Hepatocellular carcinoma (HCC) is the primary malignancy of hepatocytes and the second most common cause of cancer-related mortality across the globe. Despite significant advancements in screening, diagnosis, and treatment modalities for HCC, the mortality-to-incidence ratio remain unacceptably high. A recent study indicates that a minor population of HCCs are AFP negative or express the normal range of AFP levels. Although it is a gold standard and a more reliable biomarker in the advanced stage of HCC and poorly differentiated tumors, it does not serve as a suitable means for screening HCC. AFP plays a significant role in the development and progression of HCC and understanding its role is crucial. By examining the molecular mechanisms involved in AFP-mediated tumorigenesis, we can better understand HCC pathogenesis and identify potential therapeutic targets. This article details the role of alpha-fetoprotein (AFP) in the carcinogenic transformation of hepatocytes. The article also focuses on information about the structure, biosynthesis, and regulation of AFP at the gene level. Additionally, it discusses the immune evasion, metastasis, and control of gene expression that AFP mediates during HCC.

The purpose of this study is to develop a strategy for treating pancreatic neuroendocrine tumor (PanNET) through blocking Thymidylate Synthase (TYMS or TS), a DNA metabolic enzyme. Elevated TYMS levels are frequently observed in human PanNET and are associated with worse prognosis and resistance to cytotoxic agents such as 5FU. Elevated TYMS levels directly promote tumorigenesis in vitro and ectopic expression of human TS (hTS) in transgenic mice promotes adenoma development in the endocrine pancreas in vivo. Pancreatic islet tumor formation in hTS transgenic mice occurred with a long latency period, suggesting that additional somatic events are required for PanNET formation and progression. Men1 was shown to be a frequent target for somatic mutation in PanNETs (44% have MEN1 mutations). Therefore, we established a new mouse model designated hTS/Men1-/-, where hTS is overexpressed in pancreatic islet cells carrying conditional Men1 null alleles. We observed that ectopic hTS cooperates with Men1 inactivation to significantly accelerate PanNET progression and shorten survival. Since traditional TYMS inhibitors, such as 5-FU, consistently induce tumor resistance and cannot cure advanced disease, we have now tested the ability of TS-shRNA delivered using adeno-associated viral (AAV) vectors as a pharmacological safe and effective anti-tumor strategy. We packaged TS shRNA under the mouse insulin promoter (mIP) for islet-cell specific expression using capsid optimized Y to F double mutant AAV (AAV8-2M) to generate viral particles of scAAV8-2M-mIP-GFP-hTS-shRNA. We treated hTS/Men1-/- mice with intraperitoneal (IP) injection (1x1011 viral genomes/mice). Treated and control mice were analyzed for PanNET progression, TYMS expression and survival. In addition, we tested a human PanNET tumor cell line (BON) that was isogenic with or without hTS expression for tumor formation in xenograft model. We confirmed sustained reduction of TYMS levels 3 weeks after IP delivery of AA8-2M-mIP-GFP-hTS-shRNA into PanNET tissues of hTS/Men1-/- mice. In addition, AA8-2M-mIP-GFP-hTS-shRNA delivery blocked PanNET tumor progression and enhanced the survival of treated mice as compared to vector controls. We also confirmed that TYMS knock-down in BON cells by hTS-shRNA reduced xenograft tumor growth as compared to non-specific shRNA controls. In conclusion, the ability of AAV-mediated TS shRNA to block PanNET tumor progression directly demonstrates the importance of elevated TYMS in tumorigenesis and offers a novel anti-cancer strategy. Citation Format: Vinod Vijayakurup, Benjamin Meyer, Akbar Nawab, Frederic J. Kaye, Maria V. Guijarro, Maria Zajac-Kaye. TYMS as a novel target for AAV-based therapy [abstract]. In: Proceedings of the American Association for Cancer Research Annual Meeting 2023; Part 1 (Regular and Invited Abstracts); 2023 Apr 14-19; Orlando, FL. Philadelphia (PA): AACR; Cancer Res 2023;83(7_Suppl):Abstract nr 2733.

