tbuckley/cabot-search huggingface dataset:
Tumor mutation burden and immune microenvironment analysis of urothelial carcinoma.
Authors: Yuanyuan Jia, Ning He, Yadong Yang, Yuliang Huang, Xiaoyu Zhang, Zhichao Fu, Xiaohong Xu, Jianjun Cao, Jianfei Wang
Journal: Journal of Clinical Oncology (2021)

494 Background: Tumor mutation burden (TMB) has been established as a biomarker for response to immune therapy and prognosis in various cancers. However, the correlation between TMB and immune microenvironment remains unwell studied, especially in urothelial carcinoma. This study was aimed to investigate the relationship between TMB and other immunotherapy related biomarkers, including genetic alterations, APOBEC signature, microsatellite instability (MSI), PD-L1 expression and immune cell infiltration in urothelial carcinoma. Methods: 131 patients with urothelial carcinoma admitted from October 2018 to May 2020 were included. Total DNA was isolated from FFPE or fresh tissues. Mutation profiles, APOBEC signature and MSI scores were obtained by next-generation sequencing based a 642 cancer genes panel assay. PD-L1 expression, CD8+ T-cells and tumor-infiltrating lymphocytes density were evaluated by immunohistochemistry. The correlation was analyzed by Wilcoxon signed-rank test. Results: The mutation landscape showed that TP53 mutation is the most common alterations (n = 64/131, 48.9%), followed by KMT2D alterations (n = 49/131, 37.4%), KDM6A mutations (n = 42/131, 32.1%), MUC17 mutations (n = 42/131, 32.1%). The median TMB was 5.06 Muts/Mb (0-118 Muts/Mb). 2 of 131 patients showed MSI-H, who exhibited a much higher TMB (41, 118 Muts/Mb). Further analysis showed that TMB in the patients with certain gene mutations (such as TP53, KMT2D, KDM6A and MUC17) was significantly higher than those wild type ones (p &lt; 0.05). Meanwhile, the high APOBEC-enrichment group has a higher TMB than the low APOBEC-enrichment group (p = 0.045). Furthermore,we observed that the patients with a higher PD-L1 expression (n = 28/131, 21.4%, at a combined positive score cut-off value of 10) also showed a significantly higher TMB (p = 0.016), and TMB in the patients with higher density of CD8+ T-cells (n = 42/131, 32.1%, at a cut-off value of 5%) was also significantly higher than that of the group with lower density of CD8+ T-cells (p = 0.039). Conclusions: This study provides new insights into the correlation between the TMB and the immune microenvironment in urothelial carcinoma. The result may be a reference to immunotherapy.
The role of mRNA in the development, diagnosis, treatment and prognosis of neural tumors
Authors: Yiyang Zheng, Yanyan Luo, Xixi Chen, Huiting Li, Baojun Huang, Baofeng Zhou, Liqing Zhu, Xianhui Kang, Wujun Geng
Journal: Molecular Cancer (2021)

Abstract Neural tumors can generally be divided into central nervous system tumors and peripheral nervous tumors. Because this type of tumor is located in the nerve, even benign tumors are often difficult to remove by surgery. In addition, the majority of neural tumors are malignant, and it is particular the same for the central nervous system tumors. Even treated with the means such as chemotherapy and radiotherapy, they are also difficult to completely cure. In recent years, an increasingly number of studies have focused on the use of mRNA to treat tumors, representing an emerging gene therapy. The use of mRNA can use the expression of some functional proteins for the treatment of genetic disorders or tissue repair, and it can also be applied to immunotherapy through the expression of antigens, antibodies or receptors. Therefore, although these therapies are not fully-fledged enough, they have a broad research prospect. In addition, there are many ways to treat tumors using mRNA vaccines and exosomes carrying mRNA, which have drawn much attention. In this study, we reviewed the current research on the role of mRNA in the development, diagnosis, treatment and prognosis of neural tumors, and examine the future research prospects of mRNA in neural tumors and the opportunities and challenges that will arise in the future application of clinical treatment.
Use of preclinical models for malignant pleural mesothelioma
Authors: Marie Shamseddin, Joanna Obacz, Mathew J Garnett, Robert Campbell Rintoul, Hayley Elizabeth Francies, Stefan John Marciniak
Journal: Thorax (2021)

