Cyclic GMP-AMP (cGAMP) synthase (cGAS) stimulator of interferon genes (STING) senses pathogen-derived or abnormal self-DNA in the cytosol and triggers an innate immune defense against microbial infection and cancer. STING agonists induce both innate and adaptive immune responses and are a new class of cancer immunotherapy agents tested in multiple clinical trials. However, STING is commonly silenced in cancer cells via unclear mechanisms, limiting the application of these agonists. Here, we report that the expression of STING is epigenetically suppressed by the histone H3K4 lysine demethylases KDM5B and KDM5C and is activated by the opposing H3K4 methyltransferases. The induction of STING expression by KDM5 blockade triggered a robust interferon response in a cytosolic DNA-dependent manner in breast cancer cells. This response resulted in resistance to infection by DNA and RNA viruses. In human tumors, KDM5B expression is inversely associated with STING expression in multiple cancer types, with the level of intratumoral CD8+ T cells, and with patient survival in cancers with a high level of cytosolic DNA, such as human papilloma virus (HPV)-positive head and neck cancer. These results demonstrate a novel epigenetic regulatory pathway of immune response and suggest that KDM5 demethylases are potential targets for antipathogen treatment and anticancer immunotherapy.

p53 acetylation is indispensable for its transcriptional activity and tumor suppressive function. However, the identity of reader protein(s) for p53 acetylation remains elusive. PBRM1, the second most highly mutated tumor suppressor gene in kidney cancer, encodes PBRM1. Here, we identify PBRM1 as a reader for p53 acetylation on lysine 382 (K382Ac) through its bromodomain 4 (BD4). Notably, mutations on key residues of BD4 disrupt recognition of p53 K382Ac. The mutation in BD4 also reduces p53 binding to promoters of target genes such as CDKN1A (p21). Consequently, the PBRM1 BD4 mutant fails to fully support p53 transcriptional activity and is defective as a tumor suppressor. We also find that expressions of PBRM1 and p21 correlate with each other in human kidney cancer samples. Our findings uncover a tumor suppressive mechanism of PBRM1 in kidney cancer and provide a mechanistic insight into the crosstalk between p53 and SWI/SNF complexes.

Actin cytoskeleton is well-known for providing structural/mechanical support, but whether and how it regulates chromatin and cell fate reprogramming is far less clear. Here, we report that MKL1, the key transcriptional co-activator of many actin cytoskeletal genes, regulates genomic accessibility and cell fate reprogramming. The MKL1-actin pathway weakens during somatic cell reprogramming by pluripotency transcription factors. Cells that reprogram efficiently display low endogenous MKL1 and inhibition of actin polymerization promotes mature pluripotency activation. Sustained MKL1 expression at a level seen in typical fibroblasts yields excessive actin cytoskeleton, decreases nuclear volume and reduces global chromatin accessibility, stalling cells on their trajectory toward mature pluripotency. In addition, the MKL1-actin imposed block of pluripotency can be bypassed, at least partially, when the Sun2-containing linker of the nucleoskeleton and cytoskeleton (LINC) complex is inhibited. Thus, we unveil a previously unappreciated aspect of control on chromatin and cell fate reprogramming exerted by the MKL1-actin pathway.

SUMMARY The brain is a major site of relapse for several cancers, yet deciphering the mechanisms of brain metastasis remains a challenge because of the complexity of the brain tumor microenvironment (TME). To define the molecular landscape of brain metastasis from intact tissue in vivo, we employ an RNA-sequencing-based approach, which leverages the transcriptome of xenografts and distinguishes tumor cell and stromal gene expression with improved sensitivity and accuracy. Our data reveal shifts in epithelial and neuronal-like lineage programs in malignant cells as they adapt to the brain TME and the reciprocal neuroinflammatory response of the stroma. We identify several transcriptional hallmarks of metastasis that are specific to particular regions of the brain, induced across multiple tumor types, and confirmed in syngeneic models and patient biopsies. These data may serve as a resource for exploring mechanisms of TME co-adaptation within, as well as across, different subtypes of brain metastasis.

Metastasis is the major cause of cancer-related deaths due to the lack of effective therapies. Emerging evidence suggests that certain epigenetic and transcriptional regulators drive cancer metastasis and could be targeted for metastasis treatment. To identify epigenetic regulators of breast cancer metastasis, we profiled the transcriptomes of matched pairs of primary breast tumors and metastases from human patients. We found that distant metastases are more immune inert with increased M2 macrophages compared to their matched primary tumors. The acetyl-lysine reader, cat eye syndrome chromosome region candidate 2 (CECR2), was the top up-regulated epigenetic regulator in metastases associated with an increased abundance of M2 macrophages and worse metastasis-free survival. CECR2 was required for breast cancer metastasis in multiple mouse models, with more profound effect in the immunocompetent setting. Mechanistically, the nuclear factor κB (NF-κB) family member v-rel avian reticuloendotheliosis viral oncogene homolog A (RELA) recruits CECR2 to increase chromatin accessibility and activate the expression of their target genes. These target genes include multiple metastasis-promoting genes, such as TNC , MMP2 , and VEGFA , and cytokine genes CSF1 and CXCL1 , which are critical for immunosuppression at metastatic sites. Consistent with these results, pharmacological inhibition of CECR2 bromodomain impeded NF-κB–mediated immune suppression by macrophages and inhibited breast cancer metastasis. These results reveal that targeting CECR2 may be a strategy to treat metastatic breast cancer.