Myelodysplastic Syndromes (MDSs) are bone marrow (BM) failure malignancies characterized by constitutive innate immune activation, including NLRP3 inflammasome driven pyroptotic cell death. We recently reported that the danger-associated molecular pattern (DAMP) oxidized mitochondrial DNA (ox-mtDNA) is diagnostically increased in MDS plasma although the functional consequences remain poorly defined. We hypothesized that ox-mtDNA is released into the cytosol, upon NLRP3 inflammasome pyroptotic lysis, where it propagates and further enhances the inflammatory cell death feed-forward loop onto healthy tissues. This activation can be mediated via ox-mtDNA engagement of Toll-like receptor 9 (TLR9), an endosomal DNA sensing pattern recognition receptor known to prime and activate the inflammasome propagating the IFN-induced inflammatory response in neighboring healthy hematopoietic stem and progenitor cells (HSPCs), which presents a potentially targetable axis for the reduction in inflammasome activation in MDS. We found that extracellular ox-mtDNA activates the TLR9-MyD88-inflammasome pathway, demonstrated by increased lysosome formation, IRF7 translocation, and interferon-stimulated gene (ISG) production. Extracellular ox-mtDNA also induces TLR9 redistribution in MDS HSPCs to the cell surface. The effects on NLRP3 inflammasome activation were validated by blocking TLR9 activation via chemical inhibition and CRISPR knockout, demonstrating that TLR9 was necessary for ox-mtDNA-mediated inflammasome activation. Conversely, lentiviral overexpression of TLR9 sensitized cells to ox-mtDNA. Lastly, inhibiting TLR9 restored hematopoietic colony formation in MDS BM. We conclude that MDS HSPCs are primed for inflammasome activation via ox-mtDNA released by pyroptotic cells. Blocking the TLR9/ox-mtDNA axis may prove to be a novel therapeutic strategy for MDS.

Abstract Resistance to targeted therapy remains an ongoing challenge in lung cancer. β-Catenin (CTNNB1) mutations are observed in lung cancer, often co-occurring with known oncogenic alterations such as EGFR/KRAS/ALK. Oncogenic CTNNB1 mutations disrupt the β-catenin destruction complex upregulating Wnt signaling that may cause resistance to therapies targeting oncogenic drivers. An example of this was identified in post-mortem donated NSCLC tissue of a patient treated with a combination of carboplatin, pemetrexed, and bevacizumab that harbored both an acquired CTNNB1-T41A mutation and an EGFR exon 20 insertion. In addition, the CTNNB1 mutation spectrum was analyzed in lung cancer patients at Moffitt Cancer Center to identify prevalent CTNNB1 mutations for functional analyses. T41A, along with the most frequent Exon 3 CTNNB1 mutations were selected and transduced into HCC827 mutant cell lines to determine their ability to drive resistance to targeted therapies. Subsequently, western blotting and RNA sequencing were performed to assess differences between cells expressing wild-type and the most-resistant CTNNB1 mutant. A viability screen was also performed in which these cells were treated with a panel of drugs with known targets (COCKTAIL), in combination with EGFR TKI erlotinib, to identify new vulnerabilities of this CTNNB1 mutant erlotinib-resistant cells. Our data indicate that some CTNNB1 mutations, T41A, S37F, S45C and D32H, can cause resistance to EGFR inhibitor therapy, while others, D32Y, S33C, S33Y, S45P, and S37C, do not. Western blot analysis shows corresponding stabilization and higher accumulation of active β-catenin in cells expressing CTNNB1 mutants that are resistant to erlotinib. Of the mutations tested, cells expressing CTNNB1 T41A demonstrated the strongest resistance to erlotinib. Further analysis reveals higher levels of β-catenin regulated proteins, like axin2 and survivin, as well as EMT markers, such as vimentin and N-cadherin, in HCC827 CTNNB1 T41A cells when compared to the HCC827 CTNNB1 WT. Pathway analysis of genes differentially expressed between the WT and T41A mutant cells reveal WNT pathway to be the top upregulated pathway in the mutant cells. HCC827 T41A also showed sustained ERK, AKT and GSK3β signaling, and lower PARP cleavage compared to wild type, which may explain the resistance to EGFR TKI seen in these cells. COCKTAIL screening, comparing drug sensitivities of the WT and T41A mutant HCC827 cells to erlotinib in combination with various other targeted agents, identified PI3K, mTOR and MEK inhibitors that can reverse erlotinib resistance in the HCC827 CTNNB1 T41A cells. Our data suggests that CTNNB1 may be an important co-occurring alteration in developing resistance to targeted EGFR therapy. However, we show that different CTNNB1 mutations have differing abilities to drive resistance to EGFR TKI which correlates with the level of stabilization and activation of CTNNB1 and its downstream targets by these mutations. Citation Format: Anurima Majumder, Liznair Bridenstine, Benjamin Meyer, Fumi Kinose, J. Kevin Hicks, Theresa A Boyle, Eric B Haura. CTNNB1 mutations can mediate resistance to EGFR targeted therapies in Non-Small Cell Lung Cancer [abstract]. In: Proceedings of the AACR-NCI-EORTC Virtual International Conference on Molecular Targets and Cancer Therapeutics; 2023 Oct 11-15; Boston, MA. Philadelphia (PA): AACR; Mol Cancer Ther 2023;22(12 Suppl):Abstract nr B087.

