tbuckley/cabot-search huggingface dataset:
Topical dapsone for folliculitis decalvans: A retrospective cohort study
Authors: Ana Melián-Olivera, Patricia Burgos-Blasco, Gerald Selda-Enríquez, Ana Suárez-Valle, Laura Miguel-Gómez, Sergio Vañó-Galván, David Saceda-Corralo
Journal: Journal of the American Academy of Dermatology (2021)
Abstract 1459: PTP4A3 phosphatase is a novel drug target for epithelial ovarian cancer
Authors: John Robert Cornelison, Ettore J. Rastelli, Duncan J. Hart, Anna J. Mendelson, Elizabeth R. Sharlow, Peter Wipf, John S. Lazo
Journal: Cancer Research (2021)

Abstract High grade serous ovarian cancer (HGSOC) is the deadliest epithelial ovarian cancer (EOC) variant, with a bleak outcome that kills &amp;gt;14,000 women annually in the US. In past four decades, first line therapies have changed only modestly. While dramatic advances in targeted- and immune-based therapies have been seen in some solid tumors, they have not been reported in patients with HGSOC. Recurrent and chemoresistant HGSOC is common. Therefore, it is imperative that new HGSOC drug targets be interrogated. The Protein Tyrosine Phosphatases of Regenerating Liver (PRL or PTP4A) family is significantly upregulated in a variety of tumors, including HGSOC. A bioinformatic analysis of the ovarian cancer using the KMplot Survival Database revealed that high PTP4A3 expression was associated with poor survival in EOC (p&amp;lt;0.0001, hazard ratio (HR)=1.35). In HGSOC early stage disease, PTP4A3 expression levels were also correlated with survival (stage I/II- p=0.0013, HR=3.2), with low expressing patients surviving twice as long as high expressing patients (upper quartile survival in low expression cohort = 81.2 months compared to high expression cohort = 44.3 months). This survival difference appeared independent of myc amplification and was more pronounced in advanced disease (stage III/IV). qPCR profiling of established HGSOC cell lines, including Kuramochi, COV362 and OVCAR4, showed 5-20 fold increases in PTP4A3 gene expression versus nonmalignant control cells. A potent, specific, allosteric small molecule inhibitor of PTP4A3, KVX-053, markedly reduced the growth and survival of chemoresistant and chemosensitive EOC cell lines independent of their BRCA or p53 status. Moreover, treatment of the HGSOC OVCAR4 cell line with KVX-053 (1 μM) inhibited the oncogenic Janus kinase-signal transducer and activator of transcription (JAK-STAT) signaling pathway through loss of phosphorylation of STAT3. Evaluation of a series of next-generation KVX-053-based analogs including chemodegraders yielded chemotypes with enhanced cytotoxic effects. These results demonstrate a clear path for the development of the PTP4A family of tyrosine phosphatases as a novel therapeutic target in a HGSOC. Citation Format: John Robert Cornelison, Ettore J. Rastelli, Duncan J. Hart, Anna J. Mendelson, Elizabeth R. Sharlow, Peter Wipf, John S. Lazo. PTP4A3 phosphatase is a novel drug target for epithelial ovarian cancer [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 1459.