Malignant pleural mesothelioma (MPM) is an aggressive cancer most commonly caused by prior exposure to asbestos. Median survival is 12–18 months, since surgery is ineffective and chemotherapy offers minimal benefit. Preclinical models that faithfully recapitulate the genomic and histopathological features of cancer are critical for the development of new treatments. The most commonly used models of MPM are two-dimensional cell lines established from primary tumours or pleural fluid. While these have provided some important insights into MPM biology, these cell models have significant limitations. In order to address some of these limitations, spheroids and microfluidic chips have more recently been used to investigate the role of the three-dimensional environment in MPM. Efforts have also been made to develop animal models of MPM, including asbestos-induced murine tumour models, MPM-prone genetically modified mice and patient-derived xenografts. Here, we discuss the available in vitro and in vivo models of MPM and highlight their strengths and limitations. We discuss how newer technologies, such as the tumour-derived organoids, might allow us to address the limitations of existing models and aid in the identification of effective treatments for this challenging-to-treat disease.
Secondary cytoreduction followed by chemotherapy versus chemotherapy alone in platinum-sensitive relapsed ovarian cancer (SOC-1): a multicentre, open-label, randomised, phase 3 trial
Authors: Tingyan Shi, Jianqing Zhu, Yanling Feng, Dongsheng Tu, Yuqin Zhang, Ping Zhang, Huixun Jia, Xiao Huang, Yunlang Cai, Sheng Yin, Rong Jiang, Wenjuan Tian, Wen Gao, Jihong Liu, Huijuan Yang, Xi Cheng, Rongyu Zang
Journal: The Lancet Oncology (2021)
Abstract 14841: An Italian Survey on 4000 Healthy Young Students: An Electrocardiographic Evaluation
Authors: Alessandra D'Ambrosi, Giuseppe Giunta, Antonio Fusto, Ilaria Mancini, Azzurra Marceca, Francesco Adamo, Gennaro Alfano, Lara Fratarcangeli, Massimo Mancone, Francesco Fedele
Journal: Circulation (2012)

Purpose: In Italy, annual incidence of sudden cardiac death in patients with less than 35 years is 1/1000. While young athletes periodically undergo to cardiologic examinations, non-competitive spo...
Fractionated docetaxel and radium-223 (Ra223) in metastatic castration-resistant prostate cancer (CRPC): A phase I trial.
Authors: Brendan James Connell, Edmund Folefac, Clara Hwang, Christian Lawlor, Paul Mathew
Journal: Journal of Clinical Oncology (2021)

TPS175 Background: Disease progression following highly-active androgen-axis therapy (HAAT) in CRPC remains bone-dominant and docetaxel-responsive. Combination bone-homing Ra223 isotope therapy with docetaxel would be a logical combination therapy to follow but myelosuppression is dose-limiting. With 3-weekly bolus schedules of docetaxel (D), dose-reduction to 60mg/m2 Q3wkly and Ra223 to every 6 weeks has been required representing a reduction in the dose-intensity of both agents. Fractionated schedules of docetaxel Q2wkly (DQ2) have comparable activity to D 75mg/m2 Q3wkly (DQ3) with mitigated myelosuppression. We hypothesize that a fractionated dose-schedule of DQ2 in combination with standard Ra223 dosing will be feasible without reduction in dose-intensity of Ra-223 or D. Methods: Outcomes: The primary objective is to determine the feasibility and maximal tolerated dose (MTD) of the combination. Secondary objectives include PSA kinetics, objective response, bone marker outcomes, progression free and overall survival, and description of toxicity and quality of life. Eligibility: Progressive bone-metastatic CRPC, ECOG PS 0-2 with no prior Ra223, no prior docetaxel for CRPC, and no bulky visceral disease. Design: Phase I (6+6) design; 4 week lead-in with DQ2. Dose-level 1a: 40mg/m2; 2a: 50mg/m2, both with PEGylated G-CSF on Day 16. If tolerated (≤ Grade 2 toxicity, ANC ≥ 1500, Platelets ≥ 100,000), lead-in is followed by C1D1 of DQ2 plus Ra223 Q4wkly x 6 doses. Dose level 1a has accrued 6 subjects without DLT. Enrollment to Dose Level 2a began in August, 2020. An expansion cohort of 25 subjects is planned after the MTD is determined. Clinical trial information: NCT03737370.
Delaying surgery for clinical T1b-T2bN0M0 renal cell carcinoma: Oncologic implications in the COVID-19 era and beyond.
Authors: Arnav Srivastava, Hiren V. Patel, Sinae Kim, Brian Shinder, Joshua Sterling, Alexandra L. Tabakin, Charles Polotti, Biren Saraiya, Tina M. Mayer, Isaac Yi Kim, Saum Ghodoussipour, Hiten Dilip Patel, Thomas L Jang, Eric A. Singer
Journal: Journal of Clinical Oncology (2021)