To better understand the signaling complexity of AXL, a member of the TAM receptor tyrosine kinase family, we created a physical and functional map of AXL signaling interactions, phosphorylation events, and target-engagement of three AXL tyrosine kinase inhibitors (TKI). We assessed AXL protein-complexes using BioID, effects of AXL TKI on global phosphoproteins using mass spectrometry, and target engagement of AXL TKI using activity-based protein profiling. BioID identifies AXL-interacting proteins that are mostly involved in cell adhesion/migration. Global phosphoproteomics show that AXL inhibition decreases phosphorylation of peptides involved in phosphatidylinositol-mediated signaling and cell adhesion/migration. Comparison of three AXL inhibitors reveals that TKI RXDX-106 inhibits pAXL, pAKT and migration/invasion of these cells without reducing their viability, while Bemcentinib exerts AXL-independent phenotypic effects on viability. Proteomic characterization of these TKIs demonstrates that they inhibit diverse targets in addition to AXL, with Bemcentinib having the most off-targets. AXL and EGFR TKI co-treatment did not reverse resistance in cell line models of Erlotinib-resistance. However, a unique vulnerability was identified in one resistant clone, wherein combination of Bemcentinib and Erlotinib inhibited cell viability and signaling. We also show that AXL is overexpressed in ~30-40% of non-small but rarely in small-cell lung cancer. Cell lines have a wide range of AXL expression, with basal activation detected rarely. Implications: Our study defines mechanisms of action of AXL in lung cancers which can be used to establish assays to measure drug targetable active AXL-complexes in patient tissues and inform the strategy for targeting it's signaling as an anticancer therapy.

Clinical studies of cancer patients have shown that overexpression or amplification of thymidylate synthase (TS) correlates with a worse clinical outcome. We previously showed that elevated TS exhibits properties of an oncogene and promotes pancreatic neuroendocrine tumors (PanNETs) with a long latency. To study the causal impact of elevated TS levels in PanNETs, we generated a mouse model with elevated human TS (hTS) and conditional inactivation of the Men1 gene in pancreatic islet cells (hTS/Men1–/–). We demonstrated that increased hTS expression was associated with earlier tumor onset and accelerated PanNET development in comparison with control Men1–/– and Men1+/ΔN3-8 mice. We also observed a decrease in overall survival of hTS/Men1+/– and hTS/Men1–/– mice as compared with control mice. We showed that elevated hTS in Men1-deleted tumor cells enhanced cell proliferation, deregulated cell cycle kinetics, and was associated with a higher frequency of somatic mutations, DNA damage, and genomic instability. In addition, we analyzed the survival of 88 patients with PanNETs and observed that high TS protein expression independently predicted worse clinical outcomes. In summary, elevated hTS directly participates in promoting PanNET tumorigenesis with reduced survival in Men1-mutant background. This work will refocus attention on new strategies to inhibit TS activity for PanNET treatment.

