tbuckley/cabot-search huggingface dataset:
circRNA_0025202 Regulates Tamoxifen Sensitivity and Tumor Progression via Regulating the miR-182-5p/FOXO3a Axis in Breast Cancer
Authors: Yuting Sang, Bing Chen, Xiaojin Song, Yaming Li, Yiran Liang, Dianwen Han, Ning Zhang, Hanwen Zhang, Ying Liu, Tong Chen, Chen Li, Lijuan Wang, Wenjing Zhao, Qifeng Yang
Journal: Molecular Therapy (2021)

(Molecular Therapy 27, 1638–1652; September 2019) In the originally published article, in Figures S2E, S3D, and S6D, the transwell images were incorrectly used. The assembly of Figure S6E was wrong. The corrected images are shown below. The errors do not impact the findings or conclusions of the study. The authors apologize for this error.Figure S3. Hsa_circ_0025202 suppresses growth, metastasis and increases TAM sensitivity of HR-positive BC cells in vitroView Large Image Figure ViewerDownload Hi-res image Download (PPT)Figure S6. Has_circ_0025202 sponges miR-182-5p to regulate the tumor progression and TAM sensitivity of BC cellsView Large Image Figure ViewerDownload Hi-res image Download (PPT) circRNA_0025202 Regulates Tamoxifen Sensitivity and Tumor Progression via Regulating the miR-182-5p/FOXO3a Axis in Breast CancerSang et al.Molecular TherapyMay 16, 2019In BriefThis report demonstrates a novel circular RNA, named hsa_circ_0025202, which is downregulated in tamoxifen-resistant breast cancer cells. hsa_circ_0025202 was identified as a tumor suppressor, and it could improve tamoxifen sensitivity through regulating the miR-182-5p/FOXO3a axis, suggesting it could be a potential therapeutic target and marker for patients with hormone receptor-positive breast cancer. Full-Text PDF Open Archive
122TiP Phase III study of durvalumab with SBRT for unresected stage I/II, lymph-node negative NSCLC (PACIFIC-4/RTOG 3515)
Authors: C. Robinson, L. Xing, H. Tanaka, S. Tasaka, S.N. Badiyan, H. Nasrallah, T. Biswas, M. Shtivelband, W. Schuette, A. Shi, A. Hepner, K. Barrett, J.R. Rigas, H. Jiang, S.H. Lin
Journal: Annals of Oncology (2022)
18F-FDG PET/CT Findings in HIV-Positive Patient With Primary Pancreas Lymphoma and CMV Pancreatitis
Authors: Ediz Beyhan, Özge Erol Fenercioğlu, Rahime Şahin, Mehmet Can Baloğlu, Tevfik Fikret Çermik
Journal: Clinical Nuclear Medicine (2022)

A 35-year-old HIV-positive man with abdominal pain was referred to 18F-FDG PET/CT for metabolic characterization of mass in pancreas. PET/CT images showed intense FDG uptake in head of the pancreas, as well as diffuse moderate uptake throughout body and tail of the pancreas. Histopathological results revealed Epstein-Barr virus (EBV) associated large B-cell lymphoma and pancreatitis caused by cytomegalovirus.
Evidence Base on the Potential Carcinogenicity of Radiofrequency Radiation
Authors: David O. Carpenter, Lennart Hardell, Cindy Sage
Journal: JAMA Oncology (2022)

Our website uses cookies to enhance your experience. By continuing to use our site, or clicking "Continue," you are agreeing to our Cookie Policy | Continue JAMA Oncology HomeNew OnlineCurrent IssueFor Authors Podcast Publications JAMA JAMA Network Open JAMA Cardiology JAMA Dermatology JAMA Health Forum JAMA Internal Medicine JAMA Neurology JAMA Oncology JAMA Ophthalmology JAMA Otolaryngology–Head & Neck Surgery JAMA Pediatrics JAMA Psychiatry JAMA Surgery Archives of Neurology & Psychiatry (1919-1959) JN Learning / CMESubscribeJobsInstitutions / LibrariansReprints & Permissions Terms of Use | Privacy Policy | Accessibility Statement 2023 American Medical Association. All Rights Reserved Search All JAMA JAMA Network Open JAMA Cardiology JAMA Dermatology JAMA Forum Archive JAMA Health Forum JAMA Internal Medicine JAMA Neurology JAMA Oncology JAMA Ophthalmology JAMA Otolaryngology–Head & Neck Surgery JAMA Pediatrics JAMA Psychiatry JAMA Surgery Archives of Neurology & Psychiatry Input Search Term Sign In Individual Sign In Sign inCreate an Account Access through your institution Sign In Purchase Options: Buy this article Rent this article Subscribe to the JAMA Oncology journal
CellPhy: accurate and fast probabilistic inference of single-cell phylogenies from scDNA-seq data
Authors: Alexey Kozlov, Joao M. Alves, Alexandros Stamatakis, David Posada
Journal: Genome biology (2022)

