Alltrna

The genetic code dictates the instructions for creating proteins that carry out the majority of cell functions in the human body. Transfer RNAs (tRNAs) are the molecules that translate this code into proteins—it is impossible to make proteins without tRNAs. tRNAs have unique and diverse chemical modifications that determine their function and also break into smaller fragments that play translation-independent roles. Alltrna has successfully applied machine learning to reveal tRNA’s unique language and design rules. Through this understanding, Alltrna is systematically programming tRNAs to control protein production, from precisely correcting erroneous codes to modulating the type and expression level of proteins. As the world’s first tRNA platform company, Alltrna has an unprecedented opportunity to advance a novel class of medicines, encoding a unifying approach to treat both rare and common human diseases driven by shared genetic mutations as well as a completely new therapeutic framework that can control the protein universe to treat disease.

Origins

In 2018, Flagship General Partner David Berry and Flagship Principal Theonie Anastassiadis refocused their view on the central dogma through the tRNA lens and asked “What if we’ve overlooked a key component of the central dogma? What if tRNAs are more than adaptive molecules that build proteins, but are in fact complex signaling molecules that integrate cellular signals to control protein production and, thus, cell function and ultimately coordinate multicellular life?” Their exploration gave rise to Flagship Labs prototype company, initially called FL63 and later named Alltrna, founded to learn both the tRNA design rules and the breadth and power of tRNA biology to create tRNAs as a new therapeutic modality to treat disease.

tRNAs are fascinating molecules that are more than three billion years old. These ancient molecules have evolved modular features that are being translated into powerful and programmable therapeutics by Alltrna’s tRNA platform. There are hundreds of thousands of known tRNA sequences across all species, and orders of magnitude more unique molecules are created in nature when decorated with a vast diversity of modifications that drive function. Moreover, these molecules are known to fragment into smaller units that carry out roles beyond translation of mRNA into proteins. The Flagship team sought to discover the breadth of tRNA biology as well as the design rules of tRNA molecules to harness this ancient molecule paired with its powerful biology to create a new RNA modality to design life-improving medicines.

The hidden world of tRNA biology likely remained unexplored due to major technical hurdles that hindered many from asking the most basic biological questions. These questions require the ability to express and quantify the molecule of interest to study its effects, neither of which the scientific community knew how to do robustly for tRNAs. Indeed, due to their tight structure, many modifications, and similar sequences, quantifying tRNAs using sequencing methodologies were inconsistent and led to artifacts, which could mislead scientific discoveries. In addition, the ability to express tRNAs at levels required to observe effects was poor. Even with the tools to study tRNA biology, there were significant technical and financial challenges to chemically synthesizing tRNA oligos with modifications, until recently.

Once technical challenges were addressed, that powerful “what if” question revealed a new world in which (1) tRNAs could be programmed to precisely correct nonsense or missense mutations to restore the normal/intended full-length protein, (2) tRNAs, depending on their cellular ratio, could change the amount and type of protein being produced, unlocking treatment of diseases, such as those driven by haploinsufficiency, which causes protein level dysregulation, and (3) tRNA fragments could function within and between cells to coordinate and regulate larger biological processes, particularly through modulation of transcription.

The stable structure, small size, and vast diversity of tRNAs make them natural drugs. More than one hundred different modifications create a unique language that is key to tRNA function, stability, and selectivity. With the world’s first tRNA platform, Alltrna is using machine learning to explore the functional vastness of this new modality, program tRNAs to specifically modulate therapeutic features, and design a new modality with unprecedented therapeutic potential.

At the NewCo transition, Flagship Origination Partner Lovisa Afzelius joined Theonie Anastassiadis to execute on the promise of tRNA biology by building out the platform, growing the team, and establishing Alltrna’s machine learning capabilities to unlock tRNA therapeutic design.

Breakthrough

While many breakthroughs enabled the team to tease out and leverage the integral roles played by tRNA, three stood out. First, the team had to challenge the dogma that tRNAs are merely adapter molecules sequentially adding amino acids to the growing polypeptide code instructed by the RNA sequence. Instead, they found tRNA to be an active gatekeeper of translation, constantly sensing the cellular environment and dynamically responding to it by controlling the levels and types of proteins expressed as well as by fragmenting to carry out translation-independent functions. Second, to properly study tRNA biology, the team developed novel technologies to express, synthesize, modify, and quantify tRNA molecules. Third, they leveraged machine learning to effectively sample the vast sequence and modification space and decode the molecular language of tRNA. With these three breakthroughs, Alltrna explores the entire universe of tRNA sequences and modifications to exquisitely design optimized tRNA molecules as new targeted therapeutics.

Advantage

By asking a key question and then leveraging and creating technological breakthroughs, Alltrna has established the first and only platform to systematically decipher all tRNA biology. The Alltrna platform iteratively designs, tests, and learns to unlock the language of tRNAs and pioneer tRNA therapeutics to treat thousands of diseases. With machine learning tools, Alltrna designs novel tRNA molecules by exploring tRNA’s vast sequence space and its programmable and modular nature through modification of a structured backbone to optimize across specific therapeutic features. These molecules are then tested and characterized in the company’s fully automized, high-throughput, proprietary in vitro assays followed by confirmation in animal models. Finally, Alltrna’s digital backbone digitizes the platform for full integration of all data generated to fuel its ML-powered capabilities, analytics, and innovation. The Alltrna platform capabilities and insights translate to a broad range of therapeutic opportunities that fully leverage all tRNA biology.

Alltrna’s first platform application focuses on designing tRNA molecules that correct nonsense genetic mutations encoding a premature stop codon. These mutations represent 10 percent of all genetic diseases, both inherited and somatic. A single tRNA therapeutic has the potential to restore disrupted protein production for all diseases caused by the same underlying genetic mutation, regardless of target. Unlike other modalities, the power of tRNA medicine is the unprecedented opportunity to rapidly expand to treat thousands of indications, no matter where the mutation occurs in the genome, what protein is made, or which disease it causes. This means Alltrna can streamline therapeutic development for patient populations with no or limited treatment options no matter the prevalence, from ultra-rare genetic diseases to commonly occurring diseases.

Focus

Alltrna will further expand Flagship Pioneering’s broad expertise in RNA science and portfolio of bioplatform companies— adding another, yet differentiated, RNA modality to the arsenal of programmable medicines that can help patients with unmet need. The growing Alltrna team will continue to build out platform capabilities, expand the therapeutic applications of tRNA into regulation and expression of the protein universe to treat disease, and work on bringing its first wave of tRNA medicines to the clinic. The team will work closely with clinical investigators to identify indications where first-in-class therapies can rapidly reach patients and chart the path to leveraging tRNA’s unprecedented ability to have a single medicine treat thousands of diseases.