Ejc SupplementsPub Date : 2021-01-01Epub Date: 2021-07-01DOI: 10.21105/joss.03262
Yaroslav O Halchenko, Kyle Meyer, Benjamin Poldrack, Debanjum Singh Solanky, Adina S Wagner, Jason Gors, Dave MacFarlane, Dorian Pustina, Vanessa Sochat, Satrajit S Ghosh, Christian Mönch, Christopher J Markiewicz, Laura Waite, Ilya Shlyakhter, Alejandro de la Vega, Soichi Hayashi, Christian Olaf Häusler, Jean-Baptiste Poline, Tobias Kadelka, Kusti Skytén, Dorota Jarecka, David Kennedy, Ted Strauss, Matt Cieslak, Peter Vavra, Horea-Ioan Ioanas, Robin Schneider, Mika Pflüger, James V Haxby, Simon B Eickhoff, Michael Hanke
{"title":"DataLad: distributed system for joint management of code, data, and their relationship.","authors":"Yaroslav O Halchenko, Kyle Meyer, Benjamin Poldrack, Debanjum Singh Solanky, Adina S Wagner, Jason Gors, Dave MacFarlane, Dorian Pustina, Vanessa Sochat, Satrajit S Ghosh, Christian Mönch, Christopher J Markiewicz, Laura Waite, Ilya Shlyakhter, Alejandro de la Vega, Soichi Hayashi, Christian Olaf Häusler, Jean-Baptiste Poline, Tobias Kadelka, Kusti Skytén, Dorota Jarecka, David Kennedy, Ted Strauss, Matt Cieslak, Peter Vavra, Horea-Ioan Ioanas, Robin Schneider, Mika Pflüger, James V Haxby, Simon B Eickhoff, Michael Hanke","doi":"10.21105/joss.03262","DOIUrl":"10.21105/joss.03262","url":null,"abstract":"<p><p>DataLad is a Python-based tool for the joint management of code, data, and their relationship, built on top of a versatile system for data logistics (git-annex) and the most popular distributed version control system (Git). It adapts principles of open-source software development and distribution to address the technical challenges of data management, data sharing, and digital provenance collection across the life cycle of digital objects. DataLad aims to make data management as easy as managing code. It streamlines procedures to consume, publish, and update data, for data of any size or type, and to link them as precisely versioned, lightweight dependencies. DataLad helps to make science more reproducible and FAIR (Wilkinson et al., 2016). It can capture complete and actionable process provenance of data transformations to enable automatic re-computation. The DataLad project (datalad.org) delivers a completely open, pioneering platform for flexible decentralized research data management (RDM) (Hanke, Pestilli, et al., 2021). It features a Python and a command-line interface, an extensible architecture, and does not depend on any centralized services but facilitates interoperability with a plurality of existing tools and services. In order to maximize its utility and target audience, DataLad is available for all major operating systems, and can be integrated into established workflows and environments with minimal friction.</p>","PeriodicalId":11675,"journal":{"name":"Ejc Supplements","volume":"7 1","pages":""},"PeriodicalIF":0.0,"publicationDate":"2021-01-01","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"https://www.ncbi.nlm.nih.gov/pmc/articles/PMC11514317/pdf/","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"78458307","PeriodicalName":null,"FirstCategoryId":null,"ListUrlMain":null,"RegionNum":0,"RegionCategory":"","ArticlePicture":[],"TitleCN":null,"AbstractTextCN":null,"PMCID":"OA","EPubDate":null,"PubModel":null,"JCR":null,"JCRName":null,"Score":null,"Total":0}
Ejc SupplementsPub Date : 2020-08-01Epub Date: 2020-08-22DOI: 10.1016/j.ejcsup.2020.02.002
Elena García-Martínez , J. Alejandro Pérez-Fidalgo
