tbuckley/cabot-search huggingface dataset:
Anti–IFN-γ autoantibodies underlie disseminated<i>Talaromyces marneffei</i>infections
Authors: Jing Guo, Xin-Qiang Ning, Jing-Ya Ding, Yan-Qing Zheng, Na-Na Shi, Feng-Yao Wu, You-Kun Lin, Han-Po Shih, He-Ting Ting, Gang Liang, Xiang-Chan Lu, Jin-Ling Kong, Ke Wang, Yi-Bo Lu, Yu-Jiao Fu, Rong Hu, Tian-Min Li, Kai-Su Pan, Xiu-Ying Li, Chun-Yang Huang, Yu-Fang Lo, Ian Yi-Feng Chang, Chun-Fu Yeh, Kun-Hua Tu, Yu-Huan Tsai, Cheng-Lung Ku, Cun-Wei Cao
Journal: The Journal of Experimental Medicine (2020)

Talaromyces marneffei causes life-threatening opportunistic infections, mainly in Southeast Asia and South China. T. marneffei mainly infects patients with human immunodeficiency virus (HIV) but also infects individuals without known immunosuppression. Here we investigated the involvement of anti–IFN-γ autoantibodies in severe T. marneffei infections in HIV-negative patients. We enrolled 58 HIV-negative adults with severe T. marneffei infections who were otherwise healthy. We found a high prevalence of neutralizing anti–IFN-γ autoantibodies (94.8%) in this cohort. The presence of anti–IFN-γ autoantibodies was strongly associated with HLA-DRB1*16:02 and -DQB1*05:02 alleles in these patients. We demonstrated that adult-onset acquired immunodeficiency due to autoantibodies against IFN-γ is the major cause of severe T. marneffei infections in HIV-negative patients in regions where this fungus is endemic. The high prevalence of anti–IFN-γ autoantibody–associated HLA class II DRB1*16:02 and DQB1*05:02 alleles may account for severe T. marneffei infections in Southeast Asia. Our findings clarify the pathogenesis of T. marneffei infection and pave the way for developing novel treatments.
The prognostic impact of extracapsular lymph node involvement after neoadjuvant therapy and esophagectomy .
Authors: Sjoerd M Lagarde, Maz Navidi, Jav Sultan, Hanneke W.M. Van Laarhoven, Suzanne S Gisbertz, Sybren L. Meijer, Arul Immanuel, Michael Griffin, Mark I van Berge Henegouwen
Journal: Journal of Clinical Oncology (2015)

4058 Background: In patients with esophageal cancer, little attention has been paid to the biological significance of extracapsular lymph node involvement (LNI) in patients who underwent neoadjuvant treatment followed by esophagectomy. Therefore, the aim of the present study was to assess the incidence, extent of extracapsular LNI and prognostic significance in a consecutive multicenter series of patients with cancer of the esophagus or gastroesophageal junction who underwent neoadjuvant chemo (radio) therapy followed by surgery. Methods: From a prospectively collected database, a consecutive series of patients in two high volume centers in Europe was analyzed. All patients with potentially curable adeno- or squamous cell carcinoma of the oesophagus or gastroesophageal junction were treated with neoadjuvant chemotherapy or chemoradiation therapy followed by transthoracic esophagectomy and two-field lymphadenectomy. Results: Between January 2000 and September 2013 a consecutive series of 707 patients underwent an esophagectomy after neoadjuvant therapy. A mean number of 29 (5-77) nodes were resected and identified. 347 (49%) patients had no evidence of lymph node metastases (N0). There were 360 (51%) with positive nodes. Extracapsular LNI was identified in 197 (27%) patients. Five-year overall survival rates were 63% for N0 patients, 45% for patients with intracapsular LNI and 14% for patients with extracapsular LNI (p < 0.001). On multivariate analyses ypT, ypN and the presence of extracapsular LNI were independent factors. Conclusions: The presence of extracapsular LNI after neoadjuvant chemo(radiation) therapy identifies a subgroup of patients with a significantly worse long-term survival. Extracapsular LNI reflects a particularly aggressive biologic behavior and has significant prognostic potential and should be considered for the future edition of the TNM staging system for esophageal cancer.
Abstract 646: CRISPR/Cas9 screening to identify mechanisms of azacitidine failure in myelodysplastic syndrome
Authors: Michael Schieber, John D. Crispino
Journal: Cancer Research (2020)

