tbuckley/cabot-search huggingface dataset:
Evaluating clinical activity of MAPK targeted therapies (TT) in cancer patients (pts) with non-V600 BRAF mutations: A systematic scoping review and meta-analysis.
Authors: Matthew Dankner, Yifan Wang, Rouhi Fazelzad, Anna Spreafico, David W. Cescon, George Zogopoulos, April A. N. Rose
Journal: Journal of Clinical Oncology (2021)

3089 Background: Oncogenic nonV600 BRAF mutations (muts) can be classified according to distinct molecular characteristics. TT strategies for class 2 and 3 BRAF muts have not been established. In recent years there have been numerous reports of clinical activity for various TT in pts with nonV600 muts. We performed a systematic scoping review and meta-analysis to assess treatment outcomes with MAPK TT according to BRAF class, cancer type and TT type. Methods: An extensive literature search was conducted from 2010-20. All studies were independently reviewed and extracted by 2 reviewers and in accordance with PRISMA guidelines. Individual patient level data were collected and analyzed from studies that met the following inclusion criteria: published reports of 1) advanced cancer pts with; 2) class 2 or class 3 nonV600 BRAF muts; 3) who received MAPK TT; 4) with treatment response (TR) data available. Primary outcome was overall TR rate (TRR). To assess differences between groups, odds ratios (OR) were calculated using a multi-level mixed-effects logistic regression model. Results: 15,171 studies were screened and 168 were included for data extraction. We identified 100 studies with a total of 396 pts that met inclusion criteria. There were 17 reports (161 pts) of prospective clinical trials and 83 retrospective studies (235 pts). RECIST criteria were used for TR assessment in 183 (46%) pts. The entire study included 280 pts with class 2 and 116 pts with class 3 BRAF muts. Overall, 111 (28%) pts achieved a TR. TRR according to primary tumor type, BRAF class, and TT type is indicated in Table. TRR was lower in reports of prospective studies compared to retrospective studies (OR 0.14, P = 0.002), and in studies that employed RECIST criteria vs. those that didn’t (OR 0.29, P = 0.044). TRR was higher among pts with class 2 muts vs. those with class 3 muts (OR 2.21, P = 0.042). Conclusions: These data establish that MAPK TT have demonstrated clinical activity in cancers with oncogenic nonV600 mutations, and that BRAF mutation class may dictate responsiveness to different TT strategies. TRR may be over-estimated in the retrospective literature. This analysis will be valuable for molecular tumor boards and to guide future clinical trial design. Prospective clinical trials of TT in this pt population are warranted.[Table: see text]
Clinical and pathological response to neoadjuvant chemotherapy (NCT) in patients with triple-negative breast cancer (TNBC).
Authors: Petr Krivorotko, Elena Zhiltsova, Larisa Gigolaeva, Alexander Emelyanov, Roman Pesotskiy, Sergey Yerechshenko, Kirill Nikolaev, Alexander Komyahov, Olga Ivanova, Tengiz Tabagua, Konstantin Zernov, Vadim Ivanov, Zalina Aseeva, Alexander Bessonov, Vladimir Semiglazov
Journal: Journal of Clinical Oncology (2021)

