tbuckley/cabot-search huggingface dataset:
Abstract 2750: Prognostic impact of tumor infiltrating lymphocytes in the tumor microenvironment of vulvar squamous cell carcinoma
Authors: Maximilian Lennartz, Niclas Christian Blessin, Ann-Christin Rolschewski, Ronald Simon, Guido Sauter, Ria Uhlig, Linn Wölber, Sven Mahner, Nikolaus de Gregorio, Rüdiger Klapdor, Matthias Kalder, Stefan Steurer, Waldemar Wilczak, Eike Burandt, Simon Kind
Journal: Cancer Research (2021)

Abstract The amount of tumor infiltrating lymphocytes (TILs) is an established prognostic feature in the cancer microenvironment of colorectal and breast cancers, but data are less clear for most other solid cancer types. To study the prognostic impact of TILs in vulvar squamous cell carcinomas, a cohort of 530 cancers was analyzed by immunohistochemistry for CD3 and CD8 positive cells (CD3+, CD8+). Automated digital image analysis was used to quantitate the densities of CD3+, and CD8+ TILs in the invasive margin and the tumor center. The average immune cell density was significantly higher in the invasive margin (CD3+: 1772±1105, CD8+: 769±644 cells/mm2) as compared to the center of the tumor (CD3+: 518±570, CD8+: 301±445 cells/mm2, p≤0.0001 each). Comparison with clinic-pathological data revealed a significant prognostic impact of CD3+ but not of CD8+ cell density and a stronger link with tumor phenotype and outcome for TILs at the invasive tumor margin as compared to the tumor center. Elevated densities of CD3+ cells within the invasive margin were significantly associated with a favorable pT stage (p=0.0012) and a prolonged overall (p=0.0025) and progression free survival (p=0.0231). A high CD3+ cell density in the tumor center was linked to overall (p=0.0457) and progression free survival (p=0.0266). Unsupervised clustering of CD3+/CD8+ cell densities identified 3 major subsets corresponding to the immune desert (sparse TILs at invasive margin and tumor center), immune excluded (high TIL numbers at invasive margin but low TIL counts in the tumor center), and immune inflamed phenotypes (high TIL numbers at invasive margins and tumor center). Survival analysis revealed a particularly poor prognosis for the immune desert phenotype for overall (p=0.0071) and progression free survival (p=0.0027). In summary, our data suggest a clinical utility of TIL quantification in vulva squamous cell cancer. Citation Format: Maximilian Lennartz, Niclas Christian Blessin, Ann-Christin Rolschewski, Ronald Simon, Guido Sauter, Ria Uhlig, Linn Wölber, Sven Mahner, Nikolaus de Gregorio, Rüdiger Klapdor, Matthias Kalder, Stefan Steurer, Waldemar Wilczak, Eike Burandt, Simon Kind. Prognostic impact of tumor infiltrating lymphocytes in the tumor microenvironment of vulvar squamous cell carcinoma [abstract]. In: Proceedings of the American Association for Cancer Research Annual Meeting 2021; 2021 Apr 10-15 and May 17-21. Philadelphia (PA): AACR; Cancer Res 2021;81(13_Suppl):Abstract nr 2750.
Abstract LB072: SARS-CoV-2 proteins and anti-COVID-19 drugs induce lytic reactivation of an oncogenic virus
Authors: Zhiqiang Qin, Jungang Chen, Lu Dai, Lindsey Barrett, Steven Post
Journal: Cancer Research (2021)

