bluuebunny/crossref_metadata_2025 huggingface dataset:
Abstract 4058: TheraT - a highly versatile arenavirus based vector platform for intravenous and intratumoral cancer immunotherapy
Authors: Raguz Josipa , Schmidt Sarah , Kleisner Theresa , Zerbs Manuel , Bekic Goran , Feher Sonja , Oeler Daniel , Stemeseder Felix , Berka Ursula , Kiefmann Bettina , Schulha Sophie , Matushansky Igor , Lauterbach Henning , Orlinger Klaus
Published: September 2020

The unprecedented success of checkpoint blockade therapies clearly demonstrates the power of the immune system to fight cancer. Yet, only a minority of cancer patients respond with long-term control of the tumor or even cure, necessitating the development of other treatment modalities. Hookipa Pharma developed a novel attenuated, replication-competent viral vector platform (TheraT) that induces powerful cytotoxic T lymphocyte responses against foreign and self-antigens. In a preclinical model for human papilloma virus 16 (HPV16) associated cancer (TC-1), we evaluated immunogenicity and efficacy upon systemic and intratumoral application of TheraT vectors based on the arenaviruses lymphocytic choriomeningitis virus (LCMV) and pichinde virus (PICV). Both HB-201 (LCMV) and HB-202 (PICV) product candidates encode a non-oncogenic but highly antigenic E6/E7 fusion protein from HPV16. Independent of the route of administration, single administration of HB-201 or HB-202 induced potent peripheral E7-specific CD8+ T cell responses and led to efficient tumor growth control. Survival of TheraT treated animals was significantly longer compared to buffer treated animals. Similarly, single systemic as well as intratumoral application of HB-201 or HB-202 induced major infiltration of CD8+ T cells into the tumor microenvironment. Combination of intravenous HB-201 and anti-PD1 was well tolerated but did not further enhance efficacy in this model, implicating the presence of other immune evasion factors. In conclusion, replication-attenuated TheraT is safe, highly immunogenic and shows excellent therapeutic efficacy after single intravenous and intratumoral application. These data underline the potential and versatility of this novel vector platform. Mechanistic studies in various mouse tumor models are underway. Phase 1/2 clinical trial initiation of HB-201 monotherapy is planned for end of 2019 and preparations for an IND filing for a combination trial of HB-201 and HB-202 in H1 2020 have been initiated.

Citation Format: Josipa Raguz, Sarah Schmidt, Theresa Kleisner, Manuel Zerbs, Goran Bekic, Sonja Feher, Daniel Oeler, Felix Stemeseder, Ursula Berka, Bettina Kiefmann, Sophie Schulha, Igor Matushansky, Henning Lauterbach, Klaus Orlinger. TheraT - a highly versatile arenavirus based vector platform for intravenous and intratumoral cancer immunotherapy [abstract]. In: Proceedings of the Annual Meeting of the American Association for Cancer Research 2020; 2020 Apr 27-28 and Jun 22-24. Philadelphia (PA): AACR; Cancer Res 2020;80(16 Suppl):Abstract nr 4058.
Abstract 4188: The ERK1/2 inhibitor, JSI-1187, demonstrates preclinical efficacy in tumor models with MAPK pathway mutations
Authors: Li Ao , Jian Shanzhong , Yuan Xia , Song Fengge , Yang Shengwei , Du Chengyi , Tao Yue , Wang Liucheng , Pan Mingming , Dong Penghui , Zhou jiajun , Ge Zhengkang , Zhu Qinghong , Hao Wenshan , Xu Wen , Zhang Jintao , Li Qun , Wang Shaohui
Published: September 2020

The MAPK pathway, via RAS-RAF-MEK-ERK, is one of the most important pathways for relaying signals from cell surface receptors for cell survival, proliferation, and differentiation. Many mutations were identified in this pathway and intensely studied, resulting in a number of therapeutics for various cancers (for example, EGFR mutant inhibitors, BRAF V600 mutant inhibitors and MEK inhibitors). A common mechanism of resistance to these therapeutics has emerged to be the reactivation of ERK1/2, the terminal kinase in this pathway. Inhibition of ERK1/2 activity could therefore be instrumental in various mutations in the MAPK pathway, either as single therapy or in combination with other compounds. Through internal effort, we discovered a novel ERK1/2 small molecule inhibitor, JSI-1187, which reversibly inhibited ERK2 with a Ki of less than 1 nM. In anti-proliferation assays, JSI-1187 had IC50 of 37 NM in the BRAF V600E melanonma cell line A375 and 48 NM in the BRAF V600E CRC cell line COLO 205. For cell lines with KRAS mutations, JSI-1187 had anti-proliferation IC50 of 130 NM in the CRC cell line HCT116 and 150 NM in the NSCLC cell line Calu-6. Furthermore, JSI-1187 inhibited the phosphorylation of the ERK substrate RSK1 in these cell lines. We also tested JSI-1187 using mouse CDX models. JSI-1187 showed tumor growth inhibition in a dose dependent manner in the xenograft models of A375, COLO 205, HCT116, and Calu-6. In the COLO 205 model, JSI-1187 caused tumor regression at the dose of 20 mg/kg QD. In the Calu-6 model, BID and QD dosing schedules were compared, with the result that 10 mg/kg BID and 20 mg/kg QD inhibit xenograft tumor growth similarly. Moreover, in the HCT116 model, JSI-1187 concentrations in plasma and tumor were measured, as well as phopspho-RSK1 levels in tumor. A PK/PD correlation was observed. In addition to being tested alone, JSI-1187 was also tested in combination with the BRAF inhibitor dabrafenib in the COLO 205 xenograft model. JSI-1187 and dabrafenib demonstrated synergistic efficacy in tumor growth inhibition. In conclusion, JSI-1187 can be potentially used for treatment of cancer with MAPK pathway mutations.

