tbuckley/cabot-search huggingface dataset:
Comparison between the microbiota in lung tumor and adjacent normal tissues in lung cancer patients.
Authors: Qixing Mao
Journal: Journal of Clinical Oncology (2018)

e20548 Background: The interplay between the lung cancer and the lung microbiome has yet not been well investigated. In this study, we surveyed and compared the microbiota composition and diversity in paired tumor and adjacent normal tissues to test whether any tumor specific microbial features can be identified in tumor tissues. Methods: In total, 55 paired fresh frozen lung tissue samples were processed and sequenced at bacterial 16S V3-V4 region using Illumina Hiseq2500. The sequencing reads were further assigned with taxonomical information at 97% sequence similarity to the references. The microbial diversity was further analyzed using QIIME pipeline. The differential taxa feature by tumor status was selected using LefSe method. Results: We observed diversified microbiota in lung tissue samples. At phylum level, the dominant taxa include Proteobacteria, Firmicutes, Bacteroidetes and Actinobacteria. PERMANOVA test suggested there is no significant difference in overall microbiome dissimilarity (beta diversity) between tumor and non-tumor adjacent tissues (p-value = 0.27). The tumor samples showed significantly lower community richness (alpha diversity) measured by Shannon index(p = 0.05). We also found the microbiota is much more similar between paired tumor and adjacent tissues from the same patients than unpaired two tissues (p < 0.01). LefSe analysis found Modestobacter enriched and 8 genera including Phormidium, Propionibacterium, Rhodobacter, Finegoldia, Microbacterium and two unclassified genera reduced in tumor tissues compared to non-tumor adjacent tissues. Conclusions: Our study demonstrated that the microbiota in tumor tissues showed lower richness and reduction of many potential pro-inflammatory microbial genera, suggesting our further testing the link between the tumor microbiota to the immunosuppression tumor microenvironment.
Clinical predictive factors of overall survival and locoregional failure in advanced laryngeal cancer treated with definitive chemoradiation.
Authors: Adeel M Khan, Matthew C Ward, David J. Adelstein, Shlomo A. Koyfman, Chandana A. Reddy, Priyanka Bhateja, Pauline Funchain, Eric Lamarre, Brian Burkey, Mumtaz Khan, Joseph Scharpf, Brandon Prendes, John Greskovich, Robert Lorenz, Nikhil Joshi, Melissa L Rahe, Denise I. Ives, Bridgett Ann Harr, Joanna Bodmann, Tobenna Igweonu Nwizu
Journal: Journal of Clinical Oncology (2016)

6037 Background: Definitive chemoradiation (CRT) has become an established organ preservation treatment for patients (pts) with locoregionally advanced laryngeal cancer. Although most pts will experience long-term disease control, locoregional failure (LRF) remains a concern for a subset of pts. This study is aimed to identify predictors of LRF and overall survival (OS) after larynx-preservation therapy. Methods: Patients with AJCC stage III-IVB squamous cell carcinoma of the larynx treated with definitive CRT between 1993 and 2014 were identified at a single large tertiary institution in an IRB-approved registry. Patient, tumor, treatment, and outcome data were collected. The Cox proportional hazards method was used to identify predictors of LRF and OS. Results: There were 117 pts included in the study with median follow-up of 31 months (range: 1.8–185). Median age at diagnosis was 59 years, 74% were male, 57% were current smokers, and 21% had a history of alcohol abuse. Fourteen percent presented with T2 tumors, 70% T3 tumors, 16% had T4 disease and 62% were node-positive. Radiation therapy was administered with either a 3-field approach in 61% or with intensity modulated radiation therapy in 37%. Chemotherapy consisted of either cisplatin and 5-fluorouracil (60%) or single agent cisplatin (33%). Twenty (17%) LRFs were observed with 17 occurring within 2 years of treatment. Thirty-seven deaths (32%) were observed with median OS time of 116 months. Univariate analysis showed a higher LRF rate in pts with heavy alcohol and ≥ 20 pack-year smoking history who were currently smoking at time of diagnosis (HR 4.2, 95% CI 1.7-10.6, p = 0.002). These pts also had a lower OS rate (HR 2.2, 95% CI 1.0-4.9, p = 0.05). Their median OS time was notably reduced: 52 vs 119 months. T-stage, N-stage, or CRT regimen were not associated with LRF or OS. Conclusions: These data suggest that pts treated with definitive CRT for stage III-IVB laryngeal cancer who fail locoregionally do so within 24 months. Heavy alcohol history combined with significant smoking history and continued smoking was a significant predictor of LRF and decreased OS. Emphasis on smoking cessation and alcohol reform is warranted.
Abstract 14011: Safety of Balloon Pulmonary Angioplasty in Patients With Inoperable Chronic Thromboembolic Pulmonary Hypertension -Detail Analyses of Procedure Related Complications
Authors: Tatsuo Aoki, Koichiro Sugimura, Masanobu Miura, Shunsuke Tatebe, Saori Yamamoto, Nobuhiro Yaoita, Hideaki Suzuki, Haruka Sato, Katsuya Kozu, Kimio Satoh, Hiroaki Shimokawa
Journal: Circulation (2016)

