tbuckley/cabot-search huggingface dataset:
Abstract 5569: Discovery of tumor-specific T cell receptors (TCRs) by reverse genetic engineering platform
Authors: Yanyan Han, Xiaoling Liang, Shudan Ou, Xihe Chen, Minjun Ma, Jun Li, Yifan Ma, Xiangjun Zhou
Journal: Cancer Research (2020)

Abstract TCR-T therapy is an ideal cell therapeutic strategy against solid tumors. However, the traditional method of TCR cloning has two major problems. First, we could only develop TCRs against previously discovered tumor antigen epitopes. Second, the affinity maturation of TCR sometimes leads to mortal toxicities due to the unexpected cross-reactivities. Therefore we hereby present a reverse genetic engineering platform to clone tumor specific TCRs from immunotherapies benefit cancer patients. Multi-antigen stimulating cell therapy (MASCT) is a cell-based immunotherapy combining therapeutic DC vaccine and adoptive T cell transfer, the IND application of which was approved in China. We observed dynamic T cell responses against multiple tumor-associated antigens used in MASCT-treated HCC patients, which showed a significant correlation with clinical outcome. Based on this observation, we propose that expanded tumor-specific T cells in MASCT-benefit cancer patients could be good sources to isolate clinical relevant TCRs. A HPV positive metastatic cervical cancer patient has shown partially response after MASCT treatment alone, and survived over 5 years. Moreover, a metastatic lung cancer patient has also shown partially response and survived for longer than 2 years after combination treatment of MASCT and anti-PD1 antibody. Enhanced and persist T cell responses against several TAAs as well as HPV antigens were detected in PBMCs of both patients. We successfully expended and isolated tumor antigen-specific T cells by IFNγ-secreting cell enrichment, and obtained alpha/beta chains paired TCR sequences using single T cell NGS technology. We selected 14 pairs of TCRs isolated from cervical cancer patient for further validation. TCRs from lung cancer patient were currently under synthesis or sequencing. Among 14 TCRs, a TAA-specific TCR and a HPV18E7-specific TCR showed superior antigen specificity and optimum avidity, and would be applied for TCR-T development. Of notes, our reverse genetic engineering of TCR-T (ReGET) platform.can not only identify both HLA class I and II-restricted TCRs, but also identify novel epitopes of tumor antigens, which may provide new targets for TCR-T therapy against solid tumors. Citation Format: Yanyan Han, Xiaoling Liang, Shudan Ou, Xihe Chen, Minjun Ma, Jun Li, Yifan Ma, Xiangjun Zhou. Discovery of tumor-specific T cell receptors (TCRs) by reverse genetic engineering platform [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 5569.
Abstract 4027: Metformin treatment inhibits uterine leiomyoma and leiomyosarcoma cells growth and migration in vitro
Authors: Anamaria R. Ricci, Giovana D. Maffazioli, Edmund C. Baracat, Kátia C. Carvalho
Journal: Cancer Research (2020)

Abstract Leiomyoma (LM) and leiomyosarcoma (LMS) are uterine mesenchymal tumors that present variable clinical and biological behavior. They are associated with infertility, pelvic pain and abnormal uterine bleeding.. LM is a benign tumor commonly affecting women at reproductive age whereas LMS represents 40% of all uterine sarcomas. These tumors do not have specific therapy and their origin is still uncertain. Some researchers believe that degenerated LM may to turn to LMS. FOXO3a, a transcriptional factor, has been associated to regulation of several cellular functions as well as tumors development. Previously, we detected that FOXO3a gene and protein expression present different expression profiles in LM and LMS. In this current study, our aim was to investigate the in vitro effects of metformin and genistein, both inhibitors of AKT-mediated FOXO3a phosphorylation, treatment in LM and LMS cells behavior. LM (THESCs CRL-4003) and LMS (SK-UT-1) cell lines were grown in specific mediums and conditions (ATCC recommendations), and treated with different drugs concentrations (0.1 - 200 uM and 0.1 - 200 nM, for metformin and genistein, respectively) at several time points (0, 24, 48, 72, 96 and 120 h). After treatment, cells were evaluated for gene and protein expression, cell proliferation, migration and apoptosis. Gene expression was assessed by quantitative Real Time PCR and proteins were evaluated by immunocitochemical analysis. Genistein depicted high toxicity for the cells, due to its vehicle (DMSO), in all tested dose and times. Metformin presented higher efficiency in cell proliferation and migration inhibition for both cell lines, as well as in the apoptosis induction. Prominent effects were observed in LMS cells after treatment with 25 uM for 72h. Gene expression analysis showed a slight decrease in FOXO3a expression after treatment with these drugs. Our results suggest that treatment with metformin induces the FOXO3a function restoration in the cells, by inhibition of the AKT/PI3K pathway, and can represent a future alternative target therapy for these neoplasias. Citation Format: Anamaria R. Ricci, Giovana D. Maffazioli, Edmund C. Baracat, Kátia C. Carvalho. Metformin treatment inhibits uterine leiomyoma and leiomyosarcoma cells growth and migration in vitro [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 4027.
Abstract 5097: Pancreatic cancer cells derived exosomes stimulate pericyte phenotype switching in the tumor microenvironment
Authors: Alexander Delgado, Reed Jacobson, Dylan Wrede, Sangdeuk Ha, Jiha Kim
Journal: Cancer Research (2020)