Citation Format: Ao Li, Shanzhong Jian, Xia Yuan, Fengge Song, Shengwei Yang, Chengyi Du, Yue Tao, Liucheng Wang, Mingming Pan, Penghui Dong, jiajun Zhou, Zhengkang Ge, Qinghong Zhu, Wenshan Hao, Wen Xu, Jintao Zhang, Qun Li, Shaohui Wang. The ERK1/2 inhibitor, JSI-1187, demonstrates preclinical efficacy in tumor models with MAPK pathway mutations [abstract]. In: Proceedings of the Annual Meeting of the American Association for Cancer Research 2020; 2020 Apr 27-28 and Jun 22-24. Philadelphia (PA): AACR; Cancer Res 2020;80(16 Suppl):Abstract nr 4188.
Abstract 4228: PLAP (placental alkaline phosphatase)-CAR-T cells specifically target colorectal cancer
Authors: Golubovskaya Vita M. , Berahovich Robert , Zhou Hua , Liu Xianghong , Li Feng , Xu Shirley , Wei Yuehua , Ouaret Djamila , Bodmer Walter , Wu Lijun
Published: September 2020

Placental alkaline phosphatase, PLAP encoded by ALPP gene in humans is mainly expressed in placenta and testis, and not expressed in any other normal tissues. PLAP is overexpressed in a proportion of colorectal cancers which makes it an attractive target for CAR (chimeric antigen receptor)-T cell therapy. PLAP mRNA expression was detected in 21.4% (25 out of 117) of colorectal cancer cell lines and this expression was confirmed by FACS at the protein level. In addition, IHC staining on primary colorectal cancer tumors demonstrated PLAP expression in >20% of colorectal cancer tumors. We generated mouse and humanized PLAP ScFv-CAR-T cells and demonstrated high specificity against PLAP-positive colon cancer cells using RTCA (real-time cytotoxicity assay) and IFN-gamma secretion. In addition, humanized-CAR-T cells significantly decreased Lovo xenograft tumor growth in vivo. The combination of hPLAP-CAR-T cells with PD-1, PDL-1 or LAG-3 checkpoint inhibitors significantly increased the activity of hPLAP-CAR-T cells.

Significance: This study demonstrates ability of novel PLAP-CAR-T cells to kill colorectal cancers and that the extent of killing can be increased by combination with checkpoint inhibitors. These preclinical results suggest that PLAP-CAR-T cells combined with checkpoint inhibitors may be developed into an effective clinical therapy for PLAP expressing colorectal and other cancers.

Citation Format: Vita M. Golubovskaya, Robert Berahovich, Hua Zhou, Xianghong Liu, Feng Li, Shirley Xu, Yuehua Wei, Djamila Ouaret, Walter Bodmer, Lijun Wu. PLAP (placental alkaline phosphatase)-CAR-T cells specifically target colorectal cancer [abstract]. In: Proceedings of the Annual Meeting of the American Association for Cancer Research 2020; 2020 Apr 27-28 and Jun 22-24. Philadelphia (PA): AACR; Cancer Res 2020;80(16 Suppl):Abstract nr 4228.
Abstract 4235: A combination of CAR-NK and CAR-T cells results in rapid and persistent anti-tumor efficacy while reducing CAR-T cell mediated cytokine release and T-cell proliferation
Authors: Li Guangnan , Wu Xiumin , Chan Ivan H. , Trager James B.
Published: September 2020

CAR-NK cells show rapid and potent anti-tumor cytotoxic activity even at very low effector-to-target ratios, however, they do not typically expand upon encounter with antigen and lack long term persistence commonly associated with CAR-T cells. Conversely, CAR-T cells generally exhibit persistent killing activity, even though they are activated somewhat more slowly. In addition, the explosive expansion of CAR-T cells is frequently associated with a variety of toxicities (e.g. CRS, CRES, etc.). To address these shortcomings, Nkarta has developed a novel platform to combine both CAR-NK and CAR-T cells as a novel cancer therapeutic. To evaluate the overall outcomes of combining CAR-NK and CAR-T cells as an anti-tumor therapy, we have developed two novel in vitro assays: (a) IncuCyte-based matrixed cytotoxicity assay, which allows direct assessment of tumor killing kinetically with different E:T and NK:T ratios; (b) IncuCyte-based tumor re-challenge assay, which provides a convenient and quick assessment of anti-tumor persistence. For proof-of-concept studies, a CD19 directed CAR (CAR19) was retrovirally engineered into NK and T cells. Our newly developed assays revealed that the combination of CAR-NK and CAR-T cells clearly outperformed CAR19-NK or CAR19-T cells alone in anti-tumor efficacy and persistence. Additionally, the combination also showed an improved cytokine profile. To further investigate the cellular mechanism(s) underlying the beneficial effects of combining CAR-NK and CAR-T cells, we performed FACS-based phenotyping and a Violet Cell Trace based proliferation assay. When challenged with tumor cells, the presence of CAR19-NK cells reduced the proliferation of CAR19-T cells. Surprisingly, the presence of CAR19-T cells could trigger the proliferation of CAR19-NK cells. Finally, we evaluated the NK plus T platform in vivo with a Nalm6 xenograft model. Treatment with CAR19-NK cells combined with a low dose of CAR19-T cells (5e5 cells/animal) delayed tumor progression. Combined treatment with a medium dose of CAR19-T cells (2.5e6 cells/animal) largely prevented tumor relapse, and consequently enhanced the overall survival of the animals. In summary, our in vitro and in vivo studies strongly demonstrate that the NK plus T platform can harness the advantages of both CAR-NK and CAR-T cells, allowing for both rapid and persistent killing while potentially minimizing the toxicities associated with CAR-T cells.

