tbuckley/cabot-search huggingface dataset:
Abstract 1679: Characterization and establishment of triple negative breast cancer patient derived xenograft derived from a Nigerian woman
Authors: Uzoamaka Adaobi Okoli, Michael Tochukwu Okafor, Kenneth A. Agu, Samuel R. Ohayi, Emmanuel O. Nna, Chioli P. Chijioke, Iroka J. Udeniya
Journal: Cancer Research (2020)

Abstract Extensive literature has demonstrated the use of fresh human breast tumour tissue surgically implanted in immunodeficient mice to establish patient-derived xenograft (PDX) as a therapeutic assessment tool. Unfortunately, there is a paucity of genomic research using PDX as a preclinical tool for breast cancer metastasis in Nigerian women. Previous studies of rodent models have concentrated on cell line xenograft of other tumours usually of Caucasian or African American counterpart. To overcome this limitation, Triple-negative breast cancer (TNBC) was derived from a consenting 32-year-old Nigerian woman who had neoadjuvant therapy and had undergone a mastectomy. Triple-negative breast cancer lacks expression of hormone receptors including human epidermal receptor (HER2-), estrogen receptor (ER-) and progesterone receptor (PR-) genes. TNBC xenograft was established by orthotopic surgical implantation of breast cancer tissue fragments of 2mm3 in size with cultrex in the cleared breast pads of immunosuppressed mice and a further two passages. The size of the implanted tumour was checked twice weekly. Haematology &amp; eosin histology and immunohistochemistry analysis were used to structurally and functionally characterize the tumour xenograft and primary tumour respectively. Real-time quantitative polymerase chain reaction (RQ-PCR) was used to evaluate the genomic correlation between primary tumour and tumour xenograft. Target genes compared between the tumour xenograft and primary tumours included CXCL16; CLD10; CDC42EP3; CXCL16; EPSTI1; PALMD and ZAN. Reference genes RLP13A and GAPDH were selected as assays for endogenous controls. All tumour tissues were mechanically homogenized and lysed in guanidine isothiocyanate buffer from which RNA was extracted and converted to cDNA by random hexamer priming. RQ-PCR was performed using TaqMan chemistries. This was validated by DNA sequencing of the xenografts tumour and primary tumour using Nanopore DNA sequencing, and Ligation Sequencing ID2 chemistry. The DNA sequences were aligned with Meg Align Pro The xenografts appear to maintain characteristic human histopathology, tumour-marker production. None of the tumours showed hormone sensitivity. There was a local invasion of breast cancer in the bone. The pairwise alignment yielded significant percentage relativity. Citation Format: Uzoamaka Adaobi Okoli, Michael Tochukwu Okafor, Kenneth A. Agu, Samuel R. Ohayi, Emmanuel O. Nna, Chioli P. Chijioke, Iroka J. Udeniya. Characterization and establishment of triple negative breast cancer patient derived xenograft derived from a Nigerian woman [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 1679.
Abstract 4434: Comprehensive bioinformatic analysis of immune composition and genes for survival prediction in sarcoma
Authors: Hongmin Chen
Journal: Cancer Research (2020)

Abstract 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 2688: Pan-cancer analysis of clonality and the timing of systemic spread in paired primary tumors and metastases
Authors: Zheng Hu, Zan Li, Zhicheng Ma, Christina Curtis
Journal: Cancer Research (2020)

Abstract Metastasis is the primary cause of cancer-related deaths, but the natural history, clonal evolution and patterns of systemic spread are poorly understood. We analyzed exome sequencing data from 458 paired primary tumors (P) or metastasis (M) samples from 136 breast, colorectal and lung cancer patients, including both untreated (n=98) and treated (n=101) metastases. We find that treated metastases often harbored private driver gene mutations whereas untreated metastases did not, suggesting the acquisition and selection of additional mutations is not required for untreated metastases and treatment promotes clonal evolution. Additionally, the ratio of nonsynonymous versus synonymous mutations (dN/dS) showed decreased selection pressures in the metastasis relative to primary tumors. Polyclonal seeding was common in lymph node metastases (n=19/35, 54%; mostly untreated) and untreated distant metastases (n=20/70, 29%), but less frequent in treated metastases (n=9/90, 10%). Mathematical modeling shows that the low number of metastasis-private clonal mutations is consistent with early metastatic seeding, which commonly occurred several years prior to diagnosis in breast (2.4 years, range 0-3.3), lung (3.6 years, range 2.8-3.7) and colorectal (4.1 years, range 3.1-4.6) cancers. Thus, this pan-cancer analysis reveals early systemic spread in three common cancer types. Further, these data suggest that the natural course of metastasis is selectively relaxed relative to early tumor development and that metastasis-private mutations are not drivers of cancer spread but are instead associated with drug resistance. Citation Format: Zheng Hu, Zan Li, Zhicheng Ma, Christina Curtis. Pan-cancer analysis of clonality and the timing of systemic spread in paired primary tumors and metastases [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 2688.
Abstract 934: “GPCR-ome” modulation upon PD1 / PDL1 axis blockade
Authors: Imane Nafia, Xavier Leroy, Loic Cerf, Jean-Philippe Guegan, Anne-Laure Blayo, Antoine Italiano, Stephan Schann, Alban Bessede
Journal: Cancer Research (2020)

