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A screening approach:exploring and assessing genes responsible for neural invasion in pancreatic cancer

Pancreatology 2024年 24卷 e119-e119页

作者： Kavaklioglu, Basak Yildizhan, Saliha Elif Ertetik, Utku Sigirli, Sila Cevik, Nedim Can Baybag, Deniz Karakas, Didem Demir, Ihsan Ekin Ceyhan, Guralp Onur Department of Medical Biotechnology. Acibadem Mehmet Ali Aydinlar University Istanbul - Turkey Department of Biostatistics and Bioinformatics Acibadem Mehmet Ali Aydinlar University Istanbul Turkey Pancreatic Cancer Research Center Acibadem Mehmet Ali Aydinlar University Istanbul Turkey Pancreatic Cancer Research Center Acibadem Mehmet Ali Aydınlar University Istanbul Turkey Department of Surgery Klinikum rechts der Isar Technical University of Munich School of Medicine Munich Germany Munich Baden-Wberg Bayern Germany Department of General Surgery HPB-Unit School of Medicine Acibadem Mehmet Ali Aydinlar University Istanbul Turkey Istanbul Turkey

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111P Leveraging circulating tumor DNA sequencing for first-line cancer treatment: Insights from two prospective precision medicine studies

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Annals of Oncology 2024年 35卷 S258-S259页

作者： V. Debien S. Taleb S. Cousin L. Belcaid A. Bayle I. Taleb A. Besson N. El Ghazzi A. Moreau Y. Laizet M. Alamé D. Vasseur L. Blouin E. Khalifa L. Lacroix I. Soubeyran E. Rouleau C.P. Massard A. Italiano Early Phase Clinical Trials Unit Institute Bergonié - Centre Régional de Lutte Contre le Cancer (CLCC) Bordeaux France DITEP Institut Gustave Roussy Villejuif France Early Phase Trials Department Institut Bergonié Bordeaux France Department of Medical Oncology Copenhagen University Copenhagen Denmark Biostatistics and Epidemiology U1018 Oncostat Institut Gustave Roussy Villejuif France Radiotherapy Department Institut Bergonie Bordeaux France Department of Bioinformatics Institut Bergonié Bordeaux France Bioinformatics and AI Unit Institute Bergonié - Centre Régional de Lutte Contre le Cancer (CLCC) Bordeaux France Molecular Pathology Department Institute Bergonié - Centre Régional de Lutte Contre le Cancer (CLCC) Bordeaux France Medical Biology and Pathology Department Gustave Roussy - Cancer Campus Villejuif France Biopathology Department Institute Bergonié Bordeaux France Tumor Genetics Department Gustave Roussy - Cancer Campus Villejuif France Drug Development Department (DITEP) Gustave Roussy - Cancer Campus Villejuif France

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Correction: Circulating cell free DNA and citrullinated histone H3 as useful biomarkers of NETosis in endometrial cancer

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Journal of experimental & clinical cancer research : CR 2023年第1期42卷 278页

作者： Livia Ronchetti Irene Terrenato Margherita Ferretti Giacomo Corrado Frauke Goeman Sara Donzelli Chiara Mandoj Roberta Merola Ashanti Zampa Mariantonia Carosi Giovanni Blandino Laura Conti Anna Maria Lobascio Marcello Iacobelli Enrico Vizza Giulia Piaggio Aymone Gurtner SAFU Unit IRCCS - Regina Elena National Cancer Institute via Elio Chianesi 53 Rome 00144 Italy. Clinical Trial Center - Biostatistics & Bioinformatics IRCCS - Regina Elena National Cancer Institute Rome Italy. Department of Women and Children Health Gynecologic Oncology Unit Fondazione Policlinico Universitario A. Gemelli IRCCS - Università Cattolica del Sacro Cuore Roma Italy. Oncogenomics and Epigenetics Unit IRCCS - Regina Elena National Cancer Institute Rome Italy. Clinical Pathology Unit IRCCS - Regina Elena National Cancer Institute Rome Italy. Gynecologic Oncology Unit IRCCS - Regina Elena National Cancer Institute Rome Italy. Anatomy Pathology Unit IRCCS - Regina Elena National Cancer Institute Rome Italy. SAFU Unit IRCCS - Regina Elena National Cancer Institute via Elio Chianesi 53 Rome 00144 Italy. aymone.gurtner@ifo.it. Institute of Translational Pharmacology (IFT) National Research Council (CNR) Rome Italy. aymone.gurtner@ifo.it.