Abstract In pancreatic cancer (PC), most conventional and targeted therapies fail to provide substantial response partly due to the limited delivery efficacy of cytotoxic drugs. Poor vascular structure and stroma-rich tumor microenvironment (TME) likely contribute to such failure. We have previously shown that in breast cancer, differential perivascular investment significantly impacts vascular functionality and drug delivery efficacy. Considering unique pancreatic cancer TME, it is a promising approach to "re-invest" perivascular cells in which blood vessels are in their optimal functional status. As a first attempt to understand the perivascular phenotype of pancreatic tumors, we utilized a multiplex imaging analysis technique to map out differential pericyte markers expression on several mouse model systems for PC as well as tumor microarray (TMA) of patients with PC. Among pericyte markers examined, alpha-smooth muscle actin (α-SMA) expression was significantly increased in all cases of PC compared to normal pancreas tissues, which skewed the ratio between Desmin (mature pericyte marker) and α-SMA. To determine if eliminating pathological pericytes can normalize vascular phenotype of pancreatic tumor, we utilized PDGFRβ-TK transgenic mice in which proliferating pericytes that express PDGFRβ are depleted. However, eliminating these pericytes resulted in increased metastasis accompanied by increased vascular leakiness. This result indicates that elimination tumor-associated pericyte might result in an adverse effect instead of vascular normalization. Therefore, we hypothesize that normalizing vascular phenotype by re-investment of perivascular cells will likely contribute to improving TME for a better outcome. To understand the molecular mechanism governing pericyte phenotype switching, we established in vitro vascular cell culture system. The results indicate that PC cells derived exosomes can modify pericyte phenotype that resembles tumor-associated pericyte. Such phenotype conversion was even further enhanced in a hypoxic environment. Currently, we are investigating global gene expression changes of pericyte upon exposure to PC cell exosomes using a single-cell RNA sequencing method to have a comprehensive understanding of pericyte phenotype switching. Currently, we are performing in vivo perivascular re-investment using our candidate molecules to prove our hypothesis that perivascular re-investment will improve vascular performance and consequently enhance drug delivery efficacy. Citation Format: Alexander Delgado, Reed Jacobson, Dylan Wrede, Sangdeuk Ha, Jiha Kim. Pancreatic cancer cells derived exosomes stimulate pericyte phenotype switching in the tumor microenvironment [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 5097.
Abstract 3264: CRISPR-Cas9 library screen in primary T cells to identify cancer immunotherapeutic targets
Authors: Yangbo Yue, Qian Li
Journal: Cancer Research (2020)

