RNA self-splicing by engineered hairpin ribozyme variants

Deciphering the role of alternative splicing in neoplastic diseases for immune-oncological therapies

Alternative splicing (AS) is an important molecular biological mechanism regulated by complex mechanisms involving a plethora of cis and trans-acting elements. Furthermore, AS is tissue specific and altered in various pathologies, including infectious, inflammatory, and neoplastic diseases. Recently developed immuno-oncological therapies include monoclonal antibodies (mAbs) and chimeric antigen receptor (CAR) T cells targeting, among others, immune checkpoint (ICP) molecules. Despite therapeutic successes have been demonstrated, only a limited number of patients showed long-term benefit from these therapies with tumor entity-related differential response rates were observed. Interestingly, splice variants of common immunotherapeutic targets generated by AS are able to completely escape and/or reduce the efficacy of mAb- and/or CAR-based tumor immunotherapies. Therefore, the analyses of splicing patterns of targeted molecules in tumor specimens prior to therapy might help correct stratification, thereby increasing therapy success by antibody panel selection and antibody dosages. In addition, the expression of certain splicing factors has been linked with the patients' outcome, thereby highlighting their putative prognostic potential. Outstanding questions are addressed to translate the findings into clinical application. This review article provides an overview of the role of AS in (tumor) diseases, its molecular mechanisms, clinical relevance, and therapy response.

Chemically Cross-Linked Hammerhead Ribozyme as an Efficient RNA Interference Tool

RNA-cleaving ribozymes are promising candidates as general tools of RNA interference (RNAi) in gene manipulation. However, compared with other RNA systems, such as siRNA and CRISPR technologies, the ribozyme tools are still far from broad applications on RNAi due to their poor performance in the cellular context. In this work, we report an efficient RNAi tool based on chemically modified hammerhead ribozyme (HHR). By the introduction of an intramolecular linkage into the minimal HHR to reconstruct the distal interaction within the tertiary ribozyme structure, this cross-linked HHR exhibits efficient RNA substrate cleavage activities with almost no sequence constraint. Cellular experiments suggest that both exogenous and endogenous RNA expression can be dramatically knocked down by this HHR tool with levels comparable to those of siRNA. Unlike the widely applied protein-recruiting RNA systems (siRNA and CRISPR), this ribozyme tool functions solely on RNA itself with great simplicity, which may provide a new approach for gene manipulation in both fundamental and translational studies.

Directed Circularization of a Short RNA

Basic research and functional analyses of circular RNA (circRNA) have been limited by challenges in circRNA formation of desired length and sequence in adequate yields. Nowadays, circular RNA can be obtained using enzymatic, "ribozymatic," or modulated splice events. However, there are few records for the directed circularization of RNA. Here, we present a proof of principle for an affordable and efficient RNA-based system for the controlled synthesis of circRNA with a physiological 3',5'-phosphodiester conjunction. The engineered hairpin ribozyme variant circular ribozyme 3 (CRZ-3) performs self-cleavage poorly. We designed an activator-polyamine complex to complete cleavage as a prerequisite for subsequent circularization. The developed protocol allows synthesizing circRNA without external enzymatic assistance and adds a controllable way of circularization to the existing methods.

Elucidating the Self-cleavage Dynamics of Hairpin Ribozyme by Mode-decomposed Infrared Spectroscopy

While catalytic reactions of biomolecular processes play an indispensable role in life, extracting the underlying molecular picture often remains challenging. Based on ab initio simulations of the self-cleavage reaction of hairpin ribozyme, mode-decomposed infrared spectra, and cosine similarity analysis to correlate the product with reactant IR spectra, we demonstrate a strategy to extract molecular details from characteristic spectral changes. Our results are in almost quantitative agreement with the experimental IR band library of nucleic acids and suggest that the spectral range of 800-1200 cm-1 is particularly valuable to monitor self-cleavage. Importantly, the cosine similarities also disclose that IR peaks subject to slight shifts due to self-cleavage might be unrelated, while strongly shifting resonances can correspond to the same structural dynamics. This framework of correlating complex IR spectra at the molecular level along biocatalytic reaction pathways is broadly applicable.

DNA-catalysed alternative RNA splicing

We report DNA-catalysed alternative RNA splicing in vitro. Using modular DNA catalysts with RNA endonuclease and RNA ligase activities, we show that DNA can modulate RNA structure and activity. Furthermore, we illustrate that such DNA-catalysed reactions can yield, from a common precursor, different splicing isoforms with distinct functions.