tbuckley/cabot-search huggingface dataset:
Clinical and Genome-Wide Analysis of Multiple Severe Cisplatin-Induced Neurotoxicities in Adult-Onset Cancer Survivors
Authors: Matthew R. Trendowski, Heather E. Wheeler, Omar El-Charif, Darren R. Feldman, Robert J. Hamilton, David J. Vaughn, Chunkit Fung, Christian Kollmannsberger, Lawrence H. Einhorn, Lois B. Travis, M. Eileen Dolan
Journal: Clinical Cancer Research (2020)

Abstract Purpose: Cisplatin is a first-line chemotherapeutic for many cancers, but causes neurotoxicity including hearing loss, tinnitus, and peripheral sensory neuropathy. However, no study has comprehensively characterized risk factors for developing multiple (&amp;gt;1) severe neurotoxicities. Experimental Design: The relationship between multiple severe neurotoxicities and age, cumulative cisplatin dose, medical history, and lifestyle/behavioral factors was evaluated in 300 cisplatin-treated testicular cancer survivors using logistic regression. Case–control genome-wide association study (GWAS; cases, n = 104 and controls, n = 196) was also performed. Results: Age at clinical examination (P = 6.4 × 10−16) and cumulative cisplatin dose (P = 5.4 × 10−4) were positively associated with multiple severe neurotoxicity risk, as were high serum platinum levels (P = 0.02), tobacco use (ever smoker, P = 0.001 and current smoker, P = 0.002), and hypertension (P = 0.01) after adjustment for age and cumulative cisplatin dose. Individuals with multiple severe neurotoxicities were more likely to experience dizziness/vertigo (P = 0.01), Raynaud phenomenon (P = 3.7 × 10−9), and symptoms consistent with peripheral motor neuropathy (P = 4.3 × 10−14) after age and dose adjustment. These patients also reported poorer overall health (P = 2.7 × 10−5) and a greater use of psychotropic medications (P = 0.06). GWAS identified no genome-wide significant SNPs. Gene-based association analysis identified RGS17 (P = 3.9 × 10−5) and FAM20C (P = 5.5 × 10−5) as near genome-wide significant. Decreased FAM20C expression was associated with increased cisplatin sensitivity in tumor cell lines. Conclusions: Certain survivors are more susceptible to cisplatin-induced neurotoxicity, markedly increasing likelihood of developing numerous neuro-otological symptoms that affect quality of life. Genome-wide analysis identified genetic variation in FAM20C as a potentially important risk factor.
COMMUNITY-ACQUIRED CHRONIC HEPATITIS-C IN AN AREA OF HIGH SEROTYPE-1 ENDEMICITY - INTERFERON FOR 6 OR 12 MONTHS
Authors: A Craxi, O Loiacono, V Dimarco, P Almasio, A Vaccaro, C Camma, C Fabiano, S Magrin, P Simmonds, L Pagliaro
Journal: Hepatology (1994)
Association of Peer Comparison Emails With Electronic Health Record Documentation of Cancer Stage by Oncologists
Authors: Anna D. Sinaiko, Michael L. Barnett, Marema Gaye, Margaret Soriano, Therese Mulvey, Ephraim Hochberg
Journal: JAMA Network Open (2020)

