Spoke 2 - RNA Genetherapy

Despite continual refinements in traditional chemotherapy and radiotherapy, advancements have been made through drugs targeting specific oncogenic proteins and immune-oncology. However, the battle against most cancers remains far from victorious. This is primarily due to the rarity and diversity of druggable genetic alterations, as well as the limited efficacy of targeted therapies, acquired resistance, and the intricate heterogeneity within tumors.

The conventional focus on mutant cancer cells overlooks the complexity of tumors as ecosystems, wherein malignant cells exist within a microenvironment of normal but corrupted cells, thus contributing to phenotypic diversity or “plasticity.” Metastasis, the cause of over 90% of cancer deaths, is an increasingly understood result of normal regenerative programs co-opted by malignant cells. Metastases share genetic alterations with primary tumors, emphasizing the need to explore undruggable factors such as transcription factors, epigenetics, and signaling factors.

Despite the success of immune checkpoint inhibitors (ICI) in some cases, their benefits are frustratingly limited. This scenario prompts consideration of how Spoke 2 can contribute to its progression. Building on the success of RNA therapeutics, exemplified by the COVID vaccines, this approach offers unprecedented specificity, safety, and flexibility in cancer therapy. Spoke 2 focuses on implementing RNA therapeutics and biomarkers to address cancer trunk addictions, synthetic combinatorial approaches targeting interdependent hallmarks of cancer, and expanding the applicability of ICI.

The strategy of Spoke 2 involves targeting the undruggable, exploring the unconventional, and addressing the unseen aspects of cancer. Research projects will span different Technology Readiness Levels (TRL), with an emphasis on translational potential. Initial steps involve identifying novel targets through omics and artificial intelligence (AI) while concentrating on determinants of tumorigenesis or oncosuppressor circuits. Simultaneously, lower TRL research aims to identify new targets and biomarkers, including non-coding RNA fractions of the cancer genome. The focus extends to both malignant cells and the tumor stroma, with an emphasis on fostering anti-cancer innate and adaptive immunity and discovering diagnostic, prognostic, and treatment response biomarkers through high-throughput sequencing and AI.

PROGRAM

Spoke 2 organizes its research program into four Work Packages (WPs).
The primary objective of WP 2.1 is to identify novel target genes that fall into specific categories. Such categories include transcription factors (TFs) that mediate aberrant gene expression in cancer. WP 2.1 studies emphasize the inhibition of TFs, such as YAP, HIF, Myc, NF-Y isoforms, SOX, and FOXA through RNA therapeutics. Other objectives extend to the inhibiting of epigenetic regulators, the DNA repair/nuclear envelope, and heterochromatin packaging factors, aimed to increase tumor mutational burden and activate innate immunity. WP 2.1 focuses on specific metabolic pathways, like iron metabolism in AML, and the mitochondrial pathways, such as VDAC1 and potassium channels. WP 2.1 investigates non-coding RNAs, RNA-binding proteins, and epitranscriptomic modifiers/editors, along with alternative splicing factors targeting tumor immunogenicity.

WP 2.2 targets include in vivo effectiveness and cancer specificity. Validation involves modulating target genes and RNA molecules using various techniques, including shutdown of key enzymes, gene editing, and different RNA types. Employing intratumoral delivery of RNA therapeutics via Lipid Nanoparticles (LNPs) aims to reach clinical applications such as treating unresectable tumors and accessible metastatic lesions. WP 2.2 assesses in vivo effectiveness using Patient-Derived Avatars, while emphasizing treatments with potential systemic disease attacks (abscopal effects) through immune system reactivation.

WP 2.3 focuses on developing immune-RNA therapeutics by analyzing the tumor immune-peptidome systematically. This involves proteomics of tumor cells exposed to clinically available drugs and screening for tumor-specific immunogenic peptides. Successes include the identification of effective antigens, and the approach integrates with immunotherapy using RNA-based therapies.

WP 2.4 addresses financial aspects, including Tech transfer and fundraising activities, with a focus on collaboration with Intesa San Paolo. The goal is to create opportunities for stakeholders in the value chain, particularly small to medium enterprises (SMEs) and startups, to contribute to the outcome of Spoke 2. The emphasis is on collecting, exchanging, and connecting capabilities to streamline communication and enhance research and industrialization initiatives within the HUB.

SPOKE FLAGSHIPS

As part of the initiative focused on infrastructures and services for research activities, a cluster of laboratories will be established under the Spoke Flagship. These laboratories will be dedicated to the characterization of tumor cell receptors to facilitate the targeted transport of RNA drugs. The cluster comprises both existing infrastructures and a newly established RNA Formulation Lab, where researchers will assemble and test nanocarriers for their ability to transport nucleic acids with selective targeting properties.

These specialized laboratories will be used to assemble RNAs into transport vectors designed to target receptors expressed on cancer cells. This process will take place in a qualified and certified environment. The initiative encompasses the creation, expansion, and modernization of research infrastructures, providing innovative solutions and methodologies. Building upon existing facilities, Sapienza offers production platforms dedicated to the synthesis and formulation of RNA that serve the research groups of the National Research Center.

CROSS-SPOKE ACTIVITIES

Activities of Spoke 2 will include interactions with Spoke 6 that focus on the encapsulation of small RNAs on human ferritin constructs thus developed. Spoke 7 will offer an expansion of epitranscriptomics in silico screening with effective inhibition of RNA post-transcriptional modifying enzymes. Spoke 8 (Platforms for RNA/DNA Delivery) and Spoke 9 (From Target to therapy pharmacology, safety, and regulatory competence/center), and Spoke 10 for the translation of pre-clinical research into clinical trials (Preclinical development GMP manufacturing and clinical trials for gene therapy medicinal products – GTMPs). In addition, a collaboration with Spoke 5 will focus on target and biomarkers tuning protocols. The long-standing cooperation with the IRBM research group, which facilitates innovative research and manufacturing, will pave the way across all aspects of drug discovery and early development to accelerate the development of vaccines and medicine carrying out clinical implementation will provide a framework of cooperation with existing facilities of the SANOFI group. Antares Vision Group, also in collaboration with Spoke 8, will lead the design and implementation of a lab-scale prototype integrated modular system for continuous monitoring of formulations of nanosized EVs loaded with RNA under continuous or pulsed flow with steady-state fill volumes. The prototype will aim to characterize the formulations for EV size (based on dynamic light scattering),
RNA content (based on UV-vis spectroscopy) and (selected) membrane properties (based on microarray technology). Concerning the EV physicochemical properties, the system will aim at performances analogous to state-of-the-art low-volume batch laboratory characterization, while aiming at outperforming them in terms of processing time.

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PROGRAM

WHO WE ARE

SPOKE FLAGSHIPS

CROSS-SPOKE ACTIVITIES