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Correction to: Role of Hippo pathway dysregulation from gastrointestinal premalignant lesions to cancer

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Journal of translational medicine 2024年第1期22卷 420页

作者： Giulia Schiavoni Beatrice Messina Stefano Scalera Lorenzo Memeo Cristina Colarossi Marzia Mare Giovanni Blandino Gennaro Ciliberto Giulia Bon Marcello Maugeri-Saccà Clinical Trial Center Biostatistics and Bioinformatics Unit Department of Research Diagnosis and Innovative Technologies IRCCS Regina Elena National Cancer Institute Rome Italy. SAFU Laboratory Department of Research Advanced Diagnostic and Technological Innovation IRCCS Regina Elena National Cancer Institute Rome Italy. Pathology Unit Mediterranean Institute of Oncology Viagrande Italy. Medical Oncology Unit Mediterranean Institute of Oncology Viagrande Italy. Department of Biomedical Dental Morphological and Functional Imaging Sciences University of Messina Messina Italy. Translational Oncology Research Unit Department of Research Diagnosis and Innovative Technologies IRCCS Regina Elena National Cancer Institute Rome Italy. Scientific Directorate IRCCS Regina Elena National Cancer Institute Rome Italy. Cellular Network and Molecular Therapeutic Target Unit Department of Research Diagnosis and Innovative Technologies IRCCS Regina Elena National Cancer Institute Via Elio Chianesi 53 00144 Rome Italy. giulia.bon@ifo.it. Division of Medical Oncology 2 IRCCS Regina Elena National Cancer Institute Rome Italy.

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207 ctDNA-based WES enhances actionable alterations detection in locally advanced head and neck cancer

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Radiotherapy and Oncology 2024年 192卷 S55-S58页

作者： Gema Bruixola Jorge Martín-Arana Francisco Gimeno-Valiente Victor Seguí Jose Francisco Catalá-Senent Juan Antonio Carbonell-Asins Elena Duréndez Nuria Grimalt Delfina Dualde Clara Alfaro Olga Pons Vicente Escorihuela-García María Eugenia Iglesias Andrés Cervantes Noelia Tarazona Hospital Clínico Universitario. INCLIVA Biomedical Research Institute. Medical Oncology Valencia Spain INCLIVA Biomedical Research Institute. Bioinformatics Unit Valencia Spain INCLIVA Biomedical Research Institute. Biostatistics Unit Valencia Spain Hospital Clínico Universitario. INCLIVA Biomedical Research Insitute. University of Valencia. Radiology Valencia Spain Hospital Clínico Universitario. INCLIVA Biomedical Research Insitute. University of Valencia. Pathology Valencia Spain Hospital Clínico Universitario Radiation Oncology Valencia Spain Hospital Clínico Universitario Otorhinolaringology Valencia Spain Hospital Clínico Universitario Maxillofacial Surgery Valencia Spain CIBERONC Instituto de Salud Carlos III Medical Oncology Madrid Spain