{"title":"Immunotherapies in ovarian cancer","authors":"Elena García-Martínez , J. Alejandro Pérez-Fidalgo","doi":"10.1016/j.ejcsup.2020.02.002","DOIUrl":"10.1016/j.ejcsup.2020.02.002","url":null,"abstract":"<div><p>Ovarian cancer is the leading cause of death for gynaecological cancer, and new therapies are urgently awaited. Although the presence of tumour-infiltrating lymphocytes has been confirmed to be associated to a better prognosis, immunotherapy is not yet incorporated to the armamentarium in ovarian cancer. This review briefly summarises the strategies that have been tested or are under study for the three different groups of tumours: immune desert, inflamed and immune-excluded ovarian tumours. Finally, a better knowledge of the biology and immune microenvironment is needed for successfully developing new immunotherapy strategies.</p></div>","PeriodicalId":11675,"journal":{"name":"Ejc Supplements","volume":"15 ","pages":"Pages 87-95"},"PeriodicalIF":0.0,"publicationDate":"2020-08-01","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"https://sci-hub-pdf.com/10.1016/j.ejcsup.2020.02.002","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"38645345","PeriodicalName":null,"FirstCategoryId":null,"ListUrlMain":null,"RegionNum":0,"RegionCategory":"","ArticlePicture":[],"TitleCN":null,"AbstractTextCN":null,"PMCID":"OA","EPubDate":null,"PubModel":null,"JCR":null,"JCRName":null,"Score":null,"Total":0}
Ejc SupplementsPub Date : 2020-08-01Epub Date: 2020-08-22DOI: 10.1016/j.ejcsup.2019.11.002
Marta Gil-Martin , Beatriz Pardo , Maria-Pilar Barretina-Ginesta
{"title":"Rare ovarian tumours. Other treatments for ovarian cancer","authors":"Marta Gil-Martin , Beatriz Pardo , Maria-Pilar Barretina-Ginesta","doi":"10.1016/j.ejcsup.2019.11.002","DOIUrl":"10.1016/j.ejcsup.2019.11.002","url":null,"abstract":"<div><h3>Aim</h3><p>The description of rare malignant ovarian tumours and the most suitable treatments. Alternative therapies different from intravenous chemotherapy are also explained.</p></div><div><h3>Methods</h3><p>Literature review and ongoing trial information have been used to elaborate this guide.</p></div><div><h3>Results</h3><p>Each ovarian cancer type must be identified and treated properly from diagnostic to surgery, adjuvant treatment and metastatic disease. Hormonotherapy can be useful as an alternative treatment, especially in low-grade ovarian cancer and endometrioid subtype. Tumour characterisation is appropriated for treatment selection when targeted therapy is indicated. MEK inhibitors, tyrosine-kinase inhibitors, EGFR inhibitors, therapies against integrins, antibody–drug conjugates and other strategies are described. Antiangiogenics, PARP inhibitors and immunotherapy are discussed in other parts of this publication.</p></div><div><h3>Conclusion</h3><p>Different ovarian cancer types must receive the appropriated treatment. Alternative therapies may be evaluated beyond the standard therapy, frequently in a clinical trial, and an individualised molecular study may help to find the best treatment.</p></div>","PeriodicalId":11675,"journal":{"name":"Ejc Supplements","volume":"15 ","pages":"Pages 96-103"},"PeriodicalIF":0.0,"publicationDate":"2020-08-01","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"https://sci-hub-pdf.com/10.1016/j.ejcsup.2019.11.002","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"38645346","PeriodicalName":null,"FirstCategoryId":null,"ListUrlMain":null,"RegionNum":0,"RegionCategory":"","ArticlePicture":[],"TitleCN":null,"AbstractTextCN":null,"PMCID":"OA","EPubDate":null,"PubModel":null,"JCR":null,"JCRName":null,"Score":null,"Total":0}
Ejc SupplementsPub Date : 2020-08-01Epub Date: 2020-08-22DOI: 10.1016/j.ejcsup.2019.09.001
Marta Hergueta-Redondo, Héctor Peinado
