bluuebunny/crossref_metadata_2025 huggingface dataset:
Abstract 1156: The integrated stress response (ISR) is involved in the synergistic combinatorial efficacy of ONC201 and epigenetic modulators in brain tumor cell lines
Authors: Zhang Yiqun , Zhou Lanlan , Prabhu Varun V. , Allen Joshua E. , Seyhan Attila A. , El-Deiry Wafik S.
Published: July 2021

First-in-class small molecule ONC201 is an anti-cancer agent that activates the TRAIL pathway through ATF4 and the integrated stress response (ISR). ONC201 demonstrated durable tumor regressions and prolonged disease stabilization in some patients with histone H3K27M-mutated diffuse midline glioma (DMG). The H3K27M-mutation reduces H3K27 methylation. EZH2 inhibitors (EZH2i) reduce global H3K27 methylation. We hypothesized that ONC201 sensitivity and tumor cell death may be enhanced by reducing H3K27 methylation with EZH2i as a mimic of the H3K27M-mutation, particularly in tumor types beyond DMG. We treated cancer cells from different tissue origins including breast cancer, pancreatic cancer, colorectal cancer, glioblastoma, and DMG with single agent ONC201, EZH2 inhibitor EPZ-6438 or PF-06821497, or the combination of ONC201 plus EPZ-6438 or ONC201 plus PF-06821497. Cell viability was determined with the Cell Titer-Glo assay. Integrated stress response (ISR) activation widely observed in ONC201-treated tumor cells was evaluated using Western blot analysis of ATF4. We determined TRAIL pathway activity by analysis of DR5, and apoptosis by analysis of PARP cleavage. The effect of EPZ-6438 or PF-06821497on the target was validated by immunoblotting of H3K27me3. We knocked down ATF4 with siRNA to evaluate the role of ISR in cell death. Our results demonstrate that ONC201 synergistically reduced cell viability in combination with EZH2i, induced integrated stress response and apoptosis in combination with EZH2i. There was greater induction of ATF4 and DR5 in combinatorial therapy-treated tumor cells versus monotherapy. Knockdown of ATF4 reduced the apoptosis induced by combination therapy. EPZ-6438 or PF-06821497 decreased H3K27 tri-methylation. Our study results unravel potent synergy between ONC201 and EZH2i, highlight the role of ISR in the synergy, and provide further insights into the role of H3K27me3 in ONC201 drug sensitivity.

Citation Format: Yiqun Zhang, Lanlan Zhou, Varun V. Prabhu, Joshua E. Allen, Attila A. Seyhan, Wafik S. El-Deiry. The integrated stress response (ISR) is involved in the synergistic combinatorial efficacy of ONC201 and epigenetic modulators in brain tumor cell lines [abstract]. In: Proceedings of the American Association for Cancer Research Annual Meeting 2021; 2021 Apr 10-15 and May 17-21. Philadelphia (PA): AACR; Cancer Res 2021;81(13_Suppl):Abstract nr 1156.
Abstract 1396: Non-competitive inhibition of proteasome by kinase inhibitors
Authors: Kisselev Alexei F. , Akintola Olasubomi , Smith John
Published: July 2021

Inhibitors of Bruton's Tyrosine Kinase (BTK) and inhibitors of the proteasome are currently in use for treatment of hematologic malignancies. While the ubiquitin proteasome system is necessary for protein homeostasis in all mammalian cells, BTK is unique to some B cell malignancies. However, BTK inhibitors and LU-102, a specific inhibitor of the β2 site of the proteasome, have previously been shown to synergize in hematologic malignancies which do not express BTK, at a 100-fold higher concentration than is needed for complete inhibition of BTK, suggesting an off-target effect of these BTK inhibitors. Triple Negative Breast Cancer (TNBC), a cancer with poor prognosis and no current targeted therapy, also does not express BTK. We found that LU-102 and a specific BTK inhibitor, CGI-1764, are de-facto synthetically lethal to TNBC cells, and that effect of other BTK inhibitors varied from similar synergy to no synergy. This data further supports the idea that synergy is due to off-target effects of BTK inhibitors.We have now found that CGI-1764 is a non-competitive, allosteric inhibitor of all catalytic subunits of the proteasome 20S proteolytic core and exerts its effect in a unique, dose-dependent manner. RNA sequencing shows that the Unfolded Protein Response pathway is upregulated in TNBC cells response to treatment with the CGI-1746+LU-102 combination. We also found that accumulation of ubiquitin conjugates is synergistic indicating that the combination treatment has a synergistic effect on the inhibition of proteasome activity. These findings may pave the path to the development of more potent allosteric inhibitors of the proteasome and show that kinase inhibitors should be screened for inhibition of the proteasome as potential off-target effect.

Citation Format: Alexei F. Kisselev, Olasubomi Akintola, John Smith. Non-competitive inhibition of proteasome by kinase inhibitors [abstract]. In: Proceedings of the American Association for Cancer Research Annual Meeting 2021; 2021 Apr 10-15 and May 17-21. Philadelphia (PA): AACR; Cancer Res 2021;81(13_Suppl):Abstract nr 1396.
Abstract 1442: Targeting ATM kinase and mTOR signaling reverses bone marrow stromal cell-mediated protection of FLT3-ITD AML from FLT3-targeted therapy
Authors: Park Hae J. , Gregory Mark A. , Zaberezhnyy Vadym , DeGregori James
Published: July 2021

