tbuckley/cabot-search huggingface dataset:
Abstract 638: Enhancing the molecular diagnosis, prognosis, and treatment monitoring of retinoblastoma using cell free DNA in aqueous humor
Authors: Liya Xu, Mary E. Kim, Ashley Polski, Rishvanth K. Prabakar, Chen-Ching Peng, Patricia Chévez-Barrios, Jonathan W. Kim, Rachana Shah, Rima Jubran, Peter Kuhn, David Cobrinik, James Hicks, Jesse L. Berry
Journal: Cancer Research (2021)

Abstract Purpose: All previous studies of retinoblastoma (RB) aqueous humor (AH) analysis for tumor-derived cell-free DNA (cfDNA) have focused on sampling AH from eyes undergoing therapy; results from AH liquid biopsy at the time of diagnosis have not yet been published. Herein, we detail the diagnostic and prognostic genomic biomarkers found in the AH cfDNA from 7 RB eyes at diagnosis, each with longitudinal evaluation of over 12 months in follow-up. Methods: Subjects included 7 eyes of 6 RB patients who underwent AH sampling at diagnosis. CfDNA from each AH sample was isolated and sequenced to assess genome-wide somatic copy number alterations (SCNAs), followed by targeted resequencing and mutation detection using a custom hybridization panel for RB1 and MYCN. Results were compared to peripheral blood RB1 testing and matched tumor samples, when available. Tumor fraction (TFx) was calculated using ichorCNA. Results: Five of 7 diagnostic AH samples contained highly recurrent RB SCNAs, 4 with large scale alterations and 1 with a focal RB1 gene deletion. Mutational analysis of AH cfDNA identified pathogenic somatic variants in 5 diagnostic AH samples with high variant allele frequency, while the remaining 2 diagnostic AH samples had either a high TFx from SCNAs or a focal MYCN amplification. Taken together, somatic tumoral genomic information was detected in all 7 diagnostic AH samples. The 2 eyes that required enucleation had poor prognostic biomarkers (chromosome 6p gain and MYCN amplification) present at the time of diagnosis. TFx from longitudinal AH sampling corresponded to treatment response over time in all cases for which sequential AH samples were available. Conclusions: This study demonstrates that AH sampling at diagnosis is both feasible and safe. Molecular profiling of AH provides a plethora of diagnostic and prognostic information from only a single 0.1 mL AH sample. 1 Citation Format: Liya Xu, Mary E. Kim, Ashley Polski, Rishvanth K. Prabakar, Chen-Ching Peng, Patricia Chévez-Barrios, Jonathan W. Kim, Rachana Shah, Rima Jubran, Peter Kuhn, David Cobrinik, James Hicks, Jesse L. Berry. Enhancing the molecular diagnosis, prognosis, and treatment monitoring of retinoblastoma using cell free DNA in aqueous humor [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 638.
Development of Prognostic Prediction Model for Decision of Secondary Allogeneic Stem Cell Transplantation for Relapsed Acute Myeloid Leukemia after First Stem Cell Transplantation
Authors: Sung-Soo Park, Heeje Kim, Dae Hun Kwak, Gi June Min, Young-Woo Jeon, Jae-Ho Yoon, Seung-Hwan Shin, Seung-Ah Yahng, Sung-Eun Lee, Byung-Sik Cho, Ki-Seong Eom, Yoo-Jin Kim, Seok Lee, Chang-Ki Min, Seok-Goo Cho, Dong-Wook Kim, Jong-Wook Lee, Woo-Sung Min
Journal: Blood (2017)
Abstract 2630: Meta-analysis of pazopanib and trabectedin in 2L+ metastatic synovial sarcoma (2L+ mSS)
Authors: Charlotte Carroll, Nashita Patel, Necdet B. Gunsoy, Dan Parks, Heide A. Stirnadel-Farrant, Shibani Pokras
Journal: Cancer Research (2021)