Purpose/Objective Unresectable locally advanced head and neck cancer (LAHNSCC) presents high heterogeneity 1 , which has yet to be elucidated at the molecular level. Consequently, it hampers the guidance of standard chemoradiotherapy (ChRT) and the implementation of precision medicine. Our study aims at assessing intratumor heterogeneity (ITH) and tumor evolution by examining the mutation profiles from WES in paired tissue and plasma both at baseline and relapse. Material/Methods Primary tumor (PT) biopsies from 61 unresectable LAHNSCC patients at baseline, along with parallel biopsies at relapse and paired plasma samples (baseline and relapse) from the INCLIVA Biobank's Head and Neck Cancer Collection were obtained. Patients provided informed consent, and the study received ethical approval from our Institutional review board. WES of the collected samples was performed on a HiSeq 3000 (Illumina) using the KAPA HyperExome (Roche) panel. UMI barcodes were added to correct background noise. Samples were selected based on a minimum average coverage (50x for WBC, 100x for FFPE and 250x for plasma samples). Only patients with White Blood Cells (WBCs) and plasma samples were included. Single-Nucleotide Variants (SNV), Copy Number Variants (CNVs) and small insertions and deletions (Indel) were called with an in-house bioinformatics pipeline. Minimum Variant allele frequencies (VAF) were set to 0.1% and 10% for plasma and tissue samples, respectively. Oncogenic somatic variants and related treatments were identified and annotated with OncoKB and Ensembl v107. Functional enrichment was performed using the cluster Profiler 4.6.2 R package and databases *** 3.16.0 and MSigDB 2023.1. Results A total of 37 unresectable LAHNSCC cases meeting quality criteria were included in our analysis (Figure 1). Clinicopathologic characteristics and treatment details are given in Table 1. Download : Download high-res image (459KB) Download : Download full-size image Download : Downlo

关键词： Biology and molecular targeting whole-exome sequencing ctDNA locally advanced

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Corrigendum to "Plasmatic Membrane Expression of Adhesion Molecules in Human Cardiac Progenitor/Stem Cells Might Explain Their Superior Cell Engraftment after Cell Transplantation"

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Stem cells international 2022年第1期2022卷 9786160页

作者： Imelda Ontoria-Oviedo Itziar Palacios Joaquín Panadero Belén Sánchez Francisco García-García Adolfo López-Cerdán Akaitz Dorronsoro Delia Castellano Luis Rodríguez-Borlado Antonio Bernad Pilar Sepúlveda Regenerative Medicine and Heart Transplantation Unit Instituto de Investigación Sanitaria La Fe 46026 Valencia Spain. Coretherapix SLU Tres Cantos 28760 Madrid Spain. IGENOMIX S. L 46980 Paterna Valencia Spain. Bioinformatics and Biostatistics Unit Centro de Investigación Príncipe Felipe 46012 Valencia Spain. Biomedical Imaging Unit FISABIO-CIPF Centro de Investigación Príncipe Felipe 46012 Valencia Spain. Department of Immunology and Oncology Centro Nacional de Biotecnología (CNB-CSIC) 28048 Madrid Spain.

[This corrects the article DOI: 10.1155/2020/8872009.].

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Machine learning for MGRS risk stratification using clinical and pathology data

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Kidney International Reports 2025年

作者： Giorgio Cazzaniga Giulia Capitoli Raffaella Barretta Andrew Smith Gisella Vischini Giuliana Papalia Federico Alberici Federica Mescia Albino Eccher Jan Ulrich Becker Maarten Naesens Lucrezia Furian Bernd Schröppel Stefania Galimberti Fabio Pagni Vincenzo L'Imperio Department of Medicine and Surgery Pathology University of Milano-Bicocca San Gerardo Hospital Italy Nephrology Dialysis and Renal Transplant Unit IRCCS Azienda Ospedaliero-Universitaria di Bologna Alma Mater Studiorum University of Bologna Italy Bicocca Bioinformatics Biostatistics and Bioimaging B4 Center School of Medicine and Surgery University of Milan - Bicocca (UNIMIB) Monza Italy Biostatistics and Clinical Epidemiology Fondazione IRCCS San Gerardo dei Tintori Monza Italy Department of Health Sciences Proteomics University of Milano - Bicocca (UNIMIB) Monza Italy Department of Medical and Surgical Science (DIMEC) Alma Mater Studiorum - University of Bologna Bologna Italy Department of Pharmacy Health and Nutritional Sciences University of Calabria 87036 Rende Italy Nephrology Unit Uniersity of Brescia ASST Spedali Civili di Brescia Brescia Italy Department of Medical and Surgical Sciences for Children and Adults University of Modena and Reggio Emilia University Hospital of Modena Modena Italy Institute of Pathology University Hospital of Cologne Cologne Germany Department of Microbiology Immunology and Transplantation Nephrology and Kidney Transplantation Research Group KU Leuven Leuven Belgium Department of Nephrology and Kidney Transplantation University Hospitals Leuven Leuven Belgium Kidney and Pancreas Transplantation Unit Department of Surgical Oncological and Gastroenterological Sciences School of Medicine and Surgery University of Padua Padua Italy Section of Nephrology University Hospital Ulm Germany