Abstract We introduce CellPhy, a maximum likelihood framework for inferring phylogenetic trees from somatic single-cell single-nucleotide variants. CellPhy leverages a finite-site Markov genotype model with 16 diploid states and considers amplification error and allelic dropout. We implement CellPhy into RAxML-NG, a widely used phylogenetic inference package that provides statistical confidence measurements and scales well on large datasets with hundreds or thousands of cells. Comprehensive simulations suggest that CellPhy is more robust to single-cell genomics errors and outperforms state-of-the-art methods under realistic scenarios, both in accuracy and speed. CellPhy is freely available at https://github.com/amkozlov/cellphy .
Epidemiology, risk factors, social determinants of health, and current management for non-alcoholic fatty liver disease in sub-Saharan Africa
Authors: C Wendy Spearman, Mary Afihene, Omolade Betiku, Bilal Bobat, Lina Cunha, Chris Kassianides, Leolin Katsidzira, Hailemichael D Mekonnen, Ponsiano Ocama, Olusegun Ojo, Imran Paruk, Christian Tzeuton, Mark W Sonderup
Journal: The Lancet. Gastroenterology & hepatology (2021)
Survival outcomes of gemcitabine plus S-1 adjuvant chemotherapy after surgical resection for advanced biliary tract cancer
Authors: Hidenori Tomida, Akira Shimizu, Kouji Kubota, Tsuyosi Notake, Kentaro Umemura, Atsushi Kamachi, Takamune Goto, Shiori Yamazaki, Yuji Soejima
Journal: International Journal of Surgery (2022)
Association of PD-1/PD-L1 Co-location with Immunotherapy Outcomes in Non–Small Cell Lung Cancer
Authors: Niki Gavrielatou, Yuting Liu, Ioannis Vathiotis, Jon Zugazagoitia, Thazin Nwe Aung, Saba Shafi, Aileen Fernandez, Kurt Schalper, Amanda Psyrri, David L. Rimm
Journal: Clinical Cancer Research (2021)

Programmed cell death protein 1 (PD-1)/programmed death-ligand 1 (PD-L1) interaction suppresses local T-cell responses and promotes peripheral tolerance. In the current study, we focus on PD-1/PD-L1 co-location as a surrogate for this interaction and assess its association with immunotherapy outcomes in patients with non-small cell lung cancer (NSCLC).Pretreatment biopsies from a retrospective cohort of 154 immunotherapy-treated patients with advanced NSCLC were analyzed. Expression of PD-1 and PD-L1 was assessed by multiplexed quantitative immunofluorescence (QIF) and PD-1 expression in the same pixels as PD-L1 (called a co-location score) was measured using an algorithm to define overlapping expression areas. Co-location scores were correlated with immunotherapy outcomes and PD-L1 tumor proportion score.PD-1/PD-L1 co-location score was associated with best overall response (P = 0.0012), progression-free survival (P = 0.0341), and overall survival after immunotherapy (P = 0.0249). The association was driven by patients receiving immune checkpoint inhibitors in the second or subsequent line of treatment. PD-L1 tumor proportion score by IHC was also correlated with best overall response and progression-free survival. PD-L1 measured within the tumor compartment by QIF did not show any significant association with either best overall response or overall survival. Finally, co-location score was not associated with PD-L1 expression by either method.On the basis of our findings, co-location score shows promise as a biomarker associated with outcome after immunotherapy. With further validation, it could have value as a predictive biomarker for the selection of patients with NSCLC receiving treatment with immune checkpoint inhibitors.
A Rare Collecting Duct Carcinoma With Widespread Metastasis Visualized by 18F-FDG PET/CT
Authors: Dandan Li, Chang Fu, Yang You, Qianqian Zhang, Xiaoju Zhang
Journal: Clinical Nuclear Medicine (2021)