{"title":"The influence of secreted factors and extracellular vesicles in ovarian cancer metastasis","authors":"Marta Hergueta-Redondo, Héctor Peinado","doi":"10.1016/j.ejcsup.2019.09.001","DOIUrl":"10.1016/j.ejcsup.2019.09.001","url":null,"abstract":"<div><p>Ovarian cancer cells mainly metastasise within the peritoneal cavity, the lethal consequence of tumour progression in this cancer type. Classically, changes in tumour cells, such as epithelial to mesenchymal transition, involve the down-regulatinon of E-cadherin, activation of extracellular proteases and integrin-mediated adhesion. However, our current understanding of ovarian tumour progression suggests the implication of both intrinsic and extrinsic factors. It has been proposed that ovarian cancer metastases are a consequence of the crosstalk between cancer cells and the tumour microenvironment by soluble factors and extracellular vesicles. Characterisation of the alterations in both the tumour cells and the surrounding microenvironment has emerged as a new research field to understand ovarian cancer metastasis. In this mini review, we will summarise the most recent findings, focusing our attention on the role of secreted factors and extracellular vesicles in ovarian cancer metastasis.</p></div>","PeriodicalId":11675,"journal":{"name":"Ejc Supplements","volume":"15 ","pages":"Pages 38-48"},"PeriodicalIF":0.0,"publicationDate":"2020-08-01","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"https://sci-hub-pdf.com/10.1016/j.ejcsup.2019.09.001","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"38644503","PeriodicalName":null,"FirstCategoryId":null,"ListUrlMain":null,"RegionNum":0,"RegionCategory":"","ArticlePicture":[],"TitleCN":null,"AbstractTextCN":null,"PMCID":"OA","EPubDate":null,"PubModel":null,"JCR":null,"JCRName":null,"Score":null,"Total":0}
Ejc SupplementsPub Date : 2020-08-01Epub Date: 2020-08-22DOI: 10.1016/j.ejcsup.2020.06.001
Maria-Pilar Barretina-Ginesta
{"title":"DNA damaging agents in ovarian cancer","authors":"Maria-Pilar Barretina-Ginesta","doi":"10.1016/j.ejcsup.2020.06.001","DOIUrl":"10.1016/j.ejcsup.2020.06.001","url":null,"abstract":"<div><p>Epithelial ovarian cancer (EOC) is very sensitive to upfront chemotherapy. This condition is attributable to defects in the DNA damage repair system. Agents that damage DNA are the main drugs used for its treatment. Many EOC cells have DNA repair deficiencies that confer susceptibility to these agents. Platinum is the most important agent for first-line and also for relapses, together with other drugs that can be given as monotherapy or along with platinum or other drugs. Lately, the emerging role of PARP inhibitors has changed the landscape of opportunities for patients with EOC. All these strategies will be reviewed in this article.</p></div>","PeriodicalId":11675,"journal":{"name":"Ejc Supplements","volume":"15 ","pages":"Pages 67-72"},"PeriodicalIF":0.0,"publicationDate":"2020-08-01","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"https://sci-hub-pdf.com/10.1016/j.ejcsup.2020.06.001","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"38644505","PeriodicalName":null,"FirstCategoryId":null,"ListUrlMain":null,"RegionNum":0,"RegionCategory":"","ArticlePicture":[],"TitleCN":null,"AbstractTextCN":null,"PMCID":"OA","EPubDate":null,"PubModel":null,"JCR":null,"JCRName":null,"Score":null,"Total":0}
Ejc SupplementsPub Date : 2020-08-01Epub Date: 2020-08-22DOI: 10.1016/j.ejcsup.2020.02.001
Ignacio Romero , Susanna Leskelä , Belén Pérez Mies , Andrés Poveda Velasco , José Palacios
{"title":"Morphological and molecular heterogeneity of epithelial ovarian cancer: Therapeutic implications","authors":"Ignacio Romero , Susanna Leskelä , Belén Pérez Mies , Andrés Poveda Velasco , José Palacios","doi":"10.1016/j.ejcsup.2020.02.001","DOIUrl":"10.1016/j.ejcsup.2020.02.001","url":null,"abstract":"<div><p>Ovarian epithelial cancer (OEC) is the most lethal gynecologic malignancy. Despite current chemotherapeutic and surgical options, this high lethality can be attributed to multiple factors, including late-stage presentation. In order to optimize OEC treatment, it is important to highlight that it is composed of