The era of genome-targeted therapeutics

Changes in the genome often drive or contribute to diseases, such as cancer. Several effective cancer chemotherapies target the genome but do so somewhat indiscriminately. Many act on the first available segment of the genome that they encounter. Others broadly prevent DNA repair or the resolution of tangles (topological knots) that occur when the genome is copied or transcribed. The impact is most acutely felt by rapidly dividing cancer cells, but healthy cells are also affected. It is this collateral damage that limits the dose and duration of chemotherapy.  

Using non-selective genome-targeted chemotherapies has been an effective strategy to target cancer cells whose genome is mutated or scrambled beyond repair. However, in pediatric malignancies, cellular genomes are often relatively undamaged. In this context, subjecting the genome to a non-selective chemotherapeutic agent is undesirable, and it shines light on the unmet need for precision-tailored genome-targeting agents.

As scientists identify tell-tale changes in cancer-driving genes (or regions that control their expression) with increasing precision, the need to design and deploy agents that specifically target malfunctioning parts of the genome and remedy the dysfunction becomes more palpable. In fact, such approaches would benefit other ailments as well. Beyond cancers, the etiology of several diseases can be traced back to sequence changes in certain genes or regulatory elements that control them. Examples include sickle cell disease, immune cell dysfunction, degenerative neurological diseases and a host of inherited disorders. In such cases, scientists have long desired selective targeting and modulation of the disease-causing genomic locus. But until recently, there were no apparent means of achieving precision-targeted control of genes and genome functions.

The growing understanding of how genomic perturbations lead to disease is helping chart new paths to precision-targeting the genome therapeutically. From gene editing technologies to synthetic molecules to targeting epigenetics, laboratory findings are changing what it means to drug the genome.

Precision-targeting of genomic loci

The past decade has witnessed a revolution in targeted genome editing using a repurposed bacterial anti-viral defense system called CRISPR-Cas. The system was first described in 2012 by a former St. Jude postdoctoral fellow, Emanuelle Charpentier, in collaboration with Jennifer Doudna (for which they jointly won The Nobel Prize in Chemistry in 2020). The original CRISPR approach leveraged the bacterial protein Cas9, loading it with user-defined “guide” RNAs that directed the Cas9-RNA complex to targeted genomic sites. The first-generation CRISPR-Cas9 complexes generated double-stranded breaks at targeted genomic loci. Cells would repair these targeted breaks in a manner that would alter the underlying genomic sequence.

In the ensuing decade, a “Cambrian explosion” has led to myriad new versions of the CRISPR-Cas technology for increasingly precise genome and transcriptome editing. At St. Jude, Shondra Pruett-Miller, Shengdar Tsai, and Mitch Weiss, among other colleagues, leverage these approaches to overcome the genomic changes that lead to sickle-cell disease. While CRISPR approaches are powerful and ever-evolving, these large protein-RNA complexes face challenges in delivery, repeat dosing and long-term immune tolerability. Sequence-selective small molecules offer a complementary alternative.  

Synthetic genome “readers and regulators” (SynGRs)

Inspired by the natural antibiotics distamycin and netropsin, Peter Dervan developed a remarkable class of molecules; these synthetic DNA binders can be rationally designed to bind 6-12 base pair DNA sequences. That is roughly the length of DNA is targeted by natural human gene regulators — transcription factors such as Myc or the estrogen receptor (ER).

At the outset, researchers used such designer synthetic DNA binders to target binding sites of malfunctioning or disease-causing transcription factors. The synthetic molecules showed early promise in competitively displacing transcription factors and modulating gene circuits in tissue culture cells. Our team studied how these synthetic molecules find their target sites by mapping their genome-wide binding properties in living cells. This process led to the unexpected observation that synthetic genome readers had a longer “dwell time” at regions with clusters of their binding sites. This realization, published in Proceedings of the National Academy of Science in 2016, opened the door for targeting a number of diseases that occur because of head-to-tail, tandem repeats of short 3-6 nucleotide sequences within a gene or its regulatory regions.

