SAMHD1 silencing cooperates with radiotherapy to enhance anti-tumor immunity through IFI16-STING pathway in lung adenocarcinoma

Lung cancer is one of the most common malignant tumors with the highest mortality in the world [1]. Histopathologically, approximately 50% of lung cancers are lung adenocarcinoma (LUAD) [2]. In clinical practice, most patients were already at advantage stages when they were first diagnosed with LUAD [3]. Nowadays, the clinical application of immunotherapy has greatly improved the treatment outcome of patients. However, in advanced LUAD, the response rate of programmed death-1/programmed death-ligand 1 inhibitor monotherapy is only 17–21% [4]. The optimal treatment strategy for advanced LUAD is still controversial. It is of great importance to seek combined strategies and improve tumor immune microenvironment.

Radiotherapy enhances the immunogenicity of tumor cells [5], and has a synergistic effect with immunotherapy [6]. Radioimmunotherapy generates more effective anti-tumor immune responses, but its regulatory mechanism is still being studied. Radiotherapy can active cyclic GMP-AMP synthase (cGAS)/stimulator of interferon genes (STING) signaling pathway and promote the release of pro-immune cytokines [5, 7]. Radiation directly induces DNA damage and the formation of micronuclei in cancer cells, and cause DNA single- and double-stranded breaks [8]. The accumulation of micronuclei and double-stranded DNA in the cytoplasm result in the activation of the cytoplasmic DNA sensor cGAS, which activates the STING/type I interferon (IFN) signaling pathway, promoting the infiltration of CD8⁺ T cells in tumors [9]. DNA damage repair deficiency alone or in combination with radiotherapy enhances the immunostimulatory function through IFN-I signaling pathway [7].

Sterile alpha motif domain and histidine-aspartate domain-containing protein 1 (SAMHD1) was originally identified in 2000 as an IFN-γ-inducing protein in dendritic cells [10]. In the past decade, consequent researches revealed that SAMHD1 was a key limiting factor for human immunodeficiency virus infection [11], and that its mutation caused Aicardi–Goutières syndrome, a hereditary inflammatory encephalopathy caused by excessive interferon (IFN) production [12]. Recent studies indicated that SAMHD1 formed homo tetramers in the G1 phase, playing a role as deoxy-ribonucleoside triphosphate (dNTP) hydrolase to maintain the balance of dNTP pools [13]. However, when entering the S phase, SAMHD1 was phosphorylated at T592 to promote degradation of nascent DNA at stalled replication forks and activate the ataxia-telangiectasia-mutated-and-Rad3-related kinase/checkpoint kinase 1 checkpoint. SAMHD1 deletion led to the accumulation of single-stranded DNA (ssDNA) in the cytoplasm and activate the STING signaling pathway [14]. SAMHD1 also plays important roles in DNA damage repair. It binds to Meiotic Recombination 11 (MRE11) and recruits CtBP interacting protein (CtIP) to the DNA damage sites to promote DNA end resection, activating the DNA damage repair pathway [15].

Radiotherapy causes DNA damage and activates anti-tumor immunity, and SAMHD1 participates in DNA damage repair and innate immune responses. Therefore, we supposed that the combination of SAMHD1 silencing and radiotherapy might enhance the DNA damage and augment the anti-tumor immunity. Here, we designed experiments in vitro and in vivo to investigate and verify the function of SAMHD1 in anti-tumor immunity and radiotherapy.

SAMHD1 (72 kDa, 626aa) is located at human chromosome 20q11.23 as a dNTP hydrolase [26] and a DNA end resection factor [27], which was involved in DNA damage repair and innate immune responses [28]. In recent years, SAMHD1 mutations were reported in several cancers, such as colorectal cancer, breast cancer and chronic lymphocytic leukemia [29]. The functional consequences of SAMHD1 in cancer development and treatment still require further researches. In the colorectal cancer, high expression SAMHD1 correlated with metastasis [30] and indicated poor prognosis of stage II patients [31]. Consistent with our results, Eudald Felip et al. found that low expression of SAMHD1 was associated with a positive prognosis in breast, ovarian and non-small cell lung cancer patients [32].