Whereas VHL inactivation is a primary event in clear cell renal cell carcinoma (ccRCC), the precise mechanism(s) of how this interacts with the secondary mutations in tumor suppressor genes, including PBRM1, KDM5C/JARID1C, SETD2, and/or BAP1, remains unclear. Gene expression analyses reveal that VHL, PBRM1, or KDM5C share a common regulation of interferon response expression signature. Loss of HIF2α, PBRM1, or KDM5C in VHL-/-cells reduces the expression of interferon stimulated gene factor 3 (ISGF3), a transcription factor that regulates the interferon signature. Moreover, loss of SETD2 or BAP1 also reduces the ISGF3 level. Finally, ISGF3 is strongly tumor-suppressive in a xenograft model as its loss significantly enhances tumor growth. Conversely, reactivation of ISGF3 retards tumor growth by PBRM1-deficient ccRCC cells. Thus after VHL inactivation, HIF induces ISGF3, which is reversed by the loss of secondary tumor suppressors, suggesting that this is a key negative feedback loop in ccRCC.

PurposeBrain metastasis remains a major site of relapse for several cancer types. However, the molecular mechanisms of brain metastasis are largely unknown given the complex relationship between tumor cells and the surrounding brain tumor microenvironment (TME). We have developed a Brain Metastatic RNA‐Sequencing (BMX‐Seq) approach, which leverages xenograft models and can distinguish between the transcriptomes of human tumor and mouse stroma gene expression in vivo. These data provide an extensive molecular portrait of the co‐adaptation of brain metastasis with the brain TME.MethodsFollowing intra‐arterial injection of the human, lung adenocarcinoma (LUAD), H2030‐BrM3 cell model into athymic mice, metastatic brain tumors were macrodisasected, flash frozen and RNA extracted. Lung tumors, healthy brain regions, subcutaneous lesions and H2030‐BrM3 cells grown in monolayer were harvested in parallel. Our BMX‐Seq pipeline was engineered to analyze bulk xenograft tissue, which includes tumor lesions as well as surrounding stromal tissue. Species‐specific Taqman primers and immunofluorescent (IF) staining were used to validate our BMX‐Seq results including both human tumor and mouse stroma gene expression profiles. Models of melanoma and breast cancer brain metastasis were also included in this study.SummaryIn comparing the transcriptomic profiles of tumors grown in the brain as compared to other sites, we identify shifts in WNT signaling pathway components and epithelial and neuronal‐like gene expression programs in malignant cells (Figure 1). Further work revealed such trends are reversible once tumor cells are removed from the brain TME. In describing the neuroinflammatory response of stromal regions surrounding brain lesions, our BMX‐Seq analysis revealed increased expression of astrocyte and microglial enriched transcripts. We then utilized IF to confirm the elevated density of both of these cell types in areas directly surrounding and infiltrating tumor regions. We also detect significantly induced expression of stromal TIM3 (or HAVCR2) in areas surrounding tumor lesions and in a model system devoid of T‐Cells. Follow‐up work revealed that expression of TIM3 is induced on tumor‐associated macrophages (including microglia) within the tumor region, and we further validate such results in a syngeneic model system as well as in human, brain tissue (Figure 2).ConclusionsWe have developed a highly sensitive RNA‐sequencing based approach that can accurately map the transcriptomic adaptation of brain metastatic tumor cells and the surrounding brain TME. We believe these data may serve as a powerful resource to guide future discovery in CNS metastases.Support or Funding InformationR01CA166376, R01CA191489, W81XWH‐15‐1‐0117 (D.X.N.). Yale Lung Cancer SPORE (P50CA196530) (K.P and D.X.N); Yale SPORE Skin Cancer (P50 CA121974) K24CA172123, R01 CA216846 (H.K.M); MINECO‐Europa Excelencia SAF2015‐62547‐ERC (M.V.).This abstract is from the Experimental Biology 2019 Meeting. There is no full text article associated with this abstract published in The FASEB Journal.

Epigenetic and transcriptional changes are critical for metastasis, the major cause of cancer-related deaths. Emerging evidence suggest that metastatic tumor cells escape immune surveillance more efficiently than tumor cells in the primary sites, but the epigenetic mechanisms controlling immune evasion during cancer metastasis are poorly understood. By analyzing transcriptomes of matched metastatic and primary tumor samples from breast cancer patients, we found that immune escape genes and 14 of 29 immune-oncology targets are downregulated in matched metastatic samples compared to primary tumors. CIBERSORTx analysis identified an increase of M2-like tumor promoting macrophages in the metastasis tumors comparing to primary tumors. Among the dysregulated epigenetic regulators, acetyl-lysine reader CECR2 is the top candidate regulator of this change as its mRNA levels correlated with the ratio of M2 macrophages. Consistently, higher CECR2 protein levels are more frequently observed in metastatic tumors, and high CECR2 mRNA levels were associated with poor distant-metastasis free survival of breast cancer patients. CECR2 specifically promotes breast cancer metastasis, with more profound effect in the immunocompetent setting. Mechanistically, NF-κB family member RELA recruits CECR2 to certain NF-κB target genes, including CSF1 and CXCL1. CSF1 secreted by tumor cells is critical for CECR2 to stimulate polarization of tumor-associated macrophages to create immunosuppressive microenvironment at the metastatic sites. Pharmacological inhibition of CECR2 bromodomain blocks the expression of key NF-κB target genes and inhibit tumor cell migration and invasion. These results nominate novel therapeutic targets for the treatment of metastatic breast cancer.