LIVIVO - Search results -

Search results

Result 1 - 10 of total 90

Search options

Article ; Online: Repurposing small molecules for nephronophthisis and related renal ciliopathies.

Benmerah, Alexandre / Briseño-Roa, Luis / Annereau, Jean-Philippe / Saunier, Sophie

2023 Volume 104, Issue 2, Page(s) 245–253

Abstract: Nephronophthisis is an autosomal recessive tubulointerstitial nephropathy, belonging to the ciliopathy disorders, characterized by fibrosis and/or cysts. It is the most common genetic cause of kidney failure in children and young adults. Clinically and ... ...

Abstract	Nephronophthisis is an autosomal recessive tubulointerstitial nephropathy, belonging to the ciliopathy disorders, characterized by fibrosis and/or cysts. It is the most common genetic cause of kidney failure in children and young adults. Clinically and genetically heterogeneous, it is caused by variants in ciliary genes, resulting in either an isolated kidney disease or syndromic forms in association with other manifestations of ciliopathy disorders. No curative treatment is currently available. Over the past 2 decades, advances in understanding disease mechanisms have identified several dysregulated signaling pathways, some shared with other cystic kidney diseases. Notably, molecules previously developed to target these pathways have shown promising beneficial effects in orthologous mouse models. In addition to these knowledge-based repurposing approaches, unbiased "in cellulo" phenotypic screens of "repurposing" libraries identified small molecules able to rescue the ciliogenesis defects observed in nephronophthisis conditions. Those compounds appeared to act on relevant pathways and, when tested, showed beneficial nephronophthisis-associated kidney and/or extrarenal defects in mice. In this review, we have summarized those studies that highlight the drug repurposing strategies in the context of a rare disorders, such as nephronophthisis-related ciliopathies, with broad genetic heterogeneity and systemic manifestations but with shared disease mechanisms.
MeSH term(s)	Animals ; Mice ; Kidney/pathology ; Polycystic Kidney Diseases/genetics ; Kidney Diseases, Cystic/drug therapy ; Kidney Diseases, Cystic/genetics ; Ciliopathies/drug therapy ; Ciliopathies/genetics ; Renal Insufficiency/complications ; Fibrosis ; Cilia/pathology
Language	English
Publishing date	2023-05-25
Publishing country	United States
Document type	Journal Article ; Review ; Research Support, Non-U.S. Gov't
ZDB-ID	120573-0
ISSN	1523-1755 ; 0085-2538
ISSN (online)	1523-1755
ISSN	0085-2538
DOI	10.1016/j.kint.2023.04.027
Database	MEDical Literature Analysis and Retrieval System OnLINE

In stock of ZB MED Cologne/Königswinter

Zs.A 797: Show issues

Location:
Je nach Verfügbarkeit (siehe Angabe bei Bestand)
bis Jg. 1994: Bestellungen von Artikeln über das Online-Bestellformular
Jg. 1995 - 2021: Lesesall (1.OG)
ab Jg. 2022: Lesesaal (EG)

Order via subito

This service is chargeable due to the Delivery terms set by subito. Orders including an article and supplementary material will be classified as separate orders. In these cases, fees will be demanded for each order.

Details ▾
- See ZB MED holdings
- Order with fees

Article: Renal Ciliopathies: Sorting Out Therapeutic Approaches for Nephronophthisis.

Stokman, Marijn F / Saunier, Sophie / Benmerah, Alexandre

Frontiers in cell and developmental biology

2021 Volume 9, Page(s) 653138

Abstract: Nephronophthisis (NPH) is an autosomal recessive ciliopathy and a major cause of end-stage renal disease in children. The main forms, juvenile and adult NPH, are characterized by tubulointerstitial fibrosis whereas the infantile form is more severe and ... ...

Abstract	Nephronophthisis (NPH) is an autosomal recessive ciliopathy and a major cause of end-stage renal disease in children. The main forms, juvenile and adult NPH, are characterized by tubulointerstitial fibrosis whereas the infantile form is more severe and characterized by cysts. NPH is caused by mutations in over 20 different genes, most of which encode components of the primary cilium, an organelle in which important cellular signaling pathways converge. Ciliary signal transduction plays a critical role in kidney development and tissue homeostasis, and disruption of ciliary signaling has been associated with cyst formation, epithelial cell dedifferentiation and kidney function decline. Drugs have been identified that target specific signaling pathways (for example cAMP/PKA, Hedgehog, and mTOR pathways) and rescue NPH phenotypes in
Language	English
Publishing date	2021-05-13
Publishing country	Switzerland
Document type	Journal Article ; Review
ZDB-ID	2737824-X
ISSN	2296-634X
ISSN	2296-634X
DOI	10.3389/fcell.2021.653138
Database	MEDical Literature Analysis and Retrieval System OnLINE

Order via subito

Article ; Online: Performance and clinical utility of a new supervised machine-learning pipeline in detecting rare ciliopathy patients based on deep phenotyping from electronic health records and semantic similarity.

