KEAP-ing chemoresistance at bay in SCLC

Small cell lung cancer (SCLC) is a highly aggressive form of lung cancer that accounts for ~15% of all lung cancer cases. Despite being initially responsive to treatment, the vast majority of tumors relapse, now resistant to the original treatment. This pattern contributes to the high mortality rate: nearly 73% of patients die within five years of diagnosis.

SCLC is defined by its frequent loss of tumor suppressor genes, which normally keep cell growth in check. How these tumors develop chemoresistance so reliably remains a mystery to the field. A new study published in Science Advances by Lauren Brumage , Scott Best and Dr. David MacPherson from the MacPherson lab tackles this mystery head-on, identifying KEAP1 loss as a key mechanism behind resistance.

Using a patient-derived xenograft (PDX) that hasn’t yet acquired any chemoresistance, they performed a screen for 363 genes associated with SCLC including two — MYCN and MYCL — that they’ve previously shown to drive chemoresistance. After using lentivirus to introduce their library into the tumor-derived cells, they implanted them into mice and waited for them to grow. The established tumors were treated with either saline as a control or a combination of cisplatin and etoposide, two chemotherapeutics that target the cell cycle.  The group was encouraged to find that barcodes associated with chemoresistance-promoting MYCN appeared more frequently in the chemotherapy-treated tumors — validating the screen’s ability to detect resistance-promoting genes.

With their model system set up, co-lead author Scott Best moved forward to conduct an in vivo CRISPR-Cas9 deletion screen using a second PDX. This time, they did a loss-of-function screen using a SCLC-focused library of 400 guide RNAs (gRNA) targeting genes chosen by mining genomic data for areas with deletions or truncating mutations, as well as genes that are already implicated in chemoresistance such as members of the Wnt signaling pathway.

When they focused on guides that were enriched in in chemotherapy-treated tumors, six genes stood apart from the rest. Five of the six belong to the Spt-Ada-Gcn5-acetyltransferase complex – which Scott Best in the lab is investigating separately, so stay tuned – while the sixth enriched sgRNA targeted KEAP1, which the lab described as “a master regulator of the nuclear factor erythroid 2-related factor 2 (NRF2) oxidative stress response pathway.”

KEAP1, short for Kelch-like ECH-associated protein 1, acts as a molecular "off-switch" for the antioxidant regulator NRF2. Under normal conditions, KEAP1 targets NRF2 for degradation, keeping its activity low. But in response to cellular stress, KEAP1 changes shape and releases its grip, allowing NRF2 to accumulate and enter the nucleus. There, NRF2 triggers a gene expression program that boosts the cell’s ability to detoxify harmful molecules and survive stress.

With KEAP1 flagged as a potential driver of resistance, the authors zoomed in. Brumage used a KEAP1-targeting sgRNA from their screen to generate tumors with KEAP1 loss and treated these alongside control tumors with cisplatin and etoposide. In control tumors, chemotherapy shrank the tumors as expected. But in tumors lacking KEAP1, the drugs were completely ineffective — clearly demonstrating that KEAP1 loss is sufficient to drive chemoresistance in this model.

But how does KEAP1 loss promote resistance at the molecular level? RNA sequencing revealed upregulation of NRF2 target genes and, intriguingly, a broader shift toward metabolic reprogramming. Pathways such as glycolysis, hypoxia response, and glutathione metabolism were upregulated — consistent with enhanced antioxidant defenses and altered nutrient usage.

To investigate the metabolic angle further, the team used mass spectrometry and found that KEAP1-deficient tumors had lower glutamate levels — a clue that these tumors might rely on glutamine metabolism. They tested this by treating tumors with telaglenastat (CB-839), a glutaminase inhibitor. Strikingly, this treatment caused regression of KEAP1-deficient tumors, while tumors with intact KEAP1 remained unaffected.

Reflecting on this discovery, Brumage noted, “The most exciting and impactful aspect of this publication was identifying glutaminase inhibition as a therapeutic vulnerability in KEAP1-mutant SCLC, paired with the data from collaborators at Genentech showing that the KEAP1-NFE2L2 pathway is mutated in a subset of actual SCLC patients.”

Indeed, the final phase of the study emphasizes the importance of clinical collaboration. To assess the relevance of their findings in patients, the team partnered with Genentech and turned to data from the IMpower133 trial — a landmark clinical study that added the immune checkpoint inhibitor atezolizumab to platinum-etoposide chemotherapy. By analyzing gene expression data from trial participants, Brumage and colleagues found that a subset of patients exhibited high expression of an 11-gene KEAP1/NRF2 signature, suggesting pathway activation in real tumors. Importantly, patients with elevated signature scores had poorer clinical outcomes, reinforcing the role of KEAP1 loss in chemotherapy resistance.

As Brumage concluded, “Together, these findings demonstrate the clinical relevance of our work and point to a new way to target this subset of SCLC.”

Fred Hutch/University of Washington/Seattle Children’s Cancer Consortium Members Drs. Slobodan Beronja, Patrick Paddison, Lucas Sullivan, and David MacPherson contributed to this research.

The spotlighted research was funded by the National Institutes of Health.

Brumage L#, Best S#, Hippe DS, Grunblatt E, Chanana P, Wu F, Lee M, Ying Z, Ibrahim A, Chung J, Vigil A, Fatherree J, Beronja S, Paddison P, Sullivan L, Nabet B, MacPherson D. 2025. In vivo functional screens reveal KEAP1 loss as a driver of chemoresistance in small cell lung cancer. Science Advances. DOI: 10.1126/sciadv.adq7084.  # co-first authors