LIVIVO - Search results -

Search results

Result 1 - 10 of total 94

Search options

Article ; Online: Exploring miRNA-target gene pair detection in disease with coRmiT.

Cordoba-Caballero, Jose / Perkins, James R / García-Criado, Federico / Gallego, Diana / Navarro-Sánchez, Alicia / Moreno-Estellés, Mireia / Garcés, Concepción / Bonet, Fernando / Romá-Mateo, Carlos / Toro, Rocio / Perez, Belén / Sanz, Pascual / Kohl, Matthias / Rojano, Elena / Seoane, Pedro / Ranea, Juan A G

Briefings in bioinformatics

2024 Volume 25, Issue 2

Abstract: A wide range of approaches can be used to detect micro RNA (miRNA)-target gene pairs (mTPs ... from expression data, differing in the ways the gene and miRNA expression profiles are calculated, combined and ... by selecting the one with the highest odds ratio for each miRNA, as the optimal way to integrate the results ...

Abstract	A wide range of approaches can be used to detect micro RNA (miRNA)-target gene pairs (mTPs) from expression data, differing in the ways the gene and miRNA expression profiles are calculated, combined and correlated. However, there is no clear consensus on which is the best approach across all datasets. Here, we have implemented multiple strategies and applied them to three distinct rare disease datasets that comprise smallRNA-Seq and RNA-Seq data obtained from the same samples, obtaining mTPs related to the disease pathology. All datasets were preprocessed using a standardized, freely available computational workflow, DEG_workflow. This workflow includes coRmiT, a method to compare multiple strategies for mTP detection. We used it to investigate the overlap of the detected mTPs with predicted and validated mTPs from 11 different databases. Results show that there is no clear best strategy for mTP detection applicable to all situations. We therefore propose the integration of the results of the different strategies by selecting the one with the highest odds ratio for each miRNA, as the optimal way to integrate the results. We applied this selection-integration method to the datasets and showed it to be robust to changes in the predicted and validated mTP databases. Our findings have important implications for miRNA analysis. coRmiT is implemented as part of the ExpHunterSuite Bioconductor package available from https://bioconductor.org/packages/ExpHunterSuite.
MeSH term(s)	Consensus ; Databases, Factual ; MicroRNAs/genetics ; Odds Ratio ; RNA-Seq
Chemical Substances	MicroRNAs
Language	English
Publishing date	2024-03-04
Publishing country	England
Document type	Journal Article
ZDB-ID	2068142-2
ISSN	1477-4054 ; 1467-5463
ISSN (online)	1477-4054
ISSN	1467-5463
DOI	10.1093/bib/bbae060
Database	MEDical Literature Analysis and Retrieval System OnLINE

In stock of ZB MED Cologne/Königswinter

Zs.A 6262: Show issues

Location:
Je nach Verfügbarkeit (siehe Angabe bei Bestand)
bis Jg. 2021: Bestellungen von Artikeln über das Online-Bestellformular
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

Book ; Online ; E-Book: Epidermal stem cell niche

Perez-Moreno, Mirna

(Epidermal stem cell niche ; 3)

2019

Author's details	edited by Mirna Perez-Moreno
Series title	Epidermal stem cell niche ; 3 Advances in stem cells and their niches
Collection	Advances in stem cells and their niches
Keywords	Intestines ; Stem cells
Language	English
Size	1 Online-Ressource (xii, 219 Seiten), Illustrationen
Edition	First edition
Publisher	Elsevier AP
Publishing place	Cambridge, MA
Publishing country	United States
Document type	Book ; Online ; E-Book
Remark	Zugriff für angemeldete ZB MED-Nutzerinnen und -Nutzer
HBZ-ID	HT020245076
ISBN	978-0-12-818447-9 ; 9780128184462 ; 0-12-818447-7 ; 0128184469
Database	ZB MED Catalogue: Medicine, Health, Nutrition, Environment, Agriculture

Full text online

Accessible to users with ZB MED library card

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.

