OHSU Knight Cancer Institute scientists have identified key gene networks and signaling pathways that cancerous cells in acute myeloid leukemia use to resist treatment with the drug venetoclax, one of a new generation of targeted therapy drugs.
Image: A watercolor drawing made in 1912 of blood cells from a patient with myeloid leukemia (Wellcome Collection).
The discovery points the way to treatment strategies to overcome resistance and potentially stop the cancer long-term. It’s the latest in a series of studies showing the power of the Beat AML dataset, which includes tissue samples from more than 500 patients, gene sequencing results and other information assembled by Knight Cancer researchers.
Jeff Tyner, Ph.D., and colleagues describe the new findings in a paper in Cancer Discovery. Tyner is an associate professor of cell, developmental and cancer biology in the OHSU School of Medicine. First author Tamilla Nechiporuk, Ph.D., is a senior research associate in Tyner’s lab.
AML is the most common acute blood cancer in adults – and one of the most difficult to treat. New targeted therapy drugs have fallen short of their promise because the cancer so quickly mutates to gain resistance.
Venetoclax targets the protein BCL2, which cancer cells use to avoid the programmed death spiral, called apoptosis, that the body uses to eliminate abnormal cells. Venetoclax received an accelerated approval from the Food and Drug Administration at the end of 2018 for treating AML in combination with anticancer agents commonly used against the leukemia.
Becoming resistant to one drug led to new vulnerabilities to others, the researchers found.
Tyner and colleagues cast a wide net in their hunt for the secrets of drug resistance. His team used the gene-editing tool known as CRISPR to produce a multitude of AML cell lines, each with one of 18,000 genes rendered inoperable. They exposed these cancer cell lines to the drug venetoclax and compared the drug resistance of cells with different genes knocked out.
This strategy narrowed the search to three main suspect genes: TP53, BAX, and PMAIP1. Loss of function of any of these three genes established venetoclax resistance in a cell line.
With the large number of patient samples available in the Beat AML dataset, the researchers were able to validate the important role of TP53 and BAX gene mutations in helping cancer cells resist venetoclax. AML patient samples with inactivating mutations in the TP53 gene showed increased resistance to venetoclax, as did patient samples with less active TP53 and BAX genes. In contrast, patient samples with less active PMAIP1 did not show increased resistance to venetoclax, a result that highlights the importance of the voluminous Beat AML dataset of primary patient samples to test findings obtained from lab-grown cancer cell lines.
Further experiments showed that drug resistance resulted in part from an inability to execute programmed cell death, and more specifically from changes that protected the cells’ mitochondria from damage. Mitochondria are units within cells where energy conversion takes place.
Cells resistant to venetoclax also showed significant metabolic differences that are indicative of high rates of cell proliferation, energy production and DNA synthesis. The metabolic differences were echoed in the AML patient samples with TP53 mutations.
Becoming resistant to one drug, however, also led to new vulnerabilities to other drugs, the researchers found. They exposed TP53 and BAX gene knock-out cells to a variety of chemical inhibitors that target different signaling pathways activated in cancers.
Cells with those genes knocked out became newly sensitive to several inhibitors that disrupt NTRK/ALK/ROS1 signaling, such as entrectinib, or to the NTRK selective inhibitor, larotrectinib. Patient samples with TP53 mutations also showed increased sensitivity to entrectinib. The researchers say future studies will focus on assessing NTRK inhibitor sensitivity in TP53 mutant AML patient sample xenografts.
The TP53 Apoptotic Network is a Primary Mediator of Resistance to BCL2 inhibition in AML Cells by Tamilla Nechiporuk, Stephen Kurtz, Olga Nikolova, Tingting Liu, Courtney Jones, Angelo D’Alessandro, Rachel Culp-Hill, Amanda d’Almeida, Sunil Joshi, Mara Rosenberg, Cristina Tognon, Alexey Danilov, Brian Druker, Bill Chang, Shannon McWeeney, and Jeffrey W. Tyner. Cancer Discovery (May 2, 2019)
Studies reveal new ways to fight a deadly leukemia by Joe Rojas-Burke. Cancer Translated (Jan. 17, 2019)
OHSU-led effort results in largest cancer dataset of its kind by Amanda Gibbs. OHSU News (Oct. 17, 2018)