283 Background: During COVID-19, many operating rooms were reserved exclusively for emergent cases. As a result, many elective surgeries for renal cell carcinoma (RCC) were deferred, with an unknown impact on outcomes. Since surveillance is commonplace for small renal masses, we focused on larger, organ-confined, RCCs. Our primary endpoint was pT3a upstaging and our secondary endpoint was overall survival (OS). Methods: We retrospectively abstracted cT1b-cT2bN0M0 RCC patients from the National Cancer Database (NCDB), stratifying them by clinical stage and time from diagnosis to surgery. We selected only those patients who underwent surgery. Patients were grouped by having surgery within &lt;1 month, 1-3 months, or &gt;3 months after diagnosis. Logistic regression models measured pT3a upstaging risk. Kaplan Meier curves and Cox proportional hazards models assessed OS. Results: 29,746 patients underwent partial or radical nephrectomy. Delaying surgery &gt;3 months after diagnosis did not confer pT3a upstaging risk among cT1b (OR=0.90; 95%CI: 0.77–1.05, p = 0.170), cT2a (OR=0.90; 95%CI: 0.69–1.19, p=0.454), or cT2b (OR=0.96; 95%CI:0.62–1.51, p=0.873) masses (Table). In all clinical stage strata, non-clear cell RCCs were significantly less likely to be upstaged (p&lt;0.001). A sensitivity analysis, performed for delays of &lt;1, 1-3, 3-6, and &gt;6 months, also showed no increase in upstaging risk. Conclusions: Delaying surgery up to, and even beyond, 3 months does not significantly increase risk of tumor progression in clinically localized RCC. However, if deciding to delay surgery due to COVID-19, tumor histology, growth kinetics, patient comorbidities, and hospital capacity/resources, should be considered. [Table: see text]
The prognostic value of toxin B and binary toxin in <i>Clostridioides difficile</i> infection
Authors: Salvador López-Cárdenas, Eva Torres-Martos, Juan Mora-Delgado, Juan Manuel Sánchez-Calvo, Marta Santos-Peña, Ángel Zapata López, María Dolores López-Prieto, Salvador Pérez-Cortés, Juan Carlos Alados
Journal: Gut Microbes (2021)

To study the association between detection of the Clostridioides difficile gene encoding the binary toxin (CDT) and direct detection of toxinB (TcdB) from feces with the appearance of serious disease, complications, or recurrence in a prospective series of cases. A total of 220 confirmed cases were included, using a two-step algorithm: an initial study to detect the enzyme, glutamate dehydrogenase (GDH), followed, in cases of positivity, by detection of the tcdB. tcdB-positive patients were investigated for the presence of CDT and TcdB. Outcome variables were severe disease, the modified Illinois C. difficile infection (CDI) prognostic risk index (ZAR score), the appearance of complications (need for colectomy, CDI-related death, or toxic megacolon) and recurrence. Patients who tested positive for the presence of TcdB in feces were found to have greater disease severity than those who tested negative, with a ZAR score of 35.4% vs. 23% (p = .048), a higher recurrence rate (14.6% vs. 5.9%, p = .032), and a tendency for higher number of complications (20.7% vs. 11.5%), although without reaching statistical significance (p = .053). When presence of CDT was analyzed, higher frequencies of severe disease (39.2% vs. 21.2%, p = .005), complications and recurrence (21.6% vs. 10.9%, p = .037 and 14.9% vs. 5.8%, p = .029; respectively) were observed in patients where CDT was detected. TcdB and CDT act as prognostic markers of the appearance of serious disease, complications or recurrence in cases of CDI. Simultaneous detection of both markers, TcdB and CDT, had a greater impact on the prognosis than when they were detected separately.
Association between Smoking History and Tumor Mutation Burden in Advanced Non–Small Cell Lung Cancer
Authors: Xinan Wang, Biagio Ricciuti, Tom Nguyen, Xihao Li, Michael S. Rabin, Mark M. Awad, Xihong Lin, Bruce E. Johnson, David C. Christiani
Journal: Cancer Research (2021)

