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Natural killer cells and immune control: Deciphering the transcription factors that regulate expression of the NKG2D-ligand MICA

Subject Area Immunology
Term from 2017 to 2024
Project identifier Deutsche Forschungsgemeinschaft (DFG) - Project number 324329506
 
Final Report Year 2024

Final Report Abstract

Using a novel engineered ChIP approach in combination with mass spectrometry, we were able to identify a pharmacologically accessible transcription factor, which induces MICA expression in AML cells. Among the locus-associated chromatin components, we identified KLF4 and provided evidence for its critical role in the transcriptional regulation of MICA. Our conclusions are based on the findings that 1) the MICA promoter harbors KLF4 binding motifs and is regulated by KLF4 and that 2) the established HDACi-mediated upregulation of MICA is diminished upon chemical inhibition or genetic ablation of KLF4. Of note, KLF4 activity is known to be regulated by CBP/p300 acetyltransferases, which are the critical enzymes in the HDACi-mediated upregulation of MICA (8). Moreover, we demonstrate that 3) the small molecule APTO253, a KLF4 inducer, leads to the upregulation of MICA in AML cells. In line with this observation, 4) upregulation of MICA in response to DNA damage is also associated with KLF4 induction and abolished in chemoresistant cells, which fail to express KLF4. Interestingly and pointing towards the clinical relevance of these data, 5) APTO253-treated AML cells express surface MICA and are more susceptible to NK cell-mediated killing, although we cannot exclude that other receptor-ligand interactions may contribute to increased killing. The identification of the transcription factor network responsible for the inducible expression of a target gene remains difficult, as the chromatin composition is complex and dynamic, and single-locus proteomics remains technically challenging (17, 18). To filter promising candidates, we considered transcription factors fulfilling the following criteria as putative MICA regulators: first, regulation by CBP/p300-mediated acetylation and, second, binding motifs (if known) within the MICA promoter. Besides KLF4 we also detected PARP1, which was recently described to inhibit MICA expression on AML cells as part of the tumor immune evasion strategy (19), which validates the approach. Other factors passing the selection criteria, including the YY1 protein, were so far not described in the context of MICA transcriptional regulation. YY1 is known to antagonize PARP1 activity (20) and thus may play an analogous role in PARP1-mediated inhibition of NKG2D-L expression. Among the candidates, we focused on KLF4, because KLF4 can be induced by APTO253, a small molecule that is already in clinical testing. KLF4 has been shown to function as a tumor suppressor or oncogene in cell-dependent contexts (13). Although the role of KLF4 in AML is controversially discussed, it has been shown to play an oncogenic role in AML cell lines and the deletion of KLF4 by CRISPR/Cas9 suppresses cell growth and induces apoptosis (21, 22).These experiments were, however, performed in immunodeficient mouse models, and a putative innate immune response to NKG2D-L positive AML was not addressed. KLF4 is one of the Yamanaka factors, which induce pluripotent stem cells. In line, KLF4 was recently shown to promote leukemia stem cell division and stemness (22). This finding may seem paradoxical but makes sense considering that NKG2D-L expression is an early cellular response to malignant transformation in order to alert the innate immune system to dangerous cells – which is characterized by high KLF4 expression. In line with that, RNA expression data of sorted NKG2D-L negative AML patient cells (with stem cell properties) revealed a significantly lower KLF4 expression as compared to NKG2D-L positive AML patient cells (no stem cell properties) (p = 4.4 × 10–44, see supplement in (19). So far, APTO253 monotherapy trials to treat AML patients showed only a limited response with no severe side effects (23,24). Here, we unraveled for the first time that the KLF4-inducer APTO253 re-activates MICA expression in AML cells. This provides a novel and unexpected link of APTO253 to immune cell activation and the NKG2D/NKG2D-L axis. These results suggest that the combination of APTO253 with NK cell-based therapies may be beneficial for AML patients. Further, we extended the research to validate the effect of APTO253 in other cancer cell lines and found that the enhanced expression of NKG2D-L in response to APTO253 is limited in a tumor cell-specific manner, and for example not seen in pancreatic cancer cells. Additionally, our data suggest a link between the induced expression of MICA and the regulation of both, KLF4 and c-MYC, which might represent a mechanism underlying the induction of NKG2D-L expression upon treatment with APTO253 (ATM, Brief report, accepted and attached).

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