Introduction The prompt detection of monoclonal gammopathies of renal significance (MGRS) is clinically relevant for the initiation of chemotherapy. Although clinical and laboratory data can suggest the presence of MGRS, renal biopsy still represents the gold standard, despite not always being performed or eventually postponed because it is not deemed useful or informative. In this retrospective study, machine learning (ML) is used to build a tool to assist the pre-biopsy risk stratification of MGRS and reinforce the rationale for the histological examination. Methods The study included a total of 258 patients with MGUS, of which 168 (65%) MGRS cases and 90 (35%) non-MGRS cases based on the final renal biopsy result. Results Patients with MGRS were more frequently female (48.2% vs 28.9%, p=0.004) and had more frequent Bence-Jones proteinuria (73.2% vs. 41.1%, p<0.001), as compared to non MGRS cases, with amyloidosis being the most common diagnosis (62%). The ML model achieved an accuracy of 0.79 (95%CI: 0.67-0.88) and an AUC-ROC of 0.80 (95%CI: 0.65-0.93) in the validation set. The model is available as a free desktop and Android mobile app (MGRS Interactive Resource for AI-Guided Evaluation, MIRAGE). Conclusion The ML-based MGRS risk stratification tool can help in the selection of patients with higher probability to have MGRS on renal biopsy, aiming to direct those patients to a complete histological characterization of the disease.

关键词： MGRS digital pathology computational pathology digital health renal biopsy onconephrology

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Peri-intubation complications in critically ill obese patients: a secondary analysis of the international INTUBE cohort

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Critical Care 2025年第1期29卷 1-12页

作者： Russotto, Vincenzo Laffey, John G. Tassistro, Elena Myatra, Sheila N. Rezoagli, Emanuele Foti, Giuseppe Antolini, Laura Valsecchi, Maria Grazia Bauer, Philippe R. Szułdrzyński, Konstanty Camporota, Luigi Greif, Robert Higgs, Andy Parotto, Matteo Fumagalli, Roberto Sorbello, Massimiliano Robba, Chiara Grasselli, Giacomo Bellani, Giacomo Caironi, Pietro Lascarrou, Jean Baptiste Department of Oncology University of Turin Turin Italy Department of Anesthesia and Intensive Care University Hospital San Luigi Gonzaga Orbassano Turin Italy Anesthesia and Intensive Care Medicine School of Medicine University of Galway Galway Ireland Department of Anesthesia and Intensive Care Medicine University Hospital Galway Galway Ireland Biostatistics and Clinical Epidemiology Fondazione IRCCS San Gerardo Dei Tintori Monza Italy Bicocca Center of Bioinformatics Biostatistics and Bioimaging (B4 Center) School of Medicine and Surgery University of Milano-Bicocca Monza Italy Department of Anaesthesiology Critical Care and Pain Tata Memorial Hospital Homi Bhabha National Institute Mumbai India Department of Emergency and Intensive Care Fondazione IRCCS San Gerardo Dei Tintori Monza Italy School of Medicine and Surgery University of Milano Bicocca Monza Italy Division of Pulmonary and Critical Care Medicine Mayo Clinic Rochester United States Department of Anesthesiology and Intensive Care National Medical Institute of the Ministry of Interior and Administration Warsaw Poland Department of Adult Critical Care Health Centre for Human and Applied Physiological Sciences Guy’s and St Thomas’ NHS Foundation Trust London United Kingdom Faculty of Medicine University of Bern Bern Switzerland Anaesthesia and Intensive Care Medicine Warrington Teaching Hospitals NHS Foundation Trust Warrington United Kingdom Department of Anesthesiology and Pain Medicine Interdepartmental Division of Critical Care Medicine University of Toronto Toronto ON Canada Department of Anesthesia and Pain Management Toronto General Hospital Toronto ON Canada Department of Anesthesiology ASST Grande Ospedale Metropolitano Niguarda Milan Italy Hospital Giovanni Paolo II Ragusa Italy University of Enna KORE Enna Italy Istituto Di Ricovero E Cura a Carattere Scientifico Ospedale Policlinico San Martino Genoa Italy Department of Surgical Science and Integrated Diagnostic University