Background: Although balloon pulmonary angioplasty (BPA) is an emerging therapeutic strategy to improve hemodynamics of patients with inoperable chronic thromboembolic pulmonary hypertension (CTEPH), the original study in 2001 reported that BPA frequently induced pulmonary edema requiring mechanical ventilation. In this study, to evaluate the safety of BPA in CTEPH patients, we examined not only hemodynamics but also complications associated with latest BPA procedures by using imaging modalities. Methods and Results: From July 2009 to May 2016, we performed BPA in 78 patients with inoperable CTEPH, in whom we performed 393 sessions with combined use of imaging modalities, including optical computed tomography to select balloon size and 3D reconstructed computed tomography to determine target lesions of pulmonary arteries (PA). Mean age of the patients was 65 year-old and 65 of them were female (82%). In 72 patients (92%) who completed the treatment, hemodynamics and 5-year survival were examined after BPA. Mean follow-up period was 21 ± 15 months. After the completion of BPA treatments, mean PA pressure (38±10 to 25±7 mmHg, P&lt;0.01), pulmonary vascular resistance (7.0±3.1 to 3.7±1.7 Wood unit) and 6-min walk distance (383±156 to 489±113 meters) were all significantly improved (all P&lt;0.01). In the 393 sessions, hemoptysis was noted in 64 sessions (16%), and non-invasive positive pressure ventilation (NPPV) was used for hemoptysis and/or hypoxemia in 32 sessions (8.1%). In last 4 years, the incidence of hemoptysis and the use of NPPV have progressively decreased (Figure). Furthermore, there were no peri-procedural deaths, and 5-year survival after 1st BPA session was 94% (only one patient died for colon cancer). Conclusions: These results indicate that BPA improves hemodynamics and exercise capacity, resulting in good long-term prognosis in inoperable CTEPH patients with acceptable complication risk.
Anatomic site of metastases can influence response to nivolumab in NSCLC patients.
Authors: Andrea Botticelli, Bruna Cerbelli, Paolo Sciattella, Massimiliano Salati, Ilaria Zizzari, Michela Roberto, Giulia Poti, Federica De Galitiis, Vincenzo Picone, Giulia D'Amati, Federica Mazzuca, Marianna Nuti, Paolo Marchetti
Journal: Journal of Clinical Oncology (2018)

e15021 Background: Immune checkpoint inhibitors have revolutionized treatment and outcome of NSCLC. Unfortunately, only 25-30% of patients have a long-term benefit, while the remaining 70-75% demonstrate primary or acquired resistance. Recently, it has been demonstrated that the prevalence of PD-L1 and TILs varies based on the anatomical site of metastases. In particular liver seems to be a more immunosuppressive microenvironment while lymph node and lung metastases seem to have the highest prevalence of PD-L1 and TILS. The aim of our study was to investigate if the anatomic site of metastases could influence the outcome of patients treated with Nivolumab. Methods: Sixty-five patients, affected by stage IV NSCLC , treated with Nivolumab at Sant’Andrea Hospital, were enrolled. We studied the associations between early progression (defined as progression of the disease within 3 months from the beginning of Nivolumab treatment) and PS, age, sex and site of metastases. Furthermore we investigated the associations between PFS > 12 months and PS, age, sex and site of metastases. Statistical analysis was performed using univariate and multivariate logistic regression. Results: The median age of patients was 67 years old (range44-85) and 23 (33%) were female. Fourteen patients (21%) had liver metastases, in 21 patients (32%) only lung and/or lymph node metastases were detected. Twenty-three patients (32%) presented early progression, while 16 patients presented PFS longer than 12 months (24%). We found a significant association between the presence of liver metastases and early progression both at univariate analysis ( p = 0,001) and multivariate analysis (p = 0,005), and between PFS > 12 months and presence of only lung and/or lymph node metastases at univariate analysis (p = 0,03) . No statistical associations were demonstrated between disease progression and PS, age, sex and site of metastases. Conclusions: Our results suggest that liver metastases could predict resistance to immunotherapy .Otherwise lung or lymph node metastases could select patients with long term benefit.
FIERCE-21: Phase 1b/2 study of docetaxel + b-701, a selective inhibitor of FGFR3, in relapsed or refractory (R/R) metastatic urothelial carcinoma (mUCC).
Authors: Joaquim Bellmunt, Joel Picus, Manish Kohli, Yull Edwin Arriaga, Matthew I. Milowsky, Graeme Currie, Steve Abella, Sumanta K. Pal
Journal: Journal of Clinical Oncology (2018)