Internal tandem duplication (ITD) mutations in FMS-like tyrosine kinase 3 (FLT3) are among the most common mutations in acute myeloid leukemia (AML) and are associated with poor prognosis. FLT3-ITD causes constitutive activation of FLT3, and the strong evidence that activated FLT3 drives leukemogenesis has led to the development of several FLT3-targeted inhibitors. However, clinical studies of FLT3-targeted inhibitors have demonstrated much more effective clearing of leukemic burden in the periphery than in the bone marrow, implicating the bone marrow microenvironment as a potential contributor to drug resistance. As previously reported, the conditioned media of human bone marrow stromal cells (CM-BMSC) protects human FLT3-ITD AML cells from the killing effect of FLT3-targeted therapy despite complete inhibition of FLT3. We further show that genetic knockdown of Ataxia Telangiectasia Mutated (ATM) in combination with FLT3 inhibition substantially reverses the protection from cell death mediated by CM-BMSC. While autophosphorylation activity of ATM is downregulated upon FLT3 inhibition in regular media, CM-BMSC prevented the loss of ATM activity. Interestingly, genetic knockdown of ATM in human FLT3-ITD AML cells impaired the activity of mTOR Complex 1, and unbiased analyses of gene expression and signaling pathways by RNA-seq analysis and Reverse Phase Protein Arrays (RPPA) showed that mTOR signaling is downregulated with FLT3 inhibition in regular media, coinciding with marked inhibition of the protein translation machinery. Both mTOR signaling and protein translation were maintained during FLT3 inhibition in the presence of CM-BMSC. Furthermore, human FLT3-ITD AML cells treated with mTOR inhibitor everolimus in combination with the FLT3 inhibitor quizartinib reversed the protection mediated by CM-BMSC, and combination therapies are currently being tested in mouse models. These data suggest that ATM kinase and mTOR signaling play a key role in bone marrow stoma-mediated protection against FLT3 targeted therapy. Findings from this research provide new insights into the mechanism of bone marrow stroma-mediated protection of FLT3-ITD AML from FLT3-targeted therapy, identifying additional candidates for combinatorial therapies designed to overcome the protective effects of bone marrow stromal cells and improve patient outcomes.

Citation Format: Hae J. Park, Mark A. Gregory, Vadym Zaberezhnyy, James DeGregori. Targeting ATM kinase and mTOR signaling reverses bone marrow stromal cell-mediated protection of FLT3-ITD AML from FLT3-targeted therapy [abstract]. In: Proceedings of the American Association for Cancer Research Annual Meeting 2021; 2021 Apr 10-15 and May 17-21. Philadelphia (PA): AACR; Cancer Res 2021;81(13_Suppl):Abstract nr 1442.
Abstract 1475: Discovery of ETS-001, a highly potent allosteric SHP2 inhibitor to treat RTK/RAS-driven cancers
Authors: Xia Xi , Du Lin , Zhuge Hao , Zheng Qiangang , Cui Wenqi , Zhu Jidong , Li Guo
Published: July 2021

The non-receptor protein tyrosine phosphatase (PTP) SHP2, encoded by PTPN11, functions as a convergent node downstream of multiple receptor tyrosine kinases (RTKs) and is required for full activation of the MAPK pathway. Suppression of SHP2 activity via either genetic silencing or pharmacological inhibition has been shown to inhibit RAS/MAPK signaling and cell growth in a wide spectrum of cancers, pointing to a therapeutic opportunity for targeting SHP2 in cancer therapy. Here we report the discovery of a highly potent, selective and orally bioavailable small-molecule allosteric inhibitor of SHP2, ETS-001, that is effective in various human cancer models bearing oncogenic alterations in the RTK/RAS/MAPK pathway. Treatment with ETS-001 as a single agent resulted in dramatic growth inhibition of cancer cells as well as in vivo tumor models bearing genetic alterations of EGFR, or components in the nucleotide cycling-dependent KRAS pathway. Besides, as the effectiveness of RAS pathway inhibitors are ultimately limited by rapid emergence of drug resistance via multiple mechanisms including bypass activation of alternative RTKs, SHP2 inhibition has the potential to overcome the resistance as combinational strategies associated with various RAS pathway-targeted therapies. Here we show that ETS-001 exhibited strong synergistic effect with EGFR-TKI (osimertinib), KRASG12Ci (AMG510) or CDK4/6i (ribociclib) in appropriate cancer models in vitro and in vivo. In EGFR mutant NSCLC cells, treatment with both ETS-001 and osimertinib showed combinational benefit that was coincident with sustained ERK inhibition. In a KRASG12C mutant pancreatic cancer cell xenograft model, ETS-001 greatly enhanced the efficacy of AMG510 to suppress in vivo tumor growth. In addition, combinational benefit of ETS-001 and ribociclib was observed in esophageal cancer models, which exhibited high frequency of concurrent oncogenic alterations in RTKs and cell cycle pathway. Taken together, our findings provide preclinical evidence that ETS-001 as a potent SHP2 inhibitor, alone or in combination with other targeted-therapy agents, can effectively inhibit MAPK activation and treat cancers with diverse oncogenic mutations in the RAS/MAPK pathway.

Citation Format: Xi Xia, Lin Du, Hao Zhuge, Qiangang Zheng, Wenqi Cui, Jidong Zhu, Guo Li. Discovery of ETS-001, a highly potent allosteric SHP2 inhibitor to treat RTK/RAS-driven cancers [abstract]. In: Proceedings of the American Association for Cancer Research Annual Meeting 2021; 2021 Apr 10-15 and May 17-21. Philadelphia (PA): AACR; Cancer Res 2021;81(13_Suppl):Abstract nr 1475.
Abstract 1524: Peripheral blood mononuclear cells engineered via microfluidic Cell Squeeze® technology to generate APCs that drive mutant-KRas-specific CD8+ T cell responses
Authors: Yarar Defne , Smith Carolyne , Ramakrishnan Amritha , Loughhead Scott , Sharei Armon , Seidl Katherine , Bernstein Howard
Published: July 2021

