bluuebunny/crossref_metadata_2025 huggingface dataset:
Abstract 4155: ARID1A loss leads to chemotherapy resistance and is associated with a poor clinic outcome for patients with non-small cell lung cancer
Authors: Yang Linlin , Shen Changxian , Mo Xiaokui , Williams Terence M.
Published: September 2020

Purpose: ARID1A (AT-rich interactive domain 1A) is a member of the switch/sucrose nonfermentable (SWI/SNF) chromatin remodeling complex, and plays important roles in the regulation of gene transcription and DNA damage responses. ARID1A mutations occur frequently in non-small cell lung cancer (NSCLC), but the functions of ARID1A loss in the initiation, progression and maintenance of NSCLC remains largely unknown. This study aimed to investigate the clinical, pathological, and functional significance of ARID1A in NSCLC.

Experimental design: We first analyzed the prognostic value of ARID1A using a gene-expression microarray from the Director's Challenge Lung Study. Kaplan-Meier method and Log-rank tests were used to estimate the correlation between ARID1A expression and overall survival (OS). Univariate and multivariate Cox regression models were used to investigate the relationship between ARID1A and other clinical covariates. We further established stable ARID1A knockdown H1299 and H358 cell lines, and ARID1A exogenously expressing H460 and A549 cell lines. We performed functional assays to study the effects of ARID1A on proliferation, migration, invasion, cell cycle progression, sensitivity to chemotherapy, and in vivo tumor growth.

Results: In the Director's Challenge Study, decreased expression of ARID1A was associated with lymph node dissemination, higher T-stage (T3/T4), and worse survival compared with high expression in patients in the whole group (n=440) and subgroup who received surgery alone and no adjuvant therapy (n=328). ARID1A ablation by shRNA suppressed cell proliferation, promoted cell mobility, increased G2/M phase cell cycle distribution, and protected NSCLC cells from chemotherapy; whereas overexpression of ARID1A showed the opposite biological effects. Consistent with in vitro findings, in vivo tumor xenografts demonstrated ARID1A depletion led to reductions in cell growth but resistance of NSCLC to chemotherapy.

Conclusions: Our results suggest that loss of ARID1A suppresses NSCLC cell growth perhaps by inducing G2/M arrest, but promotes cell migration/invasion, and protect cells from chemotherapy. Further study of ARID1A is needed to better define its roles in the initiation and progression of NSCLC and response to chemotherapy.

Citation Format: Linlin Yang, Changxian Shen, Xiaokui Mo, Terence M. Williams. ARID1A loss leads to chemotherapy resistance and is associated with a poor clinic outcome for patients with non-small cell lung 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 4155.
Abstract 416: Regulation of osteosarcoma cell metastasis by FGFR and mTOR signaling
Authors: Banu Arshiya , Zandueta Carolina , Lecanda Fernando , Grigoriadis Agamemnon E.
Published: September 2020

Osteosarcoma (OS) is the most common primary malignancy of the skeleton, occurring primarily in children and adolescents. Metastatic disease is the single most important prognostic factor with survival dropping to 15-20% in patients with lung metastases. We have recently demonstrated that high FGFR1 signaling in an oncogene-induced murine model of OS as well as in human OS samples contributes to the pathogenesis and metastasis of OS. Significantly, xenograft studies showed that genetic or pharmacological inhibition of FGFR1 decreased lung metastasis.

We have identified the mTOR signaling pathway as a cooperating pathway with FGFR signaling in OS cells. Stimulation of murine and human OS cell lines with FGF2 showed an increase in both MAPK and pAkt/mTOR signaling and mTOR target genes that was inhibited by the FGFR inhibitor, PD173074. Colony growth in soft agar showed that inhibition of mTOR blocked FGF2-stimulated colony growth of OS cells and shRNA silencing of mTOR prevented FGF2-stimulated cell migration in wound/scratch assays.

To confirm pathway cooperativity in vivo, we performed xenograft studies. Silencing of mTOR in FGFR1-expressing OS cells reduced tumor formation on a chick chorioallantoic membrane, with reduced pHistone-H3 expression. Orthotopic injection of OS cells demonstrated that small molecule inhibition of both FGFR1 and mTOR signaling (AZD4547 and AZD8055, respectively), showed greater inhibition of size and diameter of lung metastatic nodules than each inhibitor alone. This was associated with a decrease in the number of Ki67+ cells in lung metastases of FGFR/mTOR inhibitor-treated mice, whereas no changes in activated caspase-3 were detected. In a complementary in vivo model, tail vein injections of OS cells showed that combined FGFR/mTOR inhibition reduced cell seeding in the lungs, suggesting that FGFR/mTOR signaling are driving lung colonization independently of the primary tumor. Finally, preliminary studies indicate that long term growth of OS cells in the lung following tail vein injection may reveal a potential for OS cells to acquire chemoresistance to mTOR inhibition. The mechanisms are not yet known but are independent of the primary tumour.

Taken together, our data suggest that combinatorial treatment significantly decreased lung metastasis of OS cells from primary xenografts. Ongoing analysis of activated FGFR and mTOR pathways in patient-derived tissue microarrays will enable patient stratification that will be useful in the clinical setting to exploit this as a potential anti-metastatic therapy in OS.

