Imagine a wildfire sweeps through a forest. Most of the vegetation is incinerated, and from a helicopter flying overhead, it looks like total destruction. But months later, the same patch of land is full with growth again. The forest that grows back is enriched for whatever survived or adapted the first time, and when another fire rips through, most of the forest survives. Tumors can behave the same way. Small cell lung cancer (SCLC) is a highly proliferative and aggressive disease. While chemotherapy initially eliminates the tumor mass, over 80% of patients with extensive-stage disease ultimately relapse with chemoresistant tumors. Chemoresistance could arise from rare pre-existing resistant cells or further adaptation of surviving cells under drug pressure. In a new study in Nature Communications, Dr. Scott Best and colleagues in the MacPherson lab at Fred Hutch tackled a fundamental question: which genes play a role in SCLC chemoresistance?
The researchers performed CRISPR-Cas9 knockout screens directly in patient-derived xenograft (PDX) tumors—human SCLC tumors grown in immunodeficient mice. This strategy maintains clinical relevance as SCLC tumors are known to lose important clinical properties upon growth in tissue culture. The team used a focused CRISPR library of ~400 candidate genes, including genes commonly altered/mutated in SCLC, implicated in SCLC chemoresistance, or identified as hits in a previous pilot screen. They isolated PDX tumors, knocked out genes in these tumor cells with the CRISPR library, implanted them back in mice, and treated mice with the standard SCLC chemotherapy combination cisplatin/etoposide or saline control. Any gene knockout where tumor cells better survive the treatment would show up as "enriched" in the treated group.
The screen identified enrichment of genes encoding subunits of SAGA, a transcriptional co-activator complex that modifies histones to control gene expression. The top hit was USP22, a deubiquitylase enzyme that removes ubiquitin tags from proteins and histones.
The team confirmed a causal relationship: deleting USP22 in two independent, highly chemosensitive PDX models made tumors resistant to chemotherapy, with USP22-deleted tumors exhibiting less apoptosis and reduced cell-cycle arrest. In line with this, they found a PDX model (JHU-LX33) that naturally harbors a truncating USP22 mutation and is chemoresistant. Restoring normal USP22 to this tumor re-sensitized it to chemotherapy, while a catalytically dead USP22 mutant failed to restore sensitivity, demonstrating that USP22's enzymatic activity is essential to chemosensitivity.
USP22 normally removes ubiquitin from histone H2A at lysine 119 (H2AK119ub), a repressive mark linked to Polycomb-mediated gene silencing. Without USP22, this mark piles up (along with the repressive mark H3K27me3) at genes controlling neuroendocrine identity, including the master regulator ASCL1 and neuronal genes like NKX2-1, NKX2-2 and SEMA6A. The authors also found decreased expression of these genes after USP22 loss. SCLC's neuroendocrine character is tightly linked to chemosensitivity, so silencing it appears to help tumors dodge the drugs.
Chemotherapy-induced DNA damage signaling was also attenuated in USP22-null tumors. Following cisplatin/etoposide treatment, these tumors showed weaker induction of γH2AX (a phosphorylation event that recruits DNA repair factors to DNA break sites), reduced phosphorylation of proteins downstream of the DNA damage checkpoint kinases ATM/ATR, and lower expression of DNA damage-response genes including BRCA1, CHEK1, and RAD51. These findings indicate that USP22-null tumors mount a diminished DNA damage response following chemotherapy.
USP22-null tumors had increased expression of glycolysis and hypoxia-related genes specifically after chemotherapy treatment—a metabolic shift that's been linked to chemoresistance in other cancers. This turned out to be a crucial susceptibility: inhibiting glycolysis with the GLUT1 inhibitor BAY-876 restored chemotherapy sensitivity in USP22-deleted tumors, boosting DNA damage signaling back to normal levels and shrinking tumors that were otherwise chemoresistant.
“These findings provide new insight into the development of chemoresistance in SCLC and identify the SAGA complex as a potential therapeutic vulnerability for overcoming treatment resistance,” lead author Scott Best shares.
“Our findings raise the broader question of how resistance to chemotherapy arises through mechanisms beyond loss-of-function alterations in small cell lung cancer,” he adds. “Moving forward, our lab will focus on systematically identifying these additional drivers of chemoresistance using orthogonal functional genomics approaches, including in vivo gain-of-function screening. We believe that defining the diverse mechanisms underlying chemoresistance will help uncover new therapeutic vulnerabilities and guide the development of more effective strategies for overcoming chemoresistance in small cell lung cancer.”
Fred Hutch/University of Washington/Seattle Children’s Cancer Consortium Members Drs. Lucas Sullivan, Patrick Paddison, Amanda Paulovich and David MacPherson contributed to this research.
The spotlighted research was funded by National Institutes of Health, including support for the Fred Hutch/University of Washington/Seattle Children’s Cancer Consortium.
Best S, Hippe DS, Grunblatt E, Fatherree J, Chanana P, Wu F, Ivey R, Kennedy JJ, Sokolov D, Ibrahim A, Xu H, Monnat Jr RJ, Sullivan LB, Paddison P, Paulovich AG, MacPherson D. 2026. Loss of the USP22 deubiquitylase confers resistance to chemotherapy in small cell lung cancer. Nat Commun. https://doi.org/10.1038/s41467-026-75117-2.
Science Spotlight writer Kelly Mitchell is a postdoctoral fellow in the Paddison Lab at Fred Hutch Cancer Center. She utilizes live cell reporters and CRISPR screening to study how glioblastoma cancer cells resist chemotherapy and radiation treatment. She obtained her PhD in cellular biology from Albert Einstein College of Medicine.