Abstract Myelodysplastic syndrome (MDS) is a heterogenous myeloid lineage malignancy characterized by blood cell morphological dysplasia, ineffective clonal hematopoiesis, and risk of secondary transformation to acute myeloid leukemia (sAML). The mainstay of treatment in patients with higher-risk MDS are the hypomethylating agents (HMAs) azacitidine and decitabine, which extend overall survival by approximately 12 to 18 months. Unfortunately, disease relapse and HMA resistance are inevitable and carry a very poor prognosis. Genomic sequencing of large MDS cohorts has led to the identification of recurrent genetic abnormalities in MDS, some of which predict sensitivity to HMA therapy. For example, abnormalities in TET2, but not ASXL1, are associated with a favorable response to the HMAs. However, it is unknown why some patients with otherwise similar clinical features have variable responses to HMA therapy. We hypothesize that there are common cellular mechanisms promoting resistance to HMA therapy and that these can be therapeutically targeted to enhance treatment responses. To uncover cellular processes promoting HMA treatment failure we performed duplicate genome-wide CRISPR/Cas9 screen in the human MDS-L cell line using resistance to azacitidine as a positive selection readout. MDS-L was established from bone marrow mononuclear cells in a 52-year-old male patient with high-risk MDS. We transduced the Brunello sgRNA CRISPR library into Cas9 expressing MDS-L cells and subjected the cells to azacitidine treatment for 7 days. Cells surviving azacitidine treatment were then expanded and harvested for genomic DNA. High throughput sequencing of the barcoded DNA produced raw reads that were analyzed using the PinAPL-Py web-based software. sgRNAs appearing in duplicate with over 10-fold enrichment compared to the control library were considered significant. We identified 125 candidate genes involved in HMA resistance from the CRISPR-Cas9 screen. Pathway analysis revealed a significant enrichment of genes involved in lipid metabolism, DNA methylation, and response to small molecule catabolism. Future experiments to validate these candidates as well as test whether they contribute in vivo to HMA resistance are underway. We conclude genome-wide CRISPR-Cas9 screens for drug-resistance in the MDS-L model are feasible and may uncover future therapeutic targets to augment HMA therapy or utilize upon HMA failure. Citation Format: Michael Schieber, John D. Crispino. CRISPR/Cas9 screening to identify mechanisms of azacitidine failure in myelodysplastic syndrome [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 646.
Abstract 3451: Non-genetic RTK-mediated cetuximab resistance in colorectal cancer offers multiple targets for therapeutic intervention
Authors: Ramona Graves-Deal, Galina Bogatcheva, Vishnu Damalanka, Lidija Klampfer, James W. Janetka, Robert J. Coffey, Bhuminder Singh
Journal: Cancer Research (2020)

Abstract Using 3D type I collagen cultures of human colorectal cancer (CRC) cell line HCA-7 derivatives (CC, SC, CC-CR), we previously identified that activation of receptor tyrosine kinases (RTKs) MET and RON contributed to resistance to anti-EGFR monoclonal antibody, cetuximab. CC cells are sensitive to cetuximab, while SC and CC-CR cells are resistant in 3D. Both de novo and acquired modes of cetuximab resistance in SC and CC-CR, respectively, could be overcome by crizotinib, a multi-RTK inhibitor that also targets MET and RON. In fact, we now show that the cetuximab/crizotinib combination leads to synergistic growth inhibition in both SC and CC-CR. In addition to steady-state upregulation of MET and RON phosphorylation in SC cells, we also observe upregulation of ERBB3 phosphorylation after cetuximab addition, indicating a need for monitoring RTK activity during treatment. We have also identified a set of KRAS wild-type human CRC patient-derived tumor xenografts (PDXs) that show increased MET/RON phosphorylation. As noted previously, addition of the MET ligand (HGF) and ERBB3 ligand (NRG1) induced cetuximab resistance in CC cells and HGF-induced cetuximab resistance was overcome by crizotinib addition. We now show that MET/RON-dependent cetuximab resistance is due to autocrine production of their cognate ligands HGF/HGFL, respectively. For these studies, we employed selective inhibitors of the proteases (HGFA, Matriptase, and Hepsin) that mediate processing and maturation of HGF/HGFL; these inhibitors (ZFH7116 and VD2173) were able to overcome cetuximab resistance in SC and CC-CR cells. Thus, RTK ligand processing is an additional therapeutic target to counter cetuximab resistance in CRC. Citation Format: Ramona Graves-Deal, Galina Bogatcheva, Vishnu Damalanka, Lidija Klampfer, James W. Janetka, Robert J. Coffey, Bhuminder Singh. Non-genetic RTK-mediated cetuximab resistance in colorectal cancer offers multiple targets for therapeutic intervention [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 3451.
Abstract 879: Functional and single-cell assessment of CRISPR-modified CAR-T cells from NSCLC patients and healthy donors
Authors: Zinkal Padalia, Andrew Dunn, Konstantinos Karagiannis, Brigid McEwan, Meghna Kuppuraju, Jason Sagert, Sushant Karnik, Mary-Lee Dequeant, Jonathan Terrett, Demetrios Kalaitzidis
Journal: Cancer Research (2020)