Citation Format: Guangnan Li, Xiumin Wu, Ivan H. Chan, James B. Trager. A combination of CAR-NK and CAR-T cells results in rapid and persistent anti-tumor efficacy while reducing CAR-T cell mediated cytokine release and T-cell proliferation [abstract]. In: Proceedings of the Annual Meeting of the American Association for Cancer Research 2020; 2020 Apr 27-28 and Jun 22-24. Philadelphia (PA): AACR; Cancer Res 2020;80(16 Suppl):Abstract nr 4235.
Abstract 4286: TGF-β signature is a therapeutic biomarker for combination immunotherapy for hepatocellular carcinoma
Authors: Chen Jian , Su Xiaoping
Published: September 2020

Background: Several immune checkpoint inhibitors have recently shown promising results in patients with advanced hepatocellular carcinoma (HCC). However, tumor response rates ranged from 14% to 17%. Thus, there remains a large unmet medical need for novel and effective immunotherapeutic strategies against HCC. Dysregulated signaling in the transforming growth factor (TGF)-β pathway plays a central role in immunomodulation, inflammation, and fibrogenesis in the HCC microenvironment. We therefore used The Cancer Genome Atlas database to analyze potential therapeutic approaches combining TGF-β inhibition and immunotherapies for HCC.

Methods: Transcriptomic analyses were performed in 193 HCC cases. Pathway analyses were performed by correlating 70 published signatures with TGF-β signatures.

Results: 1. Unsupervised hierarchical clustering of TGF-β genes in HCC revealed four distinct clusters with unique TGF-β signatures: highly activated (14.5%), activated (45.0%), normal (30.6%), and inactivated (9.9%). 2. Highly activated TGF-β signatures were significantly associated with fibrosis and activated stromal signatures. 3. TGF-β signature subtypes were significantly associated with immune cell infiltration, T cell exhaustion, and checkpoint blockade response subclasses. 4. Potentially targetable genes were associated with specific TGF-β signatures. 5. TGF-β signatures provide potential combination therapeutic options for HCC.

Conclusion: We demonstrated a specific immunosuppressive role of TGF-β in mediating immunotherapy resistance in HCC, highlighting the TGF-β signature as a potential biomarker in individualized immunotherapeutic approaches in HCC.

Citation Format: Jian Chen, Xiaoping Su. TGF-β signature is a therapeutic biomarker for combination immunotherapy for hepatocellular carcinoma [abstract]. In: Proceedings of the Annual Meeting of the American Association for Cancer Research 2020; 2020 Apr 27-28 and Jun 22-24. Philadelphia (PA): AACR; Cancer Res 2020;80(16 Suppl):Abstract nr 4286.
Abstract 4414: Single-cell analysis on the Cancer Genomics Cloud reveals changes in the transcriptome profiles of endothelial tumor cells over time - novel insights from a public dataset of a mouse model of melanoma
Authors: Vucic Nemanja , Ray Manisha , Veljkovic Dalibor , Cidilko Stefan , Davis-Dusenbery Brandi
Published: September 2020

The Cancer Genomics Cloud (CGC) powered by Seven Bridges makes the analysis of large datasets accessible from any environment, which is critical as the volume of datasets continues to expand. This expansion of the size, complexity, and location of datasets has been prominent in the field of single-cell genomics, which can present challenges for data analysis. Here we combined the rich datasets available through the Human Cell Atlas (HCA) with the tools and computational resources available on the CGC to provide a path for any scientist to explore complex biological questions. To demonstrate these capabilities, we processed a single-cell dataset of immune and stromal cells isolated from the tumor and lymph nodes of a mouse model of melanoma using an optimized version of the SmartSeq2 pipeline recommended by the HCA. This dataset contains 13.3k paired-end sequencing files for 6.6k estimated cells, with a total size of 371.60 GB. The entire dataset was transferred from Human Cell Atlas Data Portal to the CGC, where it is accessible to all users.

The goal of this study was to process a single-cell dataset on the tumor microenvironment with the SmartSeq2 pipeline and to investigate changes in transcriptome profiles of endothelial tumor cells over time. We used an alternative approach than authors in the original study, which aimed to analyze the immune and stromal cells (Davidson et al. bioRxiv 2018). To perform alignment and quantification of raw sequencing reads using the CGC execution environment, we created an implementation of the SmartSeq2 pipeline in Common Workflow Language. Quantification results were used to perform cell clustering, followed by a pseudotime analysis on the endothelial tumor cells. For the cell clustering and pseudotime analyses, we created interactive notebooks in the RMarkdown format that can be executed within the RStudio environment on the CGC. In summary, this work demonstrates the importance of developing reproducible workflows that can run on multiple environments as well as data sharing that can bring to light new insights from the existing data.

Citation Format: Nemanja Vucic, Manisha Ray, Dalibor Veljkovic, Stefan Cidilko, Brandi Davis-Dusenbery. Single-cell analysis on the Cancer Genomics Cloud reveals changes in the transcriptome profiles of endothelial tumor cells over time - novel insights from a public dataset of a mouse model of melanoma [abstract]. In: Proceedings of the Annual Meeting of the American Association for Cancer Research 2020; 2020 Apr 27-28 and Jun 22-24. Philadelphia (PA): AACR; Cancer Res 2020;80(16 Suppl):Abstract nr 4414.
Abstract 4441: CS3003, an HDAC6-selective inhibitor, improves anti-PD-1 immune checkpoint blockade therapy efficacy
Authors: Li Zhenhu , Ren Zhaoxiang , Ma Jingshu , Tang Liang , Lu Liang , Zhu Ying , Wu Yunfei , Liu Tiancheng , Zhang Juan , Bao Yuanwu , Zhang Kangyu , Wei Changqing , Chen Shuhui , Wang Xinzhong Jon
Published: September 2020

Background: Histone deacetylases (HDACs) are involved in diverse cellular regulatory function including histone modification and non-histone modification. Several publications have demonstrated that selective HDAC inhibitors (HDACi) can influence tumor growth and immunogenicity. In particular, the selective inhibition of HDAC6 has function of inhibiting tumor growth in several malignancies. However, the mechanism of this effect is still not clear.