Faviez, Carole / Vincent, Marc / Garcelon, Nicolas / Boyer, Olivia / Knebelmann, Bertrand / Heidet, Laurence / Saunier, Sophie / Chen, Xiaoyi / Burgun, Anita

Orphanet journal of rare diseases

2024 Volume 19, Issue 1, Page(s) 55

Abstract: Background: Rare diseases affect approximately 400 million people worldwide. Many of them suffer from delayed diagnosis. Among them, NPHP1-related renal ciliopathies need to be diagnosed as early as possible as potential treatments have been recently ... ...

Abstract	Background: Rare diseases affect approximately 400 million people worldwide. Many of them suffer from delayed diagnosis. Among them, NPHP1-related renal ciliopathies need to be diagnosed as early as possible as potential treatments have been recently investigated with promising results. Our objective was to develop a supervised machine learning pipeline for the detection of NPHP1 ciliopathy patients from a large number of nephrology patients using electronic health records (EHRs). Methods and results: We designed a pipeline combining a phenotyping module re-using unstructured EHR data, a semantic similarity module to address the phenotype dependence, a feature selection step to deal with high dimensionality, an undersampling step to address the class imbalance, and a classification step with multiple train-test split for the small number of rare cases. The pipeline was applied to thirty NPHP1 patients and 7231 controls and achieved good performances (sensitivity 86% with specificity 90%). A qualitative review of the EHRs of 40 misclassified controls showed that 25% had phenotypes belonging to the ciliopathy spectrum, which demonstrates the ability of our system to detect patients with similar conditions. Conclusions: Our pipeline reached very encouraging performance scores for pre-diagnosing ciliopathy patients. The identified patients could then undergo genetic testing. The same data-driven approach can be adapted to other rare diseases facing underdiagnosis challenges.
MeSH term(s)	Humans ; Rare Diseases ; Electronic Health Records ; Semantics ; Supervised Machine Learning ; Ciliopathies/diagnosis ; Ciliopathies/genetics ; Algorithms
Language	English
Publishing date	2024-02-10
Publishing country	England
Document type	Journal Article
ZDB-ID	2225857-7
ISSN	1750-1172 ; 1750-1172
ISSN (online)	1750-1172
ISSN	1750-1172
DOI	10.1186/s13023-024-03063-7
Database	MEDical Literature Analysis and Retrieval System OnLINE

Order via subito

Article ; Online: Improving Patient Similarity Using Different Modalities of Phenotypes Extracted from Clinical Narratives.

Chen, Xiaoyi / Faviez, Carole / Vincent, Marc / Saunier, Sophie / Garcelon, Nicolas / Burgun, Anita

Studies in health technology and informatics

2023 Volume 302, Page(s) 1037–1041

Abstract: In the context of medical concept extraction, it is critical to determine if clinical signs or symptoms mentioned in the text were present or absent, experienced by the patient or their relatives. Previous studies have focused on the NLP aspect but not ... ...

Abstract	In the context of medical concept extraction, it is critical to determine if clinical signs or symptoms mentioned in the text were present or absent, experienced by the patient or their relatives. Previous studies have focused on the NLP aspect but not on how to leverage this supplemental information for clinical applications. In this paper, we aim to use the patient similarity networks framework to aggregate different phenotyping modalities. NLP techniques were applied to extract phenotypes and predict their modalities from 5470 narrative reports of 148 patients with ciliopathies (a group of rare diseases). Patient similarities were computed using each modality separately for aggregation and clustering. We found that aggregating negated phenotypes improved patient similarity, but further aggregating relatives' phenotypes worsened the result. We suggest that different modalities of phenotypes can contribute to patient similarity, but they should be aggregated carefully and with appropriate similarity metrics and aggregation models.
MeSH term(s)	Humans ; Electronic Health Records ; Phenotype ; Narration ; Rare Diseases ; Natural Language Processing
Language	English
Publishing date	2023-05-19
Publishing country	Netherlands
Document type	Journal Article
ISSN	1879-8365
ISSN (online)	1879-8365
DOI	10.3233/SHTI230342
Database	MEDical Literature Analysis and Retrieval System OnLINE

Order via subito

Inter-library loan at ZB MED

Your chosen title can be delivered directly to ZB MED Cologne location if you are registered as a user at ZB MED Cologne.