Abstract 2963: A novel uterine leiomyosarcoma mouse model
Authors: Chun Wai Ng, Kwong-Kwok Wong
Journal: Cancer Research (2021)

Abstract leiomyosarcoma is an extremely rare but clinically aggressive uterine cancer arising from the smooth muscle of the uterus. Each year, it is estimated to occur in 6 out of every 1,000,000 women in the United States. The average age at diagnosis is 51 and women with uterine leiomyosarcomas have a poor prognosis. Current therapies for uterine leiomyosarcoma are not very effective and the primary treatment of uterine leiomyosarcoma is surgery. Due to the intrinsic rarity of this disease, prospective randomized clinical trials examining the outcome in individuals with uterine leiomyosarcoma is limited. Moreover, a poor understanding of the pathogenesis of this disease is also a major knowledge gap to develop effective treatment strategies. Thus, a preclinical uterine leiomyosarcoma models that recapitulate the human disease is desperately needed to support clinical trial readiness. Since both p53 mutations and Pten homozygous deletion have been observed in 61% and 64% human uterine leiomyosarcomas respectively [3], we are generating genetic mouse models with Amhr2-Cre Ptenfl/fl p53R245Wfl/fl (homozygous p53 mutation), Amhr2-Cre Ptenfl/fl p53R245Wfl/+ (heterozgyous p53 mutation) and Amhr2-Cre Ptenfl/fl (control) genotypes. Our unpublished preliminary data showed that mouse with homozygous p53 mutation and homozygous deletion of Pten developed metastatic uterine leiomyosarcoma at 24 weeks of age with 100% penetrance. However, mouse with heterozygous p53 mutation and homozygous deletion of Pten did not develop uterine leiomyosarcoma at the age of 24 weeks. From the public available human uterine leiomyosarcoma RNAseq data, 80% of those tumors with p53 mutations had homozygous mutations. Previous mouse model with homozygous deletion of p53 gene and/or BRCA1 with Amhr2-Cre only had uterine leiomyosarcoma developed in approximately 50% of mice around 13 months without metastasis. RNAseq and RPPA functional data of the uterine leiomyosarcomas from our novel mouse models are being generated for comparison with known genomic profiles of human uterine leiomyosarcomas. The RNAseq and RPPA functional proteomic data from comparing uterine tissues from homozygous and heterozygous p53 mutated mice provide insight in the understanding the development of uterine leiomyosarcoma and for future clinical trials. Citation Format: Chun Wai Ng, Kwong-Kwok Wong. A novel uterine leiomyosarcoma mouse model [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 2963.
Abstract 2279: Improving cell type and state classification in CITE-seq using probabilistic models and hierarchical cell ID matrix
Authors: Lila Fakharzadeh, Julien Tessier, Shannon McGrath, Emma Wang, Angelique Biancotto, Alexei Protopopov, Jack Pollard, Joon Sang Lee
Journal: Cancer Research (2021)

Abstract Accurate classification of cells in a population is important for most immune phenotyping applications. Surface protein marker expression measured with multiplexed platforms like Flow Cytometry and sequential gating strategies are typically employed to classify cells. However, new single-cell RNA sequencing (scRNA-seq) methods that measure RNA expression alone or Cellular Indexing of Transcriptomes and Epitopes by sequencing (CITE-seq) methods that concurrently measure both surface protein and RNA expression in single cells are providing new data and opportunities to develop methods both to classify cells and to assess their states of activation. Traditional manual gating methods using biaxial plots, where one designates a threshold separating a bimodal distribution through visual approximation, are subjective and can vary widely between individuals. Instead of manual, sequential gating for cell classification, we have implemented a probabilistic Gaussian Mixture Model (GMM) and K-means clustering to separate cell populations based on a library of marker thresholds for a variety of cell types present in human peripheral blood mononuclear cells (PBMCs) using a CITE-seq ADT expression matrix that has been preprocessed with centered-log-ratio (CLR) normalization. Furthermore, we coupled this GMM method with a hierarchical approach for cell typing. We have developed a Cell ID Matrix that outlines over 40 different immune cell types using consensus markers applicable to immune cell types across various studies. In this typing method, major cell types are identified following positive and negative marker expression as described in the Cell ID Matrix. Hierarchical gating of cells can then be used to identify subpopulations in a principled manner. The information in the Cell ID matrix is input as a binary matrix for each hierarchy level and is matched to the binarized expression values for classifying the cells. This approach can also be extended to CITE-seq datasets from disassociated tumor cells (DTCs). We conclude that automated cell gating with CITE-seq data may enhance the classification of numerous cell types in addition to significantly decreasing the amount of human intervention and time allocated for gating cells. Identifying cell states is a work in progress and will supplement this technique in the future. Citation Format: Lila Fakharzadeh, Julien Tessier, Shannon McGrath, Emma Wang, Angelique Biancotto, Alexei Protopopov, Jack Pollard, Joon Sang Lee. Improving cell type and state classification in CITE-seq using probabilistic models and hierarchical cell ID matrix [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 2279.