4534 Background: Patients with locally advanced or metastatic urothelial carcinoma (mUCC) have a poor prognosis. FGFR3 is frequently overexpressed in UCC and 15-20% of patients with mUCC have FGFR3 gene mutations or fusions (M/F). B-701 is a fully human monoclonal antibody against FGFR3 that blocks activation of the wildtype and genetically activated receptor. FIERCE-21 is a Phase 1b/2 study designed to evaluate B-701 alone or in combination with docetaxel (D). Methods: The study consists of a Phase 1b lead-in (P1b) followed by Phase 2 (P2) expansion and a randomized phase. Eligible patients P1b: the study enrolled mUCC R/R excluding prior taxane treatment, and ECOG > 1. Treatment: B-701 at 25 mg/kg and D at 75 mg/m2 q3w. Efficacy was assessed by investigators (RECIST 1.1). Primary objective: Determine P2 dose and evaluate safety and efficacy. Results: 19 patients were enrolled in P1b: median age 66 yrs, ECOG 1 = 58%, Hgb < 10 gm/dL 5%, liver metastases 26%, ≥ 2 prior regimens 63%, best response to prior therapy PD 52%. Six patients were positive for FGFR3 M/F. Grade ≥3 AEs occurring in ≥ 2 patients were typical of D at this dose and schedule [decreased neutrophil count (26.3%), neutropenia (10.5%), decreased WBC (10.5%)]. Two patients had D dose reductions and no subjects had dose reductions of B-701 or discontinued treatment due to AE. Two patients died, 1 with PD and bleeding, and 1 with MAHA associated with infection and recurrent thrombosis. Four subjects are alive (3 M/F). Median OS has not been reached in M/F vs 5.3 months in WT. Conclusions: B-701 combined with standard dose D in an every 3 week schedule in patients with mUCC was well-tolerated with expected myelosuppression. Enhanced activity was seen in the FGFR3 M/F compared to WT patients. Phase 2 expansion is currently enrolling FGFR3 M/F patients (B-701 monotherapy vs. combination B-701+D). Clinical trial information: NCT02401542.
Formal assessment of teamwork among cancer health care professionals in 3 large tertiary centers in Nigeria.
Authors: Abiola Falilat Ibraheem, Olutosin Alaba Awolude, Myhammad-yaqub Murtazha Habeebu, Anthonia Chima Sowunmi, Popoola Abiodun Olaniyi, Olufunmilayo I. Olopade, Blase N. Polite
Journal: Journal of Clinical Oncology (2017)

e18126 Background: Cancer is fast becoming a common cause of death in developing world. Over the last decade, there have been strategies to bring quality cancer care to underserved patients around the world. In low-income countries, poor utilization of principles of teamwork is a major barrier to achieving quality services. The intent of this study is to assess teamwork as perceived by the health care workers caring for cancer patients Methods: We conducted a survey among health care professionals involved in cancer care in 3 tertiary centers in the southwestern part of Nigeria from July to November 2016. Respondents rated teamwork using the previously validated ÒSafety Attitudes QuestionnaireÓ. For this analysis we focused on the teamwork climate subscale. This subscale is scored on a scale of 0-100 with mean (SD) values,in US ambulatory population of 69.7 (17). We compared ratings by professionals using analysis of variance Results: Overall 373 professionals completed the survey: Physicians (47%), nurses (14%), pharmacists (6%) and others (33%). Some results are shown in table Conclusions: Cancer care is complex and depends on teamwork amongst health care professionals to achieve optimal outcomes. While overall teamwork scores was consistent with US ambulatory studies , there are important variations that provide targets for intervention. Physicians rated teamwork poorly both intra and inter professionally. Pharmacists rated inter professional teamwork with nurses particularly poorly. Further data on additional subscales of the instrument and by individual centers will be presented. Efforts to transform cancer care need to focus on building trust among the key stakeholders. This is true in developing world where there is a need to maximize the use of limited resources to improve patient outcomes. [Table: see text]
Assessment of endotoxemia in lymphoproliferative diseases.
Authors: Irina Valerevna Neskubina, Oleg Ivanovich Kit, Irina Aleksandrovna Goroshinskaya, Liubov Yu Vladimirova, Ludmila Anatolievna Nemashkalova, Natalya Mikhailovna Tikhanovskaya, Irina Snezhko, Anna E Storozhakova
Journal: Journal of Clinical Oncology (2016)