KRAS mutations are shared across multiple cancer types and are most commonly found in cancers of the lung, pancreas, and colon. While recently developed drugs blocking signaling driven by KRAS G12C mutations have shown promise in the clinic, there is a great need for therapies targeting the more common G12V and G12D mutations. We utilize our microfluidic Cell Squeeze® technology to deliver antigens directly into the cytosol of peripheral blood mononuclear cells (PBMCs) for the generation of cancer antigen-targeted cellular vaccines. This method bypasses the need for cross-presentation and directly enables efficient antigen presentation on MHC-I in multiple cell types. Murine and human in vitro studies have demonstrated that this allows SQZ PBMCs to drive CD8+ T cell activation. Here, we demonstrate the delivery of various antigens, including KRas-derived peptides containing the most common mutations (G12D and G12V) to PBMC cell subsets. In addition, we find that human PBMCs squeezed with either KRasG12V or KRasG12D peptides can specifically stimulate KRasG12V- and KRasG12D- reactive CD8+ T cell responders. When KRasG12V and KRasG12D peptides are co-delivered via microfluidic squeezing, the human PBMCs enable activation of CD8+ T cells of both specificities. This work with KRasmutant-presenting human PBMCs lays a strong foundation for developing a potentially potent cell therapy to treat KRASmutant associated cancers.

Citation Format: Defne Yarar, Carolyne Smith, Amritha Ramakrishnan, Scott Loughhead, Armon Sharei, Katherine Seidl, Howard Bernstein. Peripheral blood mononuclear cells engineered via microfluidic Cell Squeeze® technology to generate APCs that drive mutant-KRas-specific CD8+ T cell responses [abstract]. In: Proceedings of the American Association for Cancer Research Annual Meeting 2021; 2021 Apr 10-15 and May 17-21. Philadelphia (PA): AACR; Cancer Res 2021;81(13_Suppl):Abstract nr 1524.
Abstract 1537: CD70 knockout: A novel approach to augment CAR-T cell function
Authors: Dequeant Mary-Lee , Sagert Jason , Kalaitzidis Demetri , Yu Hui , Porras Ashley , McEwan Brigid , Padalia Zinkal , Tetteh Paul , Nguyen Thao , Dunn Andrew , Spencer Sarah , Lee Nicolette , Dar Henia , Henderson Daniel , Karnik Sushant , Keerthipati Pooja , Terrett Jonathan A.
Published: July 2021

CD70 and its ligand, CD27, have been described as both activating and suppressing for different cell types including B and T cells. There has been speculation that the CD70/CD27 axis can act in a checkpoint or co-stimulatory manner in certain immuno-oncology settings. Knockout (KO) of CD70 function scored highly in a CRISPR/Cas9 screen of candidate genes for enhanced T cell activity. Deletion of other checkpoint candidates such as PD1, TIM3, LAG3 and TIGIT scored much lower than CD70, both alone and in combination with each other. T cells with CD70 KO showed resistance to exhaustion upon repeated stimulation in culture. CAR-T cells with CD70 KO similarly showed exhaustion resistance, as well as a reduction in apoptosis, increased proliferation, and improved target cell lysis upon sequential rechallenges. CTX130 is an investigational allogeneic CAR-T therapy currently being studied in patients with CD70-expressing tumors, including clear cell renal cell carcinoma and B and T cell malignancies. CTX130 contains KOs of TRAC to avoid GvHD, B2M to protect the product from patient T cells, and CD70 for enhanced CAR-T performance. Comparing CTX130 with and without CD70 KOs shows that CAR-T cells with CD70 KO have increased potency, enhanced ability to withstand multiple tumor challenges in vivo, and increased resistance to overexpression of PDL1 on target cells. Interestingly, while CD70 surface expression may be extremely low or undetectable after manufacturing of CD70-targeted CAR-T cells without CD70 KO, the beneficial properties outlined here are only achievable when the CD70 gene is genetically knocked out. In summary, KO of CD70 confers benefit to CAR-T cells that far exceeds KO of other checkpoint related genes, and this benefit was present regardless of the antigen being targeted. CD70 KO is included in the CTX130 investigational allogeneic CAR-T therapy currently in clinical trials.

Citation Format: Mary-Lee Dequeant, Jason Sagert, Demetri Kalaitzidis, Hui Yu, Ashley Porras, Brigid McEwan, Zinkal Padalia, Paul Tetteh, Thao Nguyen, Andrew Dunn, Sarah Spencer, Nicolette Lee, Henia Dar, Daniel Henderson, Sushant Karnik, Pooja Keerthipati, Jonathan A. Terrett. CD70 knockout: A novel approach to augment CAR-T cell function [abstract]. In: Proceedings of the American Association for Cancer Research Annual Meeting 2021; 2021 Apr 10-15 and May 17-21. Philadelphia (PA): AACR; Cancer Res 2021;81(13_Suppl):Abstract nr 1537.
Abstract 1578: Heating it up: Targeting RAS/RAF/PI3K pathway to make melanoma tumors ‘immunologically hot' and suitable for checkpoint blockade immunotherapies
Authors: Yan Chi , Saleh Nabil , Nebhan Caroline , Vilgelm Anna E. , Reddy E. Premkumar , Roland Joseph T. , Johnson Douglas B. , Shattuck-Brandt Rebecca L. , Chen Sheau-Chiann , Ayers Gregory D. , Richmond Ann
Published: July 2021