Details ▾
- Full text online
- Order with fees

Article ; Online: A Single Variant in Pri-miRNA-155 Associated with Susceptibility to Hereditary Breast Cancer Promotes Aggressiveness in Breast Cancer Cells.

Landeros, Natalia / Gonzalez-Hormazabal, Patricio / Pérez-Moreno, Pablo / Tapia, Julio C / Jara, Lilian

International journal of molecular sciences

2022 Volume 23, Issue 23

Abstract: Variants in genes encoding for microRNAs have been associated with their deregulation in breast cancer (BC). Sequencing of microRNAs deregulated in BC was performed using DNA from Chilean patients with a strong family history and negative for mutations ... ...

Abstract	Variants in genes encoding for microRNAs have been associated with their deregulation in breast cancer (BC). Sequencing of microRNAs deregulated in BC was performed using DNA from Chilean patients with a strong family history and negative for mutations in BRCA1/BRCA2. Seventeen variants were identified, three of which were selected for a case-control association study: rs376491654 (miR-335), rs755634302 (miR-497), and rs190708267 (miR-155). For rs190708267 C>T, the heterozygous T allele was detected in four BC cases and absent in controls, while homozygous TT cases were not detected. Variants were modelled in silico, cloned in a plasmid, expressed in BC cell lines, and functional in vitro assays were performed. Overexpression of the miR-155-T allele increased mature miR-155-5p levels in both BC cell lines, suggesting that its presence alters pre-miR-155 processing. Moreover, BC cells overexpressing the miR-155-T allele showed increased proliferation, migration, and resistance to cisplatin-induced death compared to miR-155-C overexpressing cells. Of note, the 3′UTR of APC, GSK3β, and PPP1CA genes, all into the canonical Wnt signaling pathway, were identified as direct targets. APC and GSK3β mRNA levels decreased while PP1 levels increased. These results suggest a pathogenic role of the variant rs190708267 (miR-155) in BRCA 1/2 negative BC, conferring susceptibility and promoting traits of aggressiveness.
MeSH term(s)	Female ; Humans ; 3' Untranslated Regions ; Breast Neoplasms/metabolism ; Cell Line, Tumor ; Cell Proliferation/genetics ; Gene Expression Regulation, Neoplastic ; MicroRNAs/genetics ; MicroRNAs/metabolism ; Mutation
Chemical Substances	3' Untranslated Regions ; MicroRNAs ; MIRN155 microRNA, human ; MIRN497 microRNA, human ; CYRIB protein, human
Language	English
Publishing date	2022-12-06
Publishing country	Switzerland
Document type	Journal Article
ZDB-ID	2019364-6
ISSN	1422-0067 ; 1422-0067 ; 1661-6596
ISSN (online)	1422-0067
ISSN	1422-0067 ; 1661-6596
DOI	10.3390/ijms232315418
Database	MEDical Literature Analysis and Retrieval System OnLINE

Order via subito

Article ; Online: Cluster-Partial Least Squares (c-PLS) regression analysis: Application to miRNA and metabolomic data.

Kuligowski, Julia / Pérez-Rubio, Álvaro / Moreno-Torres, Marta / Soluyanova, Polina / Pérez-Rojas, Judith / Rienda, Iván / Pérez-Guaita, David / Pareja, Eugenia / Trullenque-Juan, Ramón / Castell, José V / Verheijen, Marcha / Caiment, Florian / Jover, Ramiro / Quintás, Guillermo

Analytica chimica acta

2023 Volume 1286, Page(s) 342052

Abstract: ... suboptimal to treat omic data such as metabolic or miRNA profiles, where features cannot be distributed along ... such as miRNA-regulated metabolic pathway or lipid classes) on the predictive performance of a multivariate ...