Methods: In this study, we evaluated CS3003, a selective HDAC6 inhibitor, inhibition profile using cell-based free assays. In vivo anti-tumor efficacy was evaluated in MM.1S xenograft mouse model. CS3003 and PD-1 blockade combination effect was evaluated in CT26 syngeneic mouse model. RNA-seq method was used to explore the transcription regulation by CS3003 compared to other pan-HDAC, Class I HDAC inhibitor and selective HDAC6 inhibitors.

Results: CS3003 has distinct inhibition profile in HDAC family members. Combination of CS3003 and proteasome inhibitor synergistically enhanced anti-tumor function in human multiple myeloma mouse model (coefficient of drug interaction, CDI=0.69). In addition, CS3003 improves the anti-tumor activity of anti-PD-1 immune checkpoint blockade in solid tumor model (CDI=0.62 and 0.88 when the dosage of CS3003 was 30 and 70mg/kg, respectively). Transcriptome analysis demonstrated a unique gene expression pattern of CS3003 from other pan-HDAC and selective HDAC6 inhibitors.

Conclusions: These data provide a comprehensive pre-clinical characterization of CS3003 that supports its unique HDAC inhibition profile and its capability of improving anti-PD-1 immune checkpoint blockade therapy efficacy.

Citation Format: Zhenhu Li, Zhaoxiang Ren, Jingshu Ma, Liang Tang, Liang Lu, Ying Zhu, Yunfei Wu, Tiancheng Liu, Juan Zhang, Yuanwu Bao, Kangyu Zhang, Changqing Wei, Shuhui Chen, Xinzhong Jon Wang. CS3003, an HDAC6-selective inhibitor, improves anti-PD-1 immune checkpoint blockade therapy efficacy [abstract]. In: Proceedings of the Annual Meeting of the American Association for Cancer Research 2020; 2020 Apr 27-28 and Jun 22-24. Philadelphia (PA): AACR; Cancer Res 2020;80(16 Suppl):Abstract nr 4441.
Abstract 4791: Metabolic switch from glycolysis to oxidative phosphorylation (ox-phos) provides survival advantage to anti-androgen-treated prostate cancer cells and make them vulnerable to mitochondrial metabolism inhibitors IACS-010759 and CB-839
Authors: Basu Hirak S. , Wilganowski Nathaniel , Robertson Samantha , Ramachandran Sumankalai , Zurita-Saavedra Amado , Titus Mark , Cohen Evan , Reuben James , Wilding George
Published: September 2020

Background: Most cancer cells depend more on glycolysis for their energy need compared with their normal counterparts incubated under identical condition. In addition to glycolysis, tumor cells also engage mitochondrial ox-phos to support growth. Here, we show that PCa cells surviving under anti-androgen enzalutamide (ENZA) treatment switch from glycolysis to ox-phos for their energy need and are more vulnerable to mitochondria-targeted metabolic inhibitors. We have also standardized a high-resolution quantitative fluorescence microscopic method to detect this metabolic switch in patient circulating tumor cells (CTCs).

Methods: Seahorse assay has been used to compare mitochondrial metabolism in ENZA treated anti-androgen-sensitive LNCaP and -resistant C4-2 and PCa2b cells. The Seahorse data were supported by mass spectroscopic analysis of corresponding metabolites and metabolic fluxes. An ex vivo fluorescence staining for the CTC mitochondria with high ox-phos followed by high-resolution quantitative microscopic image analysis method has been standardized to follow such changes in cultured cells and patient CTCs.

Results: Seahorse, mass spectroscopy and high-resolution microscopy of mitochondrial ox-phos showed that ENZA significantly decreases glycolysis and increases ox-phos in all surviving PCa cells within 24h of treatment. These cells are more vulnerable to treatment with mitochondrial ox-phos inhibitor IACS-010759 and a glutaminase inhibitor CB-839. High-resolution microscopic analysis of CTCs has thus far been performed in 18 patient blood samples. Six out of the 18 patients developed resistance to anti-androgen therapy within 0-6 months of sample collection. CTCs from all six patients showed a relatively higher average fluorescence due to high mitochondrial ox-phos as compared with the rest of the patients.

Discussion: The data presented here may lead to informed combination therapy for selected PCa patients developing resistance to anti-androgen therapy for better clinical outcome.

Citation Format: Hirak S. Basu, Nathaniel Wilganowski, Samantha Robertson, Sumankalai Ramachandran, Amado Zurita-Saavedra, Mark Titus, Evan Cohen, James Reuben, George Wilding. Metabolic switch from glycolysis to oxidative phosphorylation (ox-phos) provides survival advantage to anti-androgen-treated prostate cancer cells and make them vulnerable to mitochondrial metabolism inhibitors IACS-010759 and CB-839 [abstract]. In: Proceedings of the Annual Meeting of the American Association for Cancer Research 2020; 2020 Apr 27-28 and Jun 22-24. Philadelphia (PA): AACR; Cancer Res 2020;80(16 Suppl):Abstract nr 4791.
Abstract 525: A novel anti-PD1-IL15 immunocytokine potentiates anti-tumor T cell activity of PD-1 checkpoint inhibition and IL-2R-beta-gamma agonism
Authors: Lu Dan , Polonskaya Zhanna , Chang Tzi-Pei , Martomo Stella , Luna Xenia , Zhang Zhikai , Miyara Faical , Patel Jeedar
Published: September 2020

