mRNA Regulation

In the last decade, the regulation of mRNA has become an emerging scientific discipline. Using our MOAi technology, we have exposed novel mRNA biology targets, allowing us to heavily contribute to advances in this space and become leading experts in mRNA biology.

The target space we explore encompasses proteins with specific biological roles in coordinating and regulating individual mRNA fate, and the pathways that regulate it. This allows for the discovery of small molecules that selectively modulate the mRNA fate of almost any protein of interest.

Our extensive mRNA biology knowledge and actual experimental outcomes are integrated into our Large Language Model (LLM), which is a component of our MOAi technologies. This LLM constantly works in sync with the platform components, refining our methodologies throughout each discovery project. It's like a continually updated asset in our system, making every research step smarter.

After identifying a disease's mRNA biology signature pathway, our MOAi technologies come into play to discover and validate novel targets. Compounds from our high-content screening emerge with pre-existing MOA rationale. Leveraging our vast proprietary data, the mRNA biology LLM suggests MOAs, which are then further confirmed by the co-pilot's experimental designs.

Anima's small molecule drugs act through a variety of mRNA regulatory mechanisms

Different regulatory mechanisms of the same mRNA across tissues

Cells from Tissue A or Tissue B were treated with an induction cocktail for 72 hours and imaged at different time points and a probe specific to a single mRNA was visualized (orange). Cells from Tissue A exhibited low but evident amounts of mRNA X in the cytoplasm and two transcription sites in the nucleus at steady state, before induction (upper, left image). Following induction, mRNA X levels increased over the tested period as demonstrated by increased spot sizes in the nucleus, indicating a higher transcription rate, and an increase in accumulation of mRNA in the cytoplasm (upper images). In cells from Tissue B on the other hand, mRNA X was undetectable in the cytoplasm at steady state. However, many spots were detected in the nucleus, indicating a unique mode of regulation, storing the mRNA in the nucleus. Twenty-four hours following induction, mRNA X levels in the cytoplasm remained, but an increase in the intensity of spots in the nucleus was detected, suggesting mRNA was accumulating there. Forty-eight to seventy-two hours after induction, the mRNA was transported from the nucleus to the cytoplasm, until mRNA X was completely exported from the nucleus to the cytoplasm. These findings reveal a unique regulation process on mRNA translation for the same mRNA in different cells.

Mutated mRNA selective localization

Mutated mRNA is regulated in a selective manner

Cells expressing a wildtype (W.T) or Mut (Mutated) mRNA variants of a gene of interest exhibit different mRNA localization phenotypes. This phenomenon implies different regulatory processes that operate selectively on the two forms of mRNA. In the upper panel, W.T. mRNA-expressing cells exhibit one high-intensity spot in the nucleus (transcription site) and a pool of mRNAs in the cytoplasm. In the lower panel, mutant mRNA-expressing cells show an accumulation of mRNA in many nuclear spots, a phenotype observed in patients.

Specific mRNA localization to RNA granules upon compound treatment

Compound from series X induces mRNA localization to RNA granules resulting in the decrease of mRNA translation

Cells were treated with biology modulators of a specific mRNA, identified at Anima. Compounds discovered in this project modulate the target mRNA in three different manners and belong to three different compound families. Series X compounds selectively re-localize the target mRNA from the cytoplasm to specific cytoplasmic granules (lower, second image from the left, marked by white arrows). The mRNA sequestration in the cytoplasmic granules inhibits ribosomes binding to this mRNA, resulting in the decrease of its translation. This mRNA-relocalization was series specific, indicating a unique mechanism of action for series X.

Our small molecules are targeting novel proteins involved in the regulation of mRNA

Various mechanisms enable cells to quickly respond to extracellular signals. The regulation around mRNA is extensive and those mechanisms provide novel intervention points for the development of novel therapies:

  1. Coordinated changes in translation initiation such as changing the components of the initiation complex
  2. Shuttling of mRNA, in a protected manner, to different cellular compartments where their translation is needed
  3. The use of non-protein vehicles to regulate mRNA stability, such as short-lived small noncoding RNAs (termed microRNA)

In different tissues, cells need to respond to distinct sets of cues. For example, mRNA translation in neurons is localized to different cellular compartments. Ribosomes are located around the nucleus, along exons, and at nerve endings to enable supply on demand of specific proteins required at these different cellular locations. Thus, to enable these diverse requirements and responses, mRNA translation has developed selective regulatory systems.

Ribosome accessory proteins
Epitranscriptomics (mRNA modifying proteins)
Splicing factors
Modifiers of ribosomal proteins (Kinases, methylases etc...)
tRNA abundance and control
RNA binding proteins

mRNA translation is a highly regulated process: once mRNA is transcribed, it is bound by RNA binding proteins (RBPs) in a highly specific and selective manner; an additional layer of regulation is mediated by modifications of ribonucleotides in mRNA (epitranscriptomics), that modulate RBP-mRNA interactions. Together these mechanisms regulate mRNA processing, nuclear export, and mRNA steady-state levels. RBPs regulate the localization of mRNAs in the nucleus and cytoplasm, thereby determining mRNA translation temporally and spatially. Moreover, ribosomes, much like RNA polymerases and proteasomes, have accessory proteins associated with them in a tissue and signal-specific manner, which provides mRNA translation an additional layer of selectivity.

Bi-directional mRNA translation regulation

Targeting the regulatory mechanisms of mRNA enables the discovery of compounds that not only decrease but can also selectively increase protein translation.

The images below are taken from Anima's Collagen I program. During the screening campaign, COL1A1 mRNA regulation inhibitors and activators were identified.

A compound that reduces the rate of translation of Collagen I decreases the light. Subsequently, this compound reduces Collagen I protein accumulation (middle panel).

A compound that enhances the rate of translation of Collagen I increases the light. The compound also enhances the production of Collagen I protein (right panel).