e12616 Background: Neoadjuvant chemotherapy (NCT), Triple-negative breast cancer (TNBC) including anthracyclines and taxanes for early stages of TNBC, allows to achieve pathological complete response (pCR) in 25-36% of patients. Pathological complete response (pCR) significantly correlates with an increase in disease-free survival (DFS) and overall survival (OS). Methods: Randomized, monocentric trial was conducted in NN Petrov National Medical Research Center of Oncology from 2016 to 2019. 99 patients aged from 28 to 68 years with confirmed TNBC were included in trial: 96 had invasive ductal carcinoma G3, 3 - metaplastic cancer, negative BRCA mutations (a test for Founder mutations was performed).Patients were randomized in 3 groups, depending on the NCT regimen:1st subgroup (24 patients) - Eribulin in combination with Carboplatin AUC 5 x 4 cycles 2nd subgroup (37 patients) - Paclitaxel in combination with Carboplatin AUC 5 x 4 cycles 3rd subgroup (38 patients) –Carboplatin AUC5 + Doxorubicin + Paclitaxel x 6 cycles. Patients 1 and 2 subgroups in an adjuvant mode received 4 cycles of AC. Results: Clinical complete response (cCR) by physical examination (palpation) was achieved in 44 out of 99 patients (44.4%). Clinical complete response (cCR) by ultrasound and MG - in 27 (27.2%) patients. Miller-Payne V regression stage was achieved in 55 out of 99 cases (55.6%). In clinical cT1-T2 stage (n = 70), ypCR was achieved in 49 cases (70%), cT3-T4 (n = 29) ypCR in 6 patients (20.68%). Before NCT, 71 patients had status cN0-N1. Conversion to ypN0 occurred in 57 patients (80.2%). In 28 patients with cN2-N3 status, conversion to ypN0 occurred in 7 patients (25%). The median follow-up was 58 months. Progression was observed in 15.1% of patients, mortality – 6%. Local recurrence - 6 patients (6%), all patients were with residual tumor after NCT. Distant recurrence – 8 patients (8.1 %). Local recurrence rate and distant recurrence rate did not correlate with type of surgery (BCS or ME), but correlated with ypCR. Conclusions: NCT for TNBC is advisable both for locally advanced breast cancer and early breast cancer BC. De-escalation of BC surgery is possible in the future, especially in cT1-T2 stage patients (n = 70) where ypCR rate reaches 70%. It is planned to continue the trial with the vacuum aspiration biopsy of the tumor bed and SLNB after NCT.SLNB after NCT is advisable only in cN0-N1 group of patients (n = 71), since conversion to ypN0 was achieved in 57 patients - 80.2%.
Safety of Obinutuzumab Alone or Combined with Chemotherapy in Previously Untreated (Fit or Unfit) or Relapsed/Refractory Chronic Lymphocytic Leukemia (CLL) Patients: Results from the Primary Analysis of the Phase 3b GREEN Study
Authors: Stephan Stilgenbauer, Melih Aktan, Christelle M Ferra Coll, Caroline Dartigeas, Jens Kisro, Marco Montillo, João Raposo, Jean-Louis Merot, Susan Robson, Ekaterina Gresko, Francesc Bosch, Robin Foà, Véronique Leblond
Journal: Blood (2017)
ABCB1/P-glycoprotein (Pgp) expression as stratification factor for treatment of patients with non-metastaticextremity high-grade osteosarcoma: A merged analysis of an Italian (ISG) and a Spanish (GEIS) sarcoma groups' multicentric prospective trials.
Authors: Emanuela Palmerini, Catalina Marquez, Cristina Meazza, Angela Tamburini, Gianni Bisogno, Francisco José Bautista Sirvent, Virginia Ferraresi, Sebastian Dorin Asaftei, Giuseppe Maria Milano, Roberto Luksch, Adela Canete, Aizpea Echebarria, Víctor Quintero, Cristina Mata, Rossella Bertulli, Alessandra Longhi, Piero Picci, Franca Fagioli, Nadia Hindi, Stefano Ferrari
Journal: Journal of Clinical Oncology (2021)

11527 Background: Overexpression of ABCB1/P-glycoprotein (Pgp) predicts poor outcome in retrospective osteosarcoma series.Two prospective trials with Pgp expression and post-induction histologic response as stratification factors were activated in Italy (ISG/OS-2) and Spain (GEIS-33). Methods: Patients ≤ 40 years with extremity non-metastatic high-grade osteosarcoma were eligible. Analysisi of Pgp expression from diagnostic biopsy was centralized. Preoperatively, all patients received methotrexate, adriamycin, cisplatinum (MAP). Surgery was performed at week 8. All patients received a dose of adriamycin following surgery. In case of Pgp overexpression (Pgp+), mifamurtide (2 mg/m2 twice/week for 3 months then weekly for 6 months) was added after surgery, with 4 consecutive cycles of ifosfamide 3 gr/m2/day, day 1-5 (HDIFO) in case of poor histologic response (necrosis &lt; 90%) to MAP. Patients without overexpression of Pgp (Pgp-) received MAP postoperatively, regardless the pathological response. From March 2013, an amendment increased high dose methotrexate cumulative dose from 60 g/m2 (5 cycles) to 120 mg/m2 (10 cycles). The post-amendment regimen was adopted in the observational prospective study by GEIS. Here we present the merged analysis of ISG/OS-2 patients treated post-amendment and GEIS-33. Results: From March 2013 to April 2018, 274 patients were included. Median age was 14 years (range 4-38), male/female: 163/111; 90 were Pgp-, 164 were Pgp+, 20 not evaluable. With a median follow-up of 48 months (1.3-78.5 months), the 3-year EFS and OS were 71.9% (95%CI 66-76.9) and 88% (95%CI: 83.2-91.5) respectively, with no inferior survival for Pgp positive patients and improved survival for good responders (Table). Conclusions: In this prospective uncontrolled study with a risk-adapted strategy for non-metastatic osteosarcoma, survival is superior to that of all ISG/GEIS previous series. The 3-year EFS of 71.9% compares favorably with other reports. Pgp+ patients performed well in this study, in which mifamurtide and HDIFO were added after a poor response to MAP. Clinical trial information: NCT01459484; NCT04383288. [Table: see text]
Response to: ‘Correspondence on: ‘Warfarin use and risk of knee and hip replacements’’ by He<i>et al</i>
Authors: Priyanka Ballal, Christine Peloquin, Cindy Germaine Boer, Tuhina Neogi
Journal: Annals of the Rheumatic Diseases (2021)