Abstract Background: Pazopanib (P) and trabectedin (T) are approved targeted treatments for metastatic soft tissue sarcoma (mSTS). Our objective was to evaluate the efficacy (from clinical trials [CT]) and effectiveness (from real-world studies [RW]) of P and T in second line (2L+) mSS. Methods: This meta-analysis included all English language studies assessing P or T efficacy/effectiveness in patients with 2L+ mSS, 1999 onwards, identified by a systematic literature review. Outcomes were overall response rate (ORR) representing the proportion of patients who have achieved CR or PR during the study and median overall survival (mOS) in months (mos) from start of study medication. Proportions from studies were pooled using generalized linear mixed models to account for small sample sizes, zero events and random site effects. Medians were combined using the weighted median of the medians method with 95% confidence intervals from an inverted sign test. Results: 16 studies with 405 patients with 2L+ mSS met the inclusion criteria. Response was measured variably across studies (CT: RECIST v1.0, v1.1; RW: modified RECIST or clinician assessment). ORR estimates were higher in RW than CTs (Table). OS results were consistent across CTs and RW (Table). Conclusions: This is the first study to provide estimates for patients with mSS in the 2L+ setting, distinct from mSTS and pool outcomes of targeted therapies. RW estimates of ORR for both treatments were higher than those observed in trials likely due to variable definition of response and in underlying prognostic factors. mOS was consistent across both types of studies and was similar to mOS seen on placebo (10.7 mos in PALETTE study) suggesting a high unmet need in this population. Funding: GSK (213368). Outcomes with pazopanib (P) and trabectedin (T) in clinical trials (CT) and real-world (RW) studiesPTP &amp; T pooledORR-ALL (%)N=6, n=96, 18.9 (8.5, 41.8)N=7, n=162, 12.3 (8.0, 18.9)N=13, n=258, 14.7 (9.2, 23.4)ORR-CT (%)N=1, n=38, 13.2 (2.4, 23.9)†N=3, n=57, 7.0 (2.7, 18.1)N=4, n=95, 9.5 (5.1, 17.6)ORR-RW (%)N=5, n=58, 20.2 (7.4, 54.8)N=4, n=105, 15.2 (9.7, 23.9)N=9, n=163, 17.7 (9.9, 31.5)mOS-ALL (mos)N=4, n=96, 10.3 (8.7, 13.8)N=4, n=165, 9.9 (1.5, 13.9)N=8, n=261, 9.9 (9.2, 13.9)mOS-CT (mos)ND*ND*N=3, n=113, 10.3 (8.7, 13.9)mOS-RW (mos)ND*ND*N=5, n=148, 9.9 (9.2, 13.9)*Not done due to small sample size; †results of study since N=1. N=number of studies; n=number of patients. Estimates presented with 95% confidence intervals. Citation Format: Charlotte Carroll, Nashita Patel, Necdet B. Gunsoy, Dan Parks, Heide A. Stirnadel-Farrant, Shibani Pokras. Meta-analysis of pazopanib and trabectedin in 2L+ metastatic synovial sarcoma (2L+ mSS) [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 2630.
Abstract 9550: The Impact of The Mitochondria Transfers From Mesenchymal Stem Cell to Cardiomyocytes on Functional Recovery in the Distressed Myocardium
Authors: Daisuke Mori, Shigeru Miyagawa, Takuji Kawamura, Hiroki Hata, Takayoshi Ueno, Koichi Toda, Kotoe Kawai, Hayato Kurata, Hiroyuki Nishida, Yoshiki Sawa
Journal: Circulation (2019)

Introduction: Although transplantation of Mesenchymal stem cell (MSC) shows efficacy in the treatment of ischemic cardiomyopathy, its’ therapeutic mechanisms have not been fully elucidated.It has b...
Influence of neoadjuvant chemotherapy on surgical complexity reduction in invasive UTUC
Authors: M. Pikul, S.S. Semko, O.V. Voylenko, E.S. Stakhovsky, O.S. Stakhovsky, I.V. Vitruk, B.H. Hrechko, O.K. Kononenko
Journal: European Urology (2021)
Abstract 476: Clinical characteristics and outcome of pathologic N0 NSCLC patients with false positive on FDG PET-CT
Authors: Changdong Yeo, Hye Seon Kang, Sang Haak Lee
Journal: Cancer Research (2021)