Abstract Background: Immunotherapy represents a novel weapon within the cancer armamentarium with unprecedented response observed in several indications including among others metastatic melanoma and Lung cancer. However, the limited rate of response accounting for app. 30% requires further optimization and thus calls the interest in elucidating mechanisms underlying sensitivity to immune checkpoint inhibitors. G Protein-Coupled Receptors (GPCRs) are the largest gene family of cell membrane-associated molecules mediating signal transmission, involved in several physiological functions including the shaping of the immune response but their role in tumor biology and particularly in immune evasion and resistance to immunotherapy remains to be elucidated Methods: Using a preclinical syngeneic mouse model of sarcoma based on the inoculation of murine sarcoma MCA205 cell line, we investigated - besides the evaluation of tumor growth and survival - a large set of GPCRs upon PDL1 or PD1 blockade. Gene expression analysis was performed on tumor samples by mean of RNA sequencing. Data were analyzed using computational methodology including CIBERSORT and GSEA algorithms to evaluate immune cell subset within the tumor and specific gene datasets enrichment respectively. A large set of GPCRs (1412 in total) was then investigated through conventional Differential Gene Expression (DGE) analysis. Results: PDL1/PD1 axis blockade, using specific antibodies, exhibited a strong anti-tumor effect. As highlighted by CIBERSORT analysis, anti-PD1/PDL1 antibodies triggered a CD8 and activated NK cells infiltration within the tumor. The recruitment of such effectory populations was associated with enrichment in genes from different hallmarks datasets including allograft rejection and interferon signaling thus confirming the induction of an efficient anti-tumor immune response. Concomitantly, this study revealed a significant up-regulation of several GPCRs already known to be involved in immune evasion - including Adenosine, Prostaglandins and chemokines receptors - but also highlighted the modulation of unexpected orphan or peptidic receptors. Altogether, this novel dataset confirms the induction of an effective anti-tumor immune response upon PD1 / PDL1 blockade and highlights the modulation of GPCRs that warrants further investigation to delineate their exact participation in sensitivity to immunotherapy. Citation Format: Imane Nafia, Xavier Leroy, Loic Cerf, Jean-Philippe Guegan, Anne-Laure Blayo, Antoine Italiano, Stephan Schann, Alban Bessede. “GPCR-ome” modulation upon PD1 / PDL1 axis blockade [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 934.
Tracking the tail
Authors: Alex Friedlaender, Stephen V Liu, Alfredo Addeo
Journal: Journal for ImmunoTherapy of Cancer (2020)

Immune-checkpoint inhibitors have deeply changed the therapeutic landscape of advanced non-small cell lung cancer without actionable genomic alterations. Immune-checkpoint inhibitors have become standard front-line therapy, especially among patients with tumours expressing high levels of programmed death ligand-1; yet, many patients do not respond to therapy. This has led to the adoption of front-line combination therapies, administering programmed death-1 inhibitors concomitantly either with other checkpoint inhibitors, chemotherapy or both. Today’s approved standard of care includes options with chemoimmunotherapy or dual checkpoint blockade, but each combination has only been compared to chemotherapy alone and no head-to-head trials exist. In cross-trial comparisons, combinations trials appear to show numerically superior responses to single-agent checkpoint inhibitors but the question is whether they ultimately offer a survival advantage. In this manuscript, we summarize and analyse all currently available front-line immune-checkpoint inhibitor trials in non-small cell lung cancer, whether as monotherapy or in combination with chemotherapy, second immunotherapy agents or both. Should standards of care change given the current data? While we ponder this question, we illustrate current data and conclude that the answer lies in tracking the tail of the survival curves.
Abstract 3750: STEAP2 is upregulated and necessary for hepatocellular carcinoma progression via increased copper levels and stress-activated MAP kinase activity
Authors: Carla R. Zeballos, Acarizia Easley, Hakim Bouamar, Guixi Zheng, Xiang Gu, Yang Junhua, Yidong Chen, Francisco Cigarroa, LuZhe Sun
Journal: Cancer Research (2020)

