHA.117.311335
  • Hedayatollah Hosseini, Milan M.S. Obradović, Martin Hoffmann, Kathryn Harper, Maria Soledad Sosa, Melanie Werner-Klein, Lahiri Kanth Nanduri, Christian Werno, Carolin Ehrl, Matthias Maneck, Nina Patwary, Gundula Haunschild, Miodrag Gužvić, Christian Reimelt, Michael Grauvogl, Norbert Eichner, Florian Weber, Andreas Hartkopf, Florin-Andrei Taran, Sara Y. Brucker, Tanja Fehm, Brigitte Rack, Stefan Buchholz, Rainer Spang, Gunter Meister, Julio A. Aguirre-Ghiso, Christoph A. Klein. Early dissemination seeds metastasis in breast cancer. Nature. Author manuscript; available in PMC 2017 Jun 15. Published in final edited form as: Nature. 2016 Dec 22; 540(7634): 552–558. Published online 2016 Dec 14. doi: 10.1038/nature20785 https://www.nature.com/articles/nature20785
  • Sarah M. Hücker, Tobias Fehlmann, Christian Werno, Kathrin Weidele, Florian Lüke, Anke Schlenska-Lange, Christoph A. Klein, Andreas Keller and Stefan Kirsch. Single-cell microRNA sequencing method comparison and application to cell lines and circulating lung tumor cells. Nat Commun. 2021; 12: 4316., Published online 2021 Jul 14. doi: 10.1038/s41467-021-24611-w https://www.nature.com/articles/s41467-021-24611-w
  • Piccoli MT, Gupta SK, Viereck J, Foinquinos A, Samolovac S, Kramer FL, Garg A, Remke J, Zimmer K, Batkai S, Thum T. Inhibition of the Cardiac Fibroblast-Enriched lncRNA Meg3 Prevents Cardiac Fibrosis and Diastolic Dysfunction. Circ Res. 2017;121:575-583 https://pubmed.ncbi.nlm.nih.gov/28630135/
  • Schimmel K, Jung M, Foinquinos A, José GS, Beaumont J, Bock K, Grote-Levi L, Xiao K, Bär C, Pfanne A, Just A, Zimmer K, Ngoy S, López B, Ravassa S, Samolovac S, Janssen-Peters H, Remke J, Scherf K, Dangwal S, Piccoli MT, Kleemiss F, Kreutzer FP, Kenneweg F, Leonardy J, Hobuß L, Santer L, Do QT, Geffers R, Braesen JH, Schmitz J, Brandenberger C, Müller DN, Wilck N, Kaever V, Bähre H, Batkai S, Fiedler J, Alexander KM, Wertheim BM, Fisch S, Liao R, Diez J, González A, Thum T. Natural Compound Library Screening Identifies New Molecules for the Treatment of Cardiac Fibrosis and Diastolic Dysfunction. Circulation. 2020;141:751-767 https://www.ahajournals.org/doi/10.1161/CIRCULATIONAHA.119.042559
  • Täubel J, Hauke W, Rump S, Viereck J, Batkai S, Poetzsch J, Rode L, Weigt H, Genschel C, Lorch U, Theek C, Levin AA, Bauersachs J, Solomon SD, Thum T. Novel antisense therapy targeting microRNA-132 in patients with heart failure: results of a first-in-human phase 1b randomised, double-blind, placebo-controlled study. Eur Heart J. 2021;42:178-188 https://www.ncbi.nlm.nih.gov/pmc/articles/PMC7954267/
  • Thum T, Gross C, Fiedler J, Fischer T, Kissler S, Bussen M, Galuppo P, Just S, Rottbauer W, Frantz S, Castoldi M, Soutschek J, Koteliansky V, Rosenwald A, Basson MA, Licht JD, Pena JT, Rouhanifard SH, Muckenthaler MU, Tuschl T, Martin GR, Bauersachs J, Engelhardt S (2008) MicroRNA-21 contributes to myocardial disease by stimulating MAP kinase signalling in fibroblasts. Nature. 2008;456:980-984 https://www.nature.com/articles/nature07511.
  • Ucar A, Gupta SK, Fiedler J, Erikci E, Kardasinski M, Batkai S, Dangwal S, Kumarswamy R, Bang C, Holzmann A, Remke J, Caprio M, Jentzsch C, Engelhardt S, Geisendorf S, Glas C, Hofmann TG, Nessling M, Richter K, Schiffer M, Carrier L, Napp LC, Bauersachs J, Chowdhury K, Thum T. The miRNA-212/132 family regulates both cardiac hypertrophy and cardiomyocyte autophagy. Nat Commun. 2012;3:1078. https://www.nature.com/articles/ncomms2090
  • Ucar A, Vafaizadeh V, Jarry H, Fiedler J, Klemmt PA, Thum T, Groner B, Chowdhury K. miR-212 and miR-132 are required for epithelial stromal interactions necessary for mouse mammary gland development. Nat Genet. 2010;42:1101-1108. https://pubmed.ncbi.nlm.nih.gov/21057503/
  • Viereck J, Bührke A, Foinquinos A, Chatterjee S, Kleeberger JA, Xiao K, Janssen-Peters H, Batkai S, Ramanujam D, Kraft T, Cebotari S, Gueler F, Beyer AM, Schmitz J, Bräsen JH, Schmitto JD, Gyöngyösi M, Löser A, Hirt MN, Eschenhagen T, Engelhardt S, Bär C, Thum T. Targeting muscle-enriched long non-coding RNA H19 reverses pathological cardiac hypertrophy. Eur Heart J. 2020;41:3462-3474 https://academic.oup.com/eurheartj/article/41/36/3462/5870446
  • Viereck J, Kumarswamy R, Foinquinos A, Xiao K, Avramopoulos P, Kunz M, Dittrich M, Maetzig T, Zimmer K, Remke J, Just A, Fendrich J, Scherf K, Bolesani E, Schambach A, Weidemann F, Zweigerdt R, de Windt LJ, Engelhardt S, Dandekar T, Batkai S, Thum T. Long noncoding RNA Chast promotes cardiac remodeling. Sci Transl Med. 2016;8:326ra322 https://pubmed.ncbi.nlm.nih.gov/26888430/ 
  • Melanie Werner-Klein, Ana Grujovic, Christoph Irlbeck, Milan Obradović, Martin Hoffmann, Huiqin Koerkel-Qu, Xin Lu, Steffi Treitschke, Cäcilia Köstler, Catherine Botteron, Kathrin Weidele, Christian Werno, Bernhard Polzer, Stefan Kirsch, Miodrag Gužvić, Jens Warfsmann, Kamran Honarnejad, Zbigniew Czyz, Giancarlo Feliciello, Isabell Blochberger, Sandra Grunewald, Elisabeth Schneider, Gundula Haunschild, Nina Patwary, Severin Guetter, Sandra Huber, Brigitte Rack, Nadia Harbeck, Stefan Buchholz, Petra Rümmele, Norbert Heine, Stefan Rose-John, Christoph A. Klein. Interleukin-6 trans-signaling is a candidate mechanism to drive progression of human DCCs during clinical latency. Nat Commun. 2020; 11: 4977. Published online 2020 Oct 5. doi: 10.1038/s41467-020-18701-4 https://www.nature.com/articles/s41467-020-18701-4 

Click here for a complete list of publications by Fraunhofer ITEM researchers.