Checkpoint Signaling Research Articles

An open-label, multicenter study investigating RP3 oncolytic immunotherapy in combination with first- or second-line systemic atezolizumab and bevacizumab therapy in patients with locally advanced unresectable or metastatic hepatocellular carcinoma.

TPS4178 Background: Despite advances in treatment for unresectable hepatocellular carcinoma (HCC), long-term survival rates remain poor. The combination of bevacizumab (Bev) and atezolizumab (Atezo) is the preferred frontline therapy for advanced HCC, but a minority of patients (pts) respond, and secondary resistance usually occurs within months. HCC has an immune-suppressed tumor microenvironment, mediated by activated immune checkpoint signaling and angiogenesis pathways, which may contribute to therapeutic resistance. RP3 is a genetically modified herpes simplex virus type 1 (HSV-1) that expresses the fusogenic gibbon ape leukemia virus glycoprotein with the R sequence deleted (GALV-GP-R–), an anti–CTLA-4 antibody-like molecule, CD40 ligand, and 4-1BB ligand. The direct oncolytic effect coupled with immune stimulation by RP3 in the tumor microenvironment is intended to provide systemic antitumor activity and enhance therapeutic response to anti–PD-1/PD-L1 agents, such as Atezo. Preclinical data have demonstrated improved distribution of oncolytic HSV within tumors in combination with Bev, supporting the clinical combination of RP3 with Bev. This study will evaluate the safety and efficacy of RP3 combined with Atezo and Bev as first- (1L) and second-line (2L) systemic therapies for unresectable and advanced HCC. Methods: The 1L and 2L cohorts will each enroll up to 30 pts. Pts in the 1L cohort may not have received prior systemic treatment; pts in the 2L cohort must have progressed on or following one prior line of systemic therapy, which must have included a PD-1/PD-L1−directed agent. Key inclusion criteria include advanced, unresectable HCC with ≥1 measurable tumor of ≥1 cm in longest diameter, Child-Pugh Class A, and Eastern Cooperative Oncology Group performance status of 0−1. Key exclusion criteria include untreated esophageal and/or gastric varices with bleeding or at high risk for bleeding and macroscopic invasion of tumor into any major blood vessel(s) and/or main bile ducts. Pts with a history of medically refractory hepatic encephalopathy and/or hepato-renal syndrome are also excluded. Pts in the 1L cohort will receive 1200 mg Atezo and 15 mg/kg Bev every 3 weeks (Q3W) together with RP3 intratumorally Q3W for a total of up to 8 doses. Pts in the 2L cohort will receive RP3 every 2 weeks for 4 doses with Bev Q3W starting on cycle (C) 1 day (D) 1, then RP3 and Bev Q3W for up to 4 more doses with Atezo Q3W being added on C4D1. The primary endpoint is overall response rate (ORR) by Response Evaluation Criteria in Solid Tumors (RECIST) v1.1. Secondary endpoints are safety, ORR using HCC modified RECIST, duration of response, complete response rate, and progression-free survival. Clinical trial information: NCT05733598 .

Relationship between ICOS and ICOS ligand RNA expression patterns with tumor type, tumor mutational burden, and clinically relevant immune checkpoints.

e14669 Background: ICOS (inducible T-cell co-stimulator) has a unique ligand (ICOSL). Together they contribute to both antitumor responses/immune stimulation and potentiating immunosuppression. The interaction of ICOS and ICOSL can stimulate CD4 and CD8 ICOS-positive T-cell populations, but also can increase immunosuppressive regulator T-cells. ICOS agonists and antagonists are both under development as novel therapies. We aimed to quantify ICOS and ICOSL expression relationships with tumor type and other clinically relevant checkpoint inhibitors along with evaluating relationships between ICOS and ICOSL expression patterns. Methods: Data from 514 patients with advanced solid tumors at the University of California San Diego were used in the analysis. RNA expression levels of ICOS, ICOS ligand, PD-1, PD-L1, LAG-3, and CTLA-4 from tumor specimens were analyzed at OmniSeq. Tumor mutational burden (TMB) was also evaluated. Univariate analyses (Fischer’s exact tests) and multivariate analysis (logistic regression) were conducted in SAS v 9.4 to determine relationships between high (>=75 percentile RNA rank) and low (0-24 percentile RNA rank) ICOS and ICOSL expression with age, gender, cancer type, high LAG-3, high TMB, high CTLA4, high PD-1, and high PD-L1. The relationship between ICOS and ICOSL high or low expression were also assessed. Results: Seventy patients had high ICOS (14%) and 192 had high ICOSL (37%) while low ICOS was seen in 226 (44%) and low ICOSL was seen in 76 (15%). High ICOS RNA levels were independently associated with patients not having colorectal cancer (p=0.0009), tumors with high PD-1 expression (p=0.025), tumors with high PD-L1 expression (p<0.0001), and tumors with high CTLA-4 expression (p<0.0001). Low ICOS RNA levels were independently associated with patients whose tumors did not have high PD-1 (p=0.0006), tumors that did not have high PD-L1 (p=0.01), tumors that did not have high CTLA-4 expression (p<0.0001), and those with low ICOSL expression (p=0.0007). High ICOSL was independently associated with a diagnosis of colorectal cancer (p=0.0015), tumors that did not have high PD-L1 expression (p=0.003), and tumors with high CTLA4 (p=0.0001). Low ICOSL was independently associated with patients who did not have colorectal cancer (p=0.0001) and tumors with low ICOS expression (p=0.0032). Conclusions: ICOS and ICOSL RNA expression patterns can provide insight into the complicated ICOS/ICOSL immune checkpoint signaling pathway and help support rational immunotherapy combinations as part of a precision medicine approach. Both stimulators and inhibitors of the ICOS/ICOSL axis are being developed, and their proper application may require interrogation of the individual patient’s tumor/environment.

