Genome Sequencing Method Identifies Genes Resistant to Chemotherapy

Scientists at St. Jude’s Children’s Research Hospital used a novel whole genome sequencing method to identify a gene associated with chemotherapy resistance in children with leukemia.

The team also uncovered a drug that may counter chemotherapy resistance, which could lead to improved patient outcomes and reduced mortality.  

In a study published in Nature Cancer, researchers described the novel method, which extends the momentum generated by whole genome sequencing and demonstrates the power of incorporating other dimensions of the genome.

The team used the method to identify a new gene, CELSR2, which is associated with acute lymphoblastic leukemia (ALL) resistance to glucocorticoids. CELSR2 is one of the 14 newly identified genes implicated in resistance to steroids, drugs that are critical for curing ALL.

"Drug resistance is a major cause of treatment failure for children and adults with disseminated cancers like leukemia," said corresponding author William Evans, Pharm.D., of the St. Jude Department of Pharmaceutical Sciences.

"Steroids play an essential role in the treatment of acute lymphoblastic leukemia. About 20 percent of children with acute lymphoblastic leukemia and twice as many adults are highly resistant. Yet, the underlying cause of resistance often remains unknown."

The team measured six types of genomic and epigenetic features in leukemia cells, then created a computational pipeline to aggregate each genetic feature to individual genes. Scientists were aiming to find out which genes were most strongly associated with steroid resistance.

The group then employed innovative methods like CRISPR gene editing and a sophisticated statistical tool to prioritize genes for further investigation. The methods included analyzing and validating data from 500 patients at St. Jude’s who were newly diagnosed with ALL. Investigators looked for associations between steroid resistance and gene variations, gene expression, gene regulation, and other factors.

The team developed a statistical tool to rank the contribution of more than 19,700 genes to steroid resistance, called truncated aggregation of P-values (TAP). Using the CRISPR gene cutting tool, researchers knocked out genes across the genome as another way to recognize drug resistance.

In addition to identifying novel genes, the method identified 78 percent of the 38 genes known to cause steroid resistance and 100 percent of the molecular pathways involved.

CELSR2 was the gene most strongly associated with steroid resistance. Decreased CELSR2 response in patients was associated with increased steroid resistance. About half of steroid-resistant ALL in children and adults in this study had reduced CELSR2 expression.

Reduced levels of CELSR2 protein likely contributes to steroid resistance by promoting increased expression of the protein BCL2, which inhibits a cell death pathway. Venetoclax, a drug that is commonly used to treat leukemia subtypes common in older adults, inhibits BCL2.

In a model system in the lab and in mice with human ALL expressing low CELSR2, venetoclax mitigated steroid resistance by inhibiting BCL2. Mice with steroid-resistant human ALL lived longer when steroid treatment was combined with venetoclax.

"The findings point to the potential benefit of combining venetoclax with current remission-induction therapy as a strategy to overcome steroid resistance and improve the effectiveness of ALL chemotherapy," Evans said.

Recently, genetics and genomic sequencing have played an important part in advancing leukemia treatment.

A team at Nemours Children’s Health System identified new genetic structural variants that could help deliver more personalized care and precision medicine to patients with leukemia.

“Progress in the field of genomic research and advanced technology has allowed us to find new variants that can better target treatments for kids with cancer,” said Erin Crowgey, PhD, lead author of the study and Director of Clinical Bioinformatics at Nemours.

“Pediatric leukemias have a diverse and complex genomic structure, and older sequencing techniques were missing a lot of the important information that guides our clinical evaluation, risk identification, and therapeutic strategy for patients.”

The studies suggest that genomics and precision medicine will soon improve cancer care for both adults and pediatric patients.