Therapeutic antibodies targeting immune checkpoint inhibitors (ICI) such as PD-1/PD-L1 effectively expand and reactivate T cells in patients, leading to long-lasting response in multiple tumor types. However, only a fraction of patients responded to approved ICIs, majority are either resistant or quickly become refractory. Other immunotherapy modalities including immunostimulatory cytokines IL-2, IL-12 and IL-15 demonstrated clinical benefits as monotherapy or in combination with ICIs. Cytokines exhibit in general a short half-life and systemic toxicities that limit their use as the optimal doses in treating cancer. An antibody-based immunocytokine fusion such as Kadmon lead candidate KD033 (anti-PDL1/IL15) and Roche anti-PD1/CEA/FAP-IL2v can extend the half-life of cytokine and reduce systemic toxicities. In this study, a fully human single-chain variable fragment (scFv) antibody against mouse PD1 (mPD1) have been isolated from the phage display library. The variable domains of these antibodies were fused to either human IgG1a or mouse IgG2a constant domain first, and then fused to either human IL15 receptor alpha sushi domain-hIL15 complex (hSD15) or mouse IL15 receptor alpha sushi domain-mIL15 complex (mSD15). These variations of fusion have been tested in in vitro binding and functional assays, and in vivo in PD1/PDL1 resistant mouse syngeneic model LL2 (Lewis Lung Carcinoma). We demonstrated that hSD15 fusion antibody can stimulate both IL2 dependent human and murine cells growth, surprisingly, mSD15 fusion antibody can only stimulate murine cell growth. Although mSD15 fusion antibody EC50 was 10 folds better than hSD15 fusion antibody in stimulating mouse spleen cell growth in vitro, it did not show a better efficacy than hSD15 fusion antibody in LL2 model. In vivo, mSD15 fusion antibody had higher maximum tolerate dose than hSD15 fusion antibody (up to 12mg/kg). In addition, anti-mPD1/mSD15 showed better efficacy than either the mIL15 and anti-mPD1 alone or the combination of anti-mPD1 plus mIL15 in vitro and in vivo. Together these preclinical data have confirmed that PD1-IL15 could be a promising next generation IL-15 fusion for cancer immunotherapy.

Citation Format: Dan Lu, Zhanna Polonskaya, Tzi-Pei Chang, Stella Martomo, Xenia Luna, Zhikai Zhang, Faical Miyara, Jeedar Patel. A novel anti-PD1-IL15 immunocytokine potentiates anti-tumor T cell activity of PD-1 checkpoint inhibition and IL-2R-beta-gamma agonism [abstract]. In: Proceedings of the Annual Meeting of the American Association for Cancer Research 2020; 2020 Apr 27-28 and Jun 22-24. Philadelphia (PA): AACR; Cancer Res 2020;80(16 Suppl):Abstract nr 525.
Abstract 528: EMB-01: An innovative bispecific antibody targeting EGFR and cMet on tumor cells mediates a novel mechanism to improve anti-tumor efficacy
Authors: Ren Fang , Wu Xuan , Yang Dandan , Wu Danqing , Gong Shiyong , Zhang Yingxi , Lensky Stephan , Wu Chengbin
Published: September 2020

Interruption of EGFR signaling, either by blocking EGFR binding sites on the extracellular domain of the receptor or by inhibiting intracellular tyrosine kinase activity, can prevent the growth of EGFR-expressing tumors. EGFR tyrosine kinase inhibitors (TKIs) provide a favorable treatment outcome in EGFR mutation positive NSCLC patients. However, many patients eventually develop progressive disease after treatment. Such acquired resistance limits the long-term efficacy of these EGFR TKIs in the clinic. The mechanisms of acquired resistance include a variety of mutations of the EGFR and crosstalk with the adjacent cMet receptors that allow the tumor to partially compensate the EGFR activity. EMB-01 is an innovative bispecific antibody developed based on EpimAb's proprietary FIT-Ig® platform to target EGFR and cMET on tumor cells simultaneously. The anti-EGFR and anti-cMet Fab-domains in each EMB-01 arm are fused directly in-tandem in a unique crisscross orientation without any mutations or use of peptide linkers to form a final tetravalent binding complex with the corresponding receptors on cell surface. We have demonstrated that EMB-01 can maintain all the biological activity from parental monoclonal antibody (mAb) to block ligand binding and the downstream signal pathway. In addition, such tetravalent binding feature is found to induce significant co-degradation of EGFR and cMET in various tumor cells, and such effect is unattainable by either mAb alone or in combination, demonstrating a unique synergistic function of EMB-01. At equivalent doses, EMB-01 induces significantly stronger anti-tumor activity in PDX and CDX tumor models than that of anti-EGFR mAb or anti-cMet mAb alone. Furthermore, EMB-01 shows significant anti-tumor activity in anti-EGFR mAb resistant tumor model. These results demonstrate the potential benefit of EMB-01 in treating EGFR and/or cMET driven cancers, particularly in cases where patients develop acquired resistance due to secondary EGFR mutations in the kinase domain or cMET activation. Currently, EMB-01 has initiated a Phase I/II clinical trial with advanced/metastatic solid tumors.