Abstract	Background: Biomedicine and biological research frequently involve analyzing large datasets generated by high-throughput technologies like genomics, transcriptomics, miRNomics, and metabolomics. Pathway analysis is a common computational approach used to understand the impact of experimental conditions, phenotypes, or interventions on biological pathways and networks. This involves statistical analysis of omic data to identify differentially expressed variables and mapping them onto predefined pathways. Analyzing such datasets often requires multivariate techniques to extract meaningful insights such as Partial Least Squares (PLS). Variable selection strategies like interval-PLS (iPLS) help improve understanding and predictive performance by identifying informative variables or intervals. However, iPLS is suboptimal to treat omic data such as metabolic or miRNA profiles, where features cannot be distributed along a continuous dimension describing their relationships as in e.g., vibrational or nuclear magnetic resonance spectroscopy. Results: This study introduces a novel variable selection approach called cluster PLS (c-PLS) that aims to assess the joint impact of variable groups selected based on biological characteristics (such as miRNA-regulated metabolic pathway or lipid classes) on the predictive performance of a multivariate model. The usefulness of c-PLS is shown using miRNomic and metabolomic datasets obtained from the analysis of 24 liver tissue biopsies collected in the frame of a clinical study of steatosis. Significance and novelty: Results obtained show that c-PLS enables analyzing the effect of biologically relevant variable clusters, facilitating the identification of biological processes associated with the independent variable, and the prioritization of the biological factors influencing model performance, thereby improving the understanding of the biological factors driving model predictions. While the strategy is tested for the evaluation of PLS models, it could be extended to other linear and non-linear multivariate models.
MeSH term(s)	Least-Squares Analysis ; MicroRNAs/genetics ; Metabolomics ; Gene Expression Profiling ; Biological Factors
Chemical Substances	MicroRNAs ; Biological Factors
Language	English
Publishing date	2023-11-20
Publishing country	Netherlands
Document type	Journal Article
ZDB-ID	1483436-4
ISSN	1873-4324 ; 0003-2670
ISSN (online)	1873-4324
ISSN	0003-2670
DOI	10.1016/j.aca.2023.342052
Database	MEDical Literature Analysis and Retrieval System OnLINE

Order via subito

Article ; Online: A Single Variant in Pri-miRNA-155 Associated with Susceptibility to Hereditary Breast Cancer Promotes Aggressiveness in Breast Cancer Cells

Natalia Landeros / Patricio Gonzalez-Hormazabal / Pablo Pérez-Moreno / Julio C. Tapia / Lilian Jara

International Journal of Molecular Sciences, Vol 23, Iss 15418, p

2022 Volume 15418

Abstract	Variants in genes encoding for microRNAs have been associated with their deregulation in breast cancer (BC). Sequencing of microRNAs deregulated in BC was performed using DNA from Chilean patients with a strong family history and negative for mutations in BRCA1/BRCA2. Seventeen variants were identified, three of which were selected for a case-control association study: rs376491654 (miR-335), rs755634302 (miR-497), and rs190708267 (miR-155). For rs190708267 C>T, the heterozygous T allele was detected in four BC cases and absent in controls, while homozygous TT cases were not detected. Variants were modelled in silico, cloned in a plasmid, expressed in BC cell lines, and functional in vitro assays were performed. Overexpression of the miR-155-T allele increased mature miR-155-5p levels in both BC cell lines, suggesting that its presence alters pre-miR-155 processing. Moreover, BC cells overexpressing the miR-155-T allele showed increased proliferation, migration, and resistance to cisplatin-induced death compared to miR-155-C overexpressing cells. Of note, the 3′UTR of APC, GSK3β, and PPP1CA genes, all into the canonical Wnt signaling pathway, were identified as direct targets. APC and GSK3β mRNA levels decreased while PP1 levels increased. These results suggest a pathogenic role of the variant rs190708267 (miR-155) in BRCA 1/2 negative BC, conferring susceptibility and promoting traits of aggressiveness.
Keywords	microRNA ; breast cancer ; SNV ; canonical Wnt pathway ; aggressiveness ; Biology (General) ; QH301-705.5 ; Chemistry ; QD1-999
Subject code	616
Language	English
Publishing date	2022-12-01T00:00:00Z
Publisher	MDPI AG
Document type	Article ; Online
Database	BASE - Bielefeld Academic Search Engine (life sciences selection)

Full text online

Full text

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: Translational frontiers: insight from lymphatics in skin regeneration.