Abstract An outbreak of the novel coronavirus SARS-CoV-2, the causative agent of Coronavirus Disease-2019 (COVID-19), a respiratory disease, has infected over 75,000,000 people since the end of 2019, killed over 1,600,000, and caused worldwide social and economic disruption. Because the mechanisms of SARS-CoV-2 infection of host cells and its pathogenesis remain largely unclear, there are currently no antiviral drugs with proven efficacy. Besides severe respiratory and systematic symptoms, several comorbidities increase risk of fatal disease outcome. Therefore, it is required to investigate the impacts of COVID-19 on pre-existing diseases of patients, such as cancer and other infectious diseases. Kaposi's sarcoma-associated herpesvirus (KSHV) is the etiologic agent of several human cancers, such as Kaposi's sarcoma (KS) and Primary effusion lymphoma (PEL), mostly seen in immunosuppressed patients especially people with HIV infection. In the current study, we for the first time report that SARS-CoV-2 encoded spike (S) and nucleocapsid (N) proteins and some currently used anti-COVID-19 drugs (especially Azithromycin and Nafamostat mesylate) are able to induce lytic reactivation of KSHV from virus infected normal and tumor cells, through manipulation of intracellular signaling pathways. In addition, we found the obvious upregulation of ACE2 expression, the major receptor of SARS-CoV-2, in AIDS-KS tissues, indicating that KSHV may potentially increase SARS-CoV-2 co-infection. Together, our data indicate that those KSHV+ patients especially in endemic areas exposure to COVID-19 or undergoing the treatment may have increased risks to develop these virus-associated cancers, even after they have fully recovered from COVID-19. Citation Format: Zhiqiang Qin, Jungang Chen, Lu Dai, Lindsey Barrett, Steven Post. SARS-CoV-2 proteins and anti-COVID-19 drugs induce lytic reactivation of an oncogenic virus [abstract]. In: Proceedings of the American Association for Cancer Research Annual Meeting 2021; 2021 Apr 10-15 and May 17-21. Philadelphia (PA): AACR; Cancer Res 2021;81(13_Suppl):Abstract nr LB072.
Abstract 2216: Exploration of the genomic features of pan-neuroendocrine tumors in a Chinese retrospective analysis
Authors: Jinyan Ye, Weiran Wang, Danhua Wang, Tonghui Ma
Journal: Cancer Research (2021)

Abstract Background: A neuroendocrine tumor (NET) begins in the specialized cells of the body's neuroendocrine system. Most NETs take years to develop and grow slowly. However, some NETs can be fast-growing. NETs can occur in any part of the body, including gastrointestinal (GI) tract (43%), lung (30%), pancreas (7%) and other organs. Here, we reported an analysis of genomic features in 16 GI tract, 45 lung and 13 pancreas NETs. Methods: Patients (pts) with neuroendocrine tumors were enrolled, and surgical tumor tissues or plasma samples were collected. Mutation profiling was performed by next-generation sequencing (NGS). Results: Compared with GI tract NETs patients (Age±SD, 52±11.2), lung NETs patients (Age±SD 62±8.4, P&amp;lt; 0.001) occurred in older patients, and the median age (±SD) of pancreas NETs patients was 58 (±10.8). Mutations were identified in 66 of NETs patients (89.19%), including 12 GI tract (75%), 43 lung (95.56%) and 11 pancreas (84.62%) NETs. Mutations of TP53 (43.85%, 7/16), APC (31.25%, 5/16) and KRAS (25%, 4/16) in GI tract NETs; TP53 (80%, 36/45), LRP1B (24.44%, 11/45) and EGFR (20%, 9/36) in lung NETs and MEN1 (30.77%4/13) in pancreas NETs were observed as the most commonly genetic variations in different type of NETs, which located in different signal pathways and suggested different pathogenesis. Meanwhile, there was no MEN1 mutations and only one LRP1B or EGFR mutation (6.25%, 1/16) occurring in GI tract NETs, one MEN1 mutation (2.22%, 1/44) occurring in lung NETs, and one TP53, KRAS or LRP1B mutation (7.69%, 1/12) and no APC or EGFR mutations occurring in pancreas NETs. In total, although gastrointestinal tract, lung and pancreas NETs all begin in the cells, which have traits of both hormone-producing endocrine cells and nerve cells, the mutation spectrums are very different. On the contrary, the mutations carried by NETs in different locations are related to the organ. Conclusions: In summary, genomic characterization of NETs may offer insights into tumorigenesis and identify potential therapeutic targets in this disease. Citation Format: Jinyan Ye, Weiran Wang, Danhua Wang, Tonghui Ma. Exploration of the genomic features of pan-neuroendocrine tumors in a Chinese retrospective analysis [abstract]. In: Proceedings of the American Association for Cancer Research Annual Meeting 2021; 2021 Apr 10-15 and May 17-21. Philadelphia (PA): AACR; Cancer Res 2021;81(13_Suppl):Abstract nr 2216.
Quality-adjusted Time Without Symptoms of disease or Toxicity (Q-TWiST) analysis of CPX-351 versus 7 + 3 in older adults with newly diagnosed high-risk/secondary AML
Authors: Jorge E. Cortes, Tara L. Lin, Geoffrey L. Uy, Robert J. Ryan, Stefan Faderl, Jeffrey E. Lancet
Journal: Journal of Hematology & Oncology (2021)