Immune checkpoint blockade (ICB) is the current first-line treatment for metastatic melanoma. However, ICB fails in many patients and has dangerous side effects. Rigosertib (RGS), a non-ATP-competitive small molecule RAS mimetic, has the potential to block oncogenic RAS-RAF-MEK-ERK and/or PI3K-AKT-mTOR signaling pathways. Using immunocompetent mouse models of B16F10 (BRAFwt) and YUMM3.3 (BRAFmut) melanoma, we identified that RGS treatment (300mg/kg) of melanoma tumor-bearing mice is well tolerated and results in ~50% inhibition of tumor growth as monotherapy and ~70% inhibition in synergy with αPD1+αCTLA4. RGS-induced tumor inhibition depends on the induction of CD40 expression on melanoma cells, followed by immunogenic cell death, leading to an inflamed tumor microenvironment with enrichment of dendritic cells and activated CD8+ Tc cells. The RGS-initiated suppression of tumor growth was partially reversed by either suppression of CD40 expression in the melanoma cells by shRNA, or depletion of CD8+ Tc cells. Analysis of multiple published patient melanoma studies confirms that a high CD40 expression level correlates with CD80, ICOS-L, beneficial type-I T-cell responses, and better survival in melanoma patients. The CD40 levels in melanoma cells are prognostic for therapeutic response to RGS, RAF inhibitor and ICB. Notably, multiplex IHC analysis showed that BRAF inhibitor treatment significantly induces CD40+SOX10+ melanoma cells in the tumors of melanoma patients and patient-derived xenografts. Our preclinical data support the therapeutic use of RGS plus αPD1+αCTLA4 in RAS/RAF/MEK and/or PI3K pathway-activated melanoma tumors and point to the need for clinical trials to determine the clinical benefit of RGS plus ICB for metastatic melanoma patients who do not respond to ICB alone.

The authors sincerely thank Onconova Therapeutics, Newtown, PA 18940 for kindly supplying Rigosertib for this work.

Citation Format: Chi Yan, Nabil Saleh, Caroline Nebhan, Anna E. Vilgelm, E. Premkumar Reddy, Joseph T. Roland, Douglas B. Johnson, Rebecca L. Shattuck-Brandt, Sheau-Chiann Chen, Gregory D. Ayers, Ann Richmond. Heating it up: Targeting RAS/RAF/PI3K pathway to make melanoma tumors ‘immunologically hot' and suitable for checkpoint blockade immunotherapies [abstract]. In: Proceedings of the American Association for Cancer Research Annual Meeting 2021; 2021 Apr 10-15 and May 17-21. Philadelphia (PA): AACR; Cancer Res 2021;81(13_Suppl):Abstract nr 1578.
Abstract 1664: Inhibition of arginase in combination with radiation therapy shows increased immune-activation and anti-tumor activity in syngeneic tumor models
Authors: Schuller Alwin , Doshi Aatman , Cantin Susan , Griffin Matt , Martin Maryann San , Proia Theresa , Reimer Corinne , Mlynarski Scott , Finlay Ray , Shao Wenlin
Published: July 2021

The tumor microenvironment (TME) has multiple mechanisms of immune-suppression including recruitment of arginase (ARG) expressing myeloid cells. ARG is an enzyme that catalyzes hydrolysis of L-arginine into urea and L-ornithine. Given L-arginine is essential for optimal function of both T cells and natural killer (NK) cells, inhibition of ARG has been recognized as a potential therapeutic approach to reverse immune-suppression and optimize anti-tumor immunity. We recently presented development of a novel ARG inhibitor, AZD0011, and demonstrated immune activation and anti-tumor activity as single agent and in combination with a-PD-L1 in various tumor models. We now expand these findings demonstrating combination benefit with radiation therapy. Radiation therapy (5 gray on day 6 and 9 after tumor cell implant) demonstrated an increase of both the number of arginase expressing myeloid cells, and NK cells in the TME of Lewis Lung (LL) tumors. Immuno-histochemistry also demonstrated a redistribution of the location of ARG positive myeloid cells with a marked increase at the edge of the tumor. LL tumor bearing mice receiving either AZD0011 (30 mg/kg twice daily), or radiation therapy as monotherapy did not show a significant anti-tumor response reaching 0.3% and 28% tumor growth inhibition (TGI) respectively (p>0.05 versus vehicle). In contrast, combination treatment showed a marked increased efficacy averaging 60% TGI (p<0.05 versus either monotherapy). Combination treatment also further increased several markers of immune activation including a doubling of the number of IL2+ or IFNg+ CD4+ and CD8+ T-cells in tumor draining lymph nodes. In summary, our pre-clinical data demonstrates that radiation therapy increases the number and location of intra-tumoral ARG expression myeloid cells and increased anti-tumor activity when combining the ARG inhibitor AZD0011 with radiation therapy.

Citation Format: Alwin Schuller, Aatman Doshi, Susan Cantin, Matt Griffin, Maryann San Martin, Theresa Proia, Corinne Reimer, Scott Mlynarski, Ray Finlay, Wenlin Shao. Inhibition of arginase in combination with radiation therapy shows increased immune-activation and anti-tumor activity in syngeneic tumor models [abstract]. In: Proceedings of the American Association for Cancer Research Annual Meeting 2021; 2021 Apr 10-15 and May 17-21. Philadelphia (PA): AACR; Cancer Res 2021;81(13_Suppl):Abstract nr 1664.
Abstract 1736: Antigen-specific targeting of tissue-resident gamma delta T cells with recombinant butyrophilin heterodimeric fusion proteins
Authors: de Silva Suresh , Fromm George , Lai Anne , Gonzalez Louis , Patel Arpita , Yoo Kyung Jin , Johannes Kellsey , Evans Kinsley , Wilson Keith , Schreiber Taylor H.
Published: July 2021

A major mechanism of acquired resistance to immune checkpoint inhibition involves downregulation of antigen presentation, including the MHC I complex itself. Downregulation of antigen presentation on MHC I can render tumor cells invisible to any α/β T cell directed therapy. γδ T cells (γδT) are a small subset of the overall T cell compartment, but are characterized by increased cytolytic capacity relative to α/β T cells. Rather than MHC I, γδT recognize target cells via a complex of heterodimerized butyrophilin (BTN) proteins. Thus, display of BTN heterodimers on the surface of tumor cells may enhance immunity to tumors that have downregulated MHC I, or which express low abundance or low affinity antigens.