Inferring evolutionary trajectories from cross-sectional transcriptomic data to mirror lung adenocarcinoma progression.

Lung adenocarcinoma (LUAD) is a deadly tumor with dynamic evolutionary process. Although much endeavors have been made in identifying the temporal patterns of cancer progression, it remains challenging to infer and interpret the molecular alterations associated with cancer development and progression. To this end, we developed a computational approach to infer the progression trajectory based on cross-sectional transcriptomic data. Analysis of the LUAD data using our approach revealed a linear trajectory with three different branches for malignant progression, and the results showed consistency in three independent cohorts. We used the progression model to elucidate the potential molecular events in LUAD progression. Further analysis showed that overexpression of BUB1B, BUB1 and BUB3 promoted tumor cell proliferation and metastases by disturbing the spindle assembly checkpoint (SAC) in the mitosis. Aberrant mitotic spindle checkpoint signaling appeared to be one of the key factors promoting LUAD progression. We found the inferred cancer trajectory allows to identify LUAD susceptibility genetic variations using genome-wide association analysis. This result shows the opportunity for combining analysis of candidate genetic factors with disease progression. Furthermore, the trajectory showed clear evident mutation accumulation and clonal expansion along with the LUAD progression. Understanding how tumors evolve and identifying mutated genes will help guide cancer management. We investigated the clonal architectures and identified distinct clones and subclones in different LUAD branches. Validation of the model in multiple independent data sets and correlation analysis with clinical results demonstrate that our method is effective and unbiased.

Comprehensive mutational analysis of the checkpoint signaling function of Rpa1/Ssb1 in fission yeast.

Replication protein A (RPA) is a heterotrimeric complex and the major single-strand DNA (ssDNA) binding protein in eukaryotes. It plays important roles in DNA replication, repair, recombination, telomere maintenance, and checkpoint signaling. Because RPA is essential for cell survival, understanding its checkpoint signaling function in cells has been challenging. Several RPA mutants have been reported previously in fission yeast. None of them, however, has a defined checkpoint defect. A separation-of-function mutant of RPA, if identified, would provide significant insights into the checkpoint initiation mechanisms. We have explored this possibility and carried out an extensive genetic screen for Rpa1/Ssb1, the large subunit of RPA in fission yeast, looking for mutants with defects in checkpoint signaling. This screen has identified twenty-five primary mutants that are sensitive to genotoxins. Among these mutants, two have been confirmed partially defective in checkpoint signaling primarily at the replication fork, not the DNA damage site. The remaining mutants are likely defective in other functions such as DNA repair or telomere maintenance. Our screened mutants, therefore, provide a valuable tool for future dissection of the multiple functions of RPA in fission yeast.

Replisome-cohesin interactions provided by the Tof1-Csm3 and Mrc1 cohesion establishment factors

The chromosomal cohesin complex establishes sister chromatid cohesion during S phase, which forms the basis for faithful segregation of DNA replication products during cell divisions. Cohesion establishment is defective in the absence of either of three non-essential Saccharomyces cerevisiae replication fork components Tof1-Csm3 and Mrc1. Here, we investigate how these conserved factors contribute to cohesion establishment. Tof1-Csm3 and Mrc1 serve known roles during DNA replication, including replication checkpoint signaling, securing replication fork speed, as well as recruiting topoisomerase I and the histone chaperone FACT. By modulating each of these functions independently, we rule out that one of these known replication roles explains the contribution of Tof1-Csm3 and Mrc1 to cohesion establishment. Instead, using purified components, we reveal direct and multipronged protein interactions of Tof1-Csm3 and Mrc1 with the cohesin complex. Our findings open the possibility that a series of physical interactions between replication fork components and cohesin facilitate successful establishment of sister chromatid cohesion during DNA replication.

Issue highlights-May 2023.