Abstract Background Preoperative Fluorine-18 Fluorodeoxyglucose Positron Emission Tomography/Computed Tomography (FDG PET-CT) is a non-invasive and useful diagnostic tool to evaluate mediastinal lymph node metastasis in lung cancer. However, there are often false-positive lymph node cases in FDG PET-CT. We enrolled patients diagnosed with clinical N1-3 on FDG PET-CT, but pathologic N0 after mediastinal lymph node dissection. We aimed to explore clinical characteristics and outcome of pathologic N0 non-small cell lung cancer patients with false positive mediastinal lymph nodes on FDG PET-CT. Methods We enrolled total 147 patients who took pre-operative PET-CT scan and mediastinal lymph node dissection. Among them, 40 patients were diagnosed with clinical N1-3 by PET-CT. These patients were re-evaluated by post-operative pathologic nodal metastasis and divided into false-positive group and others. We retrospectively analyzed clinicopathologic features and recurrence free survival among patients diagnosed with same pathologic stage. Results Among 40 patients diagnosed with clinical N1-3 on FDG PET-CT, 19 (47.5%) patients were pathologic N0, which means false positive lymph node by PET-CT. Preoperative absolute platelet count (279.79 x 109/L versus 218.67 x 109/L; P = 0.012) and Platelet-Lymphocyte Ratio (PLR, 16.93 versus 11.53; P = 0.012) were significantly higher in the patients with pathologic N0. Among patients with pathologic N0, the presence of lymphatic invasion was significantly lower than other group (31.6% versus 85.7%; P = 0.001). Recurrence free survival was significantly shorter in pathologic N0 patients than those with same pathologic stage (P = 0.037). In addition, cox regression analysis showed smoking status (P = 0.045) and lymphatic invasion (P = 0.047) were independent factors for recurrence, significantly. Conclusions In conclusion, higher absolute platelet count, PLR and lower proportion of lymphatic invasion were associated with false positive mediastinal lymph node on preoperative FDG PET-CT. Furthermore, recurrence free survival was significantly shorter in these patients than those with same pathologic stage. In the future, preoperative biomarkers to predict pathologic nodal status need to be investigated. Citation Format: Changdong Yeo, Hye Seon Kang, Sang Haak Lee. Clinical characteristics and outcome of pathologic N0 NSCLC patients with false positive on FDG PET-CT [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 476.
Abstract 1214: Identification of URST1 as a prognostic biomarker and therapeutic target for lung cancer
Authors: Atsushi Takano, Yohei Miyagi, Yataro Daigo
Journal: Cancer Research (2021)

Abstract This study aims to identify novel biomarkers and therapeutic targets for lung cancer. Our strategies are as follows: i) Identification of up-regulated genes in lung cancers by gene expression profile analysis, ii) Validation of clinicopathological importance of their protein expression using tissue microarray, iii) Examination of their effect on cancer cell proliferation/survival by siRNAs and/or small molecules. During this process, we identified up-regulated in solid tumor 1 (URST1). Immunohistochemical analysis of URST1 expression revealed that URST1 expression was observed in the majority of non-small cell lung cancers (NSCLCs) and SCLCs. Strong positivity of URST1 staining was correlated with tumor size and lymph node metastasis and it was significantly associated with poor prognosis for NSCLC patients. Multivariate analysis showed that strong expression of URST1 was an independent prognostic factor for NSCLCs that had undergone curative surgery. Inhibition of URST1 expression by siRNAs for URST1 suppressed the growth and invasive ability of lung cancer cells. Treatment of lung cancer cells with selective inhibitors for URST1 significantly suppressed the cell growth partly through G2/M arrest and subsequent cell death. Downstream targets of URST1 were identified by microarray analysis using lung cancer cells transfected with siRNAs for URST1. Targeting URST1 is likely to be an effective diagnostic and therapeutic approach for lung cancer. Citation Format: Atsushi Takano, Yohei Miyagi, Yataro Daigo. Identification of URST1 as a prognostic biomarker and therapeutic target for lung 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 1214.
Robotic YV plasty for bladder neck contracture or vesico-urethral anastomosis stenosis in a French university hospital: Preliminary results
Authors: L. Freton, C. Richard, J. Hascoet, Z-E. Khene, Q. Alimi, V. Graffeille, G. Verhoest, R. Mathieu, A. Manunta, L.C. Zhao, K. Bensalah, B. Peyronnet
Journal: European Urology (2021)
細胞膜で分泌腺リソソームを結合するために特に必要なmunc 13-4-rab27複合体
Authors: D Elstak Edo, Neeft Maaike, T Nehme Nadine, Voortman Jarno, Cheung Marc, Goodarzifard Monireh, C Gerritsen Hans, Callebaut Isabelle, DE Saint Basile Genevieve, Van Der Sluijs Peter
Journal: Blood (2011)
Chemoradiation triggers antitumor Th1 and tissue resident memory-polarized immune responses to improve immune checkpoint inhibitors therapy
Authors: Elodie Lauret Marie Joseph, Amos Kirilovsky, Benoît Lecoester, Carine El Sissy, Laura Boullerot, Laurie Rangan, Amélie Marguier, Florent Tochet, Magalie Dosset, Jihane Boustani, Patrice Ravel, Romain Boidot, Laurie Spehner, Nacilla Haicheur-Adjouri, Florence Marliot, Jean-René Pallandre, Francis Bonnefoy, Viorel Scripcariu, Marc Van den Eynde, Emmanuel Cornillot, Céline Mirjolet, Franck Pages, Olivier Adotevi
Journal: Journal for ImmunoTherapy of Cancer (2021)