We have previously reported the generation of a heterodimeric BTN protein targeting the CD19 antigen, referred to as BTN2A1/3A1-Fc-CD19scFv. While the BTN2A1/3A1 complex is a potent activator of γδT expressing the Vγ9δ2 T cell receptor (TCR), which is the major γδT population in human peripheral blood, Vγ9δ2 T cells are not the predominant γδT in many tissues. The murine equivalent of BTN2A1/3A1-Fc-CD19scFv, BTNL1/6-Fc-CD19scFv, stimulated specific proliferation and increased the cytolytic capacity of peripheral blood γδT in mice, but not other tissue-restricted GDT populations. These data suggested that distinct BTN heterodimers may preferentially activate tissue-restricted subsets of GDT.

To characterize potential differences between peripheral blood and tissue-restricted γδT , we performed a multi-layered analysis, including single-cell sequencing of γδ TCR from paired peripheral blood and tumor tissues from human cancer patients such as melanoma, prostate and colon cancer. These data identified tissue-specific preferences for individual γδ TCRs, with corresponding tissue-specific preferences for individual BTN proteins. Based on this information, we generated a panel of distinct heterodimeric BTN proteins, and show that specific γδT populations are preferentially activated by specific BTN heterodimers in a lock-and-key fashion. These data are a necessary pre-requisite for designing γδT specific therapeutics that may target both immune neglected and acquired resistant tumors that have limited visibility to α/β T cell directed approaches.

Citation Format: Suresh de Silva, George Fromm, Anne Lai, Louis Gonzalez, Arpita Patel, Kyung Jin Yoo, Kellsey Johannes, Kinsley Evans, Keith Wilson, Taylor H. Schreiber. Antigen-specific targeting of tissue-resident gamma delta T cells with recombinant butyrophilin heterodimeric fusion proteins [abstract]. In: Proceedings of the American Association for Cancer Research Annual Meeting 2021; 2021 Apr 10-15 and May 17-21. Philadelphia (PA): AACR; Cancer Res 2021;81(13_Suppl):Abstract nr 1736.
Abstract 1825: SAR443216, a novel trispecific T cell engager with potent T cell-dependent cytotoxicity for HER2-low tumors
Authors: Sha Wenwen , Vadde Sri , Song Zhili , Seung Edward , Xing Zhen , Chen Liqing , Cortez-Retamozo Virna , Sidhu Sukhvinder , Bangari Dinesh , Wu Lan , Wei Ronnie , Yang Zhi-yong , Nabel Gary , Pelekanou Vasiliki , Sanicola-Nadel Michele , Masciari Serena , Wiederschain Dmitri , Pao Lily
Published: July 2021

Current HER2-targeted therapies have markedly improved the outcome of cancer patients with HER2 overexpressing tumors. However, these patients may eventually relapse or develop treatment resistance. In addition, HER2-low patients that are not eligible for treatment constitute a significant portion of the breast cancer patients. To address these unmet needs, we have developed a novel HER2-targeting T cell engager, SAR443216. This is a trispecific antibody with binding sites for HER2, CD3 and CD28, and containing a mutated IgG4-Fc which lacks effector functions. CD28 binding contributes to T cell activation, including activation of IL-2 and NFκB pathways, as well as induction of anti-apoptotic protein, Bcl-xL. In the presence of HER2-positive cancer cells, SAR443216 is able to activate primary human CD4 and CD8 T cells, resulting in T cell proliferation and secretion of cytokines and granzyme B. Moreover, it has potent in vitro T cell-dependent cellular cytotoxicity (TDCC) against a panel of HER2-expressing cancer cell lines, including those that are HER2-low. The potency of in vitro TDCC is largely correlated with HER2 surface expression in the target cells. Finally, in a HER2-low breast cancer xenograft model, SAR443216 also exhibited significant anti-tumor activity in immuno-deficient NSG mice reconstituted with primary human T cells. Thus, SAR443216 represents a promising new drug for cancer patients with HER2-expressing tumors, including those who are currently ineligible for stand-of-care therapy.

Citation Format: Wenwen Sha, Sri Vadde, Zhili Song, Edward Seung, Zhen Xing, Liqing Chen, Virna Cortez-Retamozo, Sukhvinder Sidhu, Dinesh Bangari, Lan Wu, Ronnie Wei, Zhi-yong Yang, Gary Nabel, Vasiliki Pelekanou, Michele Sanicola-Nadel, Serena Masciari, Dmitri Wiederschain, Lily Pao. SAR443216, a novel trispecific T cell engager with potent T cell-dependent cytotoxicity for HER2-low tumors [abstract]. In: Proceedings of the American Association for Cancer Research Annual Meeting 2021; 2021 Apr 10-15 and May 17-21. Philadelphia (PA): AACR; Cancer Res 2021;81(13_Suppl):Abstract nr 1825.
Abstract 1966: Cell proliferation-related pathway scores (G2M Checkpoint, E2F Targets, MYC Targets V1 and V2, Mitotic Spindle, p53 pathway) as predictive and prognostic biomarkers in pancreatic cancer
Authors: Oshi Masanori , Le Lan , Tokumaru Yoshihisa , Yan Li , Matsuyama Ryusei , Endo Itaru , Takabe Kazuaki
Published: July 2021

Background: Given the poor survival and severe side effects of treatments for pancreatic cancer, we need prognostic and predictive biomarkers to guide management. We hypothesized that the cell proliferation-related pathway is associated with drug response and survival in pancreatic cancer.

Methods: We studied six hallmark cell proliferation-related gene sets (G2M Checkpoint, E2F Targets, MYC Targets V1 and V2, Mitotic Spindle, p53 pathway) defined by MSigDB in gene set variant analysis (GSVA) was evaluated in 3 independent cohorts, TCGA-PDAC (n = 176), GSE57495 (n = 63), and GSE62452 (n = 69).