Abstract Collecting duct carcinoma is a rare and highly aggressive renal tumor with a poor prognosis. The presence of metastasis is common at collecting duct carcinoma diagnosis, but widespread metastases involving multiple soft tissues are extremely unusual. Here, we describe a 65-year-old man presenting with fever and lower leg pain as the first and main manifestations. After receiving anti-infective therapy for over 6 weeks without improvement, 18 F-FDG PET/CT revealed a primary renal carcinoma with widespread metastases. A biopsy from the tubercle of fascicular spinal muscle indicated a diagnosis of collecting duct carcinoma.
Phase I/II Multicenter Trial of a Novel Therapeutic Cancer Vaccine, HepaVac-101, for Hepatocellular Carcinoma
Authors: Markus W. Löffler, Stefania Gori, Francesco Izzo, Andrea Mayer-Mokler, Paolo A. Ascierto, Alfred Königsrainer, Yuk Ting Ma, Bruno Sangro, Sven Francque, Luisa Vonghia, Alessandro Inno, Antonio Avallone, Jörg Ludwig, Diego Duarte Alcoba, Christian Flohr, Katrin Aslan, Regina Mendrzyk, Heiko Schuster, Marco Borrelli, Danila Valmori, Tanguy Chaumette, Regina Heidenreich, Cécile Gouttefangeas, Greta Forlani, Maria Tagliamonte, Caterina Fusco, Roberta Penta, Mercedes Iñarrairaegui, Ulrike Gnad-Vogt, Carsten Reinhardt, Toni Weinschenk, Roberto S. Accolla, Harpreet Singh-Jasuja, Hans-Georg Rammensee, Luigi Buonaguro
Journal: Clinical Cancer Research (2022)

Abstract Purpose: Immunotherapy for hepatocellular carcinoma (HCC) shows considerable promise in improving clinical outcomes. HepaVac-101 represents a single-arm, first-in-human phase I/II multicenter cancer vaccine trial for HCC (NCT03203005). It combines multipeptide antigens (IMA970A) with the TLR7/8/RIG I agonist CV8102. IMA970A includes 5 HLA-A*24 and 7 HLA-A*02 as well as 4 HLA-DR restricted peptides selected after mass spectrometric identification in human HCC tissues or cell lines. CV8102 is an RNA-based immunostimulator inducing a balanced Th1/Th2 immune response. Patients and Methods: A total of 82 patients with very early- to intermediate-stage HCCs were enrolled and screened for suitable HLA haplotypes and 22 put on study treatment. This consisted in a single infusion of low-dose cyclophosphamide followed by nine intradermal coadministrations of IMA970A and CV8102. Only patients with no disease relapse after standard-of-care treatments were vaccinated. The primary endpoints of the HepaVac-101 clinical trial were safety, tolerability, and antigen-specific T-cell responses. Secondary or exploratory endpoints included additional immunologic parameters and survival endpoints. Results: The vaccination showed a good safety profile. Transient mild-to-moderate injection-site reactions were the most frequent IMA970A/CV8102-related side effects. Immune responses against ≥1 vaccinated HLA class I tumor-associated peptide (TAA) and ≥1 vaccinated HLA class II TAA were respectively induced in 37% and 53% of the vaccinees. Conclusions: Immunotherapy may provide a great improvement in treatment options for HCC. HepaVac-101 is a first-in-human clinical vaccine trial with multiple novel HLA class I– and class II–restricted TAAs against HCC. The results are initial evidence for the safety and immunogenicity of the vaccine. Further clinical evaluations are warranted.
A Mediterranean-like fat blend protects against the development of severe colitis in the mucin-2 deficient murine model
Authors: Natasha Haskey, Jiayu Ye, Mehrbod Estaki, Andrea A. Verdugo Meza, Jacqueline A. Barnett, Mitra Yousefi, Blake W. Birnie, Samantha Gruenheid, Sanjoy Ghosh, Deanna L. Gibson
Journal: Gut Microbes (2022)

