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Article: Data of transcriptional effects of the merbarone-mediated inhibition of TOP2

Delgado-Chaves, Fernando M. / Martínez-García, Pedro Manuel / Herrero-Ruiz, Andrés / Gómez-Vela, Francisco / Divina, Federico / Jimeno-González, Silvia / Cortés-Ledesma, Felipe

Data in Brief. 2022 Oct., v. 44

2022

Abstract: Type II DNA topoisomerases relax topological stress by transiently gating DNA passage in a controlled cut-and-reseal mechanism that affects both DNA strands. Therefore, they are essential to overcome topological problems associated with DNA metabolism. ... ...

Abstract	Type II DNA topoisomerases relax topological stress by transiently gating DNA passage in a controlled cut-and-reseal mechanism that affects both DNA strands. Therefore, they are essential to overcome topological problems associated with DNA metabolism. Their aberrant activity results in the generation of DNA double-strand breaks, which can seriously compromise cell survival and genome integrity. Here, we profile the transcriptome of human-telomerase-immortalized retinal pigment epithelial 1 (RPE-1) cells when treated with merbarone, a drug that catalytically inhibits type II DNA topoisomerases. We performed RNA-Seq after 4 and 8 h of merbarone treatment and compared transcriptional profiles versus untreated samples. We report raw sequencing data together with lists of gene counts and differentially expressed genes.
Keywords	DNA ; cell viability ; drugs ; epithelium ; gene expression regulation ; genes ; metabolism ; sequence analysis ; topology ; transcription (genetics) ; transcriptome
Language	English
Dates of publication	2022-10
Publishing place	Elsevier Inc.
Document type	Article
ZDB-ID	2786545-9
ISSN	2352-3409
ISSN	2352-3409
DOI	10.1016/j.dib.2022.108499
Database	NAL-Catalogue (AGRICOLA)

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Article ; Online: Data of transcriptional effects of the merbarone-mediated inhibition of TOP2.

Delgado-Chaves, Fernando M / Martínez-García, Pedro Manuel / Herrero-Ruiz, Andrés / Gómez-Vela, Francisco / Divina, Federico / Jimeno-González, Silvia / Cortés-Ledesma, Felipe

Data in brief

2022 Volume 44, Page(s) 108499

Abstract	Type II DNA topoisomerases relax topological stress by transiently gating DNA passage in a controlled cut-and-reseal mechanism that affects both DNA strands. Therefore, they are essential to overcome topological problems associated with DNA metabolism. Their aberrant activity results in the generation of DNA double-strand breaks, which can seriously compromise cell survival and genome integrity. Here, we profile the transcriptome of human-telomerase-immortalized retinal pigment epithelial 1 (RPE-1) cells when treated with merbarone, a drug that catalytically inhibits type II DNA topoisomerases. We performed RNA-Seq after 4 and 8 h of merbarone treatment and compared transcriptional profiles versus untreated samples. We report raw sequencing data together with lists of gene counts and differentially expressed genes.
Language	English
Publishing date	2022-08-01
Publishing country	Netherlands
Document type	Journal Article
ZDB-ID	2786545-9
ISSN	2352-3409 ; 2352-3409
ISSN (online)	2352-3409
ISSN	2352-3409
DOI	10.1016/j.dib.2022.108499
Database	MEDical Literature Analysis and Retrieval System OnLINE

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Article ; Online: Computational Analysis of the Global Effects of

Delgado-Chaves, Fernando M / Gómez-Vela, Francisco / Divina, Federico / García-Torres, Miguel / Rodriguez-Baena, Domingo S

Genes

2020 Volume 11, Issue 7

Abstract: Gene networks have arisen as a promising tool in the comprehensive modeling and analysis of complex diseases. Particularly in viral infections, the understanding of the host-pathogen mechanisms, and the immune response to these, is considered a major ... ...

Abstract	Gene networks have arisen as a promising tool in the comprehensive modeling and analysis of complex diseases. Particularly in viral infections, the understanding of the host-pathogen mechanisms, and the immune response to these, is considered a major goal for the rational design of appropriate therapies. For this reason, the use of gene networks may well encourage therapy-associated research in the context of the coronavirus pandemic, orchestrating experimental scrutiny and reducing costs. In this work, gene co-expression networks were reconstructed from RNA-Seq expression data with the aim of analyzing the time-resolved effects of gene
MeSH term(s)	Animals ; Antigens, Surface/genetics ; Antigens, Surface/immunology ; Computational Biology/methods ; Coronavirus Infections/genetics ; Coronavirus Infections/immunology ; GPI-Linked Proteins/genetics ; GPI-Linked Proteins/immunology ; Gene Expression Regulation ; Gene Regulatory Networks ; Host-Pathogen Interactions/genetics ; Host-Pathogen Interactions/immunology ; Mice, Knockout ; Murine hepatitis virus
Chemical Substances	Antigens, Surface ; GPI-Linked Proteins ; Ly6e protein, mouse
Keywords	covid19
Language	English
Publishing date	2020-07-21
Publishing country	Switzerland
Document type	Journal Article
ZDB-ID	2527218-4
ISSN	2073-4425 ; 2073-4425
ISSN (online)	2073-4425
ISSN	2073-4425
DOI	10.3390/genes11070831
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Article ; Online: Computational Inference of Gene Co-Expression Networks for the identification of Lung Carcinoma Biomarkers: An Ensemble Approach.