e19079 Background: Lymphomas are accompanied by immunological disorders. Endogenous intoxication is one of the factors that affect the immune status of patients. The aim of this research is a screening study of the state of endotoxemia in cancer patients with some lymphoproliferative diseases. Methods: Content of medium mass molecules (MMM254 and MMM280 ), total (TCA) and effective (ECA) concentrations of albumin were studied to assess endogenous intoxication; reserve binding capacity of albumin (ABC) was calculated by ECA/TCA•100%, as well as coefficient of intoxication (CI) calculated by MMM254 / ECA•1000. These indicators have been studied in 34 patients with non-Hodgkin lymphomas (II-IVst) with a lesion of nearby and distant lymph nodes, 50 patients with Hodgkin's lymphoma (IIB-IVA st), 54 patients with chronic lymphocytic leukemia with B, C stages and advanced disease. Results: At non-Hodgkin lymphoma with a lesion of nearby and distant lymph nodes ECA and ABC were lower than normal: ECA by 35% and 23%, ABC by 34% and 26% respectively (p < 0.001). Patients with nearby lymph nodes showed an increase in both MMM fractions: by 14% (p < 0.05) and 29% (p < 0.02) and with extranodal lesions MMM280 only by 30% (p < 0.01). CI was elevated in both groups by 117% (p < 0.05) and 39% (p < 0.001). In patients with Hodgkin's lymphoma there was a decrease of ECA and ABC by 37-42% (p < 0.01-0.001), increase in both fractions of MMM by 28-34% (p < 0.01-0.001) and CI by 160% (p < 0.001). Changes in chronic lymphocytic leukemia depended on the stage of the disease, and were highest in advanced process: reduction of ECA and ABC on 48-50% and the increase in MMM by 32% (p < 0.001). At the B-stage change in ECA and ABC were at the level of 24-28%, MMM – 13%, while at the C-stage 36% and 22% respectively (p < 0.001). CI increased as tumor stage advanced: in B-stage by 46% (p < 0.01), C-stage by 89% (p < 0.001), advanced by 161% (p < 0.001). Conclusions: At non-Hodgkin lymphoma the location of tumor lesions does not significantly affect the intensity of endotoxemia. At Hodgkin's lymphoma total imbalance in the system of endotoxemia is observed. In patients with chronic lymphocytic leukemia endogenous intoxication increases depending on the extent of the process and affects all levels of the detoxification system.
Large outbreak of mumps virus genotype G among vaccinated students in Norway, 2015 to 2016
Authors: Lamprini Veneti, Katrine Borgen, Kaja Sverdrup Borge, Kostas Danis, Margrethe Greve-Isdahl, Kirsten Konsmo, Gro Njølstad, Svein Arne Nordbø, Kari Stidal Øystese, Rikard Rykkvin, Eli Sagvik, Øystein Rolandsen Riise
Journal: Eurosurveillance (2018)

From 6 September 2015-May 2016, a large mumps outbreak occurred among vaccinated students in Norway. A case was defined as a person presenting with a clinical mumps infection, notified between 1 September 2015 and 30 June 2016. Confirmed cases had positive laboratory confirmation and probable cases had an epidemiological link; PCR-positive specimens were genotyped. A total of 232 cases were notified (230 confirmed) with median age of 23 years (range 4-81) and 61% were male. Of 68 (30%) confirmed cases that were genotyped, 66 were genotype G and associated with the outbreak. Cases that had received two doses of the measles-mumps-rubella (MMR) vaccine had reduced risk of hospitalisation (adjusted relative risk (aRR): 0.14; 95%CI: 0.03-0.57), mumps-related orchitis (aRR: 0.21; 95% CI: 0.08-0.55) and severe outcome (aRR: 0.25; 95% CI: 0.10-0.62) compared with those unvaccinated. A third dose of the vaccine was offered to approximately 1,300 fully vaccinated close contacts and subsequently reported cases decreased. This large outbreak, occurring among predominately vaccinated students, suggests the current genotype A vaccine offers suboptimal protection against mumps genotype G. We recommend maintaining high vaccination coverage and offering the vaccine to all unvaccinated individuals.
Characteristics, treatment patterns and safety events from 4 cohorts of advanced or metastatic cancer patients based on health care claims data.
Authors: Leo Russo, Daina Esposito, Francois-Xavier Lamy, Stephan Lanes, Jennifer Lyons, Jose Penalvo, Ruihua Yin, Patrice Verpillat
Journal: Journal of Clinical Oncology (2018)