Article ; Online: Meta-analysis of single-cell and single-nucleus transcriptomics reveals kidney cell type consensus signatures.

Quatredeniers, Marceau / Serafin, Alice S / Benmerah, Alexandre / Rausell, Antonio / Saunier, Sophie / Viau, Amandine

Scientific data

2023 Volume 10, Issue 1, Page(s) 361

Abstract: While the amount of studies involving single-cell or single-nucleus RNA-sequencing technologies grows exponentially within the biomedical research area, the kidney field requires reference transcriptomic signatures to allocate each cluster its matching ... ...

Abstract	While the amount of studies involving single-cell or single-nucleus RNA-sequencing technologies grows exponentially within the biomedical research area, the kidney field requires reference transcriptomic signatures to allocate each cluster its matching cell type. The present meta-analysis of 39 previously published datasets, from 7 independent studies, involving healthy human adult kidney samples, offers a set of 24 distinct consensus kidney cell type signatures. The use of these signatures may help to assure the reliability of cell type identification in future studies involving single-cell and single-nucleus transcriptomics while improving the reproducibility in cell type allocation.
MeSH term(s)	Adult ; Humans ; Gene Expression Profiling ; Kidney ; Reproducibility of Results ; Transcriptome ; Single-Cell Gene Expression Analysis ; Datasets as Topic
Language	English
Publishing date	2023-06-06
Publishing country	England
Document type	Meta-Analysis ; Journal Article
ZDB-ID	2775191-0
ISSN	2052-4463 ; 2052-4463
ISSN (online)	2052-4463
ISSN	2052-4463
DOI	10.1038/s41597-023-02209-9
Database	MEDical Literature Analysis and Retrieval System OnLINE

Order via subito

Article ; Online: Identification of Similar Patients Through Medical Concept Embedding from Electronic Health Records: A Feasibility Study for Rare Disease Diagnosis.

Chen, Xiaoyi / Faviez, Carole / Vincent, Marc / Garcelon, Nicolas / Saunier, Sophie / Burgun, Anita

Studies in health technology and informatics

2021 Volume 281, Page(s) 600–604

Abstract: To identify patients with similar clinical profiles and derive insights from the records and outcomes of similar patients can help fast and precise diagnosis and other clinical decisions for rare diseases. Similarity methods are required to take into ... ...

Abstract	To identify patients with similar clinical profiles and derive insights from the records and outcomes of similar patients can help fast and precise diagnosis and other clinical decisions for rare diseases. Similarity methods are required to take into account the semantic relations between medical concepts and also the different relevance of all medical concepts presented in patients' medical records. In this paper, we introduce the methods developed in the context of rare disease screening/diagnosis from clinical data warehouse using medical concept embedding and adjusted aggregations. Our methods provided better preliminary results than baseline methods, with a significant improvement of precision among the top ranked similar patients, which is encouraging for further fine-tuning and application on a large-scale dataset for new/candidate patient identification.
MeSH term(s)	Data Warehousing ; Electronic Health Records ; Feasibility Studies ; Humans ; Rare Diseases/diagnosis ; Semantics
Language	English
Publishing date	2021-05-27
Publishing country	Netherlands
Document type	Journal Article
ISSN	1879-8365
ISSN (online)	1879-8365
DOI	10.3233/SHTI210241
Database	MEDical Literature Analysis and Retrieval System OnLINE

Order via subito

Inter-library loan at ZB MED

Your chosen title can be delivered directly to ZB MED Cologne location if you are registered as a user at ZB MED Cologne.

Article: Fluid shear stress triggers cholesterol biosynthesis and uptake in inner medullary collecting duct cells, independently of nephrocystin-1 and nephrocystin-4.

Garfa Traoré, Meriem / Roccio, Federica / Miceli, Caterina / Ferri, Giulia / Parisot, Mélanie / Cagnard, Nicolas / Lhomme, Marie / Dupont, Nicolas / Benmerah, Alexandre / Saunier, Sophie / Delous, Marion

Frontiers in molecular biosciences

2023 Volume 10, Page(s) 1254691

Abstract: Renal epithelial cells are subjected to fluid shear stress of urine flow. Several cellular structures act as mechanosensors-the primary cilium, microvilli and cell adhesion complexes-that directly relay signals to the cytoskeleton to regulate various ... ...

