Neutralization of PD-L2 is Essential for Overcoming Immune Checkpoint Blockade Resistance in Ovarian Cancer

PURPOSE

Ovarian cancer represents a major clinical hurdle for immune checkpoint blockade (ICB), with reported low patient response rates. We found that the immune checkpoint ligand PD-L2 is robustly expressed in patient samples of ovarian cancers and other malignancies exhibiting suboptimal response to ICB but not in cancers that are ICB sensitive. Therefore, we hypothesize that PD-L2 can facilitate immune escape from ICB through incomplete blockade of the PD-1 signaling pathway.

EXPERIMENTAL DESIGN

We engineered a soluble form of the PD-1 receptor (sPD-1) capable of binding and neutralizing both PD-L2 and PD-L1 with ×200 and ×10,000 folds improvement in binding affinity over wild-type PD-1 leading to superior inhibition of ligand-mediated PD-1 activities.

RESULTS

Both in vitro and in vivo analyses performed in this study demonstrated that the high-affinity sPD-1 molecule is superior at blocking both PD-L1- and PD-L2-mediated immune evasion and reducing tumor growth in immune-competent murine models of ovarian cancer.

CONCLUSIONS

The data presented in this study provide justification for using a dual targeting, high-affinity sPD-1 receptor as an alternative to PD-1 or PD-L1 therapeutic antibodies for achieving superior therapeutic efficacy in cancers expressing both PD-L2 and PD-L1.

Eliminating hypoxic tumor cells improves response to PARP inhibitors in homologous recombination-deficient cancer models

Hypoxia, a hallmark feature of the tumor microenvironment, causes resistance to conventional chemotherapy, but was recently reported to synergize with poly(ADP-ribose) polymerase inhibitors (PARPis) in homologous recombination-proficient (HR-proficient) cells through suppression of HR. While this synergistic killing occurs under severe hypoxia (<0.5% oxygen), our study shows that moderate hypoxia (2% oxygen) instead promotes PARPi resistance in both HR-proficient and -deficient cancer cells. Mechanistically, we identify reduced ROS-induced DNA damage as the cause for the observed resistance. To determine the contribution of hypoxia to PARPi resistance in tumors, we used the hypoxic cytotoxin tirapazamine to selectively kill hypoxic tumor cells. We found that the selective elimination of hypoxic tumor cells led to a substantial antitumor response when used with PARPi compared with that in tumors treated with PARPi alone, without enhancing normal tissue toxicity. Since human breast cancers with BRAC1/2 mutations have an increased hypoxia signature and hypoxia reduces the efficacy of PARPi, then eliminating hypoxic tumor cells should enhance the efficacy of PARPi therapy.

The m6A RNA demethylase FTO is a HIF-independent synthetic lethal partner with the VHL tumor suppressor

Loss of the von Hippel-Lindau (VHL) tumor suppressor is a hallmark feature of renal clear cell carcinoma. VHL inactivation results in the constitutive activation of the hypoxia-inducible factors (HIFs) HIF-1 and HIF-2 and their downstream targets, including the proangiogenic factors VEGF and PDGF. However, antiangiogenic agents and HIF-2 inhibitors have limited efficacy in cancer therapy due to the development of resistance. Here we employed an innovative computational platform, Mining of Synthetic Lethals (MiSL), to identify synthetic lethal interactions with the loss of VHL through analysis of primary tumor genomic and transcriptomic data. Using this approach, we identified a synthetic lethal interaction between VHL and the m⁶A RNA demethylase FTO in renal cell carcinoma. MiSL identified FTO as a synthetic lethal partner of VHL because deletions of FTO are mutually exclusive with VHL loss in pan cancer datasets. Moreover, FTO expression is increased in VHL-deficient ccRCC tumors compared to normal adjacent tissue. Genetic inactivation of FTO using multiple orthogonal approaches revealed that FTO inhibition selectively reduces the growth and survival of VHL-deficient cells in vitro and in vivo. Notably, FTO inhibition reduced the survival of both HIF wild type and HIF-deficient tumors, identifying FTO as an HIF-independent vulnerability of VHL-deficient cancers. Integrated analysis of transcriptome-wide m⁶A-seq and mRNA-seq analysis identified the glutamine transporter SLC1A5 as an FTO target that promotes metabolic reprogramming and survival of VHL-deficient ccRCC cells. These findings identify FTO as a potential HIF-independent therapeutic target for the treatment of VHL-deficient renal cell carcinoma.