Abstract 2508: Genomic alterations of <i>BRCA1/2</i> genes in Chinese solid tumor patients
Authors: Junjian Wang, Lingxiang Liu, Bin Ni, Xiaoqian Chen, Ling Li, Junping Shi, Jierong Chen, Ming Yao
Journal: Cancer Research (2019)

Abstract Background: BRCA1 and BRCA2 are tumor suppressor genes that play an important role in DNA repair pathways. Germline mutations in BRCA1 and BRCA2 contribute to a significant number of familial and hereditary breast and/or ovarian cancers. Additionally, BRCA 1/2 alterations induce sensitivity to poly ADP ribose polymerase inhibitors (PARPi). Therefore, the detection of BRCA 1/2 mutations in solid tumor patients is essential to predict the sensitivity to PARPi therapy. Methods: FFPE tumor and matched blood samples of 5269 Chinese patients with solid tumor were collected for next generation sequencing (NGS) based assay. Genomic alterations including single nucleotide variations (SNV), short and long insertions/deletions (Indel), copy number variations (CNV) and gene rearrangements and fusions in selected genes were assessed. Results: Three hundred patients with BRCA1/2 mutations were identified in 5269 Chinese patients with solid tumor. The patients included 177 males and 123 females with a median age of 58. Highest yields of BRCA1/2 mutations were found in patients with ovarian (24.5%) and breast (12.3%) cancers. BRCA1/2 mutations were also identified in gastric cancer (8.9%), cholangiocarcinoma (8.8%), colorectal cancer (7.1%), esophageal cancer (6.1%), gallbladder cancer (5.1%), lung cancer (4.7%), soft tissue tumor (4.1%) and pancreatic cancer (4.0%). SNVs and short Indels (84.9%) were the most common variant types of BRCA1/2, while the percentages of gene rearrangements and fusions, CNV and long Indels were 12.0%, 1.6% and 1.5%, respectively. Among patients with BRCA1/2 mutations, 224 (74.7%) patients harbored somatic mutations, 73 (24.3%) patients harbored germline mutations, 3 (1.0%) patients harbored both somatic and germline mutations. Interestingly, all of the variant types of germline mutations were SNVs and short Indels. The mutation sites were distributed in the full length of BRCA1/2 genes. No hot spot mutation was observed. Conclusions: Our data revealed that BRCA1/2 mutations occurred in 5.7% of Chinese patients with solid tumor. NGS targeted sequencing provides comprehensive and accurate information of BRCA1/2 mutations. Beyond ovarian and breast cancers, BRCA1/2 mutations could be detected in other solid tumors, which suggests potential clinical benefits from PARPi therapy. Citation Format: Junjian Wang, Lingxiang Liu, Bin Ni, Xiaoqian Chen, Ling Li, Junping Shi, Jierong Chen, Ming Yao. Genomic alterations of BRCA1/2 genes in Chinese solid tumor patients [abstract]. In: Proceedings of the American Association for Cancer Research Annual Meeting 2019; 2019 Mar 29-Apr 3; Atlanta, GA. Philadelphia (PA): AACR; Cancer Res 2019;79(13 Suppl):Abstract nr 2508.