Citation Format: Arshiya Banu, Carolina Zandueta, Fernando Lecanda, Agamemnon E. Grigoriadis. Regulation of osteosarcoma cell metastasis by FGFR and mTOR signaling [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 416.
Abstract 4178: ETH-155008, a dual inhibitor of CDK and Pim in preclinical treatment of human B-cell lymphoma xenografts
Authors: Liu Changnian , Sun Zuopeng , Xu Chunping , Zhang Pan , Ji Bin , Zhang James , Liu Laura , Yu Chengzhi
Published: September 2020

Non-Hodgkin lymphomas (NHLs) are the most common hematologic malignancies. The treatment of lymphoma presents a challenge in clinical oncology. Despite significant therapeutic efficacy achieved with combination of chemotherapy and new targeted agents, a large number of patients eventually relapse. Cyclin-dependent kinases (CDKs) are therapeutic targets frequently deregulated in various cancers including solid tumors and hematopoietic malignances. It was also reported that Moloney murine leukemia virus (PIM) kinases are overexpressed in several hematopoietic and solid tumors, especially in B-cell lymphomas. We evaluated the inhibition of kinases' activities and cell proliferation in vitro, and antitumor activities in vivo of ETH-155008, a dual inhibitor of CDK4/6 and PIM in preclinical treatment of human B-cell lymphoma xenografts. ETH-155008 was found to have strong inhibitory activities against key target enzymes with IC50s for CDK4/D1 at 0.8nM, CDK6/D1 at 1.4nM, PIM-1 at 13.3 nM, and PIM-3 at 0.9 nM. ETH-155008 showed to have highly potent antiproliferative activities against cultured human B-cell lymphoma cells of WSU-DLCL2 (diffuse large B-cell lymphoma) and JeKo-1 (mantle cell lymphoma) with IC50s at 1.7nM and 20 nM, respectively. The in vivo antitumor activities of ETH-155008 were evaluated and compared with abemaciclib (CDK4/6 inhibitor) and Imbruvica (Bruton tyrosine kinase inhibitor) in the treatment of the two lymphoma models, respectively. Treatment with ETH-155008 (40 mg/kg/daily x 14-21 days) almost completely eradicated the tumor xenografts and some of the tumor-bearing mice were cured; while as control drugs abemaciclib produced a tumor growth inhibition (TGI) of 56-60% and ibrutinib with a TGI of 60-67% in the two xenograft models. ETH-155008 treatment showed very little toxicity (only 2-4% body weight loss) which were well below the maximum tolerated dose. ETH-155008 represents a novel dual inhibitor that may yet fulfill the promise of effective B-cell lymphoma therapy through dual targeting of CDK4/6 and PIM3. These preclinical results supported the safety and efficacy observed in the preclinical studies and worthy of further clinical evaluation.

Citation Format: Changnian Liu, Zuopeng Sun, Chunping Xu, Pan Zhang, Bin Ji, James Zhang, Laura Liu, Chengzhi Yu. ETH-155008, a dual inhibitor of CDK and Pim in preclinical treatment of human B-cell lymphoma xenografts [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 4178.
Abstract 4184: Genetic and pharmacological disruption of survivin suppressed primary and metastatic tumor growth by attenuating TGFB pathway in ovarian cancer
Authors: Yue Junming
Published: September 2020

Introduction: Survivin, a member of the inhibitor of apoptosis family, is upregulated in multiple cancers including ovarian cancer, but is rarely detectable in normal tissues. Therefore, it is a potential drug target. However, targeting survivin is still challenge and small molecule inhibitors failed in clinical trials. It's very important to understand how survivin contributes to tumor development. In this study, we investigated the role of survivin in ovarian cancer using ovarian cancer cell lines in vitro and mouse models in vivo and examined how survivin contributes to ovarian primary ovarian tumor growth and metastasis by examining epithelial to mesenchymal transition (EMT).

Methods: To define the role of survivin in EMT in ovarian cancer cells, we established survivin knockout cell lines using lentiviral CRISPR/Cas9 nickase and pharmacologically inhibited survivin with a novel inhibitor MX106. We examined EMT markers, migration and invasion assays in survivin disrupted ovarian cancer cells using Transwell plates. We also assessed primary ovarian tumor growth and metastasis in an orthotopic ovarian cancer mouse models through intrabursal injecting survivin KO cell line and also treatment using MX106.

Findings: We found that disruption of survivin expression inhibited EMT by attenuating the TGFβ pathway in ovarian cancer cells. Cell proliferation, migration, and invasion were significantly inhibited in survivin knockout or MX106 treatment in SKOV3 and OVCAR3 cell lines compared to control cells. Inhibition of survivin sensitized cell responses to paclitaxel treatment and overcame chemoresistance in vitro. Lentiviral CRISPR/Cas9 mediated survivin knockout or MX106 treatment efficiently inhibited primary ovarian tumor growth and metastasis in orthotopic ovarian cancer mouse models.

Conclusions: Our data demonstrate that inhibition of survivin using either genetic knockout or a novel inhibitor MX106 suppresses primary ovarian tumor growth and metastasis by attenuating TGFβ pathway. MX106, as a novel survivin inhibitor effectively overcame chemoresistance compared to commercial YM155, which provides a novel approach for ovarian cancer therapy.