There is a growing appreciation that the interaction between diet, the gut microbiota and the immune system contribute to the development and progression of inflammatory bowel disease (IBD). A mounting body of scientific evidence suggests that high-fat diets exacerbate IBD; however, there is a lack of information on how specific types of fat impact colitis. The Mediterranean diet (MD) is considered a health-promoting diet containing approximately 40% total fat. It is not known if the blend of fats found in the MD contributes to its beneficial protective effects. Mice deficient in the mucin 2 gene (Muc 2−/−) were weaned to 40% fat, isocaloric, isonitrogenous diets. We compared the MD fat blend (high monounsaturated, 2:1 n-6:n-3 polyunsaturated and moderate saturated fat) to diets composed of corn oil (CO, n-6 polyunsaturated-rich), olive oil (monounsaturated-rich) or milk fat (MF, saturated-rich) on spontaneous colitis development in Muc2−/− mice. The MD resulted in lower clinical and histopathological scores and induced tolerogenic CD103+ CD11b+ dendritic, Th22 and IL-17+ IL-22+ cells necessary for intestinal barrier repair. The MD was associated with beneficial microbes and associated with higher cecal acetic acid levels negatively correlated with colitogenic microbes like Akkermansia muciniphila. In contrast, CO showed a higher prevalence of mucin-degraders including A. muciniphila and Enterobacteriaceae, which have been associated with colitis. A dietary blend of fats mimicking the MD, reduces disease activity, inflammation-related biomarkers and improves metabolic parameters in the Muc2−/− mouse model. Our findings suggest that the MD fat blend could be incorporated into a maintenance diet for colitis.
Abstract P160: Perceived Stress May Influence Allostatic Load When The Etiology Of Abnormal Glucose Tolerance Is β-cell Failure: The Africans In America Study
Authors: Annemarie Wentzel, M. Grace Duhuze Karera, Zoe Waldman, Blayne R Schenk, Arielle Patterson, Christopher W DuBose, Margrethe Horlyck-romanovsky, Anne E Sumner
Journal: Circulation (2022)

Background: Abnormal glucose tolerance (Abnl-GT) is a summary term for prediabetes and diabetes. The main etiologic determinant of Abnl-GT may be either β-cell failure or insulin resistance (IR). In African-born Blacks Abnl-GT may be predominantly due to β-cell failure rather than IR. Whether perceived and physiological stress profiles differ when Abnl-GT is due to β-cell failure rather than IR is uncertain. Aims: In 197 African-born Blacks living in the US (age: 38±11 (mean±SD); 58% men; BMI 28±5 kg/m 2 ) the perceived and physiological stress profiles were assessed based on Abnl-GT etiology. Methods: OGTT were performed. Abnl-GT was defined as FPG ≥100 mg/dL and/or glucose at 2h≥140 mg/dL. IR was defined by the lowest quartile of the Matsuda index (≤2.97). Abnl-GT-IR required Abnl-GT and IR. Beta-cell failure was defined as Abnl-GT without IR. The 10 question Cohen Perceived Stress Scale (PSS) was applied. Allostatic Load (ALS) included 10 variables: SBP, DBP, Pulse, cholesterol, HDL, homocysteine, BMI, A1C, Albumin, hs-CRP. Statistical analyses included t-tests, Chi-squares, and multiple regressions. Results: Abnl-GT occurred in 39% (77/197), with Abnl-GT-β-cell failure in 56% (43/77) and Abnl-GT-IR in 44% (34/77). The Abnl-GT-IR had higher BMI (31±5 vs 28±4) and WC (101±10 vs 90±11) vs Abnl-GT-β-cell failure, both P &lt;0.01. PSS did not differ between groups. ALS was higher in Abnl-GT-IR vs the Abnl-GT-β-cell failure ( P &lt;0.01). Yet, regression analyses, adjusted for age and sex, showed significant associations between PSS and ALS in the Abnl-GT-β-cell-failure-group ( P =0.01) ( Figure 1A ). However, PSS and ALS were insignificantly associated in the Abnl-GT-IR-group ( P =0.42) ( Figure 1B ). Conclusions: In Abnl-GT-β-cell failure, perceived stress may influence allostatic load. Reasons for the link between perceived stress and allostatic load in Abnl-GT due to β-cell failure need exploration.
Veliparib in Combination With Platinum-Based Chemotherapy for First-Line Treatment of Advanced Squamous Cell Lung Cancer: A Randomized, Multicenter Phase III Study
Authors: Suresh S. Ramalingam, Silvia Novello, Salih Zeki Guclu, Dmitry Bentsion, Zanete Zvirbule, Maria Szilasi, Reyes Bernabe, Konstantinos Syrigos, Lauren Averett Byers, Philip Clingan, Jair Bar, Everett E. Vokes, Ramaswamy Govindan, Martin Dunbar, Peter Ansell, Lei He, Xin Huang, Vasudha Sehgal, Jaimee Glasgow, Bruce A. Bach, Julien Mazieres
Journal: Journal of Clinical Oncology (2021)