We thank the authors for their interest in our work.1–3 Their approach and results provide yet additional support to the adverse impact of warfarin on osteoarthritis outcomes, as compared with direct oral anticoagulants.

Deidentified data were used for this work. These data …
Abstract 14080: Electrocardiographic Criteria for Silent Myocardial Infarction: Impact of Different Definitions on Detection Rates and Prognostic Significance in the Atherosclerosis Risk in Communities Study
Authors: Richard B Stacey, Ronald J Prineas, Zhu-ming Zhang, Bruce Psaty, Wayne D Rosamond, Lynne Wagenknecht, Elsayed Z Soliman
Journal: Circulation (2019)

Introduction: It is unclear how differences in the electrocardiographic (ECG) definition of myocardial infarction (MI) impact detection rates and prognostic significance of silent MI (SMI). Methods...
The Expansion of Health Care Services in the US—Reply
Authors: Larry Levitt
Journal: JAMA (2021)

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Antibodies elicited by mRNA-1273 vaccination bind more broadly to the receptor binding domain than do those from SARS-CoV-2 infection
Authors: Allison J. Greaney, Andrea N. Loes, Lauren E. Gentles, Katharine H.D. Crawford, Tyler N. Starr, Keara D. Malone, Helen Y. Chu, Jesse D. Bloom
Journal: Science Translational Medicine (2021)

The emergence of severe acute respiratory syndrome coronavirus 2 (SARS-CoV-2) variants with mutations in key antibody epitopes has raised concerns that antigenic evolution could erode adaptive immunity elicited by prior infection or vaccination. The susceptibility of immunity to viral evolution is shaped in part by the breadth of epitopes targeted by antibodies elicited by vaccination or natural infection. To investigate how human antibody responses to vaccines are influenced by viral mutations, we used deep mutational scanning to compare the specificity of polyclonal antibodies elicited by either two doses of the mRNA-1273 COVID-19 vaccine or natural infection with SARS-CoV-2. The neutralizing activity of vaccine-elicited antibodies was more targeted to the receptor-binding domain (RBD) of the SARS-CoV-2 spike protein compared to antibodies elicited by natural infection. However, within the RBD, binding of vaccine-elicited antibodies was more broadly distributed across epitopes compared to infection-elicited antibodies. This greater binding breadth means that single RBD mutations have less impact on neutralization by vaccine sera compared to convalescent sera. Therefore, antibody immunity acquired by natural infection or different modes of vaccination may have a differing susceptibility to erosion by SARS-CoV-2 evolution.
Maintenance immunosuppressive therapy with resumption of immune checkpoint inhibitor treatment to reduce recurrence of immune-mediated colitis.
Authors: Hamzah Abu-Sbeih, Fangwen Zou, Barbara Dutra, Mehmet Altan, Jennifer Leigh McQuade, John A. Thompson, Anusha Thomas, Yinghong Wang
Journal: Journal of Clinical Oncology (2021)