CPX-351 (United States: Vyxeos®; Europe: Vyxeos® Liposomal), a dual-drug liposomal encapsulation of daunorubicin and cytarabine in a synergistic 1:5 molar ratio, is approved by the US FDA and the EMA for the treatment of adults with newly diagnosed therapy-related acute myeloid leukemia or acute myeloid leukemia with myelodysplasia-related changes. In a pivotal phase 3 study that evaluated 309 patients aged 60 to 75 years with newly diagnosed high-risk/secondary acute myeloid leukemia, CPX-351 significantly improved median overall survival versus conventional 7 + 3 chemotherapy (cytarabine continuous infusion for 7 days plus daunorubicin for 3 days), with a comparable safety profile. A Quality-adjusted Time Without Symptoms of disease or Toxicity (Q-TWiST) analysis of the phase 3 study was performed to compare survival quality between patients receiving CPX-351 versus conventional 7 + 3 after 5 years of follow-up. Patients were randomized 1:1 between December 20, 2012 and November 11, 2014 to receive induction with CPX-351 or 7 + 3. Survival time for each patient was partitioned into 3 health states: TOX (time with any grade 3 or 4 toxicity or prior to remission), TWiST (time in remission without relapse or grade 3 or 4 toxicity), and REL (time after relapse). Within each treatment arm, Q-TWiST was calculated by adding the mean time spent in each health state weighted by its respective quality-of-life, represented by health utility. The relative Q-TWiST gain, calculated as the difference in Q-TWiST between treatment arms divided by the mean survival of the 7 + 3 control arm, was determined in order to evaluate results in the context of other Q-TWiST analyses. The relative Q-TWiST gain with CPX-351 versus 7 + 3 was 53.6% in the base case scenario and 39.8% among responding patients. Across various sensitivity analyses, the relative Q-TWiST gains for CPX-351 ranged from 48.0 to 57.6%, remaining well above the standard clinically important difference threshold of 15% for oncology. This post hoc analysis demonstrates that CPX-351 improved quality-adjusted survival, further supporting the clinical benefit in patients with newly diagnosed high-risk/secondary acute myeloid leukemia. Trial registration This trial was registered on September 28, 2012 at www.clinicaltrials.gov as NCT01696084 ( https://clinicaltrials.gov/ct2/show/NCT01696084 ) and is complete.
Revealing the full biosphere structure and versatile metabolic functions in the deepest ocean sediment of the Challenger Deep
Authors: Ping Chen, Hui Zhou, Yanyan Huang, Zhe Xie, Mengjie Zhang, Yuli Wei, Jia Li, Yuewei Ma, Min Luo, Wenmian Ding, Junwei Cao, Tao Jiang, Peng Nan, Jiasong Fang, Xuan Li
Journal: Genome biology (2021)

Abstract Background The full biosphere structure and functional exploration of the microbial communities of the Challenger Deep of the Mariana Trench, the deepest known hadal zone on Earth, lag far behind that of other marine realms. Results We adopt a deep metagenomics approach to investigate the microbiome in the sediment of Challenger Deep, Mariana Trench. We construct 178 metagenome-assembled genomes (MAGs) representing 26 phyla, 16 of which are reported from hadal sediment for the first time. Based on the MAGs, we find the microbial community functions are marked by enrichment and prevalence of mixotrophy and facultative anaerobic metabolism. The microeukaryotic community is found to be dominated by six fungal groups that are characterized for the first time in hadal sediment to possess the assimilatory and dissimilatory nitrate/sulfate reduction, and hydrogen sulfide oxidation pathways. By metaviromic analysis, we reveal novel hadal Caudovirales clades, distinctive virus-host interactions, and specialized auxiliary metabolic genes for modulating hosts’ nitrogen/sulfur metabolism. The hadal microbiome is further investigated by large-scale cultivation that cataloged 1070 bacterial and 19 fungal isolates from the Challenger Deep sediment, many of which are found to be new species specialized in the hadal habitat. Conclusion Our hadal MAGs and isolates increase the diversity of the Challenger Deep sediment microbial genomes and isolates present in the public. The deep metagenomics approach fills the knowledge gaps in structure and diversity of the hadal microbiome, and provides novel insight into the ecology and metabolism of eukaryotic and viral components in the deepest biosphere on earth.
Multimarker profiling identifies protective and harmful immune processes in heart failure: findings from BIOSTAT-CHF
Authors: George Markousis-Mavrogenis, Jasper Tromp, Wouter Ouwerkerk, João Pedro Ferreira, Stefan D Anker, John G Cleland, Kenneth Dickstein, Gerasimos Filippatos, Chim C Lang, Marco Metra, Nilesh J Samani, Rudolf A de Boer, Dirk J van Veldhuisen, Adriaan A Voors, Peter van der Meer
Journal: Cardiovascular Research (2021)