<h3>Importance</h3> Systematically capturing cancer stage is essential for any serious effort by health systems to monitor outcomes and quality of care in oncology. However, oncologists do not routinely record cancer stage in machine-readable structured fields in electronic health records (EHRs). <h3>Objective</h3> To evaluate whether a peer comparison email intervention that communicates an oncologist's performance on documenting cancer stage relative to that of peer physicians was associated with increased likelihood that stage was documented in the EHR. <h3>Design, Setting, and Participants</h3> This 12-month, randomized quality improvement pilot study aimed to increase oncologist staging documentation in the EHR. The pilot study was performed at Massachusetts General Hospital Cancer Center from October 1, 2018, to September 30, 2019. Participants included 56 oncologists across 3 practice sites who treated patients in the ambulatory setting and focused on diseases that use standardized staging systems. Data were analyzed from July 2, 2019, to March 5, 2020. <h3>Interventions</h3> Peer comparison intervention with as many as 3 emails to oncologists during 6 months that displayed the oncologist's staging documentation rate relative to all oncologists in the study sample. <h3>Main Outcomes and Measures</h3> The primary outcome was patient-level documentation of cancer stage, defined as the likelihood that a patient's stage of disease was documented in the EHR after the patient's first (eg, index) ambulatory visit during the pilot period. <h3>Results</h3> Among the 56 oncologists participating (32 men [57%]), receipt of emails with peer comparison data was associated with increased likelihood of documentation of cancer stage using the structured field in the EHR (23.2% vs 13.0% of patient index visits). In adjusted analyses, this difference represented an increase of 9.0 (95% CI, 4.4-13.5) percentage points (<i>P</i> = .002) in the probability that a patient's cancer stage was documented, a relative increase of 69% compared with oncologists who did not receive peer comparison emails. The association increased with each email that was sent, ranging from a nonsignificant 4.0 (95% CI, −0.8 to 8.8) percentage points (P = .09) after the first email to a statistically significant 11.2 (95% CI, 4.9-17.4) percentage points (P = .003) after the third email . The association was concentrated among an oncologist's new patients (increase of 11.8 [95% CI, 6.2-17.4] percentage points;<i>P</i> = .001) compared with established patients (increase of 1.6 [95% CI, –2.9 to 6.1] percentage points;<i>P</i> = .44) and persisted for 7 months after the email communications stopped. <h3>Conclusions and Relevance</h3> In a quality improvement pilot trial, peer comparison emails were associated with a substantial increase in oncologist use of the structured field in the EHR to document stage of disease.
Subacromial decompression versus diagnostic arthroscopy for shoulder impingement: a 5-year follow-up of a randomised, placebo surgery controlled clinical trial
Authors: Mika Paavola, Kari Kanto, Jonas Ranstam, Antti Malmivaara, Jari Inkinen, Juha Kalske, Vesa Savolainen, Ilkka Sinisaari, Simo Taimela, Teppo L Järvinen
Journal: British Journal of Sports Medicine (2020)

Objectives To assess the long-term efficacy of arthroscopic subacromial decompression (ASD) by comparing it with diagnostic arthroscopy (primary comparison), a placebo surgical intervention, and with a non-operative alternative, exercise therapy (secondary comparison). Methods We conducted a multicentre, three group, randomised, controlled superiority trial. We included 210 patients aged 35–65 years, who had symptoms consistent with shoulder impingement syndrome for more than 3 months. 175 participants (83%) completed the 5 years follow-up. Patient enrolment began on 1 February 2005 and the 5-year follow-up was completed by 10 October 2018. The two primary outcomes were shoulder pain at rest and on arm activity measured with Visual Analogue Scale (VAS). Minimally important difference (MID) was set at 15. We used a mixed-model repeated measurements analysis of variance with participant as a random factor, the baseline value as a covariate and assuming a covariance structure with compound symmetry. Results In the primary intention to treat analysis (ASD vs diagnostic arthroscopy), there were no between-group differences that exceeded the MID for the primary outcomes at 5 years: the mean difference between groups (ASD minus diagnostic arthroscopy) in pain VAS were −2.0 (95% CI −8.5 to 4.6; p=0.56) at rest and −8.0 (−17.3 to 1.3; p=0.093) on arm activity. There were no between-group differences in the secondary outcomes or adverse events that exceeded the MID. In our secondary comparison (ASD vs exercise therapy), the mean differences between groups (ASD minus exercise therapy) in pain VAS were 1.0 (−5.6 to 7.6; p=0.77) at rest and −3.9 (−12.8 to 5.1; p=0.40) on arm activity. There were no significant between-group differences for the secondary outcomes or adverse events. Conclusions ASD provided no benefit over diagnostic arthroscopy (or exercise therapy) at 5 years for patients with shoulder impingement syndrome.
Advances and novel developments in drug hypersensitivity diagnosis
Authors: Adriana Ariza, Cristobalina Mayorga, Gador Bogas, Esther Barrionuevo, Maria J. Torres, Inmaculada Doña, Tahia D. Fernandez
Journal: Allergy (2020)