Citation Format: Junming Yue. Genetic and pharmacological disruption of survivin suppressed primary and metastatic tumor growth by attenuating TGFB pathway in ovarian 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 4184.
Abstract 4227: Safety of dendtritic cell and cytokine-induced killer(DC-CIK) cell based immunotherapy in patients with solid tumor: A large retrospective study in China
Authors: Wang Shuo , Ren Jun
Published: September 2020

Background: Adoptive T cell therapy especially cytokine-induced killer cell and dendric cell treatment (DC-CIK) alone or combined with chemotherapy had significantly improved patient survival time. Although some side effects studies were briefly reported in some articles. However, systematic assessment of the adverse side effects for DC-CIK therapy, especially combined with chemotherapy has not been reported.

Patients and Methods: Totally 1099 consecutive patients (2054 trail cycles) enrolled in DC-CIK treatment trials at Beijing Shijitian hospital between August 2012 and August 2018 were retrospectively reviewed, and applying Common Terminology Criteria for Adverse Events version 4.0 [CTCAE v4.0] standards to definite adverse effects (AE).

Result: The 370 patients (34%)/ 815 cycles enrolled in our trail combined with chemotherapy. In total, there were 548(cases)/870(cycles) had AEs. The AE class mainly composed of Neurological 34 cycles (4%), Musculoskeletal 28 cycles (3%), Immunopathies 5 cycles(1%), Hematological 521 cycles(60%), General disorders and Administration site conditions 224 cycles(26%), Gastrointestinal 209 cycles(24%), Skin 15 cycles(2%), Metabolism and Nutrition disorders 119 cycles(14%). AE class of the Gastrointestinal (vomiting P=0.025), Nutrition disorders (anorexia P=0.016) and Hematological (anemia P<0.0001, leukopenia P<0.0001) appears in the DC-CIK treatment were mainly correlated with combined with chemotherapy. Multiple logistic regression analysis suggests that no matter whether DC-CIK was combined with chemotherapy, multi-line treatment was more prone to nausea, anorexia, fatigue, anemia and leukopenia than the first-line treatment. However, correlation analysis verified that increasing cycles of only DC-CIK treatment could reduce the incidence rate of fatigue (P=0.001), anorexia (P<0.0001) and anxiety (P=0.01).

Conclusion: Most of the adverse side effects that occur during autologous DC-CIK treatment were associated with combined or previously applied chemotherapeutic treatment, which also indicates that autologous DC-CIK anti-tumor therapy was safe. At the same time, the application of DC-CIK alone treatment could also reduce the occurrence rate of some side effects.

Citation Format: Shuo Wang, Jun Ren. Safety of dendtritic cell and cytokine-induced killer(DC-CIK) cell based immunotherapy in patients with solid tumor: A large retrospective study in China [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 4227.
Abstract 4283: Assessment of the tumor mutational burden in a large cohort of Chinese advanced pan-cancer patients
Authors: Liu Ping , Cui Longgang , Cai Shangli
Published: September 2020

Background: Immunotherapy have led to a paradigm shift in cancer treatment, while only a small subset of patients can benefit from the treatment. Recent studies have revealed that tumor mutational burden (TMB) is positively correlated with immunotherapy, however, by far, limited data are available for Chinese tumor patients.

Methods: We retrospectively assessed the TMB value with a validated 381-cancer-gene panel across 7,822 patients with advanced cancers, including gastric cancer (n= 457), gallbladder cancer (n=608), colorectal cancer (n=785), breast cancer (n=263), Hepatocellular carcinoma (n=904) and lung cancer (n=2135), Renal cell carcinoma (n=346), Liver cancer (904), NSCLC (2135), Melanoma (110), Ovarian cancer (177), Pancreatic cancer (363), Gastric carcinoma (457), Urinary tract cancer (166) and others.

Results: A highest 20% of TMB in each histology was selected as the cut-point. Based on our analysis, the highest and the lowest TMB level was observed in endometrial cancer and RCC, respectively. More specifically, the TMB cut-point was 10.5 for biliary tumor, 9.7 for breast cancer, 15.2 for endometrial cancer, 12.1 for CRC, 49.8 for endometrial cancer, 12.1 for oesophageal cancer, 11.1 for head and neck carcinoma, 7.3 for RCC, 10.1 for HCC, 14.5 for NSCLC, 8.9 for melanoma, 8.1 for ovarian cancer, 7.4 for pancreatic cancer, 11.3 for GC, and 20.1 for urinary tract cancer. Consistent results were observed when the median TMB was applied in the analysis.

Conclusion: This is the first study focusing on the distribution of TMB value in a large cohort of Chinese cancer patients. The results showed the varying distributions of TMB across histology and suggested that a high TMB status may not assigned by one universal cut-point across different cancer types. Our findings have provide clues to guide the treatment strategy in clinical practice and shed lights on the future trial design.

