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UC San Diego Makes Strides In Gene Modification Technology

Image Source: Tada Images / Shutterstock
UC San Diego scientists have engineered advanced genome editing mechanisms, known as multiplexed orthogonal base editors (MOBEs), that proficiently induce numerous point mutations concurrently. These mechanisms pave the way to heightened insights and experimental models of genetic ailments by enabling precise variant implantation in laboratory settings, offering innovative avenues to probe multifaceted diseases.

MOBEs, inventive genome modification implements from UC San Diego, facilitate accurate, concurrent genetic alterations, bolstering disease reconstruction and curative exploration.

The human genome is comprised of roughly 3 billion nucleotide pairs, with humans being 99.6% genetically alike. The remaining 0.4% explains the distinctions among people. Certain permutations of mutations within these pairs yield vital hints related to the genesis of complex health predicaments, such as cardiac conditions and neurodegenerative disorders like schizophrenia.

Established techniques for modeling or amending mutations in living cells are markedly inefficient, especially when introducing multiple point mutations in unison throughout the genome. Nevertheless, investigators from the University of California, San Diego have crafted novel genome modification mechanisms called multiplexed orthogonal base editors (MOBEs) that skillfully introduce various point mutations concurrently. This research, spearheaded by Assistant Professor of Chemistry and Biochemistry Alexis Komor, has been documented in Nature Biotechnology.

The Function of Single Nucleotide Variants

The investigation targeted genomes with disparities at just a single nucleotide alteration in the DNA. These constituents — C (cytosine), T (thymine), G (guanine), A (adenosine) — are recognized as bases. Whereas one person may possess a C base, another might have a T. These deviations are single nucleotide variants (SNVs) or singular point mutations, with an individual possibly harboring 4-5 million of such variations. While a number of these variations are innocuous, some are detrimental, and frequently, it’s their ensemble that indicates disease.

Obstacles in Genetic Disease Reconstruction

A frequent hindrance in harnessing the genome for disease modeling is the immense scope of potential variants. If researchers aimed to pinpoint the genetic mutations implicated in cardiac disease, they might analyze the genomes of a group afflicted with the ailment, but the numerous variations among any pair of individuals complicates the task of isolating which combination of variations prompts the condition.

“There is a fundamental hurdle in decoding genetic variants. Many variants that are identified are clinically unclassified, which means we don’t ascertain whether they are pathogenic or innocuous,” conveyed Quinn T. Cowan, a newly graduated Ph.D. from the university’s Department of Chemistry and Biochemistry and the paper’s lead author. “Our objective was to forge an implement that can be applied in disease reconstruction by implanting multiple variants within a controlled experimental setup where they can undergo further study.”

Advancement of Gene-Editing Implements

In grasping why MOBEs were conceived, it’s vital to recognize the constraints of the conventional gene-editing framework CRISPR-Cas9. CRISPR-Cas9 utilizes a guide RNA, which serves as a GPS beacon homing in on the specific spot in the genome you aim to alter. Cas9 is an enzyme that binds to DNA and shears through both strands of the DNA, effectuating a clean cleavage.

Despite its apparent simplicity, generating double-strand breaks can harm cells. This type of genome alteration can lead to indels — unpredictable sequences of insertions and deletions in the DNA — resulting from imperfect cellular reparations. Editing multiple genes with CRISPR-Cas9 amplifies these complications.

Rather than relying on CRISPR, Komor’s team champions a base-editing methodology she pioneered, inducing a chemical transformation in the DNA. However, only a single type of edit (such as C to T or A to G) can be executed at a given instance. Consequently, their strategy was to develop an approach that enables multiple, different edits concurrently.

Instead of scissors that remove a broad segment in one action, base-editing meticulously alters and substitutes individual letters sequentially. It may be slower, but it is significantly more precise and minimally damaging to the cells.

Introduction to MOBEs

Employing multiple base editors at once (transforming a C to a T at one spot, and an A to G at a different spot within the genome), facilitates the improved simulation of polygenic diseases — conditions caused by several genetic mutations. Up until now, no method could effectively implement various modifications without unintentional guide RNA “crosstalk” — accidental alterations.

Cowan’s MOBEs utilize RNA configurations known as aptamers — diminutive RNA circles that clamp onto distinct proteins — to draw base-altering enzymes to precise locations within the genome, thus allowing concurrent modifications at several sites with increased efficacy and reduced incidence of crosstalk.

Evidence of Concept and Prospective Uses

This innovative solution marks the premiere instance of employing aptamers to bring together ABEs (adenosine base editors) with CBEs (cytosine base editors) in a unique arrangement to construct the MOBEs.

The contrast is pronounced: when CBE and ABE are administered in tandem without MOBE, crosstalk happens as much as 30% of occasions. In contrast, using MOBE reduces crosstalk to beneath 5%, while realizing a 30% transformative efficiency in the targeted base amendments.

The investigation served as an evidence of concept to ascertain the viability of the MOBE system, which has been secured with a provisional patent. To subject them to further scrutiny, the group executed numerous case assessments with actual disorders, such as Kallmann syndrome, an uncommon hormonal condition. These experiments confirmed that MOBE frameworks could be employed to competently edit cells pertinent to certain polygenic ailments.

“We are engaged in the act of making the plasmids available on AddGene to ensure anyone has uninhibited access to them. We aspire that additional researchers will adopt the MOBEs to characterize genetic illnesses, comprehend their development, and thereafter devise potent treatments,” Cowan communicated.

Reference: “Formation of multiplexed orthogonal base editor (MOBE) mechanisms” by Quinn T. Cowan, Sifeng Gu, Wanjun Gu, Brodie L. Ranzau, Tatum S. Simonson, and Alexis C. Komor, 21 May 2024, Nature Biotechnology.
DOI: 10.1038/s41587-024-02240-0

This inquiry received partial funding from the National Institutes of Health (1R35GM138317, T32 GM008326, and T32 GM112584), as well as the Research Corporation for Science Advancement (28385).

The paper includes the following authors: Quinn T. Cowan, Sifeng Gu, Wanjun Gu, Brodie L. Ranzau, Tatum S. Simonson, and Alexis C. Komor (all based at UC San Diego).

Image Source: Tada Images / Shutterstock

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