Abstract Cancer patients that have undergone multiple lines of treatment can have dysfunctional immune systems. In both solid tumors and hematological malignancies, T cells have been reported to be in various states of dysfunction including senescence or exhaustion. In order to assess the potency of CAR-T cells derived from cancer patients, we created CAR-T cells targeting CD70 from non-small cell lung cancer (NSCLC) patients as well as healthy donors. Anti-CD70 CAR-T cells were created by using CRISPR/Cas9 to insert the CAR cassette into a knocked-out TRAC locus. The TRAC knock-out eliminates any TCR-mediated effector functions. CAR-T preparations from either NSCLC patients or healthy donors were assessed in vitro for T cell effector functions including cell killing, cytokine secretion and expansion in the presence of lung tumor cells expressing antigen. CAR-T cells from NSCLC patients and healthy donors were also assessed for their ability to control human lung cancer-derived tumors in immunocompromised mice. Following these functional assessments, the heterogeneity of CAR-T preparations derived from different sources was characterized further by performing single-cell RNA sequencing analysis and single-cell protein analysis (CITE-Seq and single cell cytokine secretion). A superior understanding of CAR-T cell heterogeneity and donor variability could aid in producing more efficacious drug products for cancer. Citation Format: Zinkal Padalia, Andrew Dunn, Konstantinos Karagiannis, Brigid McEwan, Meghna Kuppuraju, Jason Sagert, Sushant Karnik, Mary-Lee Dequeant, Jonathan Terrett, Demetrios Kalaitzidis. Functional and single-cell assessment of CRISPR-modified CAR-T cells from NSCLC patients and healthy donors [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 879.
Abstract 2601: Expression and clinicopathological association of RABs in pancreatic cancer
Authors: Shashi Anand, Haseeb Zubair, Mohammad Aslam Khan, Seema Singh, Ajay P. Singh
Journal: Cancer Research (2020)

Abstract Rab proteins form the largest subfamily of small GTPases and play an indispensable role in the regulation of vesicle trafficking. They control a wide variety of endocytic, transcytic and exocytic transport pathways and thus play important roles in cellular growth and behavior. Altered expression and functions of Rab proteins have been reported in various malignancies and implicated in tumorigenic processes. Pancreatic cancer (PC) is a highly lethal malignancy and molecular mechanisms associated with its pathobiology are relatively less understood. Here we mined The Cancer Genome Atlas (TCGA) Database for differential expression and clinicopathological association of RAB genes in pancreatic cancer. Out of the 62 RAB genes analyzed, 5 (RAB3A, RAB26, RAB25, RAB21, and RAB22A) were found to have significant upregulation in cancer, while 5 (RAB6B, RAB8B, RABL2A, RABL2B and RAB32) exhibited significant downregulation. Racially disparate expression was also reported for some RABs. RAB3A and RAB26 had significantly higher and lower expression, respectively, in African American (AA) and Asian PC as compared to Caucasian Americans (CA) PC, whereas RAB25 was significantly higher in Asian PC than CA PC. No clear trend of altered expression was observed with increasing stage and grade, although stage- and grade-specific differences were recorded for some RABs. RAB21, RAB22A, and RAB8B showed significantly higher expression in PC from middle-aged patients (41-60 years) compared to older age groups, but no gender-associated differential expression was observed. PC from occasional drinkers had significantly higher expression of RAB21 compared to daily or weekly drinker, whereas RAB25 expression was significantly higher in social drinkers, compared to occasional ones. Expression of RABL2A was significantly reduced in PC of diabetic patients whereas RAB26 was significantly down in pancreatitis patients. Most importantly, a significant association of high expression of RAB21, RAB22A and RAB25, and low expression of RAB6B, RABL2A, and RABL2B was observed with poorer survival of PC patients. Together, our study is suggestive of potential diagnostic and prognostic significance of RABs in PC and warrants further investigations to define their functional and mechanistic significance. Citation Format: Shashi Anand, Haseeb Zubair, Mohammad Aslam Khan, Seema Singh, Ajay P. Singh. Expression and clinicopathological association of RABs in pancreatic 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 2601.
Abstract 3369: Rapid screening of novel OX40 agonistic antibodies for cancer immunotherapy
Authors: Yuelei Shen, Zhihong Li, Yi Yang, Yunyun Chen, Yu Zhu
Journal: Cancer Research (2020)