Results: We found that although G2M and E2F correlated strongly with each other (spearman's r = 0.976), Mitotic and p53 pathway scores correlated highly with the other cell function gene sets. All pathways were significantly associated with high expression of MKI67 and with proliferation score (all p > 0.001), but none with pathologically complete resection (R0). Mitotic Spindle pathway alone associated with high cytolytic activity (p = 0.020). All pathways were significantly associated with high expression of KRAS and TP53 genes and with high rate of KRAS gene alteration except for MYC v1. The G2M, E2F, and p53 pathway were significantly associated with a high rate of TP53 gene alteration (p = 0.026, 0.011, and 0.07, respectively). Interestingly, different pathway correlated with AUC of different agents, such as Gemcitabine (Mitotic: r=0.706 [p = 0.01]), Paclitaxel (MYC v2: r = -0.636 [p < 0.05]), Apatinib (Mitotic: r = -0.556 [p = 0.03]), Palbociclib (E2F: r =0.675 [p < 0.01]), and Sorafenib (G2M: r = -0.593 [p = 0.03]), for pancreatic cancer. Among all six pathways, only G2M was significantly associated with worse patient survival consistently in all 3 cohorts.

Conclusion: Each proliferation-related pathway was predictive of unique agent, and G2M score predicts survival of pancreatic cancer.

Citation Format: Masanori Oshi, Lan Le, Yoshihisa Tokumaru, Li Yan, Ryusei Matsuyama, Itaru Endo, Kazuaki Takabe. Cell proliferation-related pathway scores (G2M Checkpoint, E2F Targets, MYC Targets V1 and V2, Mitotic Spindle, p53 pathway) as predictive and prognostic biomarkers in pancreatic cancer [abstract]. In: Proceedings of the American Association for Cancer Research Annual Meeting 2021; 2021 Apr 10-15 and May 17-21. Philadelphia (PA): AACR; Cancer Res 2021;81(13_Suppl):Abstract nr 1966.
Abstract 2044: Genomic scar score: a robust model to predict recombination repair deficient based on genomic instability
Authors: Wen Hao , Yang Shuang , Chen Xuejun , Weng Ying , Zhu Changbin , Ruan Li , Dong Hua , Wu Xiaohua
Published: July 2021

Background: Clinical benefit of PARP inhibitors or Platinum-based chemotherapy has been observed and well proved in BRCA mutation patients. However, there are other mechanisms to induce recombination repair deficient (HRD), such as BRCA methylation, ATM expression loss; HRR gene mutation in addition to BRCA mutation. Whether these complicated HRD events or phenotype could be measured by a unified model to accurately identify HRD positive patients is important.

Methods: In this study, we use support vector machine method to build genomic scar (GS) model to predict HRD events, which takes different types of chromosomal copy number into consideration to evaluate genomic instability. The accuracy of GS model was tested by different NGS platform from WGS to two captured SNP Panel. GS status association with Cisplatin-based chemotherapy was also preliminarily validated.

Results: GS model displayed more than 95% accuracy to detect BRCA-ness events and is also able to enrich different types of HRR dysfunction, such as HRR-related mutation or BRCA1 promoter methylation. Moreover, GS model can identify patient benefits from Cisplatin-based chemotherapy, and GS score (GSS) high group had longer progression free survival (PFS) than GSS low group (11 vs 8.5 months, HR=0.5, P=0.05). Meanwhile, GSS showed the high concordance among different NGS platform including WGS; two captured SNP Panels, which implied the high robustness of GS model.

Conclusion: GS was a robust model to predict HRD and had the clinical potential to enrich patients who will response to PARP inhibitors and/or Platinum-based chemotherapy.

Citation Format: Hao Wen, Shuang Yang, Xuejun Chen, Ying Weng, Changbin Zhu, Li Ruan, Hua Dong, Xiaohua Wu. Genomic scar score: a robust model to predict recombination repair deficient based on genomic instability [abstract]. In: Proceedings of the American Association for Cancer Research Annual Meeting 2021; 2021 Apr 10-15 and May 17-21. Philadelphia (PA): AACR; Cancer Res 2021;81(13_Suppl):Abstract nr 2044.
Abstract 2099: EM-seq enables accurate and precise methylome analysis of challenging DNA samples
Authors: Ponnaluri V K Chaithanya , Williams Louise , Campbell Matthew A. , Panchapakesa Vaishnavi , Vaisvila Romualdas , Langhorst Bradley , Dimalanta Eileen , Davis Theodore B.
Published: July 2021

DNA isolated from blood draws (cell-free DNA (cfDNA)) or from archival material like formalin fixed paraffin embedded (FFPE) tissues have advanced the field of cancer genetics. DNA methylation (5-methylcytosines (5mC) and 5-hydroxymethylcytosines (5hmC)) is a key epigenetic factor that plays an important role in cellular processes and it's misregulation results in diseased states like cancer. Advances in the field of sample preparation from biological matrices and genomics have enabled cancer biomarker identification based on methylation profiling. Bisulfite sequencing has been the gold standard for detection of methylation and is employed for both targeted and whole genome methylation analysis. However, the chemical based bisulfite conversion of cytosines to uracils leads to DNA damage which subsequently translates to shorter DNA insert sizes as well as biases in the data. DNA obtained from cfDNA and FFPE samples is typically of low quality and quantity making DNA methylation profiling using the harsh bisulfite conversion challenging. Robust biomarker detection relies primarily on the ability to profile methylation accurately. To overcome the drawbacks of bisulfite sequencing, we developed an enzyme based methylation detection technology, called NEBNext® Enzymatic Methyl-Seq (EM-Seq™), that minimizes damage to DNA enabling longer insert sizes, lower duplication rates and minimal GC bias resulting in more accurate quantification of methylation in the sample DNA. Using EM-Seq, we profiled cfDNA and lung FFPE DNA. Results for these challenging DNA types showed that the EM-Seq libraries had longer inserts, lower duplication rates, higher percentages of mapped reads and less GC bias compared to WGBS libraries. EM-seq libraries also identified a higher number of CpG's with even coverage facilitating accurate methylation calling. In conclusion, EM-Seq libraries have superior sequencing metrics resulting in robust methylation profiling for these types of challenging DNA samples.