Citation Format: Ping Liu, Longgang Cui, Shangli Cai. Assessment of the tumor mutational burden in a large cohort of Chinese advanced pan-cancer patients [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 4283.
Abstract 4289: Detection of germline large genomic rearrangements in BRCA1/2 genes by a capture-based NGS panel reveals its contribution to Chinese patients with solid tumors
Authors: Li Jing , Yang Bo , Huang Kefei , Liu Changhao , Dong Hua , Wang Jie , Li Fugen , Lin Zhong-qiu
Published: September 2020

Background: Germline mutations in BRCA1/2 genes have been found associate with risk to develop breast and ovarian cancer in women. Patients with these mutations are also highly sensitive to PARP inhibitors. However, current NGS-based method lacks the capability to accurately detect large genomic rearrangements (LGR) including exon level deletions and duplications.

Method: We have enhanced our capture-based NGS panel and developed an algorithm to detect LGRs in BRCA1/2 genes. We applied the method to retrospectively profile germline DNA from over 14,000 patients with solid tumors, including 367 ovarian cancers and 574 breast cancers. Samples with positive test results for exon level deletions or duplications were subsequently confirmed by MLPA.

Results: Out of the 14,000 patients, we identified 19 patients with exon level deletions (BRCA1, n = 16; BRCA2, n = 3) and 7 with duplications (BRCA1, n = 6; BRCA2, n = 1). The germline LGR events were predominantly found in ovarian and breast cancer patients with a frequency of 1.9% (7/367) in ovarian cancer and a frequency of 1.2% (7/574) in breast cancer. We also observed occasional findings in non-small cell lung cancer, colorectal cancer as well as gastric cancer. From these LGRs, BRCA1 exon 2del (n = 4), BRCA1 exon 7del (n = 4) and BRCA1 exon 17-18del (n = 3) are the most recurrent LGRs observed.

Conclusion: We here report a method to comprehensively evaluate the germline LGRs in BRCA1 and BRCA2 genes using the capture-based NGS panel. We verified the results by MLPA as an orthogonal assay and report the population frequency of LGRs occurrence in Chinese patients with solid tumors.

Citation Format: Jing Li, Bo Yang, Kefei Huang, Changhao Liu, Hua Dong, Jie Wang, Fugen Li, Zhong-qiu Lin. Detection of germline large genomic rearrangements in BRCA1/2 genes by a capture-based NGS panel reveals its contribution to Chinese patients with solid tumors [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 4289.
Abstract 432: Development of a novel engineered B2M mouse strain on B-NDG background that specifically eliminates MHC I expression while retaining normal FcRn-mediated antibody retention
Authors: An W. Frank , Gao Lan , Wang Xiaoen , Sharma Shruti , Li Kaiqi , Gao Xiqiang , Shang Chengzhang , Hu Yuting
Published: September 2020

Severely immunodeficient mouse strains, such as NOD.Cg-Prkdcscid Il2rg-/-, have been widely used to evaluate human immune responses, including applications in immuno-oncology in recent years. However, when human peripheral blood mononuclear cells (PBMCs) are engrafted in these mice, severe acute xenogeneic graft versus host disease (GvHD) arises due to engagement of human T cell receptors (TCRs) and murine major histocompatibility complex (MHC) I and II. GvHD shortens animal life span and results in only a brief window of evaluation of human immune cell functions in such mouse models. Efforts have been undertaken to reduce human PBMC-induced GvHD and to subsequently extend the window of human immunity assessment by eliminating mouse MHC I and MHC II. While these MHC deficient mice show few symptoms of GvHD, the use of beta-2-microglobulin (B2M) null allele in order to eliminate expression of all MHC I molecules resulted in an unintended consequence in that these mice had rapid antibody clearance. This is because B2M is also associated with neonatal Fc receptor (FcRn) and is important to FcRn-mediated in vivo antibody recycling and retention. Low half-lives of antibodies in B2M null mice render them unsuitable for antibody efficacy assessment. To overcome this undesired pharmacokinetic (PK) limitation of B2M null allele, while retaining its desired effect on eliminating MHC I expression and alleviating GvHD, we engineered a B2M knock-out strain in the background of B-NDG mice (NOD.Cg-Prkdcscid Il2rgtm1Wjl/Bcgen) that was deficient in MHC I expression but not antibody retention. In present study, we describe genetic, phenotypic, pharmacokinetic, and functional characterizations of the resulting mouse strain, which we believe will be a valuable addition to the collection of severely immunodeficient mouse models that permit extended and appropriate interrogation of antibody therapeutics on human immune cells.

Citation Format: W. Frank An, Lan Gao, Xiaoen Wang, Shruti Sharma, Kaiqi Li, Xiqiang Gao, Chengzhang Shang, Yuting Hu. Development of a novel engineered B2M mouse strain on B-NDG background that specifically eliminates MHC I expression while retaining normal FcRn-mediated antibody retention [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 432.
Abstract 4361: A systematic study of the impact of estrogens and selective estrogen receptor modulators on prostate cancer cell proliferation
Authors: Lafront Camille , Germain Lucas , Weidmann Cindy , Audet-Walsh Etienne
Published: September 2020