e13603 Background: Healthcare databases are valuable for epidemiological research in oncology. Our main objective was to identify patients (pts) with advanced or metastatic: ovarian cancer (mOC), urothelial carcinoma (mUC), gastric cancer (mGC) and non-small cell lung cancer (mNSCLC) and to describe their characteristics, treatments, and safety events using real-world data. Methods: Eligible pts were identified in claims data (HealthCore Integrated Research Database [HIRD]) if they had ≥1 ICD-9-CM or ICD-10 diagnosis code for considered cancer types, were continuously enrolled for ≥6 months during the study period (2010 - 2016), and confirmed to have advanced or metastatic disease by patient linkage with 3 US states cancer registries or HealthCore Integrated Research Environment Oncology data. Study outcomes were identified from diagnosis codes in the HIRD; a previously published algorithm was used to identify infusion-related reactions. Incidence rates of safety events during follow-up (62 monitored in total) were described as number of events per 100 person-years (PY). Results: We identified 1,978 pts with confirmed mOC, 791 with mUC, 937 with mGC and 8,516 with mNSCLC. Patient characteristics and selected study outcomes are described in table 1. The most frequent anticancer drug classes were alkylating agents (carboplatin) for mOC and mNSCLC and antimetabolites for mUC and mGC (respectively gemcitabine and fluorouracil). Conclusions: Confirmed cases of advanced or metastatic cancer were identified using healthcare claims data linked to cancer registries or electronic medical records and presented similar characteristics to previously published cohorts. Table 1. mOC N = 1978 mUC N = 791 mGC N = 937 mNSCLC N = 8516 Age (median) 59 70 65 67 Female (%) 100.0 30.1 33.1 47.6 Surgery (%) 62.6 61.8 18.2 9.7 Radiation (%) 9.9 19.6 30.5 48.7 Anticancer drug therapy (%) 82.4 60.9 66.8 64.0 Follow-up duration in months (median) 16 15 9 8 Safety Events (events/100 PY and 95% confidence interval) Infusion-related reactions 38.5 (35.5-41.8) 17.3 (14.8-20.0) 41.3 (36.4-46.8) 37.7 (36.2-39.4) Serious infections 13.3 (12.0-14.7) 22.3 (19.5-25.4) 30.3 (26.5-34.4) 23.3 (22.2-24.4)
Patient-reported satisfaction with multidisciplinary (MD) v serial care (SC) for lung cancer.
Authors: Kenneth Daniel Ward, Weiyu Chen, Matthew Smeltzer, Meghan Brooke Meadows, Nicholas Ryan Faris, Courtney Berryman, Bianca M Jackson, Fedoria Rugless, Meredith Ray, Raymond U. Osarogiagbon
Journal: Journal of Clinical Oncology (2018)

6535 Background: Coordinated MD lung cancer care, with all key specialists concurrently providing input to develop a consensus care plan with patients and their caregivers, is much-advocated over the usual SC model but lacks rigorous evaluation. Methods: Prospective comparative effectiveness trial enrolled newly-diagnosed lung cancer patients receiving MD or SC within the same US healthcare system. At baseline, 3 and 6 months, patients completed several satisfaction measures from the Consumer Assessment of Healthcare Providers and Systems, and the National Health Interview Survey ‘Perceived Financial Burden of Care’ instrument. All Group (MD v SC), time (baseline, 3, 6 months), and group by time interactions were analyzed in mixed linear models. Associations were adjusted for insurance, race, clinical stage, and ECOG performance status. Results: The 456 patients (159 MD, 297 SC) were similar in sex and health insurance. The MD cohort was slightly older (69 vs. 66) and had more racial minorities (37% vs. 29%). Statistically significant group by time interactions, indicating greater improvement over time for MD, were observed for satisfaction with treatment plan (p = .0036) and quality of care received from the whole care team (p = .0377). However, perceived financial burden of care increased slightly over time for MD but decreased slightly for SC (p = .0352). Collapsed across time, MD patients were more likely to perceive their cancer care to be better than that received by other patients (p = .0025). Collapsed across treatment group, depression increased significantly from baseline to 3 months (p = .0118), and improvements over time occurred for satisfaction with length of time to diagnosis, length of time to complete treatment, and communication from physicians, nurses, and about disease-specific information. Conclusions: Compared with SC, MD patients perceived their care to be better than that received by other lung cancer patients, and had greater improvements over the course of treatment in satisfaction with their treatment plan and care team. These positive patient-reported outcomes occurred despite slightly greater perceived financial burden of care. Clinical trial information: NCT02123797.