Abstract To understand potential molecular mechanisms that drive hepatocellular carcinoma (HCC) progression, we performed RNA sequencing from paired adjacent non-tumor liver and HCC tumor tissues of nine local HCC patients which revealed significant involvement of a gene coding for Six Transmembrane Epithelial Antigen of Prostate 2 (STEAP2) protein. STEAP2 is a metalloreductase involved in the reduction and indirectly, uptake, of iron and copper ions. We found significantly higher levels of total copper in HCC tissues than those in paired adjacent non-tumor tissues. The upregulation of STEAP2 expression in HCC was confirmed at its protein level and in TCGA and other published HCC gene expression datasets. Hepatic copper overload is associated with Wilson's disease and a known risk factor for HCC, therefore, we hypothesize that STEAP2 upregulation and copper accumulation contribute to HCC progression. Paired HCC and adjacent non-tumor tissues were collected for RNA sequencing, metal ion measurement, and measurements of STEAP2 levels with RT-qPCR and Western blot. Public HCC datasets were queried for STEAP2 expression in HCC and non-tumor tissues. HCC cell lines with knockdown (KD) and overexpression (OE) of STEAP2 were created to perform mechanistic studies including measurements of copper levels and MAP kinase activities, cell proliferation, migration, and anchorage independent growth in vitro and tumor growth in vivo. STEAP2 is significantly upregulated in various HCC gene expression datasets; its expression is positively associated with tumor grade. STEAP2 KD in HCC cell lines decreased cell growth, migration, invasion, and xenograft tumor growth, while STEAP2 OE showed opposite effects. STEAP2 KD in HCC cells also reduced intracellular copper levels and activation of stress-activated MAP kinases including p38 and JNK. Treatment with copper rescued the reduced HCC cell migration due to STEATP2 KD and activated p38 and JNK. Furthermore, treatment with p38 or JNK inhibitors significantly inhibited cell migration. Thus, STEAP2 appears to play a malignant-promoting role in HCC cells by driving migration/invasion via increased copper levels and MAP kinase activities. Our study uncovered a novel molecular mechanism contributing to HCC malignancy and a potential therapeutic target for HCC treatment. Citation Format: Carla R. Zeballos, Acarizia Easley, Hakim Bouamar, Guixi Zheng, Xiang Gu, Yang Junhua, Yidong Chen, Francisco Cigarroa, LuZhe Sun. STEAP2 is upregulated and necessary for hepatocellular carcinoma progression via increased copper levels and stress-activated MAP kinase activity [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 3750.
Abstract 1075: Conditionally active <i>de novo</i> IL-2 cytokine mimetics for targeted immunotherapy: <i>de novo</i> split technology
Authors: Alfredo Quijano-Rubio, Lestat R. Ali, Md A. Bhuiyan, Marc J. Lajoie, Michael Dougan, David Baker, Daniel-Adriano Silva
Journal: Cancer Research (2020)

Abstract IL-2 is a highly potent, pleiomorphic cytokine approved for the treatment of melanoma and renal cell carcinoma. The therapeutic potential of this cytokine has been restricted by dose-limiting toxicities and off-tumor effects associated with systemic IL-2 administration. Scientists have long-pursued the development of targeted IL-2 variants to control biodistribution and improve the therapeutic index, e.g. IL-2-antibody fusions or immunocytokines. However, the potential benefit of targeting IL-2 is limited by the high affinity of the cytokine for its cellular receptor, which dominates biodistribution and results in activation of cells outside the tumor microenvironment. To address this challenge, we took advantage of the remarkable stability of Neoleukin-2/15 (Neo-2/15), a fully de novo cytokine mimetic that potently activates the beta and gamma subunits shared by the IL-2 and IL-15 receptors. We demonstrate that Neo-2/15 can be divided into two pieces that cannot signal individually, but that can recover their binding and cell-signaling potential when co-localized. Fusing the split molecules to independent targeting domains creates a modular and highly specific implementation of conditional activation. We demonstrate that if one split fragment is targeted to one tumor-associated antigen, and the complementary fragment is targeted to a second tumor-associated antigen, the ability to bind the IL-2 receptor and trigger signaling is only restored when these split fragments bind to the surface of cells expressing both targets. The split Neo-2/15 molecules have anti-tumor activity in syngeneic cancer models and have the potential to enhance the therapeutic index of cytokine mimetics in immunotherapy. To our knowledge, these are the first designed examples of strictly conditionally-active, targeted, cytokine-like molecules for immunotherapy. *Current affiliation for D-A.S.: Neoleukin Therapeutics Inc, Seattle, WA, USA. Citation Format: Alfredo Quijano-Rubio, Lestat R. Ali, Md A. Bhuiyan, Marc J. Lajoie, Michael Dougan, David Baker, Daniel-Adriano Silva. Conditionally active de novo IL-2 cytokine mimetics for targeted immunotherapy: de novo split technology [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 1075.
Abstract 6472: Clonal lineage and somatic hypermutation analysis of chronic lymphocytic leukemia by long-amplicon IGH chain sequencing
Authors: Jayde Chang, Zadie Davis, Graeme Quest, Harriet Feilloter, Michelle Toro, Geoffrey Lowman, Loni Pickle, Fiona Hyland, Timothy Looney
Journal: Cancer Research (2020)