NLRP3 inflammasome and IFN-stimulated gene (ISG) induction are key biological drivers of ineffective hematopoiesis and inflammation in myelodysplastic syndromes (MDSs). Gene mutations involving mRNA splicing and epigenetic regulatory pathways induce inflammasome activation and myeloid lineage skewing in MDSs through undefined mechanisms. Using immortalized murine hematopoietic stem and progenitor cells harboring these somatic gene mutations and primary MDS BM specimens, we showed accumulation of unresolved R-loops and micronuclei with concurrent activation of the cytosolic sensor cyclic GMP-AMP synthase. Cyclic GMP-AMP synthase/stimulator of IFN genes (cGAS/STING) signaling caused ISG induction, NLRP3 inflammasome activation, and maturation of the effector protease caspase-1. Deregulation of RNA polymerase III drove cytosolic R-loop generation, which upon inhibition, extinguished ISG and inflammasome response. Mechanistically, caspase-1 degraded the master erythroid transcription factor, GATA binding protein 1, provoking anemia and myeloid lineage bias that was reversed by cGAS inhibition in vitro and in Tet2–/– hematopoietic stem and progenitor cell–transplanted mice. Together, these data identified a mechanism by which functionally distinct mutations converged upon the cGAS/STING/NLRP3 axis in MDS, directing ISG induction, pyroptosis, and myeloid lineage skewing.

Supplementary Table from Integrated Proteomics-Based Physical and Functional Mapping of AXL Kinase Signaling Pathways and Inhibitors Define Its Role in Cell Migration

Resistance to targeted therapy remains an ongoing and elusive challenge in lung cancer. β-Catenin (CTNNB1) mutations have been reported in lung cancer patients, often co-occurring with known oncogenic drivers such as rearranged ALK, and mutant EGFR and KRAS. Oncogenic CTNNB1 mutations result in aberrant accumulation of the encoded β-catenin protein and may cause resistance to targeted therapy. However, different CTNNB1 mutations may activate β-catenin differentially and thereby have varying phenotypic effects. A CTNNB1 T41A mutation was identified in donated lung cancer tissue from a patient with a clinical history of an EGFR exon 20 insertion. To investigate the functional significance of this mutation, CTNNB1 T41A was transduced into an EGFR-mutated cell line (HCC827) and one cell line harboring ALK translocation (STE1). Response to EGFR and ALK targeted therapy was then compared in the GFP-transduced control cell lines versus the CTNNB1 T41A transduced cell lines to assess for effects of this CTNNB1 mutation on targeted therapy. Both HCC827 and STE1 cells harboring the CTNNB1 T41A mutation were more resistant to EGFR and ALK targeted therapy than the control cell lines. Since, different CTNNB1 mutations may exert different phenotypic effects, the CTNNB1 mutation spectrum was analyzed in lung cancer patients at the Moffitt Cancer Center. Mutations in 19 unique residues of CTNNB1 (D32, S33, G34, S37, T41, S45, A215, C419, S29, G757, K335, N287, Q72, R151, R710, S352, S681, V62 and W383) were detected in 50 lung cancer patients. Of these, 23 had some type of EGFR abnormality that co-existed with the CTNNB1 mutation while others had ROS1, RET, BRAF, NTRK3, ALK or KRAS mutations. The most frequent Exon 3 hotspot CTNNB1 mutations (at residues D32, S33, G34, S37, and S45) were chosen for further analysis wherein these mutations were transduced into HCC827, STE1 and two KRAS mutant cell lines (H358 and LU65) to assess their ability to drive resistance to EGFR, ALK and KRAS targeted therapies in ongoing studies. Our data shows that CTNNB1 mutations can cause resistance to EGFR, ALK and KRAS inhibitor therapy to different extents. Hence, further investigation of the mechanism of action of these beta-catenin mutations and the ability of beta-catenin/other inhibitors to reverse resistance is needed. This data also suggests that CTNNB1 may be an important co-occurring alteration in the context of development of resistance to targeted therapy and should be included in comprehensive clinical genetic testing panels. Citation Format: Anurima Majumder, Benjamin S. Meyer, J Kevin Hicks, Theresa A. Boyle, Eric B. Haura. CTNNB1 mutation can mediate resistance to EGFR, ALK and KRAS targeted therapies [abstract]. In: Proceedings of the American Association for Cancer Research Annual Meeting 2022; 2022 Apr 8-13. Philadelphia (PA): AACR; Cancer Res 2022;82(12_Suppl):Abstract nr 1101.