Abstract Aims The exploration of novel immunomodulatory interventions to improve outcome in heart failure (HF) is hampered by the complexity/redundancies of inflammatory pathways, which remain poorly understood. We thus aimed to investigate the associations between the activation of diverse immune processes and outcomes in patients with HF. Methods and results We measured 355 biomarkers in 2022 patients with worsening HF and an independent validation cohort (n = 1691) (BIOSTAT-CHF index and validation cohorts), and classified them according to their functions into biological processes based on the gene ontology classification. Principal component analyses were used to extract weighted scores per process. We investigated the association of these processes with all-cause mortality at 2-year follow-up. The contribution of each biomarker to the weighted score(s) of the processes was used to identify potential therapeutic targets. Mean age was 69 (±12.0) years and 537 (27%) patients were women. We identified 64 unique overrepresented immune-related processes representing 188 of 355 biomarkers. Of these processes, 19 were associated with all-cause mortality (10 positively and 9 negatively). Increased activation of ‘T-cell costimulation’ and ‘response to interferon-gamma/positive regulation of interferon-gamma production’ showed the most consistent positive and negative associations with all-cause mortality, respectively, after external validation. Within T-cell costimulation, inducible costimulator ligand, CD28, CD70, and tumour necrosis factor superfamily member-14 were identified as potential therapeutic targets. Conclusions We demonstrate the divergent protective and harmful effects of different immune processes in HF and suggest novel therapeutic targets. These findings constitute a rich knowledge base for informing future studies of inflammation in HF.
Abstract 443: Bintrafusp alfa enhances the antitumor efficacy of anti-VEGF and VEGF receptor kinase inhibitors in preclinical solid tumor models
Authors: Tsz-Lun Yeung, Adam Lazorchak, Huakui Yu, Jin Qi, Guozhong Qin, Bo Marelli, Kai Fu, Yan Lan
Journal: Cancer Research (2021)

Abstract The targeting of pathways that regulate tumor angiogenesis is an effective strategy for the treatment of solid tumors. Transforming growth factor (TGF)-β and vascular endothelial growth factor (VEGF) are master regulators of tumor angiogenesis that limit the efficacy of cancer therapies and suppress the anti-tumor immune response. Combination therapies consisting of immune checkpoint inhibitors and tumor angiogenesis inhibitors are emerging as effective treatments for solid cancers. Bintrafusp alfa (M7824) is a bifunctional fusion protein composed of the extracellular domain of the TGF-βRII receptor (a TGF-β “trap”) fused to a human IgG1 antibody blocking PD-L1. Here, we tested the antitumor efficacy of a combination therapy consisting of bintrafusp alfa plus a VEGF receptor kinase inhibitor (pazopanib, lenvatinib, regorafenib, axitinib, or nintedanib), or a VEGF neutralizing antibody (B20) in multiple preclinical tumor models. The combination of bintrafusp alfa with lenvatinib, regorafenib, axitinib, or nintedanib showed significantly greater antitumor efficacy than the respective monotherapies in the CT26 mouse syngeneic colon carcinoma model. In the 4T1 mouse breast carcinoma model, the combination of bintrafusp alfa with anti-VEGF, lenvatinib, or regorafenib was significantly more efficacious than the respective monotherapies. Additionally, the combination of bintrafusp alfa with pazopanib also showed superior antitumor efficacy in an orthotopic Renca mouse tumor model. These data indicate that bintrafusp alfa may be a viable combination partner with multiple angiogenesis inhibitors and provide a rational for the continued development of these combination therapies to treat solid cancers. Citation Format: Tsz-Lun Yeung, Adam Lazorchak, Huakui Yu, Jin Qi, Guozhong Qin, Bo Marelli, Kai Fu, Yan Lan. Bintrafusp alfa enhances the antitumor efficacy of anti-VEGF and VEGF receptor kinase inhibitors in preclinical solid tumor models [abstract]. In: Proceedings of the American Association for Cancer Research Annual Meeting 2021; 2021 Apr 10-15 and May 17-21. Philadelphia (PA): AACR; Cancer Res 2021;81(13_Suppl):Abstract nr 443.
Patient-reported experience of diagnosis, management, and burden of renal cell carcinomas: Results from a global patient survey in 41 countries
Authors: R. Giles, D. Maskens, R. Martinez, K. Kastrati, C. Castro, J.C. Julián Mauro, R. Bick, M. Packer, D.Y.C. Heng, J. Larkin, A. Bex, E. Jonasch, S.J. Maclennan, M.A.S. Jewett
Journal: European Urology (2021)
Abstract 1833: Development of anti-CLDN18.2-anti-CD3 bispecific antibody as cancer therapeutics
Authors: Haishan Lin, Huey Li, Hunter Drobenaire, Veronica Pizzarella, Richard Zhang
Journal: Cancer Research (2021)