Cross-talk between chromatin acetylation and SUMOylation of tripartite motif-containing protein 24 (TRIM24) impacts cell adhesion

Proteins with domains that recognize and bind post-translational modifications (PTMs) of histones are collectively termed epigenetic readers. Numerous interactions between specific reader protein domains and histone PTMs and their regulatory outcomes have been reported, but little is known about how reader proteins may in turn be modulated by these interactions. Tripartite motif-containing protein 24 (TRIM24) is a histone reader aberrantly expressed in multiple cancers. Here, our investigation revealed functional cross-talk between histone acetylation and TRIM24 SUMOylation. Binding of TRIM24 to chromatin via its tandem PHD-bromodomain, which recognizes unmethylated lysine 4 and acetylated lysine 23 of histone H3 (H3K4me0/K23ac), led to TRIM24 SUMOylation at lysine residues 723 and 741. Inactivation of the bromodomain, either by mutation or with a small-molecule inhibitor, IACS-9571, abolished TRIM24 SUMOylation. Conversely, inhibition of histone deacetylation markedly increased TRIM24's interaction with chromatin and its SUMOylation. Of note, gene expression profiling of MCF7 cells expressing WT versus SUMO-deficient TRIM24 identified cell adhesion as the major pathway regulated by the cross-talk between chromatin acetylation and TRIM24 SUMOylation. In conclusion, our findings establish a new link between histone H3 acetylation and SUMOylation of the reader protein TRIM24, a functional connection that may bear on TRIM24's oncogenic function and may inform future studies of PTM cross-talk between histones and epigenetic regulators.

Generation of Stable Expression Mammalian Cell Lines Using Lentivirus

Lentiviruses are used very widely to generate stable expression mammalian cell lines. They are used for both gene down-regulation (by using shRNA) or for gene up-regulation (by using ORF of gene of interest). The technique of generating stable cell lines using 3^rd generation lentivirus is very robust and it typically takes about 1-2 weeks to get stable expression for most mammalian cell lines. The advantage of using the 3^rd generation lentivirus are that are very safe and they are replication incompetent.

Regulation of gene expression in human cancers by TRIM24

Tripartite Motif-containing protein 24 (TRIM24) functions as an E3 ligase targeting p53 for ubiquitination, a histone 'reader' that interacts with a specific signature of histone post-translational modifications and a co-regulator of nuclear receptor-regulated transcription. Although mouse models of Trim24 depletion suggest that TRIM24 may be a liver-specific tumor suppressor, several studies show that human TRIM24 is an oncogene when aberrantly over expressed. This review focuses on the mechanisms of TRIM24 functions in oncogenesis and metabolic reprogramming, which underlie recent interest in therapeutic targeting of aberrant TRIM24 in human cancers.

Abstract B17: TRIM24 links epigenetics and metabolism in cancer

The TRIpartite Motif (TRIM) family of proteins has approximately 70 proteins, which are involved in a variety of processes, including regulation of protein stability, transcription, cell proliferation and apoptosis. Our laboratory discovered TRIM24, as an E3-ubiquitin ligase of p53, using embryonic stem cells and breast cancer cell lines as model systems. Earlier reports identified TRIM24 as a transcriptional co-regulator of nuclear receptor signaling, directly interacting with retinoic-acid receptor (RAR), thyroid receptor, androgen receptor and estrogen receptor (ER). Since our laboratory's initial report showing TRIM24 over expression correlates with poor survival of breast cancer patients, several studies reported roles of TRIM24 in multiple cancers such as NSLC, head and neck carcinoma, hepatocellular carcinoma, colorectal cancer and glioblastoma.

We found that TRIM24 expression is deregulated during breast cancer progression and likely early in the process. I found that the ectopic expression of TRIM24 in immortalized Human mammary epithelial cells (HMECs) greatly increased cellular proliferation and induced malignant transformation. Subcutaneous injection of TRIM24-HMECs in nude mice displayed significantly higher xenograft volume as compared to their control counterparts. Interestingly, molecular analysis of TRIM24-HMECs revealed a glycolytic and tricarboxylic acid cycle gene signature, alongside increased glucose uptake and activated aerobic glycolysis. Using Chromatin immunoprecipitation (ChIP), I saw TRIM24 binding at the promoters of several glycolytic and TCA cycle genes such as GLUT1, IDH1, IDH2 and c-Myc Consistent with in vitro findings, the Glucose transport pathway was among the top 10 pathways positively correlated with TRIM24 expression in human breast tumors (n = 1008) from the TCGA database. Thus, TRIM24 is co-expressed with genes that regulate glucose metabolism in breast tumors, supporting clinical relevance of our findings.