PURPOSE Squamous non–small-cell lung cancer (sqNSCLC) is genetically complex with evidence of DNA damage. This phase III study investigated the efficacy and safety of poly (ADP-ribose) polymerase inhibitor veliparib in combination with conventional chemotherapy for advanced sqNSCLC ( NCT02106546 ). PATIENTS AND METHODS Patients age ≥ 18 years with untreated, advanced sqNSCLC were randomly assigned 1:1 to carboplatin and paclitaxel with veliparib 120 mg twice daily (twice a day) or placebo twice a day for up to six cycles. The primary end point was overall survival (OS) in the veliparib arm versus the control arm in current smokers, based on phase II findings. Archival tumor samples were provided for biomarker analysis using a 52-gene expression histology classifier (LP52). RESULTS Overall, 970 patients were randomly assigned to carboplatin and paclitaxel plus either veliparib (n = 486) or placebo (n = 484); 57% were current smokers. There was no significant OS benefit with veliparib in current smokers, with median OS 11.9 versus 11.1 months (hazard ratio [HR], 0.905; 95% CI, 0.744 to 1.101; P = .266). In the overall population, OS favored veliparib; median OS was 12.2 versus 11.2 months (HR, 0.853; 95% CI, 0.747 to 0.974), with no difference in progression-free survival (median 5.6 months per arm). In patients with biomarker-evaluable tumor samples (n = 360), OS favored veliparib in the LP52-positive population (median 14.0 v 9.6 months; HR, 0.66; 95% CI, 0.49 to 0.89), but favored placebo in the LP52-negative population (median 11.0 v 14.4 months; HR, 1.33; 95% CI, 0.95 to 1.86). No new safety signals were observed in the experimental arm. CONCLUSION In current smokers with advanced sqNSCLC, there was no therapeutic benefit of adding veliparib to first-line chemotherapy. The LP52 signature may identify a subgroup of patients likely to derive benefit from veliparib with chemotherapy.
Foreign Body Granuloma Masquerading as Remnant Lymphoma on 18F-FDG PET/CT
Authors: Wenjie Zhang, Hongbao Sun, Guohua Shen
Journal: Clinical Nuclear Medicine (2022)

A 54-year-old man complained of a growing nodule in the left upper arm, which was diagnosed as diffuse large B-cell lymphoma by postsurgical pathology. For baseline assessment, FDG PET/CT revealed intense uptake in the left upper arm, in addition to FDG-avid pleura lesions and regional, axillary, cervical, and mediastinal lymph nodes. After chemotherapy, the restaging scan showed complete remission of most involved lesions except for increased activity in the prior surgical site. The patient eventually underwent surgical resection again, and the diagnosis was confirmed as foreign body granuloma.
Clinical Responses of Oncolytic Coxsackievirus A21 (V937) in Patients With Unresectable Melanoma
Authors: Robert H. I. Andtbacka, Brendan Curti, Gregory A. Daniels, Sigrun Hallmeyer, Eric D. Whitman, Jose Lutzky, Lynn E. Spitler, Karl Zhou, Praveen K. Bommareddy, Mark Grose, Meihua Wang, Cai Wu, Howard L. Kaufman
Journal: Journal of Clinical Oncology (2021)