In the era of personalized medicine, the list of targeted therapeutic drugs has been greatly expanded, many of which are employed to treat hematolymphoid neoplasms. These include drugs specifically targeting immune checkpoint signaling epitopes such as programmed cell death 1 (PD1) and its ligand PDL1 to inhibit T-cell activation. Alternatively, these drugs might target the surface antigens expressed by tumor cells such as CD19 and CD22 in B-cell neoplasms. Of the latter, targeted immunotherapies include monoclonal antibodies with or without drug conjugates, bispecific T-cell engagers, or chimeric antigen receptor (CAR) T-cell therapy. The binding sites of these therapeutic antibodies are often identical or in proximity with the binding sites of the diagnostic antibodies. Therefore, use of these therapies pose great challenges for clinical cytometry labs in the assessment of post-treatment samples, especially in the detection of measurable/minimal residual disease (MRD). In this issue, Chen, Gao, et al. (2023) provided an overview of MRD detection in B-lymphoblastic leukemia/lymphoma in the era of immunotherapy, and Gao et al. (2023) focused their review on the impact of targeted therapy on mature B- and plasma cell neoplasms utilizing flow cytometry assessments. In both reviews, the authors illustrated the challenges, identified the problems, and provided a list of available options and solutions. For each of the above-mentioned disease categories, optimal gating and analysis strategies were illustrated with literature review and inputs from the authors' experience and insights. The utility and interpretation of additional B-cell markers other than CD19 and CD20 for mature or immature B-cell neoplasms such as CD22, CD24, and cCD79a (Mikhailova et al., 2022) were studied as well as VS38, CD229, and CD319 (Pojero et al., 2016; Soh et al., 2021) for plasma cell neoplasms. The authors recommended that the flow cytometry assays in the era of targeted therapies must contain significant redundancy in the antibody panels allowing the detection of the cells of interest and additionally should be ready to utilize several gating strategies for accurate and consistent population identification. Neoplastic mature B-cells often show restricted kappa or lambda light chain expression; however, light chain expression may be absent in around 5%–10% of mature B-cell lymphoma (Li et al., 2002). It is suggested that mature B-cells lacking surface light chain expression can be used as a surrogate marker to diagnose mature B-cell lymphomas. Huang et al. (2023) reported a series of 89 cases of surface light chain negative B-cell lymphoma which consisted primarily of chronic lymphocytic leukemia/small lymphocytic lymphoma (CLL/SLL). Interestingly, the authors also reported no detectable light chain expression in normal/reactive mature B cells collected from body fluids and cystic fluids from 14 patients with no clinical and pathological evidence of lymphoma/leukemia. Body fluids are often proteaceous; thus additional washing prior to kappa/lambda staining is often required to obtain adequate light chain staining and caution is needed in the interpretation of light chain expression in B-cells collected from body fluids. It is known that out of the context of chronic myeloid leukemia (CML) (Soma et al., 2016), lymphoblastic crisis is extremely rare in other chronic myeloid neoplasms, such as myelodysplastic syndrome (MDS) (Xie et al., 2019) and Philadelphia negative myeloproliferative neoplasms (MPN). Chan et al. (2023) reported the detection of a low level of abnormal B-lymphoblasts ranging from 0.012% to 3.6% in 9 out of 1262 MDS or Ph-negative MPN. Cell sorting coupled with next-generational sequencing showed that the abnormal B- lymphoblasts in myeloid neoplasms were often, but not always, clonally related to the myeloid compartment, and the molecular genetic findings suggested a mutant multipotent progenitor cell with different lineage output that might be determined by the specific mutations and the particular cell stage where the mutations occurred. Importantly, unlike CML, the presence of abnormal B-lymphoblasts in MDS and Ph-neg MPNs did not necessarily indicate blast crisis, and therapy for the underlying myeloid neoplasms with close monitoring is suggested to be a reasonable approach. The last article in this issue (Chen, Zhang, et al., 2023) studied mucosal-associated invariant T cells (MAIT) (Godfrey et al., 2019) in aplastic anemia (AA), a type of bone marrow failure directly linked to abnormal immune responses. MAIT cells exhibit an effector-memory phenotype and express several NK receptors such as NKG2D and CD161 and play an important role in the development of autoimmune diseases. The authors showed an increased frequency of MAIT cells with an activation and effector function-related cell surface marker profile in patients with aplastic anemia. The specific property of NKG2D expression on MAIT cells suggests that these cells may have a distinct mechanism involved in AA immune pathogenesis.

The Functional Role and Regulatory Mechanism of FTO m6A RNA Demethylase in Human Uterine Leiomyosarcoma.

Uterine leiomyosarcoma (uLMS) is the most frequent subtype of uterine sarcoma that presents a poor prognosis and high rates of recurrence and metastasis. The origin and molecular mechanism underlying and driving its clinical and biological behavior remain largely unknown. Recently, we and others have revealed the role of microRNAs, DNA methylation, and histone modifications in contributing to the pathogenesis of uLMS. However, the connection between reversible m6A RNA methylation and uLMS pathogenesis remains unclear. In this study, we assessed the role and mechanism of FTO m6A RNA demethylase in the pathogenesis of uLMS. Immunohistochemistry analysis revealed that the levels of RNA demethylases FTO and ALKBH5 were aberrantly upregulated in uLMS tissues compared to adjacent myometrium with a significant change by histochemical scoring assessment (p < 0.01). Furthermore, the inhibition of FTO demethylase with its small, potent inhibitor (Dac51) significantly decreased the uLMS proliferation dose-dependently via cell cycle arrest. Notably, RNA-seq analysis revealed that the inhibition of FTO with Dac51 exhibited a significant decrease in cell-cycle-related genes, including several CDK members, and a significant increase in the expression of CDKN1A, which correlated with a Dac51-exerted inhibitory effect on cell proliferation. Moreover, Dac51 treatment allowed the rewiring of several critical pathways, including TNFα signaling, KRAS signaling, inflammation response, G2M checkpoint, and C-Myc signaling, among others, leading to the suppression of the uLMS phenotype. Moreover, transcription factor (TF) analyses suggested that epitranscriptional alterations by Dac51 may alter the cell cycle-related gene expression via TF-driven pathways and epigenetic networks in uLMS cells. This intersection of RNA methylation and other epigenetic controls and pathways provides a framework to better understand uterine diseases, particularly uLMS pathogenesis with a dysregulation of RNA methylation machinery. Therefore, targeting the vulnerable epitranscriptome may provide an additional regulatory layer for a promising and novel strategy for treating patients with this aggressive uterine cancer.