Abstract Background: Current next-generation sequencing (NGS) approaches for analyzing SHM commonly rely on multiplex primers targeting the framework 1 (FR1) or leader region of the IGH variable gene in combination with joining gene primers to amplify rearranged IGH chains from gDNA template. Limitations include the potential for joining gene mutations to interfere with primer binding and an inability to evaluate isotype. Here we present a method for translational research investigations of IGH chain SHM employing multiplex FR1 and isotype (constant gene) specific primers (Oncomine IGH-LR assay primers) to amplify IGH chains from RNA template. We evaluated performance by comparing SHM values obtained from NGS of RNA from 54 CLL samples amplified using Oncomine IGH-LR primers to values obtained by Sanger sequencing or NGS of RNA amplified using FR1 or leader region/J gene primers. Methods: IGH chains from 54 CLL samples derived from two separate sequencing sites (Site 1: 24 samples, Site 2: 30 samples) were amplified from peripheral blood using Oncomine IGH-LR assay followed by sequencing via the Ion Gene Studio S5. Clonotyping, clonal lineage identification and somatic hypermutation analysis was performed by Ion Reporter via comparison to the IMGT reference database. Oncomine IGH-LR assay SHM values were compared to those obtained via NGS-based sequencing utilizing FR1/J gene primers (Site 1) or Sanger sequencing utilizing IGH-leader or FR1 and joining gene primers (Site 2). Results: IGHV SHM values were highly concordant between NGS approaches (Spearman cor =.957, Site 1) and between Sanger sequencing and NGS approaches (Spearman cor = .849, Site 2). Sequence data obtained using Oncomine IGH-LR assay enables more in-depth clonal lineage analysis, including evaluation of isotype representation and subclonal evolution. Conclusions: These results support the robustness and reliability of multiplex FR1 and constant gene based IGH chain amplification for the translational research characterization of somatic hypermutation in CLL and other B cell neoplasms. Citation Format: Jayde Chang, Zadie Davis, Graeme Quest, Harriet Feilloter, Michelle Toro, Geoffrey Lowman, Loni Pickle, Fiona Hyland, Timothy Looney. Clonal lineage and somatic hypermutation analysis of chronic lymphocytic leukemia by long-amplicon IGH chain sequencing [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 6472.
Abstract 6332: Pim kinase inhibition promotes mitochondrial fission to combat chemoresistance in non-small cell lung cancer
Authors: Shailender S. Chauhan, Rachel K. Toth, Corbin C. Jensen, David F. Kashatus, Andrea L. Casillas, Noel A. Warfel
Journal: Cancer Research (2020)

Abstract Background: Resistance to chemotherapy represents a major obstacle to the successful treatment of non-small cell lung cancer (NSCLC). A fused mitochondrial network is associated with therapeutic resistance, but the factors controlling mitochondrial dynamics in lung cancer are not fully understood. The goal of this study was to determine how PIM kinases impact mitochondrial dynamics, ROS production, and response to chemotherapy in lung cancer. Methods: Live cell imaging and microscopy were used to determine the effect of PIM on mitochondrial phenotype and ROS. Biochemical studies were performed to characterize the signaling axis linking PIM1 to Drp1 and mitochondrial fission in lung cancer. Xenograft models of lung cancer were used to evaluate the combination of PIM inhibition and chemotherapy. Immunohistochemistry and transmission electron microscopy were used to analyze mitochondrial phenotype, proliferation, and apoptosis in vivo. Results: Inhibition of PIM kinases caused excessive mitochondrial fission and significant upregulation of mitochondrial superoxide, increasing intercellular ROS. PIM inhibition significantly increased the protein levels and mitochondrial localization of Drp1. An inverse correlation between PIM1 and Drp1 was confirmed in NSCLC patient samples. Inhibition of PIM sensitized NSCLC cells to chemotherapy and produced a synergistic anti-tumor response, characterized by significantly increased ROS and apoptosis. Conclusion: PIM kinase expression is an important mechanism of intrinsic and acquired resistance to chemotherapy in NSCLC. PIM inhibition activates Drp1 to promote mitochondrial fission and superoxide production, sensitizing cancer cells to chemotherapy. These data improve our knowledge of how mitochondria are regulated in cancer and provide justification for combining PIM inhibition with chemotherapy in NSCLC. Citation Format: Shailender S. Chauhan, Rachel K. Toth, Corbin C. Jensen, David F. Kashatus, Andrea L. Casillas, Noel A. Warfel. Pim kinase inhibition promotes mitochondrial fission to combat chemoresistance in 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 6332.