Myelodysplastic syndromes (MDS) are heterogeneous hematopoietic stem cell malignancies that can phenotypically resemble other hematologic disorders. Thus, tools that may add to current diagnostic practices could aid in disease discrimination. Constitutive innate immune activation is a pathogenetic driver of ineffective hematopoiesis in MDS through Nod-like receptor protein 3 (NLRP3)-inflammasome-induced pyroptotic cell death. Oxidized mitochondrial DNA (ox-mtDNA) is released upon cytolysis, acts as a danger signal, and triggers inflammasome oligomerization via DNA sensors. By using immortalized bone marrow cells from murine models of common MDS somatic gene mutations and MDS primary samples, we demonstrate that ox-mtDNA is released upon pyroptosis. ox-mtDNA was significantly increased in MDS peripheral blood (PB) plasma compared with the plasma of healthy donors, and it was significantly higher in lower-risk MDS vs higher-risk MDS, consistent with the greater pyroptotic cell fraction in lower-risk patients. Furthermore, ox-mtDNA was significantly higher in MDS PB plasma compared with all other hematologic malignancies studied, with the exception of chronic lymphocytic leukemia (CLL). Receiver operating characteristic/area under the curve (ROC/AUC) analysis demonstrated that ox-mtDNA is a sensitive and specific biomarker for patients with MDS compared with healthy donors (AUC, 0.964), other hematologic malignancies excluding CLL (AUC, 0.893), and reactive conditions (AUC, 0.940). ox-mtDNA positively and significantly correlated with levels of known alarmins S100A9, S100A8, and apoptosis-associated speck-like protein containing caspase recruitment domain (CARD) specks, which provide an index of medullary pyroptosis. Collectively, these data indicate that quantifiable ox-mtDNA released into the extracellular space upon inflammasome activation serves as a biomarker for MDS and the magnitude of pyroptotic cell death.