Jiang, Yujia / Perez-Moreno, Mirna

Frontiers in physiology

2024 Volume 15, Page(s) 1347558

Abstract: The remarkable regenerative ability of the skin, governed by complex molecular mechanisms, offers profound insights into the skin repair processes and the pathogenesis of various dermatological conditions. This understanding, derived from studies in ... ...

Abstract	The remarkable regenerative ability of the skin, governed by complex molecular mechanisms, offers profound insights into the skin repair processes and the pathogenesis of various dermatological conditions. This understanding, derived from studies in human skin and various model systems, has not only deepened our knowledge of skin regeneration but also facilitated the development of skin substitutes in clinical practice. Recent research highlights the crucial role of lymphatic vessels in skin regeneration. Traditionally associated with fluid dynamics and immune modulation, these vessels are now recognized for interacting with skin stem cells and coordinating regeneration. This Mini Review provides an overview of recent advancements in basic and translational research related to skin regeneration, focusing on the dynamic interplay between lymphatic vessels and skin biology. Key highlights include the critical role of stem cell-lymphatic vessel crosstalk in orchestrating skin regeneration, emerging translational approaches, and their implications for skin diseases. Additionally, the review identifies research gaps and proposes potential future directions, underscoring the significance of this rapidly evolving research arena.
Language	English
Publishing date	2024-02-29
Publishing country	Switzerland
Document type	Journal Article ; Review
ZDB-ID	2564217-0
ISSN	1664-042X
ISSN	1664-042X
DOI	10.3389/fphys.2024.1347558
Database	MEDical Literature Analysis and Retrieval System OnLINE

Order via subito

Article ; Online: miRNA profile obtained by next‑generation sequencing in metastatic breast cancer patients is able to predict the response to systemic treatments.

Martinez-Gutierrez, Antonio Daniel / Catalan, Oliver Millan / Vázquez-Romo, Rafael / Porras Reyes, Fany Iris / Alvarado-Miranda, Alberto / Lara Medina, Fernando / Bargallo-Rocha, Juan E / Orozco Moreno, Luz Tonatzin / Cantú De León, David / Herrera, Luis Alonso / López-Camarillo, César / Pérez-Plasencia, Carlos / Campos-Parra, Alma D

International journal of molecular medicine

2019 Volume 44, Issue 4, Page(s) 1267–1280

Abstract: ... The aim of this study was to identify a miRNA profile for distinguishing patients with MBC who respond ... guidelines. We performed miRNA‑Seq on 9 primary tumors using the Thermo Fisher Scientific Ion S5 system ... To obtain global miRNA profiles, we carried out differentially expressed gene elimination strategy (DEGES ...