Abstract OX40, also known as TNFRSF4 or CD134, is a member of the tumor necrosis factor receptor superfamily and is an important co-stimulator of T cell responses. OX40L expressed at high levels on activated antigen presenting cells (APCs) can result in higher order multimerization of OX40 receptors, leading to stronger activation in T cells. OX40 plays an important role in memory T cell formation. The highest levels of OX40 are found on effector and central memory CD4+ T cells and regulatory T cells (Treg). Given the duality of OX40 agonism in both stimulating effector T cell activity and suppressing Treg activity, OX40 agonists have been widely explored in the setting of cancer immunotherapy. We hoped to develop novel OX40 agonists that can effectively inhibit tumor growth. YH002 is a recombinant, humanized IgG1 monoclonal antibody that specifically targets OX40. In vitro studies demonstrated that YH002 bound specifically and potently to human and monkey OX40 proteins. YH002 was able to dose-dependently potentiate the activation of human OX40 on reporter cells in the presence of FcγRIIB-expressing accessory cells. YH002 mediated ADCC activity in vitro. YH002 demonstrated robust anti-tumor efficacy with a bell-shaped dose response relationship against established MC38 syngeneic tumors in human OX40 transgenic mice (B-hOX40 mice) and Treg depletion were noted in tumor-infiltrating lymphocyte analysis using the same murine model. In conclusion, YH002 enhances anti-tumor activities by stimulating effector T cells and overcoming immune suppressions via suppressing or depleting regulatory T cells. Furthermore, we showed that YH002 works in concert with Pembrolizumab in double humanized model of h-OX40 and h-PD1. The combination of YH002 and ipilimumab is synergistic in double humanized model of h-OX40 and h-CTLA4. In the GLP-compliant single-dose toxicology study, the MTD of a single i.v. dose of YH002 in cynomolgus monkeys was considered to be 200 mg/kg/day. Repeated i.v. infusions of YH002 to male and female cynomolgus monkeys at 10, 30, or 90 mg/kg for 29 days (QW×5) were tolerated, the HNSTD was considered to be 90 mg/kg. Citation Format: Yuelei Shen, Zhihong Li, Yi Yang, Yunyun Chen, Yu Zhu. Rapid screening of novel OX40 agonistic antibodies for cancer immunotherapy [abstract]. In: Proceedings of the Annual Meeting of the American Association for Cancer Research 2020; 2020 Apr 27-28 and Jun 22-24. Philadelphia (PA): AACR; Cancer Res 2020;80(16 Suppl):Abstract nr 3369.
Abstract 4989: Introduction of a robust workflow for the whole-side acquisition and co-registration of multiplex immunofluorescence tissue images for analysis of a 9-color, 8-marker immunophenotyping assay
Authors: Anne E. Hellebust, Kyla Teplitz, Katir K. Patel, Karan Sharma, Amanda Bares, Mael Manesse, Mark Burton, Bonnie Phillips, Sean Downing, Kate Lillard
Journal: Cancer Research (2020)