Abstract Background: Immunotherapy, especially checkpoint blockers targeting programmed cell death protein 1 (PD-1) pathways, has transformed cancer treatment. Current checkpoint blockers are limited by low response rate, side effect and treatment relapse. An efficient and high-throughput screen platform in primary immune cells will accelerate the identification of key regulators in the immune response to tumor. New targets identified from the screen will be validated in in vitro and in vivo models that recapitulate key components of tumor-immune interaction. Results: We developed a CRISPR-Cas9 genome targeting system that can achieve efficient gene disruption in primary CD8+T cells isolated from mouse (~60%) or human (~70%). We have applied this method to a pooled CRISPR library screen for key modulators of T cell-induced cytotoxicity to cancer cells in vitro and in vivo. This library contains sgRNAs targeting nearly all membrane proteins expressed in both murine and human T cells. In our in vitro model, cancer cells expressing chicken ovalbumin (OVA) were co-cultured with OVA-specific CD8+T cells isolated from OT-I transgenic mice. The proliferation and function of CD8+ T cell were damped by tumor cells in an antigen dependent way. In our in vivo model, OVA-specific CD8+T cells were transplanted into C57BL/6 mice implanted with OVA-expressing tumor. The accumulation, proliferation and function dynamics of transplanted CD8+T cells were monitored in tumors. They infiltrated into tumor in 3 days, substantially decreased in number in the following 4 days, and then continuously increased. Importantly, most CD8+T cells (~70%) in tumor were CD107a negative, which means they were non-functional. Summary: We have established a high-throughput platform for identification of membrane proteins in primary CD8+ T cells to regulate T cell proliferation and function in tumor microenvironment. Citation Format: Yangbo Yue, Qian Li. CRISPR-Cas9 library screen in primary T cells to identify cancer immunotherapeutic targets [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 3264.
Abstract 1620: MDM2 P1 and P2 promoters have different roles in tumorigenesis
Authors: Narisa Phinichkusolchit, Thomas Jamieson, Rachel Ridgway, Dimitris Athineos, Kerryanne Crawford, Nikolina Vlatkovic, Mark Boyd, Owen Sansom, Karen Blyth
Journal: Cancer Research (2020)

Abstract The murine double minute 2 (MDM2) protein is an E3 ubiquitin ligase most notable for priming tumour-suppressor p53 for degradation. MDM2 contains two promoters - the constitutive P1 and the inducible P2. The p53-independent P1 promoter is responsible for basal levels of MDM2, whilst the p53-dependent P2 promoter is activated upon stress responses. Although the oncogenic functions of MDM2 are well understood, less is known about the individual roles of the promoters and their contribution to tumorigenesis and stress responses. To tease apart the roles of the promoters, we have used genetically engineered mouse (GEM) models null for the P1-promoter and mutated for the P2-promoter in the context of intestinal cancer, lymphoma and hepatocellular carcinoma (HCC). Here, we have shown that mice with heterozygous or homozygous loss of the P1-promoter in the APCMin/+ intestinal model have extended survival and reduced intestinal tumour burden in comparison to the P1- wild type (WT), APCMin/+ mice. Surprisingly, none of the P1-null APCMin/+ mice succumbed to intestinal tumours, but rather to thymic lymphomas. In the P1-null APCMin/+ lymphoma samples, we investigated the p53 functionality by examining the expression levels of p21, a p53 downstream target. Immunohistochemistry analysis clearly revealed that p53 is non-functional as p21 was not expressed, despite variations in p53 expression levels itself. This uncommon occurrence in the APCMin/+ model led us to investigate the role of the P1 and P2 promoters in the Eµ-Myc lymphoma model. Interestingly, in this model, heterozygous loss of the P1 promoter improves survival, while heterozygous loss of the P2 promoter accelerates lymphomagenesis. Our findings thus far indicate a differential role for the P1 and P2 MDM2 promoters in tumorigenesis. In addition to using GEM models, we are investigating the role of the MDM2 promoters in stress-induced HCC. These studies will allow for a better understanding of MDM2 functions, but also perhaps provide an alternative therapeutic strategy for cancers with aberrations in the p53-MDM2 signalling axis. Citation Format: Narisa Phinichkusolchit, Thomas Jamieson, Rachel Ridgway, Dimitris Athineos, Kerryanne Crawford, Nikolina Vlatkovic, Mark Boyd, Owen Sansom, Karen Blyth. MDM2 P1 and P2 promoters have different roles in tumorigenesis [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 1620.
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: Jing Li, Bo Yang, Kefei Huang, Changhao Liu, Hua Dong, Jie Wang, Fugen Li, Zhong-qiu Lin
Journal: Cancer Research (2020)