Background: Airway management in critically ill obese patients is potentially associated with a higher risk of adverse events due to a constellation of physiological and anatomical challenges. Data from international prospective studies on peri-intubation adverse events in obese critically ill patients are lacking. Methods: INTUBE (International Observational Study to Understand the Impact and Best Practices of Airway Management In Critically Ill Patients) was an international multicentre prospective cohort study enrolling critically ill adult patients undergoing in-hospital tracheal intubation in 197 sites from 29 countries worldwide from October 1, 2018, to July 31, 2019. This secondary analysis compares airway management practices and outcomes between obese (body mass index–BMI ≥ 30 kg/m²) and non-obese patients (BMI < 30 kg/m²). Results: A total of 2946 patients met inclusion criteria for this secondary analysis, 639 (21.7%) obese and 2307 (78.3%) non-obese. Severe peri-intubation hypoxemia was more frequently reported in obese compared to non-obese patients (12.1% vs 8.6% respectively, p = 0.01). Variables independently associated with a higher risk of peri-intubation hypoxemia were baseline SpO₂/FiO₂ (OR 0.996, 95% CI 0.994–0.997), 30–45° head-up position (OR 1.53, 95% CI 1.04–2.26) and first-pass intubation failure (OR for first-pass success 0.21, 95% CI 0.15–0.29). Obesity (OR 0.71, 95% CI 0.56–0.91) and 20° head-up position (OR 0.67, 95% CI 0.47–0.95) were independently associated with higher likelihood of first-pass intubation failure. In contrast, intubation by staff physician/consultant (OR 1.70, 95% CI 1.30–2.21) or anesthesiologists (OR 1.98, 95% CI 1.55–2.53) were associated with higher first-pass success. Conclusions: Compared to non-obese patients, obese critically ill exhibit a higher incidence of peri-intubation severe hypoxemia. In this population, worse baseline oxygenation and first-pass intubation fa

关键词： Airway management Critical care Intubation Obesity

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MODL-15. High-throughput combination drug screening identifies synergism between retinoic acid treatment and BCL-XL-inhibition inMYC(N)-driven medulloblastoma and neuroblastoma models

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Neuro-Oncology 2022年第SUPPLEMENT_1期24卷 i171–i172页

作者： Seiboldt, Till Zeiser, Constantia Salem-Altintas, Rabia Nguyen, Duy Holland-Letz, Tim Peterziel, Heike Witt, Olaf Oehme, Ina Hopp Children’s Cancer Center Heidelberg (KiTZ) and Clinical Cooperation Unit Pediatric Oncology (B310) German Cancer Research Center (DKFZ) Heidelberg Germany Faculty of Medicine Heidelberg University Heidelberg Germany Bioinformatics and Omics Data Analytics German Cancer Research Center (DKFZ) Heidelberg Germany Division of Biostatistics German Cancer Research Center (DKFZ) Heidelberg Germany Department of Pediatric Oncology Hematology Immunology and Pulmonology Heidelberg University Hospital Heidelberg Germany