Abstract	Metastatic breast cancer (MBC) is a challenge for oncologists, and public efforts should focus on identifying additional molecular markers and therapeutic management to improve clinical outcomes. Among all diagnosed cases of breast cancer (BC; approximately 10%) involve metastatic disease; notably, approximately 40% of patients with early‑stage BC develop metastasis within 5 years. The management of MBC consists of systemic therapy. Despite different treatment options, the 5‑year survival rate is <20%, which may be due to a lack of response with de novo or acquired resistance. MicroRNAs (miRNAs or miRs) are promising biomarkers as they are readily detectable and have a broad spectrum and potential clinical applications. The aim of this study was to identify a miRNA profile for distinguishing patients with MBC who respond to systemic treatment. Patients with MBC were treated according to the National Comprehensive Cancer Network guidelines. We performed miRNA‑Seq on 9 primary tumors using the Thermo Fisher Scientific Ion S5 system. To obtain global miRNA profiles, we carried out differentially expressed gene elimination strategy (DEGES) analysis between the responsive and non‑responsive patients. The results identified a profile of 12 miRNAs associated with the response to systemic treatment. The data were validated in an independent cohort (TCGA database). Based on the results, the upregulation of miR‑342‑3p and miR‑187‑3p was associated with the response to systemic treatment, and with an increased progression‑free survival (PFS) and overall survival (OS); by contrast, the downregulation of miR‑301a‑3p was associated with a higher PFS and OS. On the whole, the findings of this study indicate that these miRNAs may serve as biomarkers for the response to systemic treatment or the prognosis of patients with MBC. However, these data should be validated experimentally in other robust cohorts and using different specimens before implementing these miRNAs as biomarkers in clinical practice to benefit this group of patients.
MeSH term(s)	Adult ; Aged ; Biomarkers, Tumor ; Breast Neoplasms/genetics ; Breast Neoplasms/mortality ; Breast Neoplasms/pathology ; Breast Neoplasms/therapy ; Combined Modality Therapy ; Female ; Gene Expression Regulation, Neoplastic ; High-Throughput Nucleotide Sequencing ; Humans ; MicroRNAs/genetics ; Middle Aged ; Neoplasm Metastasis ; Neoplasm Staging ; Prognosis ; Reproducibility of Results ; Survival Analysis ; Transcriptome ; Treatment Outcome
Chemical Substances	Biomarkers, Tumor ; MicroRNAs
Language	English
Publishing date	2019-07-30
Publishing country	Greece
Document type	Journal Article
ZDB-ID	1444428-8
ISSN	1791-244X ; 1107-3756
ISSN (online)	1791-244X
ISSN	1107-3756
DOI	10.3892/ijmm.2019.4292
Database	MEDical Literature Analysis and Retrieval System OnLINE

In stock of ZB MED Cologne/Königswinter

Zs.A 4942: Show issues

Location:
Je nach Verfügbarkeit (siehe Angabe bei Bestand)
bis Jg. 1994: Bestellungen von Artikeln über das Online-Bestellformular
Jg. 1995 - 2021: Lesesall (2.OG)
ab Jg. 2022: Lesesaal (EG)

Order via subito

Details ▾
- See ZB MED holdings
- Order with fees

Article: The Role of MicroRNAs in Breast Cancer and the Challenges of Their Clinical Application.

Muñoz, Juan P / Pérez-Moreno, Pablo / Pérez, Yasmín / Calaf, Gloria M

Diagnostics (Basel, Switzerland)

2023 Volume 13, Issue 19

Abstract: ... tools for miRNA analysis and the challenges faced by these new biomedical approaches in its clinical ... MicroRNAs (miRNAs) constitute a subclass of non-coding RNAs that exert substantial influence ... demonstrated distinct expression patterns of miRNAs in normal and malignant breast cells. Consequently ...

Abstract	MicroRNAs (miRNAs) constitute a subclass of non-coding RNAs that exert substantial influence on gene-expression regulation. Their tightly controlled expression plays a pivotal role in various cellular processes, while their dysregulation has been implicated in numerous pathological conditions, including cancer. Among cancers affecting women, breast cancer (BC) is the most prevalent malignant tumor. Extensive investigations have demonstrated distinct expression patterns of miRNAs in normal and malignant breast cells. Consequently, these findings have prompted research efforts towards leveraging miRNAs as diagnostic tools and the development of therapeutic strategies. The aim of this review is to describe the role of miRNAs in BC. We discuss the identification of oncogenic, tumor suppressor and metastatic miRNAs among BC cells, and their impact on tumor progression. We describe the potential of miRNAs as diagnostic and prognostic biomarkers for BC, as well as their role as promising therapeutic targets. Finally, we evaluate the current use of artificial intelligence tools for miRNA analysis and the challenges faced by these new biomedical approaches in its clinical application. The insights presented in this review underscore the promising prospects of utilizing miRNAs as innovative diagnostic, prognostic, and therapeutic tools for the management of BC.
Language	English
Publishing date	2023-09-28
Publishing country	Switzerland
Document type	Journal Article ; Review
ZDB-ID	2662336-5
ISSN	2075-4418
ISSN	2075-4418
DOI	10.3390/diagnostics13193072
Database	MEDical Literature Analysis and Retrieval System OnLINE

Order via subito

Article ; Online: Isolation of Cancer Stem Cells from Squamous Cell Carcinoma.