Huntington’s disease, Fragile-X, Myotonic Dystrophy and Friedreich’s Ataxia (FA) are among the 40 (and growing) diseases that owe their origins to the tandem expansion of 3-6 nucleotide “microsatellites.” FA is a terminal neurodegenerative disease caused by GAA trinucleotide expansion within the frataxin gene. In FA, hundreds of GAA repeats prevent the expression of frataxin. Our team created a bi-functional synthetic genome reader and regulator (SynGR) to target the “diseased” genomic locus and facilitate the expression of the underlying gene. This SynGR, published in Science in 2017, can bind three GAA repeats. However, rather than displace natural proteins, it recruits proteins that license frataxin expression (dismantling the roadblock to gene expression manifested by the expanded GAA repeats) and restores the levels of the protein naturally found in asymptomatic individuals.

This prototype SynGR opened the door to selectively target a wide range of sequences enriched at disease-causing genomic loci. The coming years offer the promise of genome-tailored solutions to rare and pediatric diseases.

Targeting epigenomic marks

Beyond the DNA sequence, layers of overlapping marks and signals impact genome function. Methylation, the placement or removal of these chemical marks, can impair the ability of cellular machinery to engage the genome. Worse still, these marks might engage proteins that silence genes. In chronically stimulated T cells, genomic sequences are widely methylated and thought to result in cellular “exhaustion,” a phenomenon currently investigated at St. Jude by several researchers, including Ben Youngblood and Caitlin Zebley. CAR T–cell exhaustion also appears to contribute to reduced tumor-killing activity, a process studied by Stephen Gottschalk, Giedre Krenciute and other colleagues.

Removing such “epigenetic/epigenomic” marks by silencing the enzymes that place these marks, or by expressing enzymes that remove them, has shown promise in overcoming T-cell exhaustion. Genome-targeted small molecules that prevent the placement of such repressive marks or engage machinery to facilitate their removal present an exciting area of research.

Small molecules that act on enzymes that control access to DNA by altering its state of compaction have also led to several therapeutic agents, including EZH2 inhibitors such as tazemetostat in epitheloid sarcomas, based on work by Charles W.M. Roberts. Several classes of small molecules targeting diverse enzymes that alter chromatin states and genomic function are in development worldwide and have already yielded new classes of therapeutics. The ability to deliver such molecules to desired genomic loci will lead to the next generation of genome-targeted therapies with large therapeutic indices and minimal off-target effects.

New frontiers: St. Jude — a world leader in Transcription Therapy

Targeting genomes with small molecules and biologics is a highly promising area of scientific and clinical research at St. Jude. With over 75 clinical and research groups investigating different facets of gene regulation and genome function, St. Jude is an emerging leader in the nascent field of transcription-targeted therapy. In addition to selectively targeting the genome, transcription therapy includes targeting regulators that actuate the genome. These include transcription factors, enzymes that act on chromatin and the transcriptional machinery, architectural proteins and other modulators of genome function. Dysfunction of such genome “actuators” contribute to a broad swath of pediatric diseases.

To define the leading edge of this field, over the past three years, St. Jude has brought together thought leaders in chemistry, biology, computation and medicine through the Bringing Chemistry to Medicine symposium. Jointly organized by the Department of Chemical Biology and Therapeutics and the Comprehensive Cancer Center, the first day of the conference focuses on new and emerging trends in Transcription Therapy. Complementing the focus on gene regulation, the second day more broadly covers cutting-edge chemical approaches to studying biomedicine. Exciting advances in targeted protein degradation, exploration of biomolecular condensates and selective partitioning of chemotherapeutics or targeting of seemingly inaccessible protein-protein interfaces with small molecule inhibitors are just some of the topics discussed.

The 2023 Bringing Chemistry to Medicine symposium will be held in a hybrid format with options to attend in-person or virtually. We invite you to register to join us in exploring and developing this exciting area at the interface of science and medicine.