Background: The pathogenesis of Myelodysplastic Syndromes (MDS) is linked to constitutive innate immune stimulation that converges upon the NLRP3 inflammasome to induce pyroptosis, a caspase-1 dependent cell death. We have shown that inflammasome assembly is initiated by both cell-extrinsic stimuli such as S100A9 elaborated by Myeloid-Derived Suppressor Cells (MDSC), as well as cell-intrinsic somatic gene mutations (SGM) (Basiorka A, et. al. Blood 2016). SGM of varied classes evoke replication stress caused by transcriptional pauses that can expose genomic DNA to cytosolic sensors through unresolved R-loops or micronuclei formation. The cGMP-AMP Synthase-Stimulator of Interferon Genes (cGAS-STING) is a cell-intrinsic DNA surveillance pathway recognizing both cytosolic pathogenic and autologous DNA, leading to interferon stimulated gene (ISG) transcription and NLRP3 inflammasome activation, key biological features of MDS (Pellagatti A, et. al. Blood 2006; 108:337.). Here, we investigate the contribution of genomic cytosolic DNA engagement by cGAS-STING to NLRP3 inflammasome activation in MDS. Methods: MDS patient and healthy donor bone marrow mononuclear cells (BMMC) were isolated by Ficoll®-Hipaque method from consented participants at the Moffitt Cancer Center or the National Taiwan University Hospital (NTUH). Immortalized murine C57BL/6 Tet2 -/- and MX1Cre/ SRSF2 P95H as well as respective wild type (WT) control BMMCs were used as MDS SGM models. Results: We first assessed cGAS-STING activation in MDS BMMC by measuring ISG response by microarray, demonstrating profoundly increased expression of ISG15, CXCL10, Samd9l, and Ifi27l2 in MDS BMMC (n=213) compared to healthy control BMMC (n=20) (p Tet2 and SRSF2 SGM models have increased ISG expression compared to WT. Importantly, treatment with the cGAS inhibitor, RU.521 (0.1-1µM, 24 hours), significantly suppressed ISG expression in the SGM models. Further, we confirmed DNA sensor pathway activation in the SRSF2 SGM model by demonstrating upregulated phosphorylation of the interferon-regulatory factor (IRF)3 and IRF7 transcription factors compared to WT controls, and treatment with RU.521 decreased IRF3 phosphorylation. Caspase-1 cleavage in Tet2 and SRSF2 SGM models confirmed NLRP3 inflammasome activation in mutant cells compared to WT controls, and RU.521 treatment decreased active caspase-1 generation in both SGM models. RU.521 treatment of MDS BMMC harboring DNMT3 and Tet2 mutations induced terminal differentiation as evidenced by increased CD11b expression detected by flow cytometry and morphological assessment of Wright-Giemsa stains. Similarly, treatment with RU.521 promoted cytological differentiation in the Tet2 SGM model. We next investigated cytosolic genomic-DNA sources including micronuclei and unresolved DNA:RNA hybrids (R-loops) in the SGM models and primary MDS BMMC. Using immunofluorescence (IF), we found a significantly increased number of micronuclei in MDS BMMC (n=8) compared to controls (n=4), p=0.0248. Additionally, R-loops were increased in MDS primary BMMC (n=5) harboring varied SGM classes vs. controls (n=5) as well as in the SGM models. Finally, to confirm genomic-DNA engagement by cGAS, we used IF to assess cGAS co-localization. cGAS co-localized with micronuclei at sites of envelope collapse as well as with R-loops in MDS BMMC, thereby demonstrating cGAS/STING engagement of cytosolic self-DNA (n=4, each). Conclusion: These data indicate that cGAS-STING engages redundant sources of cytosolic genomic-DNA in MDS to initiate a Type I interferon response and NLRP3 inflammasome activation. Inhibition of the cGAS-STING axis may represent a novel therapeutic strategy for investigation in MDS. Disclosures List: Celgene: Research Funding.

Constitutive innate immune activation is a pathogenetic driver of Myelodysplastic Syndromes (MDS) that directs ineffective hematopoiesis by NLRP3 inflammasome (IFM) assembly and pyroptotic cell death. IFM activation involves recruitment of caspase-1 (casp1) through the adapter protein, ASC, to facilitate autocatalytic cleavage of the zymogen to its active form that is responsible for interleukin (IL)-1β maturation, membrane pore formation and pyroptosis. Oxidized mitochondrial DNA (ox-mtDNA) has been proposed to serve as an alarmin that can activate the IFM by interaction directly with NLRP3 or engagement by DNA sensors, Toll-like receptor 9 (TLR9) and Cyclic GMP-AMP synthase (cGAS). Upon cytolysis, ox-mtDNA is released, permitting interaction with pattern recognition receptors on neighboring cells (Grishman, Pediatric Research, 2012, Shimada, 2012, Immunity. Vollmer, 2004, Immunology). Here, we investigate ox-mtDNA as an IFM-activator and pyroptotic biomarker in MDS.