five main subtypes: high-grade serous ovarian carcinoma (HGSOC), low-grade serous ovarian carcinoma (LGSOC), endometrioid ovarian carcinoma (EOC), ovarian clear cell carcinoma (CCOC), and mucinous ovarian carcinoma (MOC). These subtypes differ in their precursor lesions, as well as in epidemiological, morphological, molecular and clinical features. OEC is one of the tumours in which most pathogenic germline mutations have been identified. Accordingly, up to 20% OC show alterations in <em>BRCA1/2</em> genes, and also, although with a lower frequency, in other low penetrance genes associated with homologous recombination deficiency (HRD), mismatch repair genes (Lynch syndrome) and <em>TP53</em>. The most important prognostic factor is the 2014 FIGO staging, while older age is also associated with worse survival. HGSOC in all stages and CCC and MOC in advanced stages have the worse prognosis among histological types. Molecular markers have emerged as prognostic factors, particularly mutations in <em>BRCA1/2,</em> which are associated with a better outcome. Regarding treatment, whereas a proportion of HGSOC is sensible to platinum-based treatment and PARP inhibitors due to HRD, the rest of the histological types are relatively chemoresistant. New treatments based in specific molecular alterations are being tested in different histological types. In addition, immunotherapy could be an option, especially for EOC carrying mismatch repair deficiency or <em>POLE</em> mutations.</p></div>","PeriodicalId":11675,"journal":{"name":"Ejc Supplements","volume":"15 ","pages":"Pages 1-15"},"PeriodicalIF":0.0,"publicationDate":"2020-08-01","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"https://sci-hub-pdf.com/10.1016/j.ejcsup.2020.02.001","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"38644500","PeriodicalName":null,"FirstCategoryId":null,"ListUrlMain":null,"RegionNum":0,"RegionCategory":"","ArticlePicture":[],"TitleCN":null,"AbstractTextCN":null,"PMCID":"OA","EPubDate":null,"PubModel":null,"JCR":null,"JCRName":null,"Score":null,"Total":0}
Ejc SupplementsPub Date : 2020-08-01Epub Date: 2020-08-22DOI: 10.1016/j.ejcsup.2019.12.001
Raquel López-Reig , José Antonio López-Guerrero
{"title":"The hallmarks of ovarian cancer: proliferation and cell growth","authors":"Raquel López-Reig , José Antonio López-Guerrero","doi":"10.1016/j.ejcsup.2019.12.001","DOIUrl":"10.1016/j.ejcsup.2019.12.001","url":null,"abstract":"<div><p>Epithelial ovarian cancer (EOC) is a heterogeneous group of diseases with distinct biological and clinical behaviour. Despite the differences between them, the capability of tumour cells to continuously proliferate and avoid death is maintained among histotypes. This ability is the result of alterations at different levels, causing the deregulation of cell cycle and proliferative-related pathways. Even if the leading role is played by RB and TP53, changes in other molecular pathways are involved in the development of EOC. This ability can be exploited to generate <em>in vitro</em> and <em>in vivo</em> models resembling the conditions of tumour development in a patient. <em>In vivo</em> models, such as patient-derived xenografts (PDX) or genetically engineered mouse models (GEMM), represent a fundamental tool in the study of the molecular mechanisms implicated in each EOC biotype for testing new therapeutic approaches. Herein we describe the major proliferation-related pathways and its disruption found in EOC and how these features can be used to establish <em>in vivo</em> models for translational research.</p></div>","PeriodicalId":11675,"journal":{"name":"Ejc Supplements","volume":"15 ","pages":"Pages 27-37"},"PeriodicalIF":0.0,"publicationDate":"2020-08-01","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"https://sci-hub-pdf.com/10.1016/j.ejcsup.2019.12.001","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"38644502","PeriodicalName":null,"FirstCategoryId":null,"ListUrlMain":null,"RegionNum":0,"RegionCategory":"","ArticlePicture":[],"TitleCN":null,"AbstractTextCN":null,"PMCID":"OA","EPubDate":null,"PubModel":null,"JCR":null,"JCRName":null,"Score":null,"Total":0}