Abstract Lung carcinogenesis is a complex and stepwise process involving accumulation of genetic mutations in signaling and oncogenic pathways via interactions with environmental factors and host susceptibility. Tobacco exposure is the leading cause of lung cancer, but its relationship to clinically relevant mutations and the composite tumor mutation burden (TMB) has not been fully elucidated. In this study, we investigated the dose–response relationship in a retrospective observational study of 931 patients treated for advanced-stage non–small cell lung cancer (NSCLC) between April 2013 and February 2020 at the Dana Farber Cancer Institute and Brigham and Women’s Hospital. Doubling smoking pack-years was associated with increased KRASG12C and less frequent EGFRdel19 and EGFRL858R mutations, whereas doubling smoking-free months was associated with more frequent EGFRL858R. In advanced lung adenocarcinoma, doubling smoking pack-years was associated with an increase in TMB, whereas doubling smoking-free months was associated with a decrease in TMB, after controlling for age, gender, and stage. There is a significant dose–response association of smoking history with genetic alterations in cancer-related pathways and TMB in advanced lung adenocarcinoma. Significance: This study clarifies the relationship between smoking history and clinically relevant mutations in non–small cell lung cancer, revealing the potential of smoking history as a surrogate for tumor mutation burden.
Genetic variation and microRNA targeting of A-to-I RNA editing fine tune human tissue transcriptomes
Authors: Eddie Park, Yan Jiang, Lili Hao, Jingyi Hui, Yi Xing
Journal: Genome biology (2021)

A-to-I RNA editing diversifies the transcriptome and has multiple downstream functional effects. Genetic variation contributes to RNA editing variability between individuals and has the potential to impact phenotypic variability. We analyze matched genetic and transcriptomic data in 49 tissues across 437 individuals to identify RNA editing events that are associated with genetic variation. Using an RNA editing quantitative trait loci (edQTL) mapping approach, we identify 3117 unique RNA editing events associated with a cis genetic polymorphism. Fourteen percent of these edQTL events are also associated with genetic variation in their gene expression. A subset of these events are associated with genome-wide association study signals of complex traits or diseases. We determine that tissue-specific levels of ADAR and ADARB1 are able to explain a subset of tissue-specific edQTL events. We find that certain microRNAs are able to differentiate between the edited and unedited isoforms of their targets. Furthermore, microRNAs can generate an expression quantitative trait loci (eQTL) signal from an edQTL locus by microRNA-mediated transcript degradation in an editing-specific manner. By integrative analyses of edQTL, eQTL, and microRNA expression profiles, we computationally discover and experimentally validate edQTL-microRNA pairs for which the microRNA may generate an eQTL signal from an edQTL locus in a tissue-specific manner. Our work suggests a mechanism in which RNA editing variability can influence the phenotypes of complex traits and diseases by altering the stability and steady-state level of critical RNA molecules.
Cardiovascular informatics: building a bridge to data harmony
Authors: John Harry Caufield, Dibakar Sigdel, John Fu, Howard Choi, Vladimir Guevara-Gonzalez, Ding Wang, Peipei Ping
Journal: Cardiovascular Research (2021)

Abstract The search for new strategies for better understanding cardiovascular (CV) disease is a constant one, spanning multitudinous types of observations and studies. A comprehensive characterization of each disease state and its biomolecular underpinnings relies upon insights gleaned from extensive information collection of various types of data. Researchers and clinicians in CV biomedicine repeatedly face questions regarding which types of data may best answer their questions, how to integrate information from multiple datasets of various types, and how to adapt emerging advances in machine learning and/or artificial intelligence to their needs in data processing. Frequently lauded as a field with great practical and translational potential, the interface between biomedical informatics and CV medicine is challenged with staggeringly massive datasets. Successful application of computational approaches to decode these complex and gigantic amounts of information becomes an essential step toward realizing the desired benefits. In this review, we examine recent efforts to adapt informatics strategies to CV biomedical research: automated information extraction and unification of multifaceted -omics data. We discuss how and why this interdisciplinary space of CV Informatics is particularly relevant to and supportive of current experimental and clinical research. We describe in detail how open data sources and methods can drive discovery while demanding few initial resources, an advantage afforded by widespread availability of cloud computing-driven platforms. Subsequently, we provide examples of how interoperable computational systems facilitate exploration of data from multiple sources, including both consistently formatted structured data and unstructured data. Taken together, these approaches for achieving data harmony enable molecular phenotyping of CV diseases and unification of CV knowledge.
Terlipressin plus Albumin for the Treatment of Type 1 Hepatorenal Syndrome
Authors: Florence Wong, S. Chris Pappas, Michael P. Curry, K. Rajender Reddy, Raymond A. Rubin, Michael K. Porayko, Stevan A. Gonzalez, Khalid Mumtaz, Nicholas Lim, Douglas A. Simonetto, Pratima Sharma, Arun J. Sanyal, Marlyn J. Mayo, R. Todd Frederick, Shannon Escalante, Khurram Jamil
Journal: New England Journal of Medicine (2021)