Abstract 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 1632: Long-term maintenance of human mature NK cells from hCD34+HSCs engraftment supported by immune humanized B-NDG hIL15 mice
Authors: Qingcong Lin, Yuting Hu, Xiaofei Zhou, Youhong Su, Yuelei Shen
Journal: Cancer Research (2020)

Abstract Human HSC (hematopoietic stem cells) engrafted humanized mice are a powerful model that allows researchers to examine the human immune system and evaluate cellular immunotherapy in the preclinical stage. Successful reconstitution of the human immune system in B-NDG mice (a complete immunodeficient mouse model previously developed by Biocytogen) has been accomplished using CD34+ hematopoietic stem cells. However, the species barrier between human immune cells and the mouse microenvironment can obstruct human immunity acquisition, as well as innate immune function development, in the mice upon the reconstitution of immune system. To address this issue, Biocytogen has developed and validated the B-NDG hIL15 mice that combines a B-NDG mouse background and expresses human IL15 cytokine, which plays important roles in the innate and adaptive cell homeostasis, as well as peripheral immune function. The targeting strategy stipulates the insertion of CDS region of the human IL15 gene after the 5′UTR of the mouse Il15. In this work, human CD34+ hematopoietic stem cells have been successfully grafted in B-NDG hIL15 mice, to reconstitute a functional human immune system. At 4 weeks post CD34+ cell implantation, the percentage of hCD45+ cells reached over 25%, containing human T, B, and NK cells. In summary, these CD34+ reconstituted B-NDG hIL15 mice are validated to be promising tools for the efficacy study of clinically relevant therapeutic agents given the mice's long-term maintenance of human NK cells upon the reconstitution of immune system. Citation Format: Qingcong Lin, Yuting Hu, Xiaofei Zhou, Youhong Su, Yuelei Shen. Long-term maintenance of human mature NK cells from hCD34+HSCs engraftment supported by immune humanized B-NDG hIL15 mice [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 1632.
Abstract 2118: Using electronic medical records to assemble a lung cancer cohort for prognosis study
Authors: Qianyu Yuan, Tianrun Cai, Chuan Hong, Tianxi Cai, David Christiani
Journal: Cancer Research (2020)

Abstract Background: Electronic medical records (EMRs) provide a low-cost means of accessing longitudinal data on large populations with detailed information regarding diagnosis, clinical procedures, medications and tests. A lung cancer cohort assembled from EMR represents a powerful resource for studying prognosis. Methods: EMRs are from the Massachusetts General Hospital and Brigham and Women's Hospital using Partners HealthCare System Research Patient Data Registry from 1988 to October 18, 2018. A previously validated phenotyping algorithm was developed to identify lung cancer patients based on a gold standard set of 200 patients. Demographics and clinical characteristics were extracted from both structured data and clinical notes utilizing natural language processing tools. The quality of EMR cohort was assessed by comparing to Boston Lung Cancer Study (BLCS) cohort using overlapped population. Specifically, we assessed: 1) absolute differences: the agreements of diagnosis dates, histological type and clinical stage; 2) relative differences: the effect sizes of variables on overall survival estimated from Cox regression models. Results: The initial study population included 76,643 patients with a diagnostic code related to primary lung cancer. The phenotyping model identified 42,069 lung cancer patients with sensitivity of 75.2%, specificity of 90.0%, PPV of 94.4% and AUC of 0.927. A total of 5,053 patients overlapped in BLCS and EMR cohorts were used for quality assessment. The diagnosis dates from EMR agreed with diagnosis dates from BLCS cohort with median of 0 days. 10.9%, 7.5%, and 5.1% of the population had an absolute date discrepancy of more than 90 days, 180 days, and one year, respectively. The agreements of histological type and clinical stage were 90.1% and 82.8% respectively. Further analysis for overall survival showed high consistency in the two cohorts as Cox regression models controlled for age, sex, race, smoking status, histological type, stages and treatments yielded similar estimates. Conclusion: We assembled a large lung cancer cohort from EMRs using phenotyping algorithm and extraction strategies combining structured and unstructured data. The quality of analytic data from EMRs were compared with the well curated epidemiology study to ensure their suitability for lung cancer prognosis research. Citation Format: Qianyu Yuan, Tianrun Cai, Chuan Hong, Tianxi Cai, David Christiani. Using electronic medical records to assemble a lung cancer cohort for prognosis study [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 2118.