Ejc SupplementsPub Date : 2020-08-01Epub Date: 2020-08-22DOI: 10.1016/j.ejcsup.2019.12.002
Diego Salas-Benito , Enric Vercher , Enrique Conde , Javier Glez-Vaz , Ibon Tamayo , Sandra Hervas-Stubbs
{"title":"Inflammation and immunity in ovarian cancer","authors":"Diego Salas-Benito , Enric Vercher , Enrique Conde , Javier Glez-Vaz , Ibon Tamayo , Sandra Hervas-Stubbs","doi":"10.1016/j.ejcsup.2019.12.002","DOIUrl":"10.1016/j.ejcsup.2019.12.002","url":null,"abstract":"<div><p>The standard first-line therapy for ovarian cancer is a combination of surgery and carboplatin/paclitaxel-based chemotherapy. Patients with longer survival and improved response to chemotherapy usually present T-cell inflamed tumours. The presence of tumour-infiltrating T cells (TILs) notably varies among the different subtypes of ovarian tumours, being highest in high-grade serous ovarian carcinoma, intermediate in endometrioid tumours, and lowest in low-grade serous, mucinous and clear cell tumours. Interestingly, the presence of TILs is often accompanied by a strong immunosuppressive tumour environment. A better understanding of the immune response against ovarian cancer and the tumour immune evasion mechanisms will enable improved prognostication, response prediction and immunotherapy of this disease. This article provides an overview of some ovarian cancer cell features relevant for antitumour response, such as tumour-associated antigens, including neoantigens, expression of inhibitory molecules, and other mechanisms of immune evasion. Moreover, we describe relevant immune cell types found in epithelial ovarian tumours, including T and B lymphocytes, regulatory T cells, natural killer cells, tumour-associated macrophages, myeloid-derived suppressor cells and neutrophils. We focus on how these components influence the burden of the tumour and the clinical outcome.</p></div>","PeriodicalId":11675,"journal":{"name":"Ejc Supplements","volume":"15 ","pages":"Pages 56-66"},"PeriodicalIF":0.0,"publicationDate":"2020-08-01","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"https://sci-hub-pdf.com/10.1016/j.ejcsup.2019.12.002","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"38645342","PeriodicalName":null,"FirstCategoryId":null,"ListUrlMain":null,"RegionNum":0,"RegionCategory":"","ArticlePicture":[],"TitleCN":null,"AbstractTextCN":null,"PMCID":"OA","EPubDate":null,"PubModel":null,"JCR":null,"JCRName":null,"Score":null,"Total":0}
Ejc SupplementsPub Date : 2020-08-01Epub Date: 2020-08-22DOI: 10.1016/j.ejcsup.2019.11.001
Alba Mota PhD , Sara S Oltra PhD , Gema Moreno-Bueno PhD
{"title":"Insight updating of the molecular hallmarks in ovarian carcinoma","authors":"Alba Mota PhD , Sara S Oltra PhD , Gema Moreno-Bueno PhD","doi":"10.1016/j.ejcsup.2019.11.001","DOIUrl":"10.1016/j.ejcsup.2019.11.001","url":null,"abstract":"<div><h3>Background and purpose</h3><p>Ovarian cancer (OC) is the deadliest gynaecologic cancer characterised by a high heterogeneity not only at the clinical point of view but also at the molecular level. This review focuses on the new insights about the OC molecular classification.</p></div><div><h3>Materials and methods</h3><p>We performed a bibliographic search for different indexed articles focused on the new molecular classification of OC. All of them have been published in PubMed and included information about the most frequent molecular alterations in OC confirmed by omics approaches. In addition, we have extracted information about the role of liquid biopsy in the OC diagnosis and prognosis.