We evaluated the activity of intratumoral Coxsackievirus A21 (V937) in 57 patients with unresectable stage IIIC or IV melanoma.In this multicenter, open-label, phase II study, patients received up to a total V937 dose of 3 × 108 TCID50 (50% tissue culture infectious dose) in a maximum 4.0-mL volume by intratumoral injection. Ten sets of V937 injections were administered between days 1 and 127 (NCT01227551). Patients who had stable disease or were responding could continue treatment in an extension study (NCT01636882). Response and progression status were based on contrast-enhanced computed tomography, magnetic resonance imaging, or caliper measurement and were categorized using immune-related Response Evaluation Criteria in Solid Tumors (irRECIST). Other evaluations included monitoring of adverse events and serum levels of V937 and anti-V937 antibody titers. The primary efficacy end point was 6-month progression-free survival (PFS) rate per irRECIST.The primary efficacy end point, 6-month PFS rate per irRECIST, was 38.6% (95% CI, 26.0 to 52.4). Durable response rate (partial or complete response for ≥ 6 months) was 21.1% per irRECIST. Best overall response rate (complete plus partial response) was 38.6% (unconfirmed) and 28.1% (confirmed) per irRECIST. Regression of melanoma was observed in noninjected lesions. Based on Kaplan-Meier estimation, 12-month PFS was 32.9% (95% CI, 19.5 to 46.9) per irRECIST and 12-month overall survival was 75.4% (95% CI, 62.1 to 84.7). No treatment-related grade ≥ 3 adverse events occurred. Viral RNA was detected in serum within 30 minutes of administration. Neutralizing antibody titers increased to > 1:16 in all patients after day 22, without effect on clinical or immunologic response.V937 was well tolerated and warrants further investigation for treatment of patients with unresectable melanoma. Studies of combination approaches with V937 and immune checkpoint inhibitors are ongoing.
The Origins of Phenotypic Heterogeneity in Cancer
Authors: Guido Lenz, Giovana R. Onzi, Luana S. Lenz, Julieti H. Buss, Jephesson A. dos Santos, Karine R. Begnini
Journal: Cancer Research (2021)

Heterogeneity is a pervasive feature of cancer, and understanding the sources and regulatory mechanisms underlying heterogeneity could provide key insights to help improve the diagnosis and treatment of cancer. In this review, we discuss the origin of heterogeneity in the phenotype of individual cancer cells. Genotype-phenotype (G-P) maps are widely used in evolutionary biology to represent the complex interactions of genes and the environment that lead to phenotypes that impact fitness. Here, we present the rationale of an extended G-P (eG-P) map with a cone structure in cancer. The eG-P cone is formed by cells that are similar at the genome layer but gradually increase variability in the epigenome, transcriptome, proteome, metabolome, and signalome layers to produce large variability at the phenome layer. Experimental evidence from single-cell-omics analyses supporting the cancer eG-P cone concept is presented, and the impact of epimutations and the interaction of cancer and tumor microenvironmental eG-P cones are integrated with the current understanding of cancer biology. The eG-P cone concept uncovers potential therapeutic strategies to reduce cancer evolution and improve cancer treatment. More methods to study phenotypes in single cells will be the key to better understand cancer cell fitness in tumor biology and therapeutics.
Controversies surrounding peripheral cannabinoid receptor 1 in fatty liver disease
Authors: Beste Mutlu, Pere Puigserver
Journal: Journal of Clinical Investigation (2021)

Cannabinoid receptor 1 (CB-1) antagonists are potential candidates for treating obesity and metabolic complications. Despite clear metabolic benefits, unwanted side effects in the brain pose issues for patients. With the hope of overcoming this obstacle, CB-1 in peripheral tissues has become a potential drug target. Previous studies had suggested that liver CB-1 would be an excellent target to prevent development of nonalcoholic steatohepatitis (NAFLD). However, in this issue of the JCI, Wang et al. showed that CB-1 was barely detectable in the liver and deletion of CB-1 in hepatocytes provided no metabolic benefits against NAFLD. These contradictory results raise substantial concerns about the potential benefits of peripheral CB-1 blockers against NAFLD.