Abstract	Renal epithelial cells are subjected to fluid shear stress of urine flow. Several cellular structures act as mechanosensors-the primary cilium, microvilli and cell adhesion complexes-that directly relay signals to the cytoskeleton to regulate various processes including cell differentiation and renal cell functions. Nephronophthisis (NPH) is an autosomal recessive tubulointerstitial nephropathy leading to end-stage kidney failure before adulthood.
Language	English
Publishing date	2023-10-17
Publishing country	Switzerland
Document type	Journal Article
ZDB-ID	2814330-9
ISSN	2296-889X
ISSN	2296-889X
DOI	10.3389/fmolb.2023.1254691
Database	MEDical Literature Analysis and Retrieval System OnLINE

Order via subito

Article: Patient-Patient Similarity-Based Screening of a Clinical Data Warehouse to Support Ciliopathy Diagnosis.

Chen, Xiaoyi / Faviez, Carole / Vincent, Marc / Briseño-Roa, Luis / Faour, Hassan / Annereau, Jean-Philippe / Lyonnet, Stanislas / Zaidan, Mohamad / Saunier, Sophie / Garcelon, Nicolas / Burgun, Anita

Frontiers in pharmacology

2022 Volume 13, Page(s) 786710

Abstract: A timely diagnosis is a key challenge for many rare diseases. As an expanding group of rare and severe monogenic disorders with a broad spectrum of clinical manifestations, ciliopathies, notably renal ciliopathies, suffer from important underdiagnosis ... ...

Abstract	A timely diagnosis is a key challenge for many rare diseases. As an expanding group of rare and severe monogenic disorders with a broad spectrum of clinical manifestations, ciliopathies, notably renal ciliopathies, suffer from important underdiagnosis issues. Our objective is to develop an approach for screening large-scale clinical data warehouses and detecting patients with similar clinical manifestations to those from diagnosed ciliopathy patients. We expect that the top-ranked similar patients will benefit from genetic testing for an early diagnosis. The dependence and relatedness between phenotypes were taken into account in our similarity model through medical concept embedding. The relevance of each phenotype to each patient was also considered by adjusted aggregation of phenotype similarity into patient similarity. A ranking model based on the best-subtype-average similarity was proposed to address the phenotypic overlapping and heterogeneity of ciliopathies. Our results showed that using less than one-tenth of learning sources, our language and center specific embedding provided comparable or better performances than other existing medical concept embeddings. Combined with the best-subtype-average ranking model, our patient-patient similarity-based screening approach was demonstrated effective in two large scale unbalanced datasets containing approximately 10,000 and 60,000 controls with kidney manifestations in the clinical data warehouse (about 2 and 0.4% of prevalence, respectively). Our approach will offer the opportunity to identify candidate patients who could go through genetic testing for ciliopathy. Earlier diagnosis, before irreversible end-stage kidney disease, will enable these patients to benefit from appropriate follow-up and novel treatments that could alleviate kidney dysfunction.
Language	English
Publishing date	2022-03-25
Publishing country	Switzerland
Document type	Journal Article
ZDB-ID	2587355-6
ISSN	1663-9812
ISSN	1663-9812
DOI	10.3389/fphar.2022.786710
Database	MEDical Literature Analysis and Retrieval System OnLINE

Order via subito

Article: 2d and 3d human induced pluripotent stem cell-based models to dissect primary cilium involvement during neocortical development

Boutaud, Lucile / Michael, Marie / Banal, Céline / Calderon, Damelys / Farcy, Sarah / Pernelle, Julie / Goudin, Nicolas / Maillard, Camille / Dimartino, Clémantine / Deleschaux, Cécile / Dupichaud, Sébastien / Lebreton, Corinne / Saunier, Sophie / Attié-Bitach, Tania / Bahi-Buisson, Nadia / Lefort, Nathalie / Thomas, Sophie

Journal of visualized experiments. 2022 Mar. 25, , no. 181

2022

Abstract: Primary cilia (PC) are non-motile dynamic microtubule-based organelles that protrude from the surface of most mammalian cells. They emerge from the older centriole during the G1/G0 phase of the cell cycle, while they disassemble as the cells re-enter the ...