Multiple synergistic combination approaches with cancer drugs are developed to overcome primary resistance to immunotherapy; however, the mechanistic rationale to combine chemoradiotherapy (CRT) with immune checkpoint inhibitors remains elusive. This study described the immunological landscape of tumor microenvironment (TME) exposed to CRT. Tumor samples from patients with rectal cancer (n=43) treated with neoadjuvant CRT or radiotherapy were analyzed by nanostring and immunohistochemistry. Studies in mice were performed using three syngeneic tumors (TC1, CT26 and MC38). Tumor-bearing mice were treated either with platinum-based CRT, radiotherapy or chemotherapy. Anti-CTLA-4 and/or anti-Programmed Cell Death Receptor-1 (PD-1) therapy was used in combination with CRT. The therapy-exposed TME was screened by RNA sequencing and flow cytometry and tumor-infiltrating T lymphocyte functionality was evaluated by interferon (IFN)-γ ELIspot and intracellular cytokine staining. Front-to-front comparison analysis revealed the synergistic effect of CRT to establish a highly inflamed and Th1-polarized immune signature in the TME of patients and mice. In both settings, CRT-exposed TMEs were highly enriched in newly-infiltrated tumor-specific CD8+ T cells as well as tissue resident memory CD103+CD8+ T cells. In mice, CD8 T cells were involved in the antitumor response mediated by CRT and were primed by CRT-activated CD103+ dendritic cells. In the three tumor models, we showed that concurrent combination of CRT with a dual CTLA-4 and PD-1 blockade was required to achieve an optimal antitumor effect and to establish a broad and long-lasting protective antitumor T cell immunity. Our results highlight the ability of CRT to stimulate strong antitumor T-cell-mediated immunity and tissue resident memory T activation in TME, to foster immune checkpoint inhibitors action. These findings have implications in clinic for the design clinical trials combining chemoradiation with immunotherapy.
Acquired Resistance to Third-Generation EGFR Tyrosine Kinase Inhibitors in Patients With De Novo EGFRT790M-Mutant NSCLC
Authors: Ha-Ram Park, Tae Min Kim, Yusoo Lee, Soyeon Kim, Seongyeol Park, Young Seok Ju, Miso Kim, Bhumsuk Keam, Yoon Kyung Jeon, Dong-Wan Kim, Dae Seog Heo
Journal: Journal of Thoracic Oncology (2021)
Abstract 2243: Comprehensive genomic profiling - does timing matter
Authors: Bicky Thapa, Gulrayz Ahmed, Matthew Lasowski, James P. Thomas, Honey V. Reddi, Michael T. Zimmerman, Raul Urrutia, Aniko Szabo, Ben George
Journal: Cancer Research (2021)