The estrogen receptors ERα and ERβ are expressed in prostate cancer (PCa) cells and are believed to act as an oncogene and a tumor suppressor, respectively, and thus to be attractive therapeutic targets. Indeed, compounds modulating the activity of these receptors already exist and are currently used to treat ERα-positive breast tumors. However, there is a lot of discrepancies regarding the efficacy of anti-estrogen treatments for the management of PCa. Several factors explain these discrepancies, including unspecific antibodies against ERβ, lack of proper estrogenic positive controls, and usage of estrogens and anti-estrogens molecules at high dosages were off-target effects are observed. Our objective was to conduct a systematic study on the impact of estrogenic and anti-estrogenic ligands on PCa cell proliferation and survival. After optimization of our cellular assay using the human breast cancer cell line MCF7, we used five of the most commonly studied human PCa cell models, namely LNCaP, 22Rv1, LAPC4, DU145, and PC3 cells. These cells were treated with nine estrogenic/anti-estrogenic compounds, including five selective estrogen receptor modulators (SERMs), with and without co-treatment with androgens for androgen receptor (AR)-positive cells. In both AR-positive and AR-negative cells, we observed no significant modulation of proliferation following modulation of ERs activity. Using both RNA-seq and Western Blots, ERs expression was mostly undetectable in these models. Our study indicate that commonly used PCa models in vitro are not appropriate models to study the estrogen signaling pathway in PCa. Yet, expression data from PCa tissues indicate a significant expression of both receptors, and indicate that usage of new PCa models or of in vivo models are required to properly study drug repurposing of anti-estrogens and SERMs for PCa treatment.

Citation Format: Camille Lafront, Lucas Germain, Cindy Weidmann, Etienne Audet-Walsh. A systematic study of the impact of estrogens and selective estrogen receptor modulators on prostate cancer 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 4361.
Abstract 4376: OP-1250, a complete estrogen receptor antagonist (CERAN) that shrinks estrogen receptor positive tumors and exhibits favorable pharmacokinetics
Authors: Hodges-Gallagher Leslie , Harmon Cyrus L. , Sun Richard , Myles David C. , Kushner Peter
Published: September 2020

Fulvestrant (FASLODEX), a Complete Estrogen Receptor ANtagonist (CERAN) is recognized as the most effective endocrine therapy for estrogen receptor positive (ER+) metastatic breast cancer. Unfortunately, fulvestrant must be injected i.m. and has poor drug exposure. Thus, an oral compound that shares fulvestrant's drug virtues with improved drug exposure might be both more effective and more convenient than fulvestrant. This realization has sparked intensive efforts to develop such a compound, however most efforts have focused on discovering novel selective estrogen receptor degraders (SERDS) most of which have also displayed agonist activities on gene expression and uterus, and are therefore are also selective estrogen receptor modulators (SERMs). We predict that CERANs that fully block the activities of estrogen receptor alpha (ERalpha) will have a clinical advantage over SERM/SERDs in shrinking breast tumors as well as preventing and treating endocrine resistance.

We have developed a small molecule, OP-1250 that, like fulvestrant, is a CERAN that completely turns off both transcriptional activation functions of ERalpha, as can be seen in a uterine cell assay, and also prevents uterine weight gain in ovariectomized mice. In addition, it blocks degrades ERalpha and blocks the proliferation of a large variety of ER+ breast cells. Using RNAseq, we found many estrogen-regulated biomarkers that are also regulated by SERM/SERDs, however CERANS such as OP-1250 and fulvestrant have no, or even an inverse effect on many such genes.

Unlike fulvestrant, OP-1250 gives high and stable oral drug exposure in multiple species. Consequentially, OP-1250 effectively shrinks ER+ tumors in multiple human tumor xenografts in mice at very low daily doses of 3 mg/kg, even in models containing activating ERalpha mutant receptors. Importantly, the pharmacokinetics and biodistribution of OP-1250 has a favorable profile that results in unusual potency of OP-1250 in vivo.

Citation Format: Leslie Hodges-Gallagher, Cyrus L. Harmon, Richard Sun, David C. Myles, Peter Kushner. OP-1250, a complete estrogen receptor antagonist (CERAN) that shrinks estrogen receptor positive tumors and exhibits favorable pharmacokinetics [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 4376.
Abstract 439: Withaferin A attenuates the induction of cardiac cachexia by ovarian cancer
Authors: Kelm Natia Q. , Straughn Alex R. , Ratajczak Mariusz Z. , Kakar Sham S.
Published: September 2020