SAMHD1 was reported to suppress innate immune responses in human monocytic cells and macrophages via inhibiting interferon pathways [33]. The IFN-I responses in SAMHD1-deficient myeloid cells required the cGAS-STING cytosolic DNA sensing pathway [25]. Another study showed that SAMHD1 deficiency led to ssDNA accumulate in the cytosol and activated the cGAS-STING pathway to induce IFN-I [14]. Since cGAS is a DNA sensor which preferentially binds to double-stranded DNA [34], we wondered how ssDNA activated STING pathway. Ahmed Emam et al. found that the increased cytosolic ssDNA contains ribosomal DNA that can bind to cGAS and activate of the innate immune response [35]. Kiwon Park et al. found that SAMHD1 prevents R-loop formation to preserve genome integrity [36]. R-loops, nucleic acid structures containing RNA: DNA hybrids and ssDNAs, could be recognized by cGAS and activate cGAS-STING activity [37]. Here, we suggested SAMHD1 silencing activated STING pathway through IFI16. IFI16 is a key DNA sensor which could sense ssDNA. The non-canonical IFI16/STING pathway was reported in recent year [38]. IFI16 could promote production and function of cGAMP [39] and cooperate with cGAS in the activation of STING [23]. Our studies suggested that SAMHD1 silencing in LUAD cells caused cytosolic ssDNA accumulation and IFI16 was upregulated and translocated from nucleus to cytosol and then activated STING-IFN-I signaling pathway.

Macrophage constitutes a predominant component of tumor immune microenvironment in lung cancer [40]. The activation states of macrophages are complex. There are two main macrophage phenotypes, proinflammatory (M1) and anti-inflammatory (M2) macrophages [41]. M1 macrophages can directly mediate cytotoxicity to kill tumor cells or kill tumor cells by antibody-dependent cell-mediated cytotoxicity [42]. M1 macrophages can also enhance antigen processing and presentation and T cell responses [43]. We found that SAMHD1 silencing in lung cancer cells promoted macrophage M1 polarization, which might improve the tumor immune microenvironment.

SAMHD1 promotes DNA end resection which is the initiation of DNA repair by homologous recombination [15]. SAMHD1 silencing causes homologous recombination deficiency which may sensitize tumor cells to radiotherapy. We verified the combination effects of SAMHD1silencing and radiotherapy on tumor growth inhibition and anti-tumor immunity activation. The combination treatment inhibited cell proliferation, regulated cell cycle and increased apoptosis. In vivo, SAMHD1 deficiency and radiotherapy cooperated to inhibit tumor growth and increased M1 macrophages and CD8⁺ T cell infiltration.

There is one therapeutic implication of our findings that SAMHD1 inhibition and radiotherapy may be a rational combination to inhibit tumor growth and enhance anti-tumor immunity. The Vpx protein could induce the degradation of SAMHD1 [44]. TRIM21 is an E3 ubiqutin ligase, a key regulator of SAMHD1 which specifically degrades SAMHD1 through the proteasomal pathway [45]. But a protein-based therapy have some limitations and they also have other targets. Selective CDK4/6 inhibitors could control SAMHD1 function by inhibiting its phosphorylation [46]. CDK4/6 inhibitors might inhibit the DNA end resection ability of SAMHD1 and enhance the dNTP hydrolase function, since SAMHD1 formed homotetramers to Hydrolyze dNTP and was phosphorylated to promote DNA end resection [28]. We supposed that CDK4/6 inhibitors and radiotherapy might be a promising therapeutic combination for cancer therapy to enhance anti-tumor immune responses. Another potential therapeutic implication is that LUAD with low SAMHD1 expression might receive more benefits and immunostimulatory effects from radiotherapy.

SAMHD1 deficiency induced IFN-I production through the cytosolic DNA sensing IFI16-STING signaling pathway in LUAD cells. The combination of SAMHD1 silencing and radiation enhanced the activation of TBK1-IRF3-IFN-I signaling pathway in LUAD cells (Fig. 9). In addition, SAMHD1 knockdown combined with radiotherapy inhibited tumor growth and induced anti-tumor immunity via promoting macrophage M1 polarization and CD8⁺ T cell infiltration.