The role of kinetochore dynein in checkpoint silencing is restricted to disassembly of the corona.

During mitosis, kinetochore-microtubule attachments are monitored by a molecular surveillance system known as the spindle assembly checkpoint. The prevailing model posits that dynein evicts checkpoint proteins (e.g., Mad1, Mad2) from stably attached kinetochores by transporting them away from kinetochores, thus contributing to checkpoint silencing. However, the mechanism by which dynein performs this function, and its precise role in checkpoint silencing remain unresolved. Here, we find that dynein's role in checkpoint silencing is restricted to evicting checkpoint effectors from the fibrous corona, and not the outer kinetochore. Dynein evicts these molecules from the corona in a manner that does not require stable, end-on microtubule attachments. Thus, by disassembling the corona through indiscriminate microtubule encounters, dynein primes the checkpoint signaling apparatus so it can respond to stable end-on microtubule attachments and permit cells to progress through mitosis. Accordingly, we find that dynein function in checkpoint silencing becomes largely dispensable in cells in which checkpoint effectors are excluded from the corona.

Abstract LB044: Modeling the role of ARID1A in colon cancer using patient-derived organoids

Abstract Loss-of-function (LOF) mutations in genes encoding subunits of SWI/SNF chromatin remodeling complexes are found in approximately 25% of human cancers. Colorectal cancers (CRC), the second leading cause of cancer related deaths, are particularly vulnerable to SWI/SNF driver mutations, harboring subunit alterations in up to 55% of patient tumors. ARID1A, a BAF subcomplex specific subunit, is the most frequently mutated subunit in human cancers (12%) and CRCs (10-12%). Additionally, ARID1A was recently identified as a leading genetic alteration in inflammatory bowel diseases such as Crohn’s and Ulcerative Colitis, conditions which are at higher risk of developing CRC. These data suggest an important role in ARID1A regulation of colonic tissue homeostasis and the potential for ARID1A mutation as an initiating or early driving event in CRC, which has not yet been modeled in human colon tissues. To examine the role of ARID1A in colon cancer development, we took a bottom-up strategy using CRISPR edited patient-derived colon organoids to model ARID1A LOF mutations in combination with classic CRC mutations APC and TP53. We evaluated the functional consequences of ARID1A mutation on cell growth using colony formation and proliferation assays. To systematically investigate the phenotypic contribution of ARID1A loss in these cell contexts, we employed transcriptomic and epigenomic profiling with RNAseq and ATACseq. We found that triple knock-out (TKO) of ARID1A, APC and TP53 confers a growth advantage in colon organoids, and induces dramatic morphological changes such as loss of symmetry and the breakdown of cystic architectures. At the gene expression level, ARID1A mutations led to shared and cell context specific transcriptional changes enriched for pathways such as G2M checkpoint, KRAS Signaling, and STAT5 signaling. Mechanistically, we show that ARID1A dependent chromatin accessibility changes at putative enhancers are linked to promoters of differentially expressed genes. These data suggest that ARID1A can regulate multiple cancer hallmark pathways depending on the cellular context and indicate a pleiotropic tumor suppressive function requiring further investigation in clinically relevant genetic backgrounds. Citation Format: Luke T. Deary, Nicholas Sugiarto, Cameron Pigeon, Sara W. Mayo, Matthew Z. Wilson, Xiaofeng Wang. Modeling the role of ARID1A in colon cancer using patient-derived organoids [abstract]. In: Proceedings of the American Association for Cancer Research Annual Meeting 2023; Part 2 (Clinical Trials and Late-Breaking Research); 2023 Apr 14-19; Orlando, FL. Philadelphia (PA): AACR; Cancer Res 2023;83(8_Suppl):Abstract nr LB044.

Meiotic cells escape prolonged spindle checkpoint activity through kinetochore silencing and slippage.

To prevent chromosome mis-segregation, a surveillance mechanism known as the spindle checkpoint delays the cell cycle if kinetochores are not attached to spindle microtubules, allowing the cell additional time to correct improper attachments. During spindle checkpoint activation, checkpoint proteins bind the unattached kinetochore and send a diffusible signal to inhibit the anaphase promoting complex/cyclosome (APC/C). Previous work has shown that mitotic cells with depolymerized microtubules can escape prolonged spindle checkpoint activation in a process called mitotic slippage. During slippage, spindle checkpoint proteins bind unattached kinetochores, but the cells cannot maintain the checkpoint arrest. We asked if meiotic cells had as robust of a spindle checkpoint response as mitotic cells and whether they also undergo slippage after prolonged spindle checkpoint activity. We performed a direct comparison between mitotic and meiotic budding yeast cells that signal the spindle checkpoint through two different assays. We find that the spindle checkpoint delay is shorter in meiosis I or meiosis II compared to mitosis, overcoming a checkpoint arrest approximately 150 minutes earlier in meiosis than in mitosis. In addition, cells in meiosis I escape spindle checkpoint signaling using two mechanisms, silencing the checkpoint at the kinetochore and through slippage. We propose that meiotic cells undertake developmentally-regulated mechanisms to prevent persistent spindle checkpoint activity to ensure the production of gametes.