2642 Background: Immune-mediated colitis (IMC) may limit immune checkpoint inhibitors (ICI) treatment. Current guidelines recommend consideration of resuming ICI when IMC symptoms subside to ≤ grade 1. We aimed to investigate the effect of maintenance immunosuppressive therapy (IST) on the outcome of IMC in patients who resume ICI therapy. Methods: We retrospectively studied patients who resumed ICI therapy after adequate treatment of IMC from March 2015 to June 2020 at MD Anderson Cancer Center. Relevant demographic, oncologic, and ICI data were collected and analyzed. Univariate logistic regression analysis was conducted to assess risk factors of IMC recurrence. Results: We included 102 patients with a median age of 61 years. 66% were males and 97% were Caucasians. 48 patients (47%) received IST maintenance in conjunction with ICI resumption and 54 patients did not. Symptoms of IMC recurred in 28 patients, 8 (17%) in the concurrent IST group and 20 (37%) in the other group. Compared to no concurrent IST group, patients on concurrent IST were more likely to have received combined ICI regimen (60% vs 41%, p = 0.003) and more initial ICI doses (9 vs 5 doses, p = 0.030). Concurrent IST group had significantly longer ICI treatment duration on resumption (72 vs 62 days, p = 0.023), more ICI resumed doses (5 vs 4 doses, p = 0.038), and lower IMC recurrence (17% vs 37%, p = 0.027). Patient who received more IST doses, both therapeutic and prophylactic, had lower rate of IMC recurrence (OR 0.72, p = 0.012; table). IST maintenance treatment (OR 0.34, p = 0.024) was associated with lower IMC recurrence rate after ICI resumption. Vedolizumab was the predominant IST used. Overall survival was comparable among the two groups (p = 0.934). Conclusions: Concurrent IST treatment with ICI resumption after IMC was associated with significantly lower IMC recurrence and more extended ICI treatment while reserving similar overall survival to patients without IST maintenance therapy. Future prospective randomized trial of concurrent IST is still merited for further clarification.[Table: see text]
The impact of antibiotic (Ab) exposure on clinical outcomes in patients with metastatic renal cell carcinoma (mRCC) treated with immune checkpoint inhibitors (ICI) or VEGF targeted therapy (VEGF-TT).
Authors: Matthew Scott Ernst, Sarah Abou Alaiwi, Nazli Dizman, Chris Labaki, Pier Vitale Nuzzo, Elio Adib, Andrew Lachlan Schmidt, Luis A Meza, Chun Loo Gan, J Connor Wells, Ziad Bakouny, Sumanta K. Pal, Toni K. Choueiri, Daniel Yick Chin Heng, Shaan Dudani
Journal: Journal of Clinical Oncology (2021)

4552 Background: Retrospective studies have shown an association between Ab exposure and inferior clinical outcomes in patients receiving ICI across various tumor types, including mRCC. However, it is unclear whether Ab exposure has a unique interaction with ICI or is an independent prognostic marker, regardless of treatment. We sought to examine Ab exposure and its association with clinical outcomes in patients with mRCC treated with ICI compared to VEGF-TT. Methods: We identified patients treated with ICI (anti-PD-L1 alone or in combination with VEGF or CTLA4 inhibitor) or VEGF-TT alone in first to fourth line settings from 2009-2020 across 3 academic centers in North America. Ab exposure was defined as administration of Ab within 60 days prior to initiation of systemic therapy. Outcomes of interest were response rate (RR), time to treatment failure (TTF) and overall survival (OS). Multivariable Cox regression was performed to control for imbalances in International mRCC Database Consortium (IMDC) risk factors, histology, and treatment line. Results: We identified 748 patients. Among the ICI (n=427) and VEGF-TT (n=321) cohorts, 13% vs 15% (p=0.47) had Ab exposure and 57% vs 48% (p=0.046) were treated in the first line setting. The proportion of favorable, intermediate, and poor risk disease by IMDC criteria differed between Ab exposed and unexposed patients in the ICI (14% vs 18%, 47% vs 62%, 39% vs 21% p=0.03) and VEGF-TT (7% vs 13%, 43% vs 60%, 50% vs 27%, p=0.01) cohorts. RR, TTF and OS results are displayed in Table 1. Multivariable analysis did not show a significant independent association between Ab exposure and OS in both the ICI (HR 1.13, p=0.62) and VEGF-TT (HR 1.32, p=0.16) cohorts. Treatment modality (ICI vs VEGF-TT) did not modify the effect of Ab exposure on OS (p=0.84). Conclusions: Ab exposure was associated with higher IMDC risk scores in both the ICI and VEGF-TT cohorts as well as inferior OS on univariable analysis. After adjusting for IMDC risk factors, histology and treatment line, we were unable to find an independent association between Ab exposure and OS in multivariable analysis for either cohort.[Table: see text]
RNA sequencing effectively identifies gene fusions undetected by DNA sequencing in lung adenocarcinomas.
Authors: Ruiying Zhao, Yuchen Han, Chan Xiang, Shengnan Chen, Jikai Zhao, Lianying Guo, Anbo Yu, Jinchen Shao, Lei Zhu, Yue Tian, Fan Yang, Lin Shao, Xuejing Li, Lu Zhang
Journal: Journal of Clinical Oncology (2021)