Delgado-Chaves, Fernando M / Gómez-Vela, Francisco / García-Torres, Miguel / Divina, Federico / Vázquez Noguera, José Luis

Genes

2019 Volume 10, Issue 12

Abstract: ... biomarkers, genes N C K A P 1 L and D M D are highlighted due to their implications in a considerable portion ...

Abstract	Gene Networks (GN), have emerged as an useful tool in recent years for the analysis of different diseases in the field of biomedicine. In particular, GNs have been widely applied for the study and analysis of different types of cancer. In this context, Lung carcinoma is among the most common cancer types and its short life expectancy is partly due to late diagnosis. For this reason, lung cancer biomarkers that can be easily measured are highly demanded in biomedical research. In this work, we present an application of gene co-expression networks in the modelling of lung cancer gene regulatory networks, which ultimately served to the discovery of new biomarkers. For this, a robust GN inference was performed from microarray data concomitantly using three different co-expression measures. Results identified a major cluster of genes involved in SRP-dependent co-translational protein target to membrane, as well as a set of 28 genes that were exclusively found in networks generated from cancer samples. Amongst potential biomarkers, genes N C K A P 1 L and D M D are highlighted due to their implications in a considerable portion of lung and bronchus primary carcinomas. These findings demonstrate the potential of GN reconstruction in the rational prediction of biomarkers.
MeSH term(s)	Algorithms ; Biomarkers, Tumor/genetics ; Computational Biology ; Dystrophin/genetics ; Gene Expression ; Gene Regulatory Networks ; Humans ; Lung/metabolism ; Lung Neoplasms/genetics ; Membrane Proteins/genetics ; Mutation ; Smoking/genetics
Chemical Substances	Biomarkers, Tumor ; DMD protein, human ; Dystrophin ; Membrane Proteins ; NCKAP1L protein, human (144351-15-5)
Language	English
Publishing date	2019-11-22
Publishing country	Switzerland
Document type	Journal Article ; Research Support, Non-U.S. Gov't
ZDB-ID	2527218-4
ISSN	2073-4425 ; 2073-4425
ISSN (online)	2073-4425
ISSN	2073-4425
DOI	10.3390/genes10120962
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Article ; Online: Data of transcriptional effects of the merbarone-mediated inhibition of TOP2

Fernando M. Delgado-Chaves / Pedro Manuel Martínez-García / Andrés Herrero-Ruiz / Francisco Gómez-Vela / Federico Divina / Silvia Jimeno-González / Felipe Cortés-Ledesma

Data in Brief, Vol 44, Iss , Pp 108499- (2022)

2022

Abstract	Type II DNA topoisomerases relax topological stress by transiently gating DNA passage in a controlled cut-and-reseal mechanism that affects both DNA strands. Therefore, they are essential to overcome topological problems associated with DNA metabolism. Their aberrant activity results in the generation of DNA double-strand breaks, which can seriously compromise cell survival and genome integrity. Here, we profile the transcriptome of human-telomerase-immortalized retinal pigment epithelial 1 (RPE-1) cells when treated with merbarone, a drug that catalytically inhibits type II DNA topoisomerases. We performed RNA-Seq after 4 and 8 h of merbarone treatment and compared transcriptional profiles versus untreated samples. We report raw sequencing data together with lists of gene counts and differentially expressed genes.
Keywords	Topoisomerase inhibition ; Differential gene expression ; DNA supercoiling ; Merbarone ; RNA-Seq ; Computer applications to medicine. Medical informatics ; R858-859.7 ; Science (General) ; Q1-390
Subject code	612
Language	English
Publishing date	2022-10-01T00:00:00Z
Publisher	Elsevier
Document type	Article ; Online
Database	BASE - Bielefeld Academic Search Engine (life sciences selection)

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Article ; Online: Computational Analysis of the Global Effects of Ly6E in the Immune Response to Coronavirus Infection Using Gene Networks

Fernando M. Delgado-Chaves / Francisco Gómez-Vela / Federico Divina / Miguel García-Torres / Domingo S. Rodriguez-Baena

Genes, Vol 11, Iss 831, p

2020 Volume 831

Abstract	Gene networks have arisen as a promising tool in the comprehensive modeling and analysis of complex diseases. Particularly in viral infections, the understanding of the host-pathogen mechanisms, and the immune response to these, is considered a major goal for the rational design of appropriate therapies. For this reason, the use of gene networks may well encourage therapy-associated research in the context of the coronavirus pandemic, orchestrating experimental scrutiny and reducing costs. In this work, gene