Abstract 4117: Molecular insights into resistance mechanisms to therapy with T cell bispecific antibodies

Abstract T Cell Bispecific Antibodies (TCBs) are potent molecules that induce durable complete remissions with a favorable safety profile in Relapsed Refractory Non Hodgkin Lymphoma patients. Despite the promising clinical efficacy, a proportion of patients escape under treatment due to the occurrence of primary and acquired resistance mechanisms that may involve the modulation of target antigen expression, cancer cell intrinsic mechanisms, T cell functionality or treatment-induced changes in the tumor microenvironment (TME). Therefore, a better understanding of TCB-induced resistance mechanisms is of great importance to enable the design of novel therapeutic approaches and/or combination strategies to overcome resistance. We present the results of exploratory preclinical analysis using an aggressive lymphoma model in humanized mice and a syngeneic melanoma model in immunocompetent mice, focusing on the assessment of T cell functionality, TME reprogramming, and cancer cell intrinsic changes upon longitudinal TCB treatments, encompassing tumor regression and escape. Flow cytometry, IHC, scRNAseq and ex vivo functional analysis of T cell cytotoxicity and cytokine release demonstrate that intra-tumor T cell functionality is preserved over serial TCB treatments, including tumor escape. On the other hand, TCB treatment induced a reprogramming of the TME consisting of rapid myeloid cell infiltration, followed by the expansion of intra-tumor T cells at a later time point (favoring higher CD8:CD4 ratio). Cumulative evidence from in vitro and in vivo scRNAseq experiments provided insights into macrophage reaction to TCB-mediated T cell inflammation, consisting of a rapid (as early as 2 h) activation and upregulation of several pro-inflammatory molecules (IL-1b, CXCL8, CXCL9, CXCL10, CXCL1, CCL2, CCL3, CCL4, CCL5, IFN-g-induced genes: GBP2 -8 and BATF2). This was followed by a shift towards a more suppressive phenotype at later time points (20-96 h) as evidenced by the expression of PD-L1, INHBA, IDO, FLT1 genes. The analysis of cancer cells showed upregulation of Wnt/beta catenin, p53 and Hedgehog signaling pathways at tumor escape. In contrast, proliferation signatures including MYC, E2F target genes, MTORC signaling, and G2M checkpoint, along with metabolic pathways of oxidative phosphorylation and glycolysis were enriched in cancer cells at regression. Taken together, our data show that T cell cytotoxicity and functional states are preserved during tumor regression and tumor escape phases, suggesting that T cell dysfunctionality is unlikely to be the sole cause of TCB resistance. TME reprogramming, consisting of a rapid myeloid cell infiltration and their acquisition of a suppressive phenotype over time, along with a selection of cancer cell clones that escape the TCB-mediated cytotoxicity and upregulate Wnt, p53 and Hedgehog pathways could contribute to TCB-mediated resistance, leading to tumor escape. Citation Format: Johannes Sam, Llucia Alberti Servera, Sina Nassiri, Atul Sethi, Alison Ribeiro, Gabrielle Leclercq-Cohen, Petra Schwalie, Tamara Hüsser, Emilio Yangueez, Sylvia Herter, Christian Klein, Pablo Umana, Marina Bacac. Molecular insights into resistance mechanisms to therapy with T cell bispecific antibodies. [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 4117.

Abstract 1414: The role of chromosome arm 3p and human papillomavirus on proliferation, differentiation, and metastasis in squamous cancers

Abstract Squamous Cell Carcinoma (SCC) is an aggressive form of cancer that develops in the mucosal epithelium of the digestive and respiratory tracts as well as on the skin. Two major risk factors for development of SCC are carcinogen exposures, such as alcohol and tobacco, and Human Papillomavirus (HPV) infection. Viral- and carcinogen-driven SCCs have differential responses to radiation, chemotherapy, and immunotherapy, with HPV+ SCCs responding better to these treatments than HPV- carcinomas. Analysis of aneuploidy patterns of genomic samples from The Cancer Genome Atlas (TCGA) have shown that squamous cancers cluster together and are characterized by gain of chromosome arm 3q gain and loss of chromosome arm 3p. However, while HPV+ SCCs show similar rates of 3q gain, they have significantly lower rates of 3p loss, suggesting that 3p deletion and HPV infection might have overlapping roles in cancer initiation and/or progression. In addition, the degree to which these two paths of tumor development contribute to differences in disease progression and outcome has been largely unexplored. We have identified a strong correlation between 3p deletion and high epithelial-mesenchymal transition (EMT) gene signature across all cancer types. Interestingly, interferon signaling has been found to be upregulated in non-squamous cancers upon 3p deletion but downregulated in squamous cancers with 3p deletion. SCCs positive for HPV infection show decreased expression of EMT genes and increased expression of genes in interferon signaling and cell cycle checkpoint pathways. Together, the results of these TCGA analyses suggest mechanisms by which chromosome 3p deletion and HPV infection may affect cancer progression and are currently being validated in vitro in a panel of squamous cancer cell lines. Additionally, we will use a targeted CRISPR-Cas9 system developed in our lab to delete chromosome 3p, as well as transfect HPV oncoproteins, in normal keratinocytes to create isogenic models. With these models, we will study the role of individual aneuploidy events in tumorigenesis, tumor development, and metastasis in the context of HPV positive and negative SCC. Citation Format: Samyukta Mallick, Alison M. Taylor. The role of chromosome arm 3p and human papillomavirus on proliferation, differentiation, and metastasis in squamous cancers [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 1414.