Abstract 2569: miR520a inhibits Fzd9 in bronchial epithelial cells and NSCLC
Authors: Alex J. Smith, Paulina Do, Kayla M. Sompel, Alamelu Elango
Journal: Cancer Research (2021)

Abstract Non-small cell lung cancer (NSCLC) continues to be the most diagnosed cancer type worldwide and has the highest mortality rate. Treatment is highly researched, but 5 year survival remains around 20%. Chemoprevention could combat the development of lung cancer in individuals who are at high risk, such as former cigarette smokers. Iloprost is a prostacyclin analogue demonstrated to reduce the presence of endobronchial dysplasia in former smokers. Increased Frizzled-9 (Fzd9) expression is induced by Iloprost, resulting in activation of peroxisome proliferator activated receptor γ (PPARγ) and inhibition of transformed growth. The goal of this study is to elucidate the relationship of cigarette smoke, NSCLC, and miRNA regulation of Fzd9 expression. We hypothesized that miRNA regulate Fzd9 expression when NSCLC cells are exposed to both cigarette smoke condensate (CSC) and Iloprost. miR520a5p was predicted in silico to bind Fzd9 and we validated binding with a miR520a5p mimic and Fzd9 3'UTR luciferase in an immortalized human bronchial epithelial cell line (HBEC) and NSCLC cell lines. A549 and H322 NSCLC cells and HBEC were exposed to cigarette smoke condensate (CSC) and Iloprost. CSC increased miR520a expression, while the opposite was observed in Iloprost treated cells. We also measured Fzd9 3'UTR activity and demonstrated that CSC decreases both Fzd9 3'UTR and PPRE activity, while Iloprost does the opposite. We investigated the effect of miR520a5p on targets downstream of Fzd9, including PPARγ response element (PPRE), a direct measure of PPARγ activity, and epithelial to mesenchymal transition (EMT) gene expression, including Cox2, E-cadherin, and CRB3. We found that when Fzd9 is inhibited by miR520a5p, PPRE activity and epithelial gene expression are inhibited, while mesenchymal gene expression is stimulated. Rescue experiments combining CSC with a miR520a5p inhibitor or iloprost with a miR520a5p mimic supported a role for miR-520a-5p in inhibition of Fzd9 in a CSC carcinogenic pathway in lung epithelial cells that is reversed with iloprost treatment. Overall, these findings suggest a mechanism for miRNA regulation of Fzd9 in lung epithelial cells exposed to cigarette smoke and a potential chemoprevention target. Citation Format: Alex J. Smith, Paulina Do, Kayla M. Sompel, Alamelu Elango. miR520a inhibits Fzd9 in bronchial epithelial cells and NSCLC [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 2569.
Abstract 2339: Halting head &amp; neck squamous cell carcinoma progression by broadly targeting glutamine metabolic pathways
Authors: Michael Allevato, Yumi Yokoyama, Robert Wild, Silvio Gutkind
Journal: Cancer Research (2021)

Abstract Head and neck squamous cell carcinoma (HNSCC) is the sixth most common cancer worldwide, resulting in over 14,600 deaths each year in the United States alone. HNSCC is associated with human papillomavirus (HPV) infection, and tobacco use and abusive alcohol intake. Recent revolutionary immunotherapy approaches have changed the landscape of treatment options in HNSCC. However, less than 20% of HNSCC patients respond to FDA-approved anti-PD1 immune checkpoint blockade (ICB) (pembrolizumab and nivolumab), often not leading to durable responses. This highlights the unmet need to identify novel therapeutic options and biomarkers predicting more favorable response to maximize the efficacy of immune-oncology (IO) strategies for HNSCC treatment. Glutamine is a conditionally essential amino acid for rapidly proliferating cancer cells making glutamine pathway inhibition an attractive approach for anti-cancer therapy. Treatment with the glutamine antagonist (DRP-104), which irreversibly inhibits all known enzymes involved in glutamine metabolism within the tumor, resulted in metabolically halted cell growth in vitro in a large panel of cell lines (n=8) representing the spectra of HPV- and HPV+ HNSCC, with an IC50 of 0.2-25uM, Interestingly, HNSCC cells bearing genetic alterations in PIK3CA/PTEN were significantly more sensitive to glutamine antagonism in comparison to unaltered HNSCC cells. The dependence of glutamine in HNSCC