Citation Format: Fang Ren, Xuan Wu, Dandan Yang, Danqing Wu, Shiyong Gong, Yingxi Zhang, Stephan Lensky, Chengbin Wu. EMB-01: An innovative bispecific antibody targeting EGFR and cMet on tumor cells mediates a novel mechanism to improve anti-tumor efficacy [abstract]. In: Proceedings of the Annual Meeting of the American Association for Cancer Research 2020; 2020 Apr 27-28 and Jun 22-24. Philadelphia (PA): AACR; Cancer Res 2020;80(16 Suppl):Abstract nr 528.
Abstract 539: Novel engineered toxin bodies targeting SLAMF7 (CS1)
Authors: Iberg Aimee , Cornelison Garrett L. , Howard Caleigh , Robinson Garrett L. , Zhao Jay , Ramos Hilario J. , Willert Erin K.
Published: September 2020

Engineered toxin bodies (ETBs) are comprised of a proprietarily engineered form of Shiga-like Toxin A subunit (SLT-A) genetically fused to antibody-like binding domains. ETBs work through novel mechanisms of action and are capable of forcing internalization, self-routing through intracellular compartments to the cytosol, and inducing potent cell-kill via the enzymatic and permanent inactivation of ribosomes. Three ETBs are in clinical development (MT-3724 targeting CD20, MT-5111 targeting HER2, and TAK-169 targeting CD38). The novel mechanism of action has potential benefit in different indications including in the relapsed setting, when disease has progressed after chemotherapies and other targeted therapies, and additionally may be able to be combined with standard of care. Additional ETBs are being developed that target other cell surface receptors for solid and hematological malignancies, including SLAMF7 (CS1). SLAMF7 is a clinically validated target of monoclonal antibody therapy. Although clinical responses to the monotherapy were not observed, patients treated with combination therapy using standard of care agents that are known to stimulate immune effector cell activity have improved responses. Thus, a SLAMF7 targeted agent that can act independent of effector cells by directly killing tumor cells has the potential to provide broader benefit to patients. ETBs targeting SLAMF7 harbor the catalytic activity of the SLTA subunit and can effectively and specifically kill multiple myeloma cell lines expressing the target protein in vitro. The coupling of specific targeting to myeloma cells with potent and direct cell kill activity has the potential to deplete malignant cells without reliance on effector functions of the patient immune system, such as antibody or complement dependent cellular cytotoxicity or phagocytosis, and could be beneficial when disease progresses post antibody therapy. Additionally, the novel mechanism of action of an ETB also has potential to be combined with standard of care therapies and/ or to be effective in the relapsed or refractory setting.

Citation Format: Aimee Iberg, Garrett L. Cornelison, Caleigh Howard, Garrett L. Robinson, Jay Zhao, Hilario J. Ramos, Erin K. Willert. Novel engineered toxin bodies targeting SLAMF7 (CS1) [abstract]. In: Proceedings of the Annual Meeting of the American Association for Cancer Research 2020; 2020 Apr 27-28 and Jun 22-24. Philadelphia (PA): AACR; Cancer Res 2020;80(16 Suppl):Abstract nr 539.
Abstract 5455: Identifying somatic variants with defined confidence level in targeted sequencing of tumor DNA without a matched normal sample
Authors: Huang Yanmei , Young Amanda G. , Hughes Jason D.
Published: September 2020

Sequencing tumor DNA without a matched normal sample is currently routine practice for many clinical diagnostic services that use NGS to identify somatic mutations in a panel of cancer-relevant genes, due to cost constraints. Various computational algorithms have been developed to distinguish somatic mutations from germline variations in this “single sample” setting. However, the sensitivity and specificity of these methods have not been rigorously investigated, and factors affecting accuracy of the somatic classification have not been thoroughly mapped out. We seek to address these inadequacies and identify avenues towards better somatic variant identification in “single sample” setting. We use tumor/matched normal pairs to establish true somatic/germline status of variants and analyze how adjustments in the algorithms for variant calling and somatic/germline classification affect the ability to identify true somatic variants. We show that somatic variants can be identified with varying degrees of certainty under different circumstances and demonstrate that our algorithmic methods can effectively identify a substantial subset of calls that have a very high likelihood of being truly somatic. Tunable filtering methods and confidence scoring for somatic likelihood has utility in the development of complex biomarkers such as tumor mutational burden and ctDNA measurements.

Citation Format: Yanmei Huang, Amanda G. Young, Jason D. Hughes. Identifying somatic variants with defined confidence level in targeted sequencing of tumor DNA without a matched normal sample [abstract]. In: Proceedings of the Annual Meeting of the American Association for Cancer Research 2020; 2020 Apr 27-28 and Jun 22-24. Philadelphia (PA): AACR; Cancer Res 2020;80(16 Suppl):Abstract nr 5455.
Abstract 5474: Identification of novel druggable fusions enabled through the use of an automated RNA fusion prioritization pipeline
Authors: Islam Sumaiya A. , Huether Robert , Kudalkar Emily
Published: September 2020

Gene fusions can serve as key drivers in the development of various cancers and represent important therapeutic targets and diagnostic biomarkers. Due to high detection of candidate fusions from RNA-sequencing data, there is a recognized need to build tools that will make reasonable and automated predictions to identify clinically or biologically relevant fusion events in a tumor sample. We developed a computational pipeline which scores and prioritizes all detected fusion transcripts within a sample to determine which fusions are likely driver events in the tumor. Specifically, the pipeline implements a categorization scheme that bins all scored fusion events into Low, Medium and High Confidence levels based on threshold read support levels and a DriverScore metric, which is derived from a binary classification algorithm using specific features, such as reading frame, breakpoint region, kinase domain and transcript isoform. We systematically analyzed 3200 fusion candidates from a previously published cohort of 500 paired tumor-normal samples sequenced with the Tempus xT assay. We found that 1.7% and 20.1% of fusion candidates were categorized in the High and Medium Confidence levels, respectively, while 78.2% of fusion events were deprioritized as Low Confidence calls. Of the 35 clinically-relevant fusions, 27 (77.1%) were captured in our prioritized set (High/Medium Confidence), including National Comprehensive Cancer Network actionable gene rearrangements involving RET, STAT6 and FUS, while the remaining 8 were assigned as Low Confidence due to an out of frame fusion transcript and insufficient read support. The frequency of prioritized fusions varied by cancer type, with prostate and breast cancer having the highest frequency of prioritized fusions. In addition to well-established canonical fusions, we also sought to characterize novel fusions, identifying a subset of 21 novel prioritized fusions which were also observed in The Cancer Genome Atlas tumor samples. Within this subset, 3% of fusion candidates contained a druggable domain such as a tyrosine kinase or Ras-binding domain, signifying the potential of categorization to enable novel fusion drug target discovery. Overall, our analysis highlights the utility of using an automated prioritization tool to detect known canonical fusion drivers and explore novel fusion drug targets and biomarkers.

Citation Format: Sumaiya A. Islam, Robert Huether, Emily Kudalkar. Identification of novel druggable fusions enabled through the use of an automated RNA fusion prioritization pipeline [abstract]. In: Proceedings of the Annual Meeting of the American Association for Cancer Research 2020; 2020 Apr 27-28 and Jun 22-24. Philadelphia (PA): AACR; Cancer Res 2020;80(16 Suppl):Abstract nr 5474.
Abstract 5619: PBMC humanized NSG-(KbDb)null (IA)null mouse model to evaluate immune-oncology drug efficacy
Authors: Yao Li-Chin , Cheng Mingshan , Shultz Leonard D. , Keck James G.
Published: September 2020

Multiple types of humanized mouse models using immunodeficient NOD-scid IL2rgnull (NSG) mice have been developed by The Jackson Laboratory for preclinical studies of new cancer therapies. Humanized NSG mice engrafted with both human peripheral blood mononuclear cells (PBMC) and human cancers have been used for evaluating antibody-based therapeutics targeting T cells. Compared to CD34+ HSC-mediated humanization, NSG mice engrafted with PBMC are ready to use more quickly and are more cost-effective. The major limitation of PBMC engrafted NSG is the development of acute xenogeneic graft-versus-host disease (GVHD) due to human T cell activation through mouse MHC class I and class II molecules. The experimental window for drug efficacy evaluation is limited to three-four weeks post PBMC injection and strong xeno-GVHD may hinder drug-induced T cell activation. A new strain lacking murine MHC molecules, NSG-(KbDb)null (IA)null, was created to address this limitation. Here we engrafted non-irradiated adult NSG and MHC double knockout NSG-(KbDb)null (IA)null mice using the same human PBMC donors to compare their survival and engraftment level. We found that most of the MHC deficient mice can survive over 100 days and can support human T cell engraftment. We also evaluated drug efficacy response using checkpoint inhibitors anti-CTLA-4 (lpilimumab) and anti-PDL-1 (Avelumab) in human tumor xenograft models. Anti-CTLA-4 treatment resulted in reduced growth of mantle cell lymphoma Jeko-1. Anti-PDL-1 treatment reduced growth of a melanoma PDX. In consistent with their anti-tumor response, flow analysis showed increased T cell frequency in blood and tumor in the drug treated group when compared to the vehicle control. Additional cancer treatment evaluated in the PBMC engrafted NSG-(KbDb)null (IA)null mice will also be discussed.

Citation Format: Li-Chin Yao, Mingshan Cheng, Leonard D. Shultz, James G. Keck. PBMC humanized NSG-(KbDb)null (IA)null mouse model to evaluate immune-oncology drug efficacy [abstract]. In: Proceedings of the Annual Meeting of the American Association for Cancer Research 2020; 2020 Apr 27-28 and Jun 22-24. Philadelphia (PA): AACR; Cancer Res 2020;80(16 Suppl):Abstract nr 5619.
Abstract 5747: A single center's ten-year experience in sustaining a cancer survivorship program
Authors: Palos Guadalupe , Gilmore Katherine R. , Bi Weiqi , Chapman Patricia Hansberry , Carpenter Kathy , Pancho-Acorda Maree Joy , Rodriguez Maria Alma
Published: September 2020

Introduction: In 2009, our institution's leadership supported the creation of the Cancer Survivorship Program founded on core elements from the 2006 Institute of Medicine report “From Cancer Patient to Cancer Survivor: Lost in Transition.” These elements align with those recently posited in the 2019 Commission on Cancer (CoC) Standard 4.8. to establish and monitor a Survivorship Program. Here we describe our program model and present data collected over a decade to evaluate the program's outcomes.

Procedures: Six key components guided the program's implementation and sustainability. These factors included: 1) inclusion of patients treated with curative intent, 2) recruitment of a transdisciplinary program staff, 3) delivery of clinical services based on 4 domains of survivorship care, 4) provision of consultative services available on-site or through referrals, 5) use of a quality improvement plan to monitor services provided, and 6) the creation and dissemination of treatment summaries and survivorship care plans. We reviewed electronic health records (EHR) of patients seen in the 12-survivorship clinics between 2009 and 2019. Data sources consisted of OneConnect, EPIC universes, and a departmental database. Data elements collected on arrived or missed appointments, no-show rate, and completion rates for the treatment summary and 30-day Passport (Survivorship Care Plans). Descriptive statistics summarized metrics per clinic and as a group.

Results: Twelve site-specific cancer survivorship clinics scheduled appointments for survivors who had completed their curative treatment. A medical and operations director led the 6-member team who coordinated and monitored program activities. Patients had access to consultative services (i.e. cardiologists, nutritionists, social workers, etc.) provided by the institution or through community referrals. Table 1 summarizes data related to clinic visits for 10 years. In FY 2019, clinics with the highest number of arrived appointments included breast (4985), GU (1709), and head and/neck (1175). Clinics with the highest treatment summary compliance rates were lymphoma (97%), thyroid (77%), and stem cell transplant (72%). Each year, about 20% of patients scheduled are being seen for the first time in a survivorship clinic (rates vary by clinic).

Conclusions: Results from our 10-year program experience suggest the newly proposed CoC survivorship program model can be practical and successful.

Citation Format: Guadalupe Palos, Katherine R. Gilmore, Weiqi Bi, Patricia Hansberry Chapman, Kathy Carpenter, Maree Joy Pancho-Acorda, Maria Alma Rodriguez. A single center's ten-year experience in sustaining a cancer survivorship program [abstract]. In: Proceedings of the Annual Meeting of the American Association for Cancer Research 2020; 2020 Apr 27-28 and Jun 22-24. Philadelphia (PA): AACR; Cancer Res 2020;80(16 Suppl):Abstract nr 5747.
Abstract 5778: Hernia and Ewing sarcoma
Authors: He Di , Hansen Johnni , Federman Noah , Olsen Jorn , Ritz Beate , Heck Julia E.
Published: September 2020

Introduction: Ewing sarcoma (ES) is a rare cancer with an incidence that peaks in adolescence and young adulthood. The tumor occurs in bone and soft tissue and the etiology is unclear. Several studies have observed increased ES risk in children and young adults with hernia, including umbilical and inguinal hernia, suggesting a mechanism for a common causal pathway. A meta-analysis of 3 case-control studies reported a threefold increased risk of ES among hernia patients. The purpose of this study is to examine the association between hernia and ES in a population-based study.

Methods: We ascertained Ewing sarcoma cases (age <20 years) from the Danish Cancer Registry (diagnoses 1977-2016; births 1977-2013), then randomly selected controls free of cancer at the date of corresponding cases diagnosis and matched (25:1) by sex and year of birth from the Central Population Register (N=4,160). Ewing sarcoma cases (N=122) were identified with the International Classification of Diseases for Oncology (ICD-O-1 and ICD-O-3 code 9260). Information on birth outcomes and gestational factors were taken from the Medical Birth Registry (1973+) and information on mother's and child's health was taken from the National Patient Register (1977+). We also searched this Register for diagnoses of hernia in the child based on procedure codes (a Nordic coding system from 1977-1995, and an extended version of ICD-10 thereafter). We used conditional logistic regression to determine associations for hernia and ES.

Results: 122 ES cases were identified, among whom 6 cases had a diagnosis of hernia (1 of them had hernia diagnosed within the first 3 years of life). Among controls, 203 (6.7%) had a diagnosis of hernia. Of all children diagnosed with hernia, 27 (12.9%) presented hernia during the first year of life and 74 (35.4%) presented during the first 3 years of life. In ES cases there was no increase in risk of hernia (OR= 0.53, 0.17-1.72). Adjustment for presence of other congenital malformations did not change the results for hernia (OR=0.65). Restriction to younger cases (diagnosed ≤15 years) showed similar results for hernia.

Conclusions: Previous studies have raised the possibility that inherited genes causing both developmental anomalies and cancer might be involved with the etiology of ES. However, based on registry and hospitalization data, we were not able to confirm previous associations with hernia. Either this study or earlier studies may have been influenced by small sample size. There is also a possibility that previous reports of positive associations are due to recall or publication biases.

Citation Format: Di He, Johnni Hansen, Noah Federman, Jorn Olsen, Beate Ritz, Julia E. Heck. Hernia and Ewing sarcoma [abstract]. In: Proceedings of the Annual Meeting of the American Association for Cancer Research 2020; 2020 Apr 27-28 and Jun 22-24. Philadelphia (PA): AACR; Cancer Res 2020;80(16 Suppl):Abstract nr 5778.
Abstract 6248: Engineered probiotics for local delivery of checkpoint blockade nanobodies
Authors: Gurbatri Candice , Lia Ioana , Vincent Rosa , Coker Courtney , Castro Samuel , Treuting Piper , Hinchliffe Taylor , Arpaia Nicholas , Danino Tal
Published: September 2020

Checkpoint inhibitors have revolutionized cancer therapy but only work in a subset of patients and can lead to a multitude of toxicities, suggesting the need for more targeted delivery systems. Because of their preferential colonization of tumors, microbes are a natural platform for the local delivery of cancer therapeutics. Here, we engineer a probiotic bacteria system for the controlled production and intratumoral release of nanobodies targeting programmed cell death-ligand 1 (PD-L1) and cytotoxic T lymphocyte-associated protein-4 (CTLA-4) using a stabilized lysing release mechanism. We used computational modeling coupled with experimental validation of lysis circuit dynamics to determine the optimal genetic circuit parameters for maximal therapeutic efficacy. A single injection of this engineered system demonstrated an enhanced therapeutic response compared to analogous clinically relevant antibodies, resulting in tumor regression in syngeneic mouse models. Supporting the potentiation of a systemic immune response, we observed a relative increase in activated T cells, an abscopal effect, and corresponding increases in systemic T cell memory populations in mice treated with probiotically delivered checkpoint inhibitors. Last, we leveraged the modularity of our platform to achieve enhanced therapeutic efficacy in a poorly immunogenic syngeneic mouse model through effective combinations with a probiotically produced cytokine, granulocyte-macrophage colony-stimulating factor (GM-CSF). Together, these results demonstrate that our engineered probiotic system bridges synthetic biology and immunology to improve upon checkpoint blockade delivery.

Citation Format: Candice Gurbatri, Ioana Lia, Rosa Vincent, Courtney Coker, Samuel Castro, Piper Treuting, Taylor Hinchliffe, Nicholas Arpaia, Tal Danino. Engineered probiotics for local delivery of checkpoint blockade nanobodies [abstract]. In: Proceedings of the Annual Meeting of the American Association for Cancer Research 2020; 2020 Apr 27-28 and Jun 22-24. Philadelphia (PA): AACR; Cancer Res 2020;80(16 Suppl):Abstract nr 6248.