Abstract	Primary cilia (PC) are non-motile dynamic microtubule-based organelles that protrude from the surface of most mammalian cells. They emerge from the older centriole during the G1/G0 phase of the cell cycle, while they disassemble as the cells re-enter the cell cycle at the G2/M phase boundary. They function as signal hubs, by detecting and transducing extracellular signals crucial for many cell processes. Similar to most cell types, all neocortical neural stem and progenitor cells (NSPCs) have been shown harboring a PC allowing them to sense and transduce specific signals required for the normal cerebral cortical development. Here, we provide detailed protocols to generate and characterize two-dimensional (2D) and three-dimensional (3D) cell-based models from human induced pluripotent stem cells (hIPSCs) to further dissect the involvement of PC during neocortical development. In particular, we present protocols to study the PC biogenesis and function in 2D neural rosette-derived NSPCs including the transduction of the Sonic Hedgehog (SHH) pathway. To take advantage of the three-dimensional (3D) organization of cerebral organoids, we describe a simple method for 3D imaging of in toto immunostained cerebral organoids. After optical clearing, rapid acquisition of entire organoids allows detection of both centrosomes and PC on neocortical progenitors and neurons of the whole organoid. Finally, we detail the procedure for immunostaining and clearing of thick free-floating organoid sections preserving a significant degree of 3D spatial information and allowing for the high-resolution acquisition required for the detailed qualitative and quantitative analysis of PC biogenesis and function.
Keywords	biogenesis ; centrioles ; humans ; organoids ; quantitative analysis ; spatial data
Language	English
Dates of publication	2022-0325
Size	p. e62667.
Publishing place	Journal of Visualized Experiments
Document type	Article
ZDB-ID	2259946-0
ISSN	1940-087X
ISSN	1940-087X
DOI	10.3791/62667
Database	NAL-Catalogue (AGRICOLA)

Order via subito

Article ; Online: Diagnosis support systems for rare diseases: a scoping review.

Faviez, Carole / Chen, Xiaoyi / Garcelon, Nicolas / Neuraz, Antoine / Knebelmann, Bertrand / Salomon, Rémi / Lyonnet, Stanislas / Saunier, Sophie / Burgun, Anita

Orphanet journal of rare diseases

2020 Volume 15, Issue 1, Page(s) 94

Abstract: Introduction: Rare diseases affect approximately 350 million people worldwide. Delayed diagnosis is frequent due to lack of knowledge of most clinicians and a small number of expert centers. Consequently, computerized diagnosis support systems have been ...

Abstract	Introduction: Rare diseases affect approximately 350 million people worldwide. Delayed diagnosis is frequent due to lack of knowledge of most clinicians and a small number of expert centers. Consequently, computerized diagnosis support systems have been developed to address these issues, with many relying on rare disease expertise and taking advantage of the increasing volume of generated and accessible health-related data. Our objective is to perform a review of all initiatives aiming to support the diagnosis of rare diseases. Methods: A scoping review was conducted based on methods proposed by Arksey and O'Malley. A charting form for relevant study analysis was developed and used to categorize data. Results: Sixty-eight studies were retained at the end of the charting process. Diagnosis targets varied from 1 rare disease to all rare diseases. Material used for diagnosis support consisted mostly of phenotype concepts, images or fluids. Fifty-seven percent of the studies used expert knowledge. Two-thirds of the studies relied on machine learning algorithms, and one-third used simple similarities. Manual algorithms were encountered as well. Most of the studies presented satisfying performance of evaluation by comparison with references or with external validation. Fourteen studies provided online tools, most of which aimed to support the diagnosis of all rare diseases by considering queries based on phenotype concepts. Conclusion: Numerous solutions relying on different materials and use of various methodologies are emerging with satisfying preliminary results. However, the variability of approaches and evaluation processes complicates the comparison of results. Efforts should be made to adequately validate these tools and guarantee reproducibility and explicability.
MeSH term(s)	Humans ; Rare Diseases/diagnosis ; Reproducibility of Results
Language	English
Publishing date	2020-04-16
Publishing country	England
Document type	Journal Article ; Research Support, Non-U.S. Gov't ; Review
ISSN	1750-1172
ISSN (online)	1750-1172
DOI	10.1186/s13023-020-01374-z
Database	MEDical Literature Analysis and Retrieval System OnLINE

Order via subito

Inter-library loan at ZB MED

Your chosen title can be delivered directly to ZB MED Cologne location if you are registered as a user at ZB MED Cologne.

To top

More links

Kategorien

In stock of ZB MED Cologne/Königswinter

Order via subito

More links

Kategorien

Order via subito

More links

Kategorien

Order via subito

More links

Kategorien

Order via subito

Inter-library loan at ZB MED

More links

Kategorien

Order via subito

More links

Kategorien

Order via subito

Inter-library loan at ZB MED

More links

Kategorien

Order via subito

More links

Kategorien

Order via subito

More links

Kategorien

Order via subito

More links

Kategorien

Order via subito

Inter-library loan at ZB MED