Fontenete, Silvia / Perez-Moreno, Mirna

Methods in molecular biology (Clifton, N.J.)

2018 Volume 1879, Page(s) 407–414

Abstract: Different cancer stem cell (CSC) populations can be found in many types of cancer, including squamous cell carcinoma (SSC). Diverse reports showed that CSC play a crucial role in the relapse of different types of cancer. CSC sustains tumor growth due to ... ...

Abstract	Different cancer stem cell (CSC) populations can be found in many types of cancer, including squamous cell carcinoma (SSC). Diverse reports showed that CSC play a crucial role in the relapse of different types of cancer. CSC sustains tumor growth due to their capacity to self-renew and their potential to initiate secondary tumors with metastatic cancer features. Therefore, the development of methods for the isolation of CSC is a key step to explore the mechanisms underlying CSC maintenance. In this chapter, we provide a method for isolating CSC from cutaneous SSC using immunofluorescence labeling to allow the specific purification of CSC by fluorescence-activated cell sorting (FACS). This method is based on the use of CSC membrane markers, allowing as well the isolation CSC from different mouse strains.
MeSH term(s)	Animals ; Carcinoma, Squamous Cell/pathology ; Cell Separation/methods ; Flow Cytometry/methods ; Fluorescent Antibody Technique/methods ; Mice ; Neoplastic Stem Cells/pathology ; Skin Neoplasms/pathology
Language	English
Publishing date	2018-06-19
Publishing country	United States
Document type	Journal Article ; Research Support, Non-U.S. Gov't
ISSN	1940-6029
ISSN (online)	1940-6029
DOI	10.1007/7651_2018_162
Database	MEDical Literature Analysis and Retrieval System OnLINE

Full text online

Accessible to users with ZB MED library card

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.

Details ▾
- Full text online
- Order with fees

Article: Variation of extrachromosomal circular DNA in cancer cell lines.

Dos Santos, Carl Rung / Hansen, Lasse Bøllehuus / Rojas-Triana, Monica / Johansen, Astrid Zedlitz / Perez-Moreno, Mirna / Regenberg, Birgitte

Computational and structural biotechnology journal

2023 Volume 21, Page(s) 4207–4214

Abstract: The presence of oncogene carrying eccDNAs is strongly associated with carcinogenesis and poor patient survival. Tumour biopsies ... ...

Abstract	The presence of oncogene carrying eccDNAs is strongly associated with carcinogenesis and poor patient survival. Tumour biopsies and
Language	English
Publishing date	2023-08-28
Publishing country	Netherlands
Document type	Journal Article
ZDB-ID	2694435-2
ISSN	2001-0370
ISSN	2001-0370
DOI	10.1016/j.csbj.2023.08.027
Database	MEDical Literature Analysis and Retrieval System OnLINE

Order via subito

To top

More links

Kategorien

In stock of ZB MED Cologne/Königswinter

Order via subito

Full text online

Kategorien

Order via subito

Inter-library loan at ZB MED

More links

Kategorien

Order via subito

More links

Kategorien

Order via subito

Full text online

More links

Kategorien

Inter-library loan at ZB MED

More links

Kategorien

Order via subito

More links

Kategorien

In stock of ZB MED Cologne/Königswinter

Order via subito

More links

Kategorien

Order via subito

Full text online

More links

Kategorien

Order via subito

Inter-library loan at ZB MED

More links

Kategorien

Order via subito