A correct diagnosis of drug hypersensitivity reactions (DHRs) is very important for both the patient and health system. However, DHRs diagnosis is complex, time consuming, requires trained personnel, is not standardized for many drugs, involves procedures not exempt of risk, and in most cases lacks standardized in vivo and in vitro tests. Thus, there is an urgent need for improving the different approaches to diagnose patients with suspected DHRs. In this review, we have analyzed the advances performed in immediate and nonimmediate DHRs diagnosis during the last two years and obtained several conclusions: the significant heterogeneity in current practice among centers illustrates the need to re-evaluate, update, and standardize in vivo tests and protocols for the diagnosis and management of patients with suspected drug allergy. Regarding in vitro tests, the latest studies have focused on increasing their sensitivity or on establishing the sensitivity and specificity for the tests performed with new drugs. There seems to be a consensus about combining in vivo and in vitro tests as the best way to increase the diagnostic accuracy.
Genome and Transcriptome Biomarkers of Response to Immune Checkpoint Inhibitors in Advanced Solid Tumors
Authors: Alexandra Pender, Emma Titmuss, Erin D. Pleasance, Kevin Y. Fan, Hillary Pearson, Scott D. Brown, Cameron J. Grisdale, James T. Topham, Yaoqing Shen, Melika Bonakdar, Gregory A. Taylor, Laura M. Williamson, Karen L. Mungall, Eric Chuah, Andrew J. Mungall, Richard A. Moore, Jean-Michel Lavoie, Stephen Yip, Howard Lim, Daniel J. Renouf, Sophie Sun, Robert A. Holt, Steven J.M. Jones, Marco A. Marra, Janessa Laskin
Journal: Clinical Cancer Research (2020)

Abstract Purpose: Immune checkpoint inhibitors (ICI) have revolutionized the treatment of solid tumors with dramatic and durable responses seen across multiple tumor types. However, identifying patients who will respond to these drugs remains challenging, particularly in the context of advanced and previously treated cancers. Experimental Design: We characterized fresh tumor biopsies from a heterogeneous pan-cancer cohort of 98 patients with metastatic predominantly pretreated disease through the Personalized OncoGenomics program at BC Cancer (Vancouver, Canada) using whole genome and transcriptome analysis (WGTA). Baseline characteristics and follow-up data were collected retrospectively. Results: We found that tumor mutation burden, independent of mismatch repair status, was the most predictive marker of time to progression (P = 0.007), but immune-related CD8+ T-cell and M1-M2 macrophage ratio scores were more predictive for overall survival (OS; P = 0.0014 and 0.0012, respectively). While CD274 [programmed death-ligand 1 (PD-L1)] gene expression is comparable with protein levels detected by IHC, we did not observe a clinical benefit for patients with this marker. We demonstrate that a combination of markers based on WGTA provides the best stratification of patients (P = 0.00071, OS), and also present a case study of possible acquired resistance to pembrolizumab in a patient with non–small cell lung cancer. Conclusions: Interpreting the tumor-immune interface to predict ICI efficacy remains challenging. WGTA allows for identification of multiple biomarkers simultaneously that in combination may help to identify responders, particularly in the context of a heterogeneous population of advanced and previously treated cancers, thus precluding tumor type–specific testing.
Long-Term Outcomes of Patients With Mediastinal Radiation–Associated Coronary Artery Disease Undergoing Coronary Revascularization With Percutaneous Coronary Intervention and Coronary Artery Bypass Grafting
Authors: Aaron N. Dunn, Eoin Donnellan, Douglas R. Johnston, Alaa Alashi, Grant W. Reed, Christine Jellis, Amar Krishnaswamy, A. Marc Gillinov, Lars G. Svensson, Stephen Ellis, Brian P. Griffin, Samir R. Kapadia, Gosta B. Pettersson, Milind Y. Desai
Journal: Circulation (2020)
SUV39H1 deficiency suppresses clear cell renal cell carcinoma growth by inducing ferroptosis
Authors: Jianfeng Wang, Xiaomao Yin, Wei He, Wei Xue, Jin Zhang, Yiran Huang
Journal: Acta Pharmaceutica Sinica B (2020)

Clear cell renal cell carcinoma (ccRCC) is a common kidney malignancy characterized by a poor prognosis. Suppressor of variegation 3–9 homolog 1 (SUV39H1), which encodes a histone H3 lysine 9 methyltransferase, has been reported to act as an oncogene in many cancers. However, it is unclear whether SUV39H1 is involved in ccRCC. Here, we report that SUV39H1 expression is frequently upregulated in ccRCC tumors and is significantly correlated with ccRCC progression. SUV39H1 expression level is an independent risk factor for cancer prognosis, and integration with several known prognostic factors predicted ccRCC patient prognosis with improved accuracy than the conventional SSIGN (stage, size, grade and necrosis) prognostic model. Mechanistically, we discovered that siRNA knockdown or pharmacological inhibition of SUV39H1 induced iron accumulation and lipid peroxidation, leading to ferroptosis that disrupted ccRCC cell growth in vitro and in vivo. We also show that SUV39H1 deficiency modulated the H3K9me3 status of the DPP4 (dipeptidyl-peptidase-4) gene promoter, resulting in upregulation of its expression that contributes to ferroptosis. Taken together, our findings provide the mechanistic insight into SUV39H1-dependent epigenetic control of ccRCC tumor growth and indicate that SUV39H1 may serve as a potential therapeutic target for ccRCC treatment.
Seroprevalence of SARS-CoV-2 antibodies in people with an acute loss in their sense of smell and/or taste in a community-based population in London, UK: An observational cohort study
Authors: Janine Makaronidis, Jessica Mok, Nyaladzi Balogun, Cormac G. Magee, Rumana Z. Omar, Alisia Carnemolla, Rachel L. Batterham
Journal: PLoS Medicine (2020)