growth and the increased sensitivity of PIK3CA/PTEN aberrant cells was also observed in orosphere assays and 6 distinct HNSCC tumor xenografts in NOD SCID mice. We next investigated the efficacy of glutamine suppression in the context of an intact immune system, taking advantage of new syngeneic HNSCC model system, 4MOSC and MOC1. Specifically, we recently developed orthotopic syngeneic mouse models, 4MOSC, reflecting human tobacco-related HNSCC genomic alterations and mutational landscape (Wang et al., Nature Comm 2019), while MOC1 is a DMBA-induced mouse HNSCC cell line grown in the subcutaneous flank of mice (Judd et al. Cancer Res 2011). Monotherapy administration of DRP- 104 (1.4mg/kg) was potent as a monotherapy in all three syngeneic HNSCC models. We also observed a trend of increased sensitivity when DRP-104 was combined with anti-PD-1 therapy. Our data suggest that broad glutamine antagonism using DRP-104 has therapeutic potential in HNSCC by both dismantling cancer metabolism and enhancing the anti-tumor immune response of immune checkpoint blockade. Clinical trials of DRP-104 are currently ongoing. Citation Format: Michael Allevato, Yumi Yokoyama, Robert Wild, Silvio Gutkind. Halting head &amp; neck squamous cell carcinoma progression by broadly targeting glutamine metabolic pathways [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 2339.
Impact of health-related quality of life on repeat protocol biopsy compliance on active surveillance for favorable prostate cancer: Results from a prospective cohort in the PRIAS-JAPAN study
Authors: Y. Tohi, T. Kato, A. Yokomizo, K. Mitsuzuka, R. Tomida, J. Inokuchi, R. Matsumoto, T. Saito, H. Sasaki, K. Inoue, H. Kinoshita, H. Fukuhara, S. Maruyama, S. Sakamoto, T. Tanikawa, S. Egawa, H. Ichikura, T. Abe, M. Nakamura, Y. Kakehi, M. Sugimoto
Journal: European Urology (2021)
The use of 3D augmented reality during Robot-assisted living donor nephrectomy (RALDN): A case report technical overview
Authors: R. Schiavina, L. Bianchi, F. Chessa, M. Salvador, L. Cercenelli, B. Bortolani, S. Lodi, G. Comai, M. Busutti, A. Angiolini, E. Molinaroli, S. Diciotti, E. Marcelli, E. Brunocilla, G. La Manna, M. Ravaioli
Journal: European Urology (2021)
Dietary N‐Nitroso Compounds and Risk of Hepatocellular Carcinoma: A USA‐Based Study
Authors: Jiali Zheng, Carrie R. Daniel, Rikita I. Hatia, Janice Stuff, Ahmed A. Abdelhakeem, Asif Rashid, Yun Shin Chun, Prasun K. Jalal, Ahmed O. Kaseb, Donghui Li, Manal M. Hassan
Journal: Hepatology (2021)

Background and Aims N-nitroso compounds (NOCs) are among the most potent dietary carcinogens. N-nitrosodiethylamine (NDEA), N-nitrosodimethylamine (NDMA), and N-nitrosopiperidine (NPIP) are abundant in foods and carcinogenic to the liver. We investigated the relationship between dietary NOCs and HCC risk. Approach and Results In this large, hospital-based, case-control study of 827 pathologically or radiologically confirmed HCC cases and 1,013 controls, NOC intake was calculated by linking food frequency questionnaire–derived dietary data with a comprehensive NOC concentration database. Multivariable-adjusted ORs and 95% CIs of HCC by quartiles of NOC consumption were estimated using logistic regression models, with the lowest quartile as the referent. We further investigated joint effects of consuming the highest quartile of NOCs that were associated with increased HCC risk and hepatitis, diabetes, or alcohol drinking on HCC risk. After adjustment for confounding factors, higher intake of NDEA from plant sources (ORQ4 vs. Q1 = 1.58; 95% CI = 1.03-2.41), NDMA from plant sources (ORQ4 vs. Q1 = 1.54; 95% CI = 1.01-2.34), and NPIP (ORQ4 vs. Q1 = 2.52; 95% CI = 1.62-3.94) was associated with increased HCC risk. No association was observed for nitrate or total NOC intake and HCC risk. Higher consumption of HCC-inducing NOCs and positive hepatitis virus status jointly increased the risk of developing HCC. Conclusions In conclusion, though some of our findings may indicate the presence of reverse causation owing to lower meat intake among cases with chronic liver diseases before HCC diagnosis, the potent dietary HCC carcinogens, NDEA, NDMA, and NPIP, and their enhanced carcinogenic effects among chronic carriers of hepatitis virus warrant further prospective investigation.