PURPOSE: Despite remarkable improvements in childhood cancer survival, certain high-risk entities including malignancies of the nervous system still carry dismal prognoses. Retinoic acid (RA) treatment has long been administered in high-risk neuroblastoma patients and preclinical data suggest a benefit in applying retinoids in selected brain tumor entities. However, limited single-agent efficacy and developing treatment resistance provide a rationale for investigating improved combination ***: We assessed the RA sensitivity of 16 cell lines and patient-derived cultures of pediatric nervous system tumors from the INFORM (INdividualized Therapy FOr Relapsed Malignancies in Childhood) registry. Bulk RNA sequencing was performed for five sensitive models undergoing RA treatment. All models were screened for drug sensitivity to 76 clinically relevant drugs alone and combined with RA. Beneficial hit combinations were further investigated for synergy, as well as their effect on differentiation and apoptosis by high-content fluorescence microscopy and caspase activity assay. Results fromin vivoexperiments are ***: Group 3 medulloblastoma and high-risk neuroblastoma models were most sensitive to RA treatment leading to significant changes in gene expression of apoptotic regulation. Drug sensitivity screening revealed similar patterns of response to combination treatments inMYC-driven Group 3 medulloblastomas andMYCN-amplified neuroblastomas. Apoptosis regulating BCL-XL-inhibitors (A-1155463, navitoclax) were identified as top hits across RA sensitive models, whereas epigenetic BET family inhibitor I-BET151 and histone deacetylase inhibitor entinostat suggested entity-specific combination benefits in neuroblastoma and medulloblastoma models, respectively. In both entities, combining RA with navitoclax was synergistic and significantly increased caspase-3 activity. The combination led to a morphological shift from differentiation under RA treatment t

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BIMCV COVID-19+: a large annotated dataset of RX and CT images from COVID-19 patients

arXiv

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arXiv 2020年

作者： Vayá, Maria de la Iglesia Saborit, Jose Manuel Montell, Joaquim Angel Pertusa, Antonio Bustos, Aurelia Cazorla, Miguel Galant, Joaquin Barber, Xavier Orozco-Beltrán, Domingo García-García, Francisco Caparrós, Marisa González, Germán Salinas, Jose María Unidad Mixta de Imagen Biomédica FISABIO-CIPF. Fundación para el Fomento de la Investigación Sanitario y Biomédica de la Comunidad Valenciana Valencia Spain Universidad de Alicante Spain Medbravo. Hospital San Juan de Alicante Spain Universidad Miguel Hernández Spain Sierra Research SL Bioinformatics & Biostatistics Unit Principe Felipe Research Center Valencia Spain

This paper describes BIMCV COVID-19+, a large dataset from the Valencian Region Medical ImageBank (BIMCV) containing chest X-ray images CXR (CR, DX) and computed tomography (CT) imaging of COVID-19+ patients along with their radiological findings and locations, pathologies, radiological reports (in Spanish), DICOM metadata, Polymerase chain reaction (PCR), Immunoglobulin G (IgG) and Immunoglobulin M (IgM) diagnostic antibody tests. The findings have been mapped onto standard Unified Medical Language System (UMLS) terminology and cover a wide spectrum of thoracic entities, unlike the considerably more reduced number of entities annotated in previous datasets. Images are stored in high resolution and entities are localized with anatomical labels and stored in a Medical Imaging Data Structure (MIDS) format. In addition, 10 images were annotated by a team of radiologists to include semantic segmentation of radiological findings. This first iteration of the database includes 1,380 CX, 885 DX and 163 CT studies from 1,311 COVID-19+ patients. This is, to the best of our knowledge, the largest COVID-19+ dataset of images available in an open format. The dataset can be downloaded from http://***/bimcv-projects/bimcv-covid19/.MSC Codes 92B20, 92C50, 68T50, 92B10 Copyright © 2020, The Authors. All rights reserved.

关键词： Computerized tomography

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