Mechanistically, we have previously reported that TRIM24 acts as a transcriptional co-regulator by “reading” a specific signature of histone post-translational modifications (H3K4me0-H3K23ac) via a tandem plant homeodomain (PHD) and bromodomain (Bromo) within the C-terminus of TRIM24. Additionally, TRIM24 via its RING domain acts as an E3-ubiquitin ligase of p53 and targets it for proteasome-mediated degradation. Currently, I am performing studies to determine if chromatin association of TRIM24 via the PHD/Bromo-domain and/or RING-domain activity is critical for oncogenic transformation linked with metabolic reprograming in cancer. In summary, our studies suggest a unique role for TRIM24 in early steps of mammary carcinogenesis that involves reprogramming of glucose metabolism and the results provide the groundwork to test chemical therapeutics that disrupt TRIM24 functions, e.g. Bromodomain inhibitors.

Citation Format: Kaushik N. Thakkar, Shiming Jiang, Sabrina Stratton, Michelle Barton. TRIM24 links epigenetics and metabolism in cancer. [abstract]. In: Proceedings of the AACR Special Conference: Metabolism and Cancer; Jun 7-10, 2015; Bellevue, WA. Philadelphia (PA): AACR; Mol Cancer Res 2016;14(1_Suppl):Abstract nr B17.

Abstract 2213: Aberrant expression of TRIM24 in breast cancer progression is linked to loss of repressive histone marks at the promoter

We recently discovered that TRIM24 is an E3-ubiquitin ligase that targets p53 for degradation in embryonic stem cells and breast cancer cell lines. TRIM24 functions in human cells as a reader of dual histone marks and binds chromatin and estrogen receptor (ER) to activate estrogen-dependent genes associated with cellular proliferation and tumor development. Intriguingly, we and others have shown that over-expression of TRIM24 is associated with poor prognosis and worse survival in breast cancer patients. Whether TRIM24 is causal in malignant transformation of breast epithelial cells during breast tumor development and progression is not known. Furthermore the mechanism that drives deregulated expression of TRIM24 in breast cancer is not understood. To develop a timeline of TRIM24 deregulation during malignant transformation, we used an isogenic human mammary epithelial cell (HMEC) model system that allows for assessment of molecular changes that occur at the earliest stages of multistep human breast carcinogenesis. Our analysis of TRIM24 expression in HMECs transitioning from finite lifespan, to immortality and to malignantly transformed HMECs showed gradual up-regulation of TRIM24 at both RNA and protein levels early in the transformation process. Consistent with these findings, Immunohistochemical (IHC) staining of TRIM24 in clinical breast tumor samples from a breast cancer progression array showed increased TRIM24 expression in hyperplasia, ductal carcinoma in situ (DCIS) and invasive carcinoma, compared to normal breast tissues. To understand the mechanism of TRIM24 deregulation in breast tumor progression, we studied the TRIM24 promoter region for aberrant DNA methylation changes by bisulfite genomic sequencing. There were no aberrant DNA methylation changes in HMEC transitioning from finite lifespan to malignant transformation suggesting that TRIM24 gene expression is regulated by mechanisms other than DNA methylation. Interestingly, Chromatin Immunoprecipitation (ChIP) studies in finite lifespan HMECs at the TRIM24 promoter showed an enrichment of repressive histone marks H3K9me2 and H3K9me3 which gradually decreased in immortal and malignantly transformed mammary epithelial cells. Further studies to see if TRIM24 is involved in transformation of normal mammary epithelial cells by stably overexpressing TRIM24 in HMECs are currently ongoing. Also more studies are ongoing to define additional levels of regulation of TRIM24, and which transcription factors are involved in its deregulated expression in breast cancer. Our studies suggest a unique role of TRIM24 in early steps of mammary carcinogenesis. Therefore, our study may provide valuable insights into the rational development of TRIM24-targeted therapeutic strategies against breast cancer.

Citation Format: {Authors}. {Abstract title} [abstract]. In: Proceedings of the 103rd Annual Meeting of the American Association for Cancer Research; 2012 Mar 31-Apr 4; Chicago, IL. Philadelphia (PA): AACR; Cancer Res 2012;72(8 Suppl):Abstract nr 2213. doi:1538-7445.AM2012-2213