The vasoconstrictor terlipressin is used for type 1 hepatorenal syndrome (HRS-1) in many parts of the world and is part of the clinical practice guidelines in Europe.We conducted a phase 3 trial to confirm the efficacy and safety of terlipressin plus albumin in adults with HRS-1. The patients were randomly assigned in a 2:1 ratio to receive terlipressin or placebo for up to 14 days; in both groups, concomitant use of albumin was strongly recommended. The primary end point was verified reversal of HRS, defined as two consecutive serum creatinine measurements of 1.5 mg per deciliter or less at least 2 hours apart and survival without renal-replacement therapy for at least 10 days after the completion of treatment. Four prespecified secondary end points were analyzed with the Hochberg procedure to account for multiple comparisons.A total of 300 patients underwent randomization - 199 were assigned to the terlipressin group and 101 to the placebo group. Verified reversal of HRS was reported in 63 patients (32%) in the terlipressin group and 17 patients (17%) in the placebo group (P = 0.006). With respect to the prespecified secondary end points, HRS reversal, defined as any serum creatinine level of 1.5 mg per deciliter or less during the first 14 days, was reported in 78 patients (39%) in the terlipressin group and 18 (18%) in the placebo group (P<0.001); HRS reversal without renal-replacement therapy by day 30, in 68 (34%) and 17 (17%), respectively (P = 0.001); HRS reversal among patients with systemic inflammatory response syndrome (84 patients in the terlipressin group and 48 patients in the placebo group), in 31 (37%) and 3 (6%), respectively (P<0.001); and verified reversal of HRS without recurrence by day 30, in 52 (26%) and 17 (17%), respectively (P = 0.08). At day 90, liver transplantations had been performed in 46 patients (23%) in the terlipressin group and 29 patients (29%) in the placebo group, and death occurred in 101 (51%) and 45 (45%), respectively. More adverse events, including abdominal pain, nausea, diarrhea, and respiratory failure, occurred with terlipressin than with placebo. Death within 90 days due to respiratory disorders occurred in 22 patients (11%) in the terlipressin group and 2 patients (2%) in the placebo group.In this trial involving adults with cirrhosis and HRS-1, terlipressin was more effective than placebo in improving renal function but was associated with serious adverse events, including respiratory failure. (Funded by Mallinckrodt Pharmaceuticals; CONFIRM ClinicalTrials.gov number, NCT02770716.).
Analysis of rectal dose during prostate stereotactic body radiotherapy in MR-guided radiotherapy.
Authors: Kobika Sritharan, Alex Dunlop, Adam Mitchell, Jonathan Mohajer, Gillian Smith, Alison Tree
Journal: Journal of Clinical Oncology (2021)

242 Background: The Unity MR-Linac combines a 7-MV Linac with 1.5T magnetic resonance (MR) imaging capability and it enables adaptive radiotherapy, whereby the target and organs at risk are recontoured and a plan is optimised daily. During treatment a session MR image is taken first, on which the target and organs-at-risk are contoured, and a plan created. A verification image is taken prior to dose delivery to identify intra-fractional changes. If present, the daily treatment plan is shifted to reflect the anatomy. A post-treatment image is acquired at the end of treatment. This study evaluates the dosimetric changes to the rectum caused by intra-fractional changes during treatment delivery for prostate stereotactic body radiotherapy (SBRT) calculated on the verification and post-treatment images. Methods: The first five patients treated on the MR-Linac with 5-fraction SBRT to the prostate are included in this study. For each patient, the rectum was contoured on the verification and post-treatment MR images for each of the five fractions. The dose delivered to the rectum with the original treatment plan was then calculated on each image and the V36Gy rectal dose constraint was noted. Results: Out of the 25 fractions, a post treatment image was not performed in one fraction; 24 fractions were therefore analysed in total. The rectal V36Gy dose constraint exceeded the mandatory target of 2cc on 50% of the verification images and 46% of the post-treatment images. In 6 fractions the rectal V36Gy was greater than 2cc on both the verification and post-treatment images suggesting this rectal constraint was exceeded throughout treatment. In 17% of patients, the volume of rectum receiving 36Gy increased at each timepoint an image was taken during the treatment workflow. Conclusions: The rectal V36Gy dose constraint is susceptible to minor changes in rectal filling, which may often lead to higher than the accepted dose constraint. Thus, a single planning CT scan is unlikely to be representative of dose delivered. Adaptive radiotherapy can reduce this uncertainty somewhat, but intra-fraction dose re-optimisation would be required to ensure the rectal V36Gy remains acceptable at all times.