Background Loss of smell and taste are commonly reported symptoms associated with coronavirus disease 2019 (COVID-19); however, the seroprevalence of severe acute respiratory syndrome coronavirus 2 (SARS-CoV-2) antibodies in people with acute loss of smell and/or taste is unknown. The study aimed to determine the seroprevalence of SARS-CoV-2 antibodies in a community-based population with acute loss of smell and/or taste and to compare the frequency of COVID-19 associated symptoms in participants with and without SARS-CoV-2 antibodies. It also evaluated whether smell or taste loss are indicative of COVID-19 infection. Methods and findings Text messages, sent via primary care centers in London, United Kingdom, invited people with loss of smell and/or taste in the preceding month, to participate. Recruitment took place between 23 April 2020 and 14 May 2020. A total of 590 participants enrolled via a web-based platform and responded to questions about loss of smell and taste and other COVID-19–related symptoms. Mean age was 39.4 years (SD ± 12.0) and 69.1% (n = 392) of participants were female. A total of 567 (96.1%) had a telemedicine consultation during which their COVID-19–related symptoms were verified and a lateral flow immunoassay test that detected SARS-CoV-2 immunoglobulin G (IgG) and immunoglobulin M (IgM) antibodies was undertaken under medical supervision. A total of 77.6% of 567 participants with acute smell and/or taste loss had SARS-CoV-2 antibodies; of these, 39.8% (n = 175) had neither cough nor fever. New loss of smell was more prevalent in participants with SARS-CoV-2 antibodies, compared with those without antibodies (93.4% versus 78.7%, p < 0.001), whereas taste loss was equally prevalent (90.2% versus 89.0%, p = 0.738). Seropositivity for SARS-CoV-2 was 3 times more likely in participants with smell loss (OR 2.86; 95% CI 1.27–6.36; p < 0.001) compared with those with taste loss. The limitations of this study are the lack of a general population control group, the self-reported nature of the smell and taste changes, and the fact our methodology does not take into account the possibility that a population subset may not seroconvert to develop SARS-CoV-2 antibodies post-COVID-19. Conclusions Our findings suggest that recent loss of smell is a highly specific COVID-19 symptom and should be considered more generally in guiding case isolation, testing, and treatment of COVID-19. Trials registration ClinicalTrials.gov NCT04377815
Acute Statin Treatment Improves Antibody Accumulation in EGFR- and PSMA-Expressing Tumors
Authors: Patrícia M.R. Pereira, Komal Mandleywala, Ashwin Ragupathi, Jason S. Lewis
Journal: Clinical Cancer Research (2020)

Abstract Purpose: Statins are cholesterol-depleting drugs used to treat patients with hypercholesterolemia. Preclinically, statins disrupt trafficking of receptors present at the cell membrane. Membrane receptors, defined as tumor biomarkers and therapeutic targets, are often internalized by an endocytic pathway. Indeed, receptor endocytosis and recycling are dynamic mechanisms that often affect receptor density at the cell surface. In therapies using monoclonal antibodies (mAb), a downregulation in receptor density at the cell surface decreases antibody binding to the extracellular domain of the membrane receptor. Here, we determined the potential of lovastatin, simvastatin, and rosuvastatin in preclinically modulating epidermal growth factor receptor (EGFR) and prostate-specific membrane antigen (PSMA) receptor density at the tumor cell surface. Experimental Design: Small-animal PET was used to study the binding of 89Zr-labeled antibodies in ectopic xenografts. Ex vivo analyses were performed to determine changes in endocytic proteins, EGFR, and PSMA surface levels. Results: Acute statin treatment using lovastatin, simvastatin, or rosuvastatin enhanced tumors' avidity for the mAbs panitumumab, cetuximab, and huJ591. Statins temporarily modulated caveolin-1, cavin-1, endophilin, clathrin, and dynamin proteins in EGFR- and PSMA-overexpressing xenografts. Conclusions: These data show the potential of statins as pharmacologic modulators of endocytic proteins for improved tumors' accumulation of mAbs. The translational significance of these findings lies in the potential of statins to temporarily modulate the heterogeneous presence of receptors at the cell membrane, a characteristic often associated with poor response in tumors to therapeutic antibodies.
The role of alternative splicing in cancer: From oncogenesis to drug resistance
Authors: Rocco Sciarrillo, Anna Wojtuszkiewicz, Yehuda G. Assaraf, Gerrit Jansen, Gertjan J.L. Kaspers, Elisa Giovannetti, Jacqueline Cloos
Journal: Drug Resistance Updates (2020)