Abstract 4438: Bypassing immune evasion in colorectal cancer by integrin inhibition-mediated downregulation of PD-L1

Abstract Integrin receptors have long posed a potentially attractive target for disrupting cancer hallmarks. Promising preliminary findings with integrin inhibition as an adjuvant to chemotherapy have not translated to clinical success. However, the effect of integrin inhibition on tumor-immune cell interactions remains largely unexplored. Further investigation could shed light on a connection between integrin signaling and immune checkpoint expression, opening the path for using integrin inhibitors to sensitize otherwise resistant tumors to immunotherapy. Fluorescently labeled wild-type HCT-116 colorectal cancer cells and TALL-104 T-cells were co-cultured and treated with GLPG0187, a small molecule integrin inhibitor, at various doses. Co-cultures were observed at different time points using fluorescence microscopy and cell counts were quantified using ImageJ software. The co-culture included the cell viability marker ethidium homodimer so the number of viable cells of each type could be determined using colocalization. This assay revealed synergistic cancer cell killing, indicating that integrin inhibition may be sensitizing cancer cells to immune cells. The hypothesized mechanism involves TGF-beta-mediated PD-L1 expression in cancer cells. GLPG0187 has been shown to inhibit the ɑvβ6 integrin receptor, which is responsible for the activation of latent-TGFβ into the active form. By blocking this receptor, there would potentially be a reduction of TGFβ signaling and therefore a reduced expression of PD-L1 leading to an enhanced immune response. To investigate this mechanism, both WT and p53-/- HCT-116 cells were pre-treated with GLPG0187 and subsequently with latent-TGFβ. Western blot analysis demonstrated that the addition of latent-TGFβ increased the expression of PD-L1 in cancer cells. Additionally, a low dose of integrin inhibitor rescued these effects, returning PD-L1 expression back to control levels. However, the higher dose of the drug did not reduce PD-L1 expression. This could potentially be due to off-target effects conflicting with the proposed pathway, however, these findings are still under active investigation. Ongoing proteomic experiments include a larger range of both drug and latent-TGFβ doses. Probing for additional downstream markers of TGFβ and up-stream markers of PD-L1 will help to further elucidate the mechanism. Further co-culture experiments include anti-PD-L1 and anti-PD-1 therapy to investigate the viability of integrin inhibition as an adjuvant to immune checkpoint blockade. Citation Format: William J. MacDonald, Brooke Verschleiser, Lindsey Carlsen, Kelsey E. Huntington, Wafik S. El-Deiry. Bypassing immune evasion in colorectal cancer by integrin inhibition-mediated downregulation of PD-L1. [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 4438.

Abstract 2667: PARG inhibition augments CHK1 inhibitor-induced replication stress and synergistically kills ovarian cancer cells

Abstract Ovarian cancer (OC) is one of the leading causes of cancer-related deaths in women in the United States. PARP inhibitors showed promising clinical responses; however, most of the patients eventually relapse and succumb to the resistant disease. Currently, it lacks effective therapies to prevent and treat OC, which warrants novel drugs and combination therapies to improve patients' prognoses. Epithelial OCs are heavily dependent on ATR-CHK1-mediated DNA damage checkpoint signaling for survival, which is also regulated by hedgehog/GLI1 (Hh) signaling in cancer cells. However, both Hh/GLI1 and CHK1 inhibitors failed to show promising results in clinical trials as single agents. Poly(ADP-ribose) glycohydrolase (PARG) is the critical enzyme that removes Poly-ADP ribosylated (PARylated) proteins upon replication stress. We hypothesized that inhibition of PARG could amplify CHK1 inhibitor-induced replication stress by trapping PARylated proteins on the chromatin and compromising DNA repair and causing a metabolic and mitotic catastrophe. We evaluated CHK1 inhibitor prexasertib in combination with PARG inhibitor (PARGi) to target metabolic and DNA repair crosstalk to effectively kill OC cells and to overcome resistance. Our studies demonstrate that prexasertib treatment induces PARylation by inducing replication stress. Similarly, PARG inhibition by (PDD00017273) fails to remove PARylation and activates checkpoint kinase 1 (CHK1) by phosphorylating at S296, S317, and S345 in OC cells. Based on these observations, we hypothesized that a combination of CHK1 and PARG inhibition would augment oncogenic replication stress in OC cells and cause increased DNA damage and cell death. Interestingly, our evaluation of prexasertib and PARGi combination treatment by clonogenic survival and MTT assays showed synergistic killing in a panel of OC cells, including in isogenic chemoresistant models as well as 3D organoid models of primary OC cells compared to individual drugs. As predicted, combined treatment increased DNA double-strand breaks as demonstrated by COMET assays, and increased γH2AX foci, pRPA32 foci, perturbed S/G2 phase arrest, and nuclear disintegration relative to individual-drug treatment. Furthermore, significant depletion of NAD+ levels was seen in PARGi-treated OC cells compared to untreated cells. Together, these results indicate that this combination treatment cause persistence of heavy PARylation at DNA damage sites abrogates cell cycle checkpoint mechanisms, exhausts cellular NAD+ levels, and inhibits DNA repair leading to the metabolic and mitotic collapse of cancer cells and synergistic lethality in OC cells. Currently, prexasertib is under clinical trials and our studies will provide novel mechanistic insight into the therapeutic potential of this combination and provides preclinical evidence to develop further this combination therapy in treating OC. Citation Format: Ganesh Acharya, Chinnadurai Mani, Mark B. Reedy, Komaraiah Palle. PARG inhibition augments CHK1 inhibitor-induced replication stress and synergistically kills ovarian cancer cells [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 2667.