Abstract Claudin-18 (CLDN18) is a member of the large Claudin family of four-span transmembrane proteins, which are essential components of the mammalian tight junctions (TJs) in the epithelial cells. Claudin-18 has two splice variants, CLDN18.1 and CLDN18.2. While CLDN18.1 is specifically expressed in the lung tissue, CLDN18.2 expression in normal tissue is more restricted and is only detected in small patches of stomach mucosal. CLDN18.2 expression is elevated in many types of epithelial cancers including stomach, esophagus, pancreatic and ovarian cancers. Anti-CLDN18.2 monoclonal antibody Claudiximab (IMAB362) demonstrated promising results in clinical trials for gastric cancers. Using a combination of DNA, protein, and transfected cells as immunogens, we have generated a panel of mouse monoclonal antibodies which are highly specific for CLDN18.2 but do not cross-react to CLDN18.1. The lead antibody E9 had higher binding affinity for CLDN18.2, compared to the IMAB362. The humanized anti-CLDN18.2 antibody showed a strong antibody dependent cytotoxicity (ADCC) activity against Mia PaCa-2 cells overexpressing CLDN18.2. To redirect T-cell-mediated lysis toward CLDN18.2-overexpressed tumor cells, we generated an anti-CLDN18.2/anti-CD3 bispecific antibody. We demonstrated that the bispecific antibody binds to both human T cells and CLDN18.2-expressing tumor cells. Furthermore, the anti-CLDN18.2/anti-CD3 bispecific antibody had robust activity in killing Mia PaCa-2 cells overexpressing CLDN18.2 in the in vitro T cell-dependent cellular cytotoxicity (TDCC) assay. In addition, the bispecific antibody retained the in vitro ADCC activity against Mia PaCa-2 cells overexpressing CLDN18.2. Taken together, our data suggest that the anti-CLDN18.2/anti-CD3 bispecific antibody is a promising cancer therapeutic candidate utilizing multiple anti-tumor mechanisms of action, including ADCC and TDCC. Citation Format: Haishan Lin, Huey Li, Hunter Drobenaire, Veronica Pizzarella, Richard Zhang. Development of anti-CLDN18.2-anti-CD3 bispecific antibody as cancer therapeutics [abstract]. In: Proceedings of the American Association for Cancer Research Annual Meeting 2021; 2021 Apr 10-15 and May 17-21. Philadelphia (PA): AACR; Cancer Res 2021;81(13_Suppl):Abstract nr 1833.
Identification of neoantigen-reactive T lymphocytes in the peripheral blood of a patient with glioblastoma
Authors: Vid Leko, Gal Cafri, Rami Yossef, Biman Paria, Victoria Hill, Devikala Gurusamy, Zhili Zheng, Jared J Gartner, Todd D Prickett, Stephanie L Goff, Paul Robbins, Yong-Chen Lu, Steven A Rosenberg
Journal: Journal for ImmunoTherapy of Cancer (2021)

The adoptive transfer of naturally occurring T cells that recognize cancer neoantigens has led to durable tumor regressions in select patients with cancer. However, it remains unknown whether such T cells can be isolated from and used to treat patients with glioblastoma, a cancer that is refractory to currently available therapies. To answer this question, we stimulated patient blood-derived memory T cells in vitro using peptides and minigenes that represented point mutations unique to patients' tumors (ie, candidate neoantigens) and then tested their ability to specifically recognize these mutations. In a cohort of five patients with glioblastoma, we found that circulating CD4+ memory T cells from one patient recognized a cancer neoantigen harboring a mutation in the EED gene (EEDH189N) that was unique to that patient's tumor. This finding suggests that neoantigen-reactive T cells could indeed be isolated from patients with glioblastoma, thereby providing a rationale for further efforts to develop neoantigen-directed adoptive T cell therapy for this disease.