Citation Format: V K Chaithanya Ponnaluri, Louise Williams, Matthew A. Campbell, Vaishnavi Panchapakesa, Romualdas Vaisvila, Bradley Langhorst, Eileen Dimalanta, Theodore B. Davis. EM-seq enables accurate and precise methylome analysis of challenging DNA samples [abstract]. In: Proceedings of the American Association for Cancer Research Annual Meeting 2021; 2021 Apr 10-15 and May 17-21. Philadelphia (PA): AACR; Cancer Res 2021;81(13_Suppl):Abstract nr 2099.
Abstract 2112: Epigenetic control of heparanase expression using CRISPR/dCas9
Authors: Chen Zixin , Zeng Guihua , Li Xiaogang , Liang Fu-Sen , Cui Lina
Published: July 2021

Heparanase (HPSE) is the only known enzyme that cleaves the polymeric heparan sulfate (HS), a key component of the extracellular matrix (ECM). Heparanase has been implicated in various pathophysiological conditions involving ECM remodeling, such as tumor progression, metastasis angiogenesis, and inflammation. To study the role of heparanase in diseases, we developed a strategy to epigenetically modulate its expression in cells based on the clustered regularly interspaced short palindromic repeats (CRISPR) system. A fusion protein of dCAS9 can be directed to the HPSE gene via one or a combination of single guide RNAs. By linking dCas9 with different histone modification enzymes (eg. P300, hHDAC3, LSD1), the expression of heparanase can be up- or down-regulated through histone acetylation, deacetylation and demethylation. This approach allows us to tune heparanase expression in various cell lines on demand, enabling the study of heparanase activity in real-time. This work will also lead to novel therapeutics targeting heparanase.

Citation Format: Zixin Chen, Guihua Zeng, Xiaogang Li, Fu-Sen Liang, Lina Cui. Epigenetic control of heparanase expression using CRISPR/dCas9 [abstract]. In: Proceedings of the American Association for Cancer Research Annual Meeting 2021; 2021 Apr 10-15 and May 17-21. Philadelphia (PA): AACR; Cancer Res 2021;81(13_Suppl):Abstract nr 2112.
Abstract 2161: A transcriptomic signature for measuring YAP1 activity in patient samples and tumor models
Authors: Spanakis Emmanuel , Calvet Loreley , Santos Odette Dos , Dib Colette , Sidhu Sukhvinder , Moll Jurgen , Debussche Laurent , Pollard Jack , Valtingojer Iris
Published: July 2021

Over the past years, the HIPPO tumor suppressor pathway and its downstream effector Yes1-associated transcriptional regulator (YAP1) present increasing interest in cancer research. The YAP1-TEAD complex regulates transcription for cell proliferation, survival, plasticity, and migration. Aberrant activation of YAP1 has been reported for multiple different cancer types. To estimate the proportion of cases where YAP1/TEAD-dependent transcription may be responsible for tumor development or evolution and evaluate the pharmacodynamics of novel TEAD-inhibitors, we have identified a transcriptional signature of YAP1 activity. The signature comprises 500 genes, positive and negative downstream effectors at about equal proportions, selected by differential expression analyses from 10 published datasets reporting, in total, 19 YAP1-activation and 18 YAP1-inhibition experiments. YAP1/TEAD-dependent transcription was scored in single samples as the difference Rp - Rn, where Rp is the mean fractional rank of the positive YAP1-effectors, and Rn, that of the negative effectors. We so scored, and called, YAP1 activation in normal tissues (GTEx collection; N~9000), in primary, recurrent, or metastatic tumors (TCGA; N~10000), and in cell lines (CCLE; N~1000) for the selection of models. We further applied the signature to follow the degree of YAP1 inhibition in cell and tumor models either after genetic knockdown of HIPPO-YAP1 pathway components or by pharmacologic inhibition using small-molecule TEAD-inhibitors. Our data confirm the robustness of the YAP1-transcription signature as a biomarker for both, tumor indication selection and pharmacodynamics of YAP1-TEAD activity.

Citation Format: Emmanuel Spanakis, Loreley Calvet, Odette Dos Santos, Colette Dib, Sukhvinder Sidhu, Jurgen Moll, Laurent Debussche, Jack Pollard, Iris Valtingojer. A transcriptomic signature for measuring YAP1 activity in patient samples and tumor models [abstract]. In: Proceedings of the American Association for Cancer Research Annual Meeting 2021; 2021 Apr 10-15 and May 17-21. Philadelphia (PA): AACR; Cancer Res 2021;81(13_Suppl):Abstract nr 2161.
Abstract 2413: POLE gene mutations in African Americans colorectal cancer
Authors: Brim Hassan , Shokrani Babak , Azimi Hamed , Varma Sudhir , Lee Edward , Ashktorab Hassan
Published: July 2021

Background: Most focus in genetic instability in colon carcinogenic transformation was on DNA Mismatch Repair (MMR) genes alterations as they relate to the microsatellite instability phenotype. However, POLE gene mutations can also be instrumental in triggering genetic instability, at even higher magnitude of genome mutation rate.

Aim: To assess POLE gene mutations in African Americans with colorectal cancer (CRC).

Methods: Data from Whole exome sequencing of 12 CRC African American tumors was searched to scan POLE gene mutations. All detected mutations were checked in tumors and matched normal. The detected mutations were validated in a second set of samples that were sequenced using POLE gene targeted sequencing. Detected and validated mutations were checked in available databases such as COSMIC and dbSNP to determine novel mutations in our population that is at high risk of aggressive CRC.