A DNA damage–induced phosphorylation circuit enhances Mec1ATR Ddc2ATRIP recruitment to Replication Protein A

The cell cycle checkpoint kinase Mec1ATR and its integral partner Ddc2ATRIP are vital for the DNA damage and replication stress response. Mec1-Ddc2 "senses"single-stranded DNA (ssDNA) by being recruited to the ssDNA binding Replication Protein A (RPA) via Ddc2. In this study, we show that a DNA damage-induced phosphorylation circuit modulates checkpoint recruitment and function. We demonstrate that Ddc2-RPA interactions modulate the association between RPA and ssDNA and that Rfa1-phosphorylation aids in the further recruitment of Mec1-Ddc2. We also uncover an underappreciated role for Ddc2 phosphorylation that enhances its recruitment to RPA-ssDNA that is important for the DNA damage checkpoint in yeast. The crystal structure of a phosphorylated Ddc2 peptide in complex with its RPA interaction domain provides molecular details of how checkpoint recruitment is enhanced, which involves Zn2+. Using electron microscopy and structural modeling approaches, we propose that Mec1-Ddc2 complexes can form higher order assemblies with RPA when Ddc2 is phosphorylated. Together, our results provide insight into Mec1 recruitment and suggest that formation of supramolecular complexes of RPA and Mec1-Ddc2, modulated by phosphorylation, would allow for rapid clustering of damage foci to promote checkpoint signaling.

Principles and dynamics of spindle assembly checkpoint signalling.

The transmission of a complete set of chromosomes to daughter cells during cell division is vital for development and tissue homeostasis. The spindle assembly checkpoint (SAC) ensures correct segregation by informing the cell cycle machinery of potential errors in the interactions of chromosomes with spindle microtubules prior to anaphase. To do so, the SAC monitors microtubule engagement by specialized structures known as kinetochores and integrates local mechanical and chemical cues such that it can signal in a sensitive, responsive and robust manner. In this Review, we discuss how SAC proteins interact to allow production of the mitotic checkpoint complex (MCC) that halts anaphase progression by inhibiting the anaphase-promoting complex/cyclosome (APC/C). We highlight recent advances aimed at understanding the dynamic signalling properties of the SAC and how it interprets various naturally occurring intermediate attachment states. Further, we discuss SAC signalling in the context of the mammalian multisite kinetochore and address the impact of the fibrous corona. We also identify current challenges in understanding how the SAC ensures high-fidelity chromosome segregation.

Anthracycline Therapy Modifies Immune Checkpoint Signaling in the Heart.

Cancer survival rates have increased significantly because of improvements in therapy regimes and novel immunomodulatory drugs. Recently, combination therapies of anthracyclines and immune checkpoint inhibitors (ICIs) have been proposed to maximize neoplastic cell removal. However, it has been speculated that a priori anthracycline exposure may prone the heart vulnerable to increased toxicity from subsequent ICI therapy, such as an anti-programmed cell death protein 1 (PD1) inhibitor. Here, we used a high-dose anthracycline mouse model to characterize the role of the PD1 immune checkpoint signaling pathway in cardiac tissue using flow cytometry and immunostaining. Anthracycline treatment led to decreased heart function, increased concentration of markers of cell death after six days and a change in heart cell population composition with fewer cardiomyocytes. At the same time point, the number of PD1 ligand (PDL1)-positive immune cells and endothelial cells in the heart decreased significantly. The results suggest that PD1/PDL1 signaling is affected after anthracycline treatment, which may contribute to an increased susceptibility to immune-related adverse events of subsequent anti-PD1/PDL1 cancer therapy.

What do we know about co-stimulatory and co-inhibitory immune checkpoint signals in ankylosing spondylitis?