The purpose of this study was to investigate whether cardiac cachexia occurs in the context of ovarian cancer and whether Withaferin A could ameliorate the cachectic phenotype. We believe that treatment with Withaferin A can ameliorate cancer-induced cachexia and preserve heart function. Ovarian cancer is the fifth leading cause of cancer-related deaths among women in the United States. Cachexia is a common syndrome in advanced cancer patients and accounts for approximately 20% of all cancer-related fatalities. Withaferin A is a steroidal lactone with anti-inflammatory properties that is known to inhibit the growth of ovarian cancer and was recently demonstrated to attenuate the skeletal muscle cachectic phenotype induced by a xenograft model of ovarian cancer. The ovarian cancer cell line A2780 was xenografted into severely immunodeficient female NSG mice via an intraperitoneal (i.p.) injection. Tumor-free control groups received an equivalent volume of sterile saline. Following an engraftment period of 8 days, tumor-free and tumor-bearing mice were treated with vehicle or Withaferin A at one of two doses (2 mg/kg or 4 mg/kg) via i.p. injections every 3 days until the end of the study (4 weeks). Bodyweight and grip strength were assessed on a weekly basis. Heart function was evaluated at the terminal week of the study by echocardiography using Vevo3100 system (FUJIFILM VisualSonics Inc.), followed by histological assessment of the heart for evidence of fibrosis and cardiomyocyte size changes. Cancer induced heart failure in female NSG mice (Systolic dysfunction: FS - 35±3.2; diastolic dysfunction: E/A - 0.45±0.12, IVRT - 22±1.2 msec) and reduced cardiac mass (normalized cardiac mass 9±1.1 (tumor-bearing, vehicle-treated) compared to 13±1.3 (tumor-free, vehicle-treated). Treatment with Withaferin A preserved systolic function in tumor-bearing mice (FS - 58±5.2), but diastolic dysfunction was only modestly improved (E/A - 0.83±0.98, IVRT -17±1.2 msec). Further, Withaferin A ameliorated the reduction in myofibrillar cross-sectional area induced by ovarian cancer. Lastly, treatment with Withaferin A ameliorated fibrotic depositions in the hearts in the tumor-bearing animals. In conclusion, ovarian cancer was shown to induce cardiac cachectic phenotype. Further, it was demonstrated that WFA treatment preserved systolic function, reduced diastolic dysfunction, and attenuated the atrophying and fibrotic effects of the xenografted tumors.

Citation Format: Natia Q. Kelm, Alex R. Straughn, Mariusz Z. Ratajczak, Sham S. Kakar. Withaferin A attenuates the induction of cardiac cachexia by ovarian 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 439.
Abstract 4397: Pathway-based drug combinatory synergy prediction using gene expression and essentiality data
Authors: Li Jin , Wu Xue , Huo Yang , Liu Enze , Zeng Zhi , Cheng Lijun , Li Lang
Published: September 2020

Background: Experiment based drug combinatory synergy discovery is limited in a moderate scale. Systems biology models can substantially widen the search space, and discover novel mechanisms. While most of systems pharmacology models were designed to optimize the predictive performance for the drug combination synergy, they were limited by their lack of mechanistic interpretations. The gene essentiality data generated from RNAi screening have not been integrated into the systems pharmacology model yet.

Methods: Drug combinatory synergy data from NCI-ALMANAC was used in this research. Cancer cell line gene expression and essential score (RNAi screening from DepMap portal), drug targets and KEGG pathways were used in our systems pharmacology model. Two types of models were constructed. The first model predicts a drug combination's synergy using various pathways among various cell lines. The second model predicts various drug combinatory synergy in a cell line. Machine learning approaches, such as SVR, Ridge regression, Random forest and Logistic regulation were investigated in developing this model. Our predictive models were built upon 43 cell lines with both baseline gene expression and essential scores, 165 KEGG pathways, and 198 drug pairs who have at least synergistic drug combinatory effects in 3 or more cell lines.

Results: In predicting drug combinatory synergy from both predictive models, the mean R square was merely 0.006 using individual gene expression or essentiality data. The mean R-square increased to 0.022 when using pathways. In drug combination specific predictive model (model 1), 64 and 62 drug combinations were related to more than 10 pathways which had enriched essential and expression genes, respectively. The correlation between expression enrich pathways and essential enriched pathways is only 0.04. In the cell line specific predictive model (model 2), drug combination synergy score from 14 cell lines can be predicted with more than 150 pathways, and 5 cell lines can be predicted with less than 10 pathways.

Conclusion: Pathway-based models are more powerful than gene level-based models in predicting drug combination synergy. Gene expressions and essential genes provide much different information in predicting drug combination synergy. Drug combination synergy prediction and its related pathways are dramatically different among different cancer cell lines.

Citation Format: Jin Li, Xue Wu, Yang Huo, Enze Liu, Zhi Zeng, Lijun Cheng, Lang Li. Pathway-based drug combinatory synergy prediction using gene expression and essentiality data [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 4397.
Abstract 4434: Comprehensive bioinformatic analysis of immune composition and genes for survival prediction in sarcoma
Authors: Chen Hongmin
Published: September 2020

Introduction

Sarcomas, a broad family of mesenchymal malignancies, exhibit remarkable histologic diversity. Previous study has reported that the infiltration of immune and stromal cells in tumor microenvironment contribute significantly to prognosis. ESTIMATE, an algorithm to calculate immune and stromal scores, predicts the infiltration of non-cancer components. The Cancer Genome Atlas (TCGA) database is available to grasp potential correlations between gene set prolife and overall survival of malignancies, including sarcomas. To better understand the proportions of immune cells in the tumor microenvironment, We used CIBERSORT deconvolution software and ssGSEA to infer the relative proportions of several distinct leukocyte cell types in the tumors from microarray gene expression data of sarcoma patients. By taking advantage of both TCGA database of sarcomas cohorts and ESTIMATE algorithm, we extracted a list of genes that predict poor outcomes in sarcoma patients. Finally, we validated these genes in an independent sarcoma cohort from the GSE17679. Thus, we obtained a list of tumor microenvironment-related genes that predict poor outcomes in sarcoma patients.