</p></div><div><h3>Results</h3><p>New molecular insights into OC have allowed novel clinical entities to be defined. Among OC, high-grade serous ovarian carcinoma (HGSOC) which is the most common OC is characterised by omics approaches, mutations in <em>TP53</em> and in other genes involved in the homologous recombination repair, especially <em>BRCA1/2</em>. Recent studies in HGSOC have allowed a new molecular classification in subgroups according to their mutational, transcriptional, methylation and copy number variation signatures with a real impact in the characterisation of new therapeutic targets for OC to be defined. Furthermore, despite the intrinsic intra-tumour heterogeneity, the advances in next generation sequencing (NGS) analyses of ascetic liquid from OC have opened new ways for its characterisation and treatment.</p></div><div><h3>Conclusions</h3><p>The advances in genomic approaches have been used for the identification of new molecular profiling techniques which define OC subgroups and has supposed advances in the diagnosis and in the personalised treatment of OC.</p></div>","PeriodicalId":11675,"journal":{"name":"Ejc Supplements","volume":"15 ","pages":"Pages 16-26"},"PeriodicalIF":0.0,"publicationDate":"2020-08-01","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"https://sci-hub-pdf.com/10.1016/j.ejcsup.2019.11.001","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"38644501","PeriodicalName":null,"FirstCategoryId":null,"ListUrlMain":null,"RegionNum":0,"RegionCategory":"","ArticlePicture":[],"TitleCN":null,"AbstractTextCN":null,"PMCID":"OA","EPubDate":null,"PubModel":null,"JCR":null,"JCRName":null,"Score":null,"Total":0}
Ejc SupplementsPub Date : 2020-08-01Epub Date: 2020-08-22DOI: 10.1016/j.ejcsup.2019.11.003
V. Heredia-Soto , J.A. López-Guerrero , A. Redondo , M. Mendiola
{"title":"The hallmarks of ovarian cancer: Focus on angiogenesis and micro-environment and new models for their characterisation","authors":"V. Heredia-Soto , J.A. López-Guerrero , A. Redondo , M. Mendiola","doi":"10.1016/j.ejcsup.2019.11.003","DOIUrl":"10.1016/j.ejcsup.2019.11.003","url":null,"abstract":"<div><p>Cancers develop by sustained growth, migration and invasion properties of tumour cells, supported by complex interactions with stromal cells within the tumour micro-environment.</p><p>This review is focused on the latest discoveries regarding the highlighted role of angiogenesis and tumour micro-environment in ovarian cancer. This cancer milieu encompasses non-cancerous cells present in the tumour or nearby, including vessel-forming cells, fibroblasts and immune cells amongst others that work in a cooperative way with cancer cells, impacting tumour behaviour. Angiogenesis, migration and invasion, and more recently immune evasion, are cancer hallmarks clearly dependent on these supporting cells. Moreover, these stromal cells are more genetically stable than tumour cells and thus represent an attractive therapeutic target. A better understanding of the stromal cells function, and their complex interplay with cancer cells, will open additional areas to target, as the tumour–host interface.</p></div>","PeriodicalId":11675,"journal":{"name":"Ejc Supplements","volume":"15 ","pages":"Pages 49-55"},"PeriodicalIF":0.0,"publicationDate":"2020-08-01","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"https://sci-hub-pdf.com/10.1016/j.ejcsup.2019.11.003","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"38644504","PeriodicalName":null,"FirstCategoryId":null,"ListUrlMain":null,"RegionNum":0,"RegionCategory":"","ArticlePicture":[],"TitleCN":null,"AbstractTextCN":null,"PMCID":"OA","EPubDate":null,"PubModel":null,"JCR":null,"JCRName":null,"Score":null,"Total":0}
求助内容：
应助结果提醒方式：
京公网安备 11010802042870号