Alternative splicing is a tightly regulated process whereby non-coding sequences of pre-mRNA are removed and protein-coding segments are assembled in diverse combinations, ultimately giving rise to proteins with distinct or even opposing functions. In the past decade, whole genome/transcriptome sequencing studies revealed the high complexity of splicing regulation, which occurs co-transcriptionally and is influenced by chromatin status and mRNA modifications. Consequently, splicing profiles of both healthy and malignant cells display high diversity and alternative splicing was shown to be widely deregulated in multiple cancer types. In particular, mutations in pre-mRNA regulatory sequences, splicing regulators and chromatin modifiers, as well as differential expression of splicing factors are important contributors to cancer pathogenesis. It has become clear that these aberrations contribute to many facets of cancer, including oncogenic transformation, cancer progression, response to anticancer drug treatment as well as resistance to therapy. In this respect, alternative splicing was shown to perturb the expression a broad spectrum of relevant genes involved in drug uptake/metabolism (i.e. SLC29A1, dCK, FPGS, and TP), activation of nuclear receptor pathways (i.e. GR, AR), regulation of apoptosis (i.e. MCL1, BCL-X, and FAS) and modulation of response to immunotherapy (CD19). Furthermore, aberrant splicing constitutes an important source of novel cancer biomarkers and the spliceosome machinery represents an attractive target for a novel and rapidly expanding class of therapeutic agents. Small molecule inhibitors targeting SF3B1 or splice factor kinases were highly cytotoxic against a wide range of cancer models, including drug-resistant cells. Importantly, these effects are enhanced in specific cancer subsets, such as splicing factor-mutated and c-MYC-driven tumors. Furthermore, pre-clinical studies report synergistic effects of spliceosome modulators in combination with conventional antitumor agents. These strategies based on the use of low dose splicing modulators could shift the therapeutic window towards decreased toxicity in healthy tissues. Here we provide an extensive overview of the latest findings in the field of regulation of splicing in cancer, including molecular mechanisms by which cancer cells harness alternative splicing to drive oncogenesis and evade anticancer drug treatment as well as splicing-based vulnerabilities that can provide novel treatment opportunities. Furthermore, we discuss current challenges arising from genome-wide detection and prediction methods of aberrant splicing, as well as unravelling functional relevance of the plethora of cancer-related splicing alterations.
TGF-β and Eomes control the homeostasis of CD8+ regulatory T cells
Authors: Shruti Mishra, Wei Liao, Yong Liu, Ming Yang, Chaoyu Ma, Haijing Wu, Ming Zhao, Xin Zhang, Yuanzheng Qiu, Qianjin Lu, Nu Zhang
Journal: The Journal of Experimental Medicine (2020)

In addition to Foxp3+ CD4+ regulatory T cells (CD4+ T reg cells), Foxp3− CD8+ regulatory T cells (CD8+ T reg cells) are critical to maintain immune tolerance. However, the molecular programs that specifically control CD8+ but not CD4+ T reg cells are largely unknown. Here, we demonstrate that simultaneous disruption of both TGF-β receptor and transcription factor Eomesodermin (Eomes) in T cells results in lethal autoimmunity due to a specific defect in CD8+ but not CD4+ T reg cells. Further, TGF-β signal maintains the regulatory identity, while Eomes controls the follicular location of CD8+ T reg cells. Both TGF-β signal and Eomes coordinate to promote the homeostasis of CD8+ T reg cells. Together, we have identified a unique molecular program designed for CD8+ T reg cells.