Despite their similar morphological appearance, related cancers often exhibit significant differences in clinical characteristics, treatment responses, and overall outcomes. Identification of specific molecular subtypes can lead to better drug design and improved patient outcomes by predicting optimal therapeutic strategies. In recent years, two transcriptional subtypes of pancreatic ductal adenocarcinoma (PDAC), the most aggressive form of pancreatic cancer, have been identified: classical and basal. A recent study led by Jessica Gianopulos, a graduate student in Dr. Sita Kugel's lab, an Assistant Professor in the Human Biology Division, identified sirtuin 6 (SIRT6) as a differential marker for PDAC subtypes. “We have identified the first subtype-specific therapy for PDAC,” Jessica said. “For decades, the standard of care treatment for PDAC has remained relatively unchanged, resulting in a dire need for new therapeutic options,” she added. The identification of specific markers for each subtype will “provide an important insight into why patient responses are dramatically different with standard chemotherapy.”
First, the authors analyzed the susceptibility of PDAC cell lines to THZ1, a potent inhibitor of CDK7. They found that THZ1 treatment significantly decreased MYC protein expression, a well-established driver of tumorigenesis, in both classical and basal PDAC cells. However, cell death was observed only in basal PDAC cells, suggesting that THZ1-induced cell death is independent of MYC suppression. Moreover, overexpression of MYC in basal PDAC cells failed to prevent THZ1-mediated cell death. Additionally, the authors examined whether inhibition of CDK’s by THZ1 was required to induce cell death in basal PDAC cells. Knockout (KO) of CDK7 in both basal and classical PDAC cells resulted in cell growth inhibition and induction of apoptosis only in basal PDAC cells. The authors concluded that inhibition of CDK7, but not MYC, is essential for THZ1-induced cell death in basal PDAC cells.
For a better understanding of THZ1-induced cell death in PDAC cells, the authors performed RNA sequencing in classical and basal PDAC cells treated with THZ1. The authors found that transcription-related genes were potently and specifically repressed in basal PDAC cells. The authors then examined mRNA translation in classical and basal PDAC cells. The researchers found that translation was increased in basal PDAC cells compared to classical PDAC cells. Furthermore, THZ1 treatment dramatically inhibited translation in basal PDAC cells but not in classical PDAC cells.
The integrated stress response (ISR) is activated in response to various stressors, including cancer. Activation of ISR results in a decrease in global translation and the induction of selected genes, including transcription factor ATF4, that together promote cellular recovery or death. The Kugel lab discovered that classical PDAC cells express high levels of ATF4 consistent with low translation levels. Conversely, they found that basal PDAC exhibited low ATF4 and, therefore, increased translation. Interestingly, the NAD-dependent deacetylase SIRT6 has previously been reported to bind to ATF4. Hence, the authors investigated whether the increase in ISR in the classical PDAC was due to the interaction between these proteins. The authors found that loss of SIRT6 resulted in a decrease in both ATF4 protein levels and ATF4 target gene levels. Although ATF4 is predominantly regulated through translation, the authors discovered that SIRT6 controls the stability of ATF4 protein in PDAC. Mechanistically, SIRT6 binds to ATF4 and localizes it to nuclear speckles, which protects ATF4 from proteasomal degradation. Thus, SIRT6 stabilization of ATF4 enables transcriptional activation of ATF4 target genes and control of the ISR in classical PDAC.
Next, the authors examined whether ISR activation could protect basal PDAC cells from CDK7 inhibition. Activation of the ISR decreased cell death in basal PDAC cells following THZ1 treatment. In contrast, blocking ISR activation in classical PDAC cells increased cell death. Knocking down ATF4 in classical PDAC cells had the same effect. Finally, the authors validated their findings in vivo using the CDK inhibitor flavopiridol which is approved for use in the clinical. Immunocompetent mice were implanted with SIRT6 KO or wild-type (WT) PDAC organoids and then treated with flavopiridol. Unlike SIRT6 WT organoid tumors, SIRT6 KO organoid tumors could not grow in the presence of flavopiridol. In PDAC, SIRT6 expression correlates with the classical subtype and can be used to predict sensitivity to CDK inhibitors. “We have uncovered the mechanism by which regulation of a stress-induced pathway controls the sensitivity of PDAC to these inhibitors,” Jessica commented. In future work, the authors will continue investigating “PDAC subtypes to better understand their biological differences and identify more vulnerable pathways that can be targeted for therapeutic development,” Jessica concluded.
The spotlighted research was supported by grants from the National Institute of Health, the V Foundation for Cancer Research, the Swim across America Pancreas Cancer Development Research Award, Chromosome Metabolism, Cancer training grant, America Cancer Society Postdoctoral Fellowship, and the Walter Benjamin fellowship from the German Research Foundation.
Fred Hutch/University of Washington/Seattle Children's Cancer Consortium members Andrew C. Hsieh and Sita Kugel contributed to this work.
Kartha N, Gianopulos JE, Schrank Z, Cavender SM, Dobersch S, Kynnap BD, Wallace-Povirk A, Wladyka CL, Santana JF, Kim JC, Yu A, Bridgwater CM, Fuchs K, Dysinger S, Lampano AE, Notta F, Price DH, Hsieh AC, Hingorani SR, Kugel S. Sirtuin 6 is required for the integrated stress response and resistance to inhibition of transcriptional cyclin-dependent kinases. Sci Transl Med. 2023 May 3;15(694):eabn9674. doi: 10.1126/scitranslmed.abn9674.