3052 Background: Next-generation sequencing of DNA, which can provide valid information for clinical therapeutic decision-making, has been widely used in the management of lung cancer especially adenocarcinoma. However, due to its technical limitations for detecting certain alterations such as gene rearrangement, the DNA-based sequencing (DNA-seq) may miss the actionable alteration in some cases, who would have benefited from targeted therapy. The study aimed to evaluate the capability of RNA sequencing (RNA-seq) in identifying DNA-seq undetectable gene alterations in lung adenocarcinomas. Methods: A total of 219 lung adenocarcinomas, which had no driver alteration detected by DNA-seq (OncoScreen Plus, Burning Rock Biotech) and had a max AF ≥5%, underwent capture-based RNA-seq using a custom panel (OncoRNA, Burning Rock Biotech) spanning full transcripts of 115 genes commonly involved in cancer genomic rearrangements. Furthermore, an independent cohort of 100 DNA-seq driver–negative lung adenocarcinomas were also subjected to RNA-seq with the same panel. Results: In the discovery cohort, 166/219 samples (75.8%) generated qualified RNA-seq data for subsequent analyses. RNA-seq identified 44 previously undetected alterations (26.5%), including 40 gene fusions (24.1%), 1 MET exon14 skipping variant ( METex14, 0.6%) and 3 other alternative splicing variants (1.8%). Among them, 14 (8.4%) were potential actionable alterations, consisting of METex14 and in-frame fusions containing functional domain of the driver gene (4 ROS1 fusions, 3 BRAF fusions, 2 NRG1 fusions, 2 EGFR fusions, 1 ALK fusion and 1 MET fusion). In the validation cohort, 69/100 samples (69.0%) generated qualified data. RNA-seq identified 22 DNA-seq undetected alterations (31.9%), with 7 of them being potential actionable fusions (10.1%). ROS1 fusion remained as the most common actionable alteration (n = 3), followed by ALK fusion (n = 2), EGFR fusion (n = 1) and MET fusion (n = 1). Further analyses of the two datasets revealed that lacking sufficient coverage spanning the rearrangement breakpoint in the DNA-seq panel mainly accounted for the failure of DNA-seq on detecting these fusions. This can be improved by increasing the corresponding probe coverage in the DNA-seq panel. In addition, complex genomic rearrangement at DNA level and the presence of repetitive sequence in the intronic region spanning or adjacent to the breakpoint might lead to missed calling of canonical fusions by DNA-seq. Conclusions: Targeted RNA-seq can effectively identify genomic rearrangements that are undetectable by DNA-seq and provide lung adenocarcinoma patients with more opportunities for targeted therapy. Therefore, it should be recommended for all patients, in whom DNA-seq fails to detect driver alteration.
Reactive oxygen species as potential signal mediators in all-trans retinoic acid mediated differentiation of neuroblastoma
Authors: Kinsley K. Kiningham, Carla Cook
Journal: Cancer Research (2005)

1854  Retinoids, active vitamin A metabolites, are signaling molecules that are involved in proliferation, differentiation and apoptosis during development. Retinoids exert their effects, in part, through binding to nuclear hormone receptors, thereby modulating gene expression. The clinical effectiveness of retinoid therapy in the treatment of neuroblastoma and other tumors is of interest due to their success in management of acute promyelocytic leukemia; however, one limitation to their use is the potential for induction of chemoresistance. Several studies have reported that reactive oxygen species (ROS), including superoxide anion, are generated upon exposure to retinoids. Therefore, we evaluated the role of ROS in ATRA-mediated signaling in neuroblastoma. Administration of all trans retinoic acid (ATRA) to a human neuroblastoma cell line (SK-N-SH) increased immunoreactive 4-hydroxy-2-nonenal-adducted proteins in a time dependent manner, verifying increases in lipid peroxidation products that could be the result of increased ROS production. In addition, the p50 and p65 components of the redox sensitive transcription factor, NFκB, translocated to the nucleus within 24 h, resulting in an increase in DNA binding and transcriptional activity. Protein and activity levels of the mitochondrial antioxidant and NFκB target gene, manganese superoxide dismutase (MnSOD), increased in a concentration and time dependent manner upon ATRA administration. The increase in ROS and MnSOD, a protein reported to enhance differentiation, increased prior to expression of neuronal markers (NeuN, NMDAR1, tau), suggesting an early event in ATRA-mediated signaling. The antiapoptotic protein and NFκB target gene, bcl-xL, increased within 24 h of exposure to ATRA, an effect that was attenuated in the presence of antioxidants. Taken together, these results suggest that generation of ROS upon ATRA administration may represent an indirect, yet novel pathway by which retinoids modulate signaling events and may serve as a pharmacological target to increase the efficacy of ATRA therapy. (Supported by 1P20RR020180)