Ankylosing Spondylitis is the main entity of a family of inflammatory diseases affecting many musculoskeletal (sacroiliac joints, spine, peripheral joints) and extra-musculoskeletal sites, termed spondyloarthritis. While it is debated whether disease onset is primarily driven by autoimmune or autoinflammatory processes, what is certain is that both innate and adaptive immune responses orchestrate local and systemic inflammation, which leads to chronic pain and immobility. Immune checkpoint signals are one key player for keeping the immune system in check and in balance, but their role in disease pathogenesis is still rather elusive. Therefore, we ran a MEDLINE search utilizing the PubMed platform for a variety of immune checkpoint signals in regard to ankylosing spondylitis. In this review, we summarise the experimental and genetic data available and evaluate the relevance of immune checkpoint signalling in the pathogenesis of ankylosing spondylitis. Markers such as PD-1 and CTLA-4 have been extensively studied and facilitate the concept of an impaired negative immune regulation in ankylosing spondylitis. Other markers are either neglected completely or insufficiently examined, and the data is conflicting. Still, some of those markers remain interesting targets to decipher the pathogenesis of ankylosing spondylitis and to develop new treatment strategies.

Association of DNA Promoter Methylation and BRAF Mutation in Thyroid Cancer.

The BRAF V600E mutation and DNA promoter methylation play important roles in the pathogenesis of thyroid cancer (TC). However, the association of these genetic and epigenetic alterations is not clear. In this study, using paired tumor and surrounding normal tissue from the same patients, on a genome-wide scale we tried to identify (a) any association between BRAF mutation and DNA promoter methylation, and (b) if the molecular findings may provide a basis for therapeutic intervention. We included 40 patients with TC (female = 28, male = 12) without distant metastasis. BRAF mutation was present in 18 cases. We identified groups of differentially methylated loci (DML) that are found in (a) both BRAF mutant and wild type, (b) only in BRAF mutant tumors, and (c) only in BRAF wild type. BRAF mutation-specific promoter loci were more frequently hypomethylated, whereas BRAF wild-type-specific loci were more frequently hypermethylated. Common DML were enriched in cancer-related pathways, including the mismatch repair pathway and Wnt-signaling pathway. Wild-type-specific DML were enriched in RAS signaling. Methylation status of checkpoint signaling genes, as well as the T-cell inflamed genes, indicated an opportunity for the potential use of PDL1 inhibitors in BRAF mutant TC. Our study shows an association between BRAF mutation and methylation in TC that may have biological significance.

Abstract P3-05-33: High expression of MiR-99b in breast cancer is associated with cell proliferation signaling and worse patient survivals in breast cancer

Abstract Background: MicroRNA (miR) is single stranded RNA which regulates the gene expression epigenetically by inhibiting the mRNA translation as well as promoting mRNA degradation. MiR-99b is known as a regulator of mechanistic target of rapamycin (mTOR) signaling and was reported as both onco-miR that promote cell proliferation and tumor suppressor-miR in multiple cancers. We hypothesized that there is a complex interaction between miR-99b and cancer signaling pathways as well as tumor microenvironment, which may influence outcomes. Methods: We studied the clinical relevance of miR-99b expression by performing in silico analyses of 1,961 breast cancer patients using two independent large cohorts; METABRIC and TCGA. Results: We found that high miR-99b breast cancer enriched MTORC1 signaling gene set (normalized enrichment score (NES)&amp;gt;1.50 in both cohorts), but not epithelial mesenchymal transition, NF-kB, nor TGF-β signaling gene sets (all false discovery rate (FDR)&amp;gt;0.40). High miR-99b breast cancer was significantly associated with high rates of mutation scores; silent- and non-silent-mutation rate, fraction altered, single-nucleotide variant neoantigens, as well as intratumor heterogeneity and homologous recombination defects. MiR-99b high tumors also enriched several cell proliferation-related gene sets; E2F targets, G2M checkpoint, and Mitotic spindle signaling, and was significantly associated with pathological grade, but not with subtype nor AJCC stage. High miR-99b breast cancer was significantly associated with low fraction of several stromal cells, including adipocytes cells, keratinocytes cells, and lymphatic endothelial cells in tumor microenvironment (all p&amp;lt; 0.001). On the other hand, miR-99b expression was not associated with immune function nor immune cell infiltration in breast cancer, except for dendritic cells (p=0.006 and 0.020, respectively). Finally, breast cancer with high miR-99b expression was significantly associated with worse overall survival (OS) (hazard ratio (HR)=1.23 (p&amp;lt; 0.001) and 1.26 (p=0.027), respectively) and disease-specific survival (DSS) (HR=1.28 (p&amp;lt; 0.001) and 1.39 (p=0.022), respectively), particularly DSS for ER-positive/HER2-negative breast cancer (HR=1.29 (p&amp;lt; 0.001) and 1.82 (p=0.017), respectively), consistently in two cohorts. In conclusion, we found that high miR-99b expressing breast cancer was significantly associated with not only MTORC1 but also cell proliferation and worse patient outcomes particularly in ER-positive/HER2-negative breast cancer. Citation Format: Masanori Oshi, Yoshihisa Tokumaru, Nobuhiko Sugito, Mahato Sasamoto, Rongrong Wu, Li Yan, Akimitsu Yamada, Takashi Ishikawa, Itaru Endo, Kazuaki Takabe. High expression of MiR-99b in breast cancer is associated with cell proliferation signaling and worse patient survivals in breast cancer [abstract]. In: Proceedings of the 2022 San Antonio Breast Cancer Symposium; 2022 Dec 6-10; San Antonio, TX. Philadelphia (PA): AACR; Cancer Res 2023;83(5 Suppl):Abstract nr P3-05-33.