Results: Six out of 12 patients (50%) displayed mutations in POLE gene. There were 41 detected mutations, 11 are novel mutations and 15 are amino-acid changing. Nine of these were non-synonymous and predicted to have deleterious effects. All these mutations were validated using targeted sequencing. In comparison to DNA MMR, POLE gene has four folds more mutations than MSH2gne (10 mutations and MSH6 (11 mutations and two fold more than MSH3 gene (20 mutations) in the same set of 12 cancer/matched normals. The POLE mutations heterozygous/homozygous status was overall similar in normal and matched normal. However, most of the mutations were homozygous.

Conclusion: POLE gene mutations are increasingly recognized as another important element in genetic instability. Our data shows that mutations affecting this gene are likely more significant than those affecting DNA MMR genes. Moreover, POLE mutations might be more consequential, especially those affecting its exonuclease domain of polymerase epsilon, proofreading catalytic subunit. Microsatellite-stable, hypermutated CRCs might need to be explored for POLE gene mutations to track the origin of high mutation rates.

Citation Format: Hassan Brim, Babak Shokrani, Hamed Azimi, Sudhir Varma, Edward Lee, Hassan Ashktorab. POLE gene mutations in African Americans colorectal cancer [abstract]. In: Proceedings of the American Association for Cancer Research Annual Meeting 2021; 2021 Apr 10-15 and May 17-21. Philadelphia (PA): AACR; Cancer Res 2021;81(13_Suppl):Abstract nr 2413.
Abstract 2425: Prevalence of NTRK fusions and clinico-pathological characteristics of Middle Eastern papillary thyroid cancer revealed enrichment in BRAF wild-type PTC
Authors: Siraj Abdul K. , Bu Rong , Parvathareddy Sandeep K. , Kong Yan , Annaiyappanaidu Padmanaban , Ahmed Saeeda O. , Al-Rasheed Maha , Al-Kuraya Khawla S.
Published: July 2021

Fusions involving neurotrophic tyrosine receptor kinase (NTRK) are known oncogenic drivers in a broad range of tumor types. It recently gained attention as predictor of targeted therapy, since selective NTRK inhibitor are now approved in US and Europe for patients with solid tumor harboring gene fusions. However, estimation of NTRK gene fusion/alteration frequency and its clinico-pathological characteristics in papillary thyroid cancer (PTC) is limited, especially in a population with high incidence for PTC like Middle Eastern population. This study aims to characterize the NTRK gene fusion frequency using FISH analysis and investigate the utility of pan-Trk immunohistochemistry as predictor of NTRK fusion in a large cohort of Middle Eastern PTC. FISH analysis for NTRK gene fusions as well as immunohistochemical (IHC) staining was conducted on a cohort of 315 Middle Eastern PTC. Correlation of NTRK with clinico-pathological markers and patient outcome were determined. 6.0% (19/315) patients were identified with NTRK gene fusions and significantly associated with pediatric PTC, lymph node metastasis and BRAF wild-type. Pan-Trk IHC was positive in 9.2% (29/315) and significantly associated with NTRK gene fusion with a sensitivity of 73.7% and specificity of 94.9% in this cohort. In conclusion, this study confirms the presence of NTRK fusions in Middle Eastern PTC and mostly enriched in BRAF wild-type and pediatric age group and propose the usefulness of IHC to screen for PTC patients with NTRK fusion that might benefit from TRK inhibitors.

Citation Format: Abdul K. Siraj, Rong Bu, Sandeep K. Parvathareddy, Yan Kong, Padmanaban Annaiyappanaidu, Saeeda O. Ahmed, Maha Al-Rasheed, Khawla S. Al-Kuraya. Prevalence of NTRK fusions and clinico-pathological characteristics of Middle Eastern papillary thyroid cancer revealed enrichment in BRAF wild-type PTC [abstract]. In: Proceedings of the American Association for Cancer Research Annual Meeting 2021; 2021 Apr 10-15 and May 17-21. Philadelphia (PA): AACR; Cancer Res 2021;81(13_Suppl):Abstract nr 2425.
Abstract 2568: Use of kinase inhibitors in Fanconi anemia oral cancercell lines
Authors: Jungbauer Walter N. , Ali Mustafa M. , Wuertz Beverly R. , Ondrey Frank G.
Published: July 2021

Successful Fanconi anemia (FA) treatment allows greater longevity for these patients. However, there is a greatly increased risk of squamous malignancies of the head and neck which are quite deadly in these young patients. There is an unmet need for non DNA damaging therapies for this malignancy which could augment surgery. Our approach has been to examine potential treatments based on known pathophysiology of the disease which would be acceptable for this population so we examined the effects of metformin and pioglitazone, as well as two cell cycle kinase inhibitors, in FA and leukoplakia cell lines. We examined dose-dependent and combination effects on cell proliferation, as judged by MTT assay. We examined metformin, pioglitazone, the polo-like kinase 1 inhibitor, GSK461364, and Wee1 kinase inhibitor, AZD1775.In single agent studies, we observed dose-dependent decreases in cell proliferation with all 4 single agents. We observed decreased cell proliferation in all cell lines at 72 hours at clinically achievable serum levels of 85% to 55% of control levels (P<0.0001). Additionally, we found decreases beyond single agent treatment levels when cells were treated with metformin combined with GSK461364 or AZD1775 and similarly, with combination therapies of pioglitazone and GSK461364 or AZD1775. Our current data demonstrate feasibility and preclinical efficacy of a combined agent approach for FA associated head and neck cancer. The low reported toxicity of these agents clinically allows for all of these agents to potentially move forward clinically, once additional experiments are conducted in mechanistic and animal studies.

Citation Format: Walter N. Jungbauer, Mustafa M. Ali, Beverly R. Wuertz, Frank G. Ondrey. Use of kinase inhibitors in Fanconi anemia oral cancercell lines [abstract]. In: Proceedings of the American Association for Cancer Research Annual Meeting 2021; 2021 Apr 10-15 and May 17-21. Philadelphia (PA): AACR; Cancer Res 2021;81(13_Suppl):Abstract nr 2568.