Abstract Background: Comprehensive Genomic Profiling (CGP) is performed routinely in patients (pts) with metastatic solid tumors (MSTs) to guide treatment. However, there is variability in the interval between metastatic diagnosis (MDx) and performance of CGP based on histology and/or provider preference. We analyzed the CGP utilization patterns and its impact on outcomes at our academic medical center. Methods: All MST pts with CGP data (January 2012 - April 2020), their date of MDx, and the date of CGP were identified by electronic medical record review. Pts who had CGP after MDx were divided into tertiles (T1-earliest, T3-latest) within each cancer type, while some pts had CGP performed prior to MDx (pre-mets). Overall survival (OS) was estimated from the time of MDx with left truncation at the CGP time. Cox regression model was used to estimate the impact of ‘timing of CGP' on survival for individual cancer (CA) types. Results: Among 1,358 pts identified, 710 (52%) were female, 1,109 (82%) Caucasian, 186 (14%) Afro-Americans, and 1,320 (97%) non-Hispanic. Lung (254; 19%), colorectal (203; 15%), gynecologic (121; 8.9%), pancreatic (106; 7.8%) and connective tissue/soft tissue CAs (95; 7%) were the most frequently identified. Sex, race, and ethnicity had no impact on the time interval between MDx and CGP with 2 exceptions - Hispanics with lung CA and females with pancreas CA had delayed CGP compared to non-Hispanics and males respectively (p =0.019, p =0.025). The median time to CGP after MDx was shortest for urothelial CA (2.4 months) and longest for prostate CA (22 months). Pts with lung [T2 Hazard ratio (HR) of 2.25, p&amp;lt;0.001; T3 HR of 2.67, p&amp;lt;0.001], gastro-esophageal (T2 HR of 1.88, p=0.079; T3 HR of 2.49, p= 0.024), and gynecologic CAs (T2 HR of 2.58, p=0.012; T3 HR of 5.19, p=0.003) had better survival if they had CGP performed during the first tertile after MDx. Conclusion: Early CGP after MDx may have a greater impact on OS in CA types with more actionable therapeutic targets. The inherent bias associated with limiting the analyses only to pts who had CGP performed hampers our ability to contrast these results with those who did not have CGP performed. The establishment of national quality metrics for CGP utilization by CA type is imperative. Citation Format: Bicky Thapa, Gulrayz Ahmed, Matthew Lasowski, James P. Thomas, Honey V. Reddi, Michael T. Zimmerman, Raul Urrutia, Aniko Szabo, Ben George. Comprehensive genomic profiling - does timing matter [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 2243.
2021 American College of Rheumatology/Vasculitis Foundation Guideline for the Management of Polyarteritis Nodosa
Authors: Sharon A. Chung, Mark Gorelik, Carol A. Langford, Mehrdad Maz, Andy Abril, Gordon Guyatt, Amy M. Archer, Doyt L. Conn, Kathy A. Full, Peter C. Grayson, Maria F. Ibarra, Lisa F. Imundo, Susan Kim, Peter A. Merkel, Rennie L. Rhee, Philip Seo, John H. Stone, Sangeeta Sule, Robert P. Sundel, Omar I. Vitobaldi, Ann Warner, Kevin Byram, Anisha B. Dua, Nedaa Husainat, Karen E. James, Mohamad Kalot, Yih Chang Lin, Jason M. Springer, Marat Turgunbaev, Alexandra Villa‐Forte, Amy S. Turner, Reem A. Mustafa
Journal: Arthritis & Rheumatology (2021)

Objective To provide evidence‐based recommendations and expert guidance for the management of systemic polyarteritis nodosa (PAN). Methods Twenty‐one clinical questions regarding diagnostic testing, treatment, and management were developed in the population, intervention, comparator, and outcome (PICO) format for systemic, non–hepatitis B–related PAN. Systematic literature reviews were conducted for each PICO question. The Grading of Recommendations Assessment, Development and Evaluation methodology was used to assess the quality of evidence and formulate recommendations. Each recommendation required ≥70% consensus among the Voting Panel. Results We present 16 recommendations and 1 ungraded position statement for PAN. Most recommendations were graded as conditional due to the paucity of evidence. These recommendations support early treatment of severe PAN with cyclophosphamide and glucocorticoids, limiting toxicity through minimizing long‐term exposure to both treatments, and the use of imaging and tissue biopsy for disease diagnosis. These recommendations endorse minimizing risk to the patient by using established therapy at disease onset and identify new areas where adjunctive therapy may be warranted. Conclusion These recommendations provide guidance regarding diagnostic strategies, use of pharmacologic agents, and imaging for patients with PAN.
Abstract 15333: Vascular and Pericardial Complications of Atrial Fibrillation Ablation in the VA Health Care System
Authors: Bilal M Alqam, Zaid H Gheith, Fuad J Habash, Khaldia T Khaled, Amjad M Abualsoud, Mohammed Eid Madmani, Srikanth Vallurupalli, Waddah Maskoun
Journal: Circulation (2018)

Introduction: Atrial fibrillation (AF) ablation procedure is a complex procedure that carries high risk for causing vascular complications and pericardial effusion. To decrease the risk of stroke, ...
Incidence of non-typhoidal Salmonella invasive disease: A systematic review and meta-analysis
Authors: Christian S. Marchello, Fabio Fiorino, Elena Pettini, John A. Crump, Laura B. Martin, Gianluca Breghi, Rocio Canals, Melita A Gordon, Brama Hanumunthadu, Jan Jacobs, Samuel Kariuki, Jong-Hoon Kim, Stefano Malvolti, Carsten Mantel, Florian Marks, Donata Medaglini, Vittal Mogasale, Esther Muthumbi, Robert Onsare, Ellis Owusu-Dabo, Michael Owusu, Tonney Niyrenda, Maheshi Ramasamy, J. Anthony Scott, Bassiahi Abdramane Soura, Tiziana Spadafina, Bieke Tack
Journal: Journal of Infection (2021)

We sought to collate and summarize high-quality data on non-typhoidal Salmonella invasive disease (iNTS) incidence to provide contemporary incidence estimates by location and year.