Science

RESEARCH

Susumu Tonegawa, 1987 Nobel Prize in Medicine: "Creativity is made of 3 simple concepts: 1) You have to be very curious about something; 2) You have to have unfailing urge to address the question you have; 3) Try to combine knowledge in at least two different fields where people don't necessarily interact."

Our laboratory is studying the mechanisms that promote DNA Repair and Genome Editing.

 

The lab employs cutting-edge genome editing technologies, high-throughput genetic screens, biochemical assays, cell biology experiments, and mouse models to interrogate and manipulate the cellular mechanisms that protect our genome. Studying and controlling the cellular DNA damage response will provide new insights into the mechanisms that promote genome stability, and improve genome editing applications.

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DNA damage response pathways being targeted in the clinic.

 

DNA repair pathways (MMR, SSB//BER, HR, NHEJ) are activated by various DNA lesions (mismatch, single-strand or double-strand breaks). DNA repair factors are targeted by small molecule inhibitors to induce genomic instability in a range of human cancers.

DNA REPAIR. Genomic instability is an enabling characteristic of cancer, a leading cause of death and disease worldwide.

Cells have developed highly sophisticated and complex mechanisms, collectively referred to as the DNA Damage Response (DDR), that detect and repair DNA damage. The DDR suppresses tumorigenesis and modulates the response to cancer therapies by conferring exploitable vulnerabilities to tumor cells. The targeting of the DDR, that protects against genomic instability, has proven to be an effective strategy for counteracting cancer development and improving therapy. Consequently, it is crucial to comprehensively study the fundamental mechanisms regulating the DDR under physiological and pathological conditions in order to develop targeted therapeutic strategies. The lab aims to leverage the DDR to better understand cancer development and to enhance therapy.

 

Recent advances in genome editing technologies enable the interrogation of encoded regulatory information with single base resolution. This provides new opportunities for development of a range of approaches to elucidating the fundamental molecular mechanisms underlying cancer progression and to enhance the efficiency of DNA damage-based cancer treatments. Deciphering the regulatory mechanisms that maintain genome stability is crucial not only for allowing new insights into the cellular response to conventional cancer therapies, but also for developing new strategies to facilitate drug discovery.

Read our recent work here.

Modern CRISPR-based genome editing technologies.

Several site-specific DNA lesions, including double-strand breaks, nicks, deaminated bases and flaps, are induced by modern CRISPR-based genome editing technologies that are detected and repaired by the DDR resulting in editing.

a) CRISPR-Cas9. Cas9 initiates genome editing by introducing a site-specific double-strand break.

b) Base editing. Nickase Cas9 is fused to deaminases for targeted base deamination.

c) Prime editing. Nickase Cas9 is fused to an engineered reverse transcriptase that directly copies the information contained in the guide RNA.

GENOME EDITING. DNA is the precious hereditary material of biological systems. Genomes contain genetic variants that can cause or predispose humans to disease. Emerging genome editing technologies have the potential to prevent or cure human disorders by eliminating pathogenic variants.

Genome editing technologies operate by triggering cellular DNA repair systems to resolve site-specific DNA lesions in living systems. The ability to introduce site-specific double-strand breaks by engineered nucleases or natural CRISPR-associated nucleases (a) laid the foundations for the recent genome editing revolution. Modern sophisticated DSB-free genome editing agents, such as programmable base editors (b), prime-editors (c) and integrases, are exploited to generate precise base modifications, and insertions and deletions of desired sequences by inducing genomic lesions and by stabilizing certain repair intermediates at specific genomic sequences. These include single-strand breaks, deaminated bases, abasic sites, mismatched nucleotides and flap structures. Accurate, specific and predictable editing can be modulated by manipulating cellular DNA repair effectors. The lab aims to control DNA repair to improve the efficiency, accuracy and safety of modern precision genome editing technologies.

The manipulation of the cellular DNA repair mechanisms will enable a fine control of editing in therapeutic cellular systems. The insights gained from this work will not only improve the applications of genome editing technologies but also help generate important knowledge on the fundamental mechanisms of DNA repair. An adequate control of the cellular response to DNA damage will lay the foundation for precise therapeutic genome editing and contribute to precisely modelling and functionally studying pathogenic variants.

Read our recent work here.