Abstract Background: Profiling multiple cell types in tissue samples requires more markers than can be supported by conventional approaches to immunohistochemistry. InSituPlex® multiplex immunofluorescence (mIF) technology enables biomarker multiplexing in tissue samples with an automated workflow to support discovery of immune cell signatures in the tumor immune microenvironment (TiME). Here we have designed and tested an 8-plex immunophenotyping panel using the InSituPlex approach to detect and classify T cells, macrophages, and tumor cells in non-small cell lung cancer (NSCLC) and colorectal cancer (CRC) FFPE tissue. Methods: An 8-plex UltiMapper™ immunofluorescence was developed to stain FFPE tissue, including colorectal cancer, human tonsil, and non-small cell lung cancer. Each sample was stained for the following 8 markers: CD3, CD4, CD8, CD68, FoxP3, PD-1, PD-L1, and pan-CK. Whole-slide imaging was performed in two imaging rounds on the RareCyte CyteFinder II HT slide scanner, and same-slide image alignment and phenotypic analysis was performed using the HALO Highplex FL module from Indica Labs. Results: Co-registration of two 4-plex imaging rounds and fusing into a single image file allowed for the seamless cell phenotyping of markers across imaging rounds. The 8-plex assay and workflow is compatible across multiple tumor sample types. The samples were characterized based on binned expression and co-expression of biomarkers. The following major cell phenotypes were detected: PD-L1 checkpoint expression, T cells (CD3+), cytotoxic T cells (CD3+/CD8+), T-helper cells (CD3+/CD4+), regulatory T-cells (CD3+/CD4+/FoxP3+), exhausted T cells (CD3+/PD-1+), macrophages (CD68+), and tumor cells (pan-CK+). Conclusions: The 8-plex assay workflow involving InSituPlex mIF, CyteFinder HT scanner, and HALO analysis supports the ability to measure biomarkers in situ in streamlined and scalable approach. Citation Format: Anne E. Hellebust, Kyla Teplitz, Katir K. Patel, Karan Sharma, Amanda Bares, Mael Manesse, Mark Burton, Bonnie Phillips, Sean Downing, Kate Lillard. Introduction of a robust workflow for the whole-side acquisition and co-registration of multiplex immunofluorescence tissue images for analysis of a 9-color, 8-marker immunophenotyping assay [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 4989.
Abstract 3615: Profiling of BRCA1 &amp; BRCA2 mutations in Egyptian colorectal cancer patients via next generation sequencing
Authors: Amira Salah El-Din Youssef, Ahmed Osama Touny, Zeinab K. Hassan, Mohammed Mohey Eldin, Mai M. Lotfy, Auhood Nassar, Mohamed El-Hadidi, Ali Kishk, ola sayed, Abdel-Rahman N. Zekri
Journal: Cancer Research (2020)

Abstract Aim: This study aimed to sequence BRCA1 &amp; BRCA2 genes to identify the frequency of the detected genetic mutations in the disease progression of colorectal cancer (CRC) and to estimate colorectal cancer risks in those BRCA mutation carriers. Material and methods: 140 biopsy samples were collected from Egyptian patients categorized into inflammatory bowel disease (IBD) (n=20), colonic polyp (CP) (n=38) and CRC (n=62) patients as well as subjects with chronic colitis served as a control group (n=20). The libraries were performed using Qiaseq UMI-based targeted panel and sequenced via Ion proton sequencer. The detected genetic variants at 500x were annotated against Cosmic, dbSNP, exac all, Polyphen2, Sift and Clinvar databases. Results: Analysis revealed that BRCA1 gene harbored 26, 19, 8 and 11 variants in the CRC, CP, IBD and control groups; respectively. Exon 10 was the most affected exon harbored 7 pathogenic variants in the CRC group. Two out of 7 were the most frequently detected common pathogenic variants associated with disease progression from colitis to CRC (c.1961delA (11%) &amp; c.3214delC (16%). Moreover, 3 common begnin SNP variants were found to be related to ethnicity (c.3548A&amp;gt;G (58%), c.2612C&amp;gt;T (60%), c.4900A&amp;gt;G (69%). Moreover, BRCA2 gene harbored 48, 29, 24 and 18 variants in the CRC, CP, IBD and control groups respectively. Exon 2, 11, 23 were the most affected exons harbored 12 pathogenic variants in the CRC group. Four out of 12 were the most frequently detected common pathogenic variants associated with disease progression from colitis to CRC (c.3860delA (8%), c.5351delA (18%), c.9097delA (24%) &amp; c.36delT (34%). Conclusion: Our data showed that BRCA1 &amp; BRCA2 genes analyzed by Next-Generation Sequencing (NGS) identifies large number of pathogenic and begnin variants that are crucial for understanding CRC predisposition and early detection. Also, developing personalized therapies that efficiently target the individual CRC-specific mutations. Key words: Egyptian Colorectal cancer, BRCA1, BRCA2, pathogenic, begnin, Next Generation Sequencing Citation Format: Amira Salah El-Din Youssef, Ahmed Osama Touny, Zeinab K. Hassan, Mohammed Mohey Eldin, Mai M. Lotfy, Auhood Nassar, Mohamed El-Hadidi, Ali Kishk, ola sayed, Abdel-Rahman N. Zekri. Profiling of BRCA1 &amp; BRCA2 mutations in Egyptian colorectal cancer patients via next generation 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 3615.