Abstract 2334: Discovery of selective inhibitors of carbamoyl phosphate synthetase I (CPS1) to modulate cancer relevant metabolic pathways
Authors: Shihua Yao, Tuong-Vi Nguyen, Alan Rolfe, Anant A. Agrawal, Jiyuan Ke, Shouyong Peng, Federico Colombo, Sean Yu, Patricia Bouchard, Jiayi Wu, Kuan-Chun Huang, Xingfeng Bao, Kiyoyuki Omoto, Anand Selvaraj, Lihua Yu, Stephanos Ioannidis, Frédéric H. Vaillancourt, Ping Zhu, Nicholas A. Larsen, David M. Bolduc
Journal: Cancer Research (2021)

Abstract Carbamoyl Phosphate Synthetase 1 (CPS1) catalyzes the first and rate-limiting step in ammonia detoxification through the urea cycle, generating carbamoyl phosphate from ammonia, bicarbonate and ATP. CPS1 is overexpressed in several cancers, including LKB1-deficient non-small cell lung carcinoma (NSCLC), where its activity has been proposed to support tumor growth by generating carbamoyl phosphate for use in pyrimidine synthesis. In other cancers, CPS1 has been reported to remove toxic ammonia from growing tumors to allow for sustained growth. Currently, no small molecule inhibitors of CPS1 have been identified, limiting researcher's ability to dissect the involvement of CPS1 function in cancer biology. We describe here the discovery of the first known small molecule inhibitors of CPS1. From a high throughput screen, we identify two chemical series, which achieve inhibition of CPS1 by blocking bicarbonate phosphorylation in the first step of carbamoyl phosphate synthesis. Biochemical experiments reveal inhibition of bicarbonate phosphorylation occurs through competition between inhibitor and ATP. High-resolution co-crystal structures demonstrate that these novel inhibitors bind to a previously unidentified allosteric pocket located between the integrating domain and carbamate synthetase domain of CPS1. This allosteric mechanism of action allows for highly selective CPS1 inhibition, with no inhibition of CPS2 observed. Analogs with increased potency were developed, which are able to inhibit CPS1 cellular activity, blocking both urea production and the CPS1-mediated pyrimidine biosynthetic pathway in cultured cells. These novel CPS1 inhibitors are valuable, first-in-class tools for probing CPS1 biology. We will also discuss the opportunity to utilize these novel inhibitors of CPS1, along with genetic approaches, to probe the functional roles of CPS1 in LKB1-deficient NSCLC. Citation Format: Shihua Yao, Tuong-Vi Nguyen, Alan Rolfe, Anant A. Agrawal, Jiyuan Ke, Shouyong Peng, Federico Colombo, Sean Yu, Patricia Bouchard, Jiayi Wu, Kuan-Chun Huang, Xingfeng Bao, Kiyoyuki Omoto, Anand Selvaraj, Lihua Yu, Stephanos Ioannidis, Frédéric H. Vaillancourt, Ping Zhu, Nicholas A. Larsen, David M. Bolduc. Discovery of selective inhibitors of carbamoyl phosphate synthetase I (CPS1) to modulate cancer relevant metabolic pathways [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 2334.