Methods

Gene expression profile and clinical data for sarcoma patients was obtained from the TCGA data portal. Immune scores and stromal scores were calculated by applying the ESTIMATE algorithm to the downloaded database. Batch adjusted data was subsequently analyzed using CIBERSORT to resolve the immune composition. For validation, gene expression profiles for Ewing sarcoma patients were obtained from the Gene Expression Omnibus dataset GSE17679.

Results

The immune and stromal score are associated with prognosis. The type 2 macrophages in sarcoma makes up the largest composition of all immune cells in the tumor microenvironment of sarcoma (except synovial sarcoma), which predicts poor outcomes. From functional enrichment analysis of TCGA database applied by ESTIMATE algorithm-based immune scores, we extracted that NR1H3, VAMP5, GIMAP2, GBP2, HLA-E and CRIP1 are highly expressed in the immune microenvironment, predicting good outcomes in sarcoma patients.

Conclusion

We extracted a list of tumor microenvironment related genes. These genes were validated in an independent sarcoma cohort and that may represent promising novel signatures for the diagnosis and prognosis prediction of sarcoma. The immune composition analysis could be useful for outlining the prognosis.

Citation Format: Hongmin Chen. Comprehensive bioinformatic analysis of immune composition and genes for survival prediction in 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 4434.
Abstract 447: Integrated omics modeling of transcriptional regulation in medulloblastoma subtypes
Authors: Chapman Owen S. , Ehrenberger Tobias , Archer Tenley C. , Gold Maxwell P. , Mundt Filip , Adam Miriam , Mah Clarence K. , Krug Karsten , Chandran Sahaana , Dixon Jesse R. , Pomeroy Scot L. , Fraenkel Ernest , Mesirov Jill P. , Chavez Lukas
Published: September 2020

Medulloblastoma (MB) is one of the most common pediatric brain tumors. Current treatment options carry substantial risk for lifelong cognitive and neurological impairment. Consequently, there is a pressing need to elucidate molecular mechanisms with the ultimate goal of developing targeted tumor-specific therapies. In a recent study on proteomes and phospho-proteomes of primary MB tumors, we identified proteomic MB subtypes that were not apparent from transcriptional or methylation data. To identify gene regulatory circuitries that drive these MB subtypes, we have now mapped accessible chromatin and 3D chromosome conformation in 23 and 13 MB tumors from the same cohort, using ATAC-seq and Hi-C respectively. We identify subtype-specific accessible regulatory chromatin regions, including a subset of regions not identifiable by the enhancer mark H3K27ac. We associate regulatory regions to their target gene promoters by correlating transcription with ATAC-seq signal strength, and confirm these relationships using the newly generated Hi-C data. Using an unpublished adaptation of the GSEA algorithm, which we tailored for an enrichment analysis of non-coding regulatory elements instead of genes, we identify transcription factors and master regulators with binding sites specific to an MB subtype. By associating these master regulators with their transcriptional targets, we have derived models of regulatory circuitry in MB which implicate central mechanisms of MB pathogenesis and may inform future therapeutic targeting.

Citation Format: Owen S. Chapman, Tobias Ehrenberger, Tenley C. Archer, Maxwell P. Gold, Filip Mundt, Miriam Adam, Clarence K. Mah, Karsten Krug, Sahaana Chandran, Jesse R. Dixon, Scot L. Pomeroy, Ernest Fraenkel, Jill P. Mesirov, Lukas Chavez. Integrated omics modeling of transcriptional regulation in medulloblastoma subtypes [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 447.
Abstract 4485: Comparison of two commercially available T cell receptor repertoire sequencing assays
Authors: Mason Jennifer , Buchkovich Martin , Sims Jennifer , Hurban Patrick
Published: September 2020

Background: Deep sequencing of the T-cell receptor complementarity-determining regions assists with resolving T-cell diversity, and, in oncology, detects specific clones or changes in clonality associated with anti-tumor responses. However, the extreme diversity of the T-cell repertoire represents a major analytical challenge, while a gold standard method for the repertoire analysis has not yet been identified. Here, we evaluated performance of the Oncomine TCR Beta squencing assay in PBMC and formalin-fixed paraffin-embedded (FFPE) tissues, and compared it to another commercially available TCR sequencing assay.

Method: RNA derived from PBMCs or tumor FFPE tissue were prepared using the Oncomine TCR Beta-SR (short read) and LR (long read) assays, and a comparator assay. Library preparation using the TCR Beta SR and LR assays required cDNA synthesis followed by TCR gene specific amplification, sample barcoding, and sequencing on the Ion Torrent S5. Comparator assay entailed gene specific cDNA synthesis, preparation of sequencing libraries, TCR gene specific amplification, sample barcoding and 2 × 150 bp sequencing on Illumina's NextSeq. Libraries generated from RNA derived from PBMCs and FFPE were sequenced to a depth of 25M and 10M reads, respectively, for the TCR Beta-SR and a comparator assay. All samples prepared with the TCR Beta-LR assay were sequenced to 3M reads. On target reads, reproducibility, sensitivity, and robustness of input were used to measure assay performance.

Results: Higher fractions of on target TCR reads were identified in PBMC and FFPE libraries generated with the TCR Beta-SR and LR assays. The TCR Beta-SR and LR assays had mean pairwise correlations for replicate samples of 0.95 and 0.99, respectively, and 0.86 for a comparator assay. Rare clones at frequencies 10−5 and 10−6 in PBMC samples were detected by the Oncomine TCR Beta-SR and LR assays in samples with an input of 50 - 300 ng, where a comparator assay had inconsistent detection of the rare clones at a frequency of 10−5, independent of input.

Conclusions: Thermo Fisher's Oncomine TCR Beta assay reproducibly amplifies TCR specific sequences with high sensitivity. The assay is suitable for characterization of TCR clones from RNA derived from PBMC and tissue FFPEs.

Citation Format: Jennifer Mason, Martin Buchkovich, Jennifer Sims, Patrick Hurban. Comparison of two commercially available T cell receptor repertoire sequencing assays [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 4485.
Abstract 4555: Selection of CD3 affinity allows generation of T-cell redirecting bispecific antibodies with unique pharmacokinetic and biodistribution properties
Authors: Haber Lauric , Olson Kara , Babb Robert , Kelly Marcus , Crawford Alison , Retter Marc , DiLillo David , Ullman Erica , Finney Jennifer , Canova Lauren , Pawashe Arpita , Chiu Danica , Vazzana Kristin , Ram Priyanka , Mohrs Katja , Dorvilliers Amanda , Xiao Jenny , Makonnen Sosina , Hickey Carlos , Arnold Cody , Giurleo Jason , Patel Supriya , Tavare Richard , Chen Ya Ping , Chen Gang , Olson William , Thurston Gavin , Lin John Chia-Yang , Hermann Aynur , Kirshner Jessica , Smith Eric J.
Published: September 2020

T-cell redirecting bispecific antibodies are an emerging class of therapeutic agents designed to simultaneously bind to T cells (via CD3) and tumor cell specific antigens (TSA), with the goal of inducing T cell-mediated killing of tumor cells. Despite promising pre-clinical and clinical efficacy from TSAxCD3 antibodies, these agents have associated toxicities that remain challenging. Here we present findings from a series of bispecific antibodies that were engineered to have a range of CD3 affinities, but which retained the same binding affinity to the selected tumor antigen. These agents were tested for killing of tumor cells in vitro, and for biodistribution, serum half-life, and anti-tumor activity in vivo. By altering the binding strength for CD3, bispecifics were generated that maintained potent killing of TSA+ cells but displayed differential profiles of cytokine release, pharmacokinetics, and biodistribution. Our results suggest that tuning CD3 affinity is a promising method to improve the therapeutic window of T cell-engaging bispecific antibodies.

Citation Format: Lauric Haber, Kara Olson, Robert Babb, Marcus Kelly, Alison Crawford, Marc Retter, David DiLillo, Erica Ullman, Jennifer Finney, Lauren Canova, Arpita Pawashe, Danica Chiu, Kristin Vazzana, Priyanka Ram, Katja Mohrs, Amanda Dorvilliers, Jenny Xiao, Sosina Makonnen, Carlos Hickey, Cody Arnold, Jason Giurleo, Supriya Patel, Richard Tavare, Ya Ping Chen, Gang Chen, William Olson, Gavin Thurston, John Chia-Yang Lin, Aynur Hermann, Jessica Kirshner, Eric J. Smith. Selection of CD3 affinity allows generation of T-cell redirecting bispecific antibodies with unique pharmacokinetic and biodistribution properties [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 4555.
Abstract 4560: Conditionally active biologics (CAB): A novel class of molecules targeting solid tumors
Authors: Wang Jing , Xing Charles , Liu Haizhen , Cugnetti Ana Paula G. , Wheeler Christina , Lucas Matthew , Frey Gerhard , Chang Cathy , Boyle William J. , Short Jay M.
Published: September 2020

Conditionally Active Biologics (CAB) technology is a proprietary platform that selects antibodies binding to target antigens in the context of diseased tissues, but not normal tissues, taking advantage of the unique conditions in the tumor microenvironment. Using our CAB technology, we have developed CAB ADCs to various well-established tumor associated antigens (TAA), including Nectin-4, Her2 and CD46. Each of these molecules play an important role in cancer biology and are attractive targets for the development of therapeutic antibodies. These targets, however, are expressed on many normal tissues and have been implicated in a wide range of biological processes; therefore, limiting the use of traditional ADCs as cancer therapy. Using CAB technology, we have developed conditionally active ADCs that have no or very little binding to the target antigen in healthy tissue (normal physiological conditions), but have strong binding in the context of diseased tissues (tumor microenvironment) based on the glycolytic tumor metabolism (including Warburg effect). In vitro and in vivo efficacy data demonstrating the abilities of CAB ADCs to induce cytotoxicity of human target-expressing tumor cell lines, and to inhibit tumor growth in human tumor xenograft models will be presented. In conclusion, our data is consistent with our previous work on EpCAM, our clinical stage AXL and ROR2 CAB ADCs, and suggests that conditionally active ADCs generated using the CAB technology will provide a new generation of biologics with increased safety margin and therapeutic index in the clinic.

Citation Format: Jing Wang, Charles Xing, Haizhen Liu, Ana Paula G. Cugnetti, Christina Wheeler, Matthew Lucas, Gerhard Frey, Cathy Chang, William J. Boyle, Jay M. Short. Conditionally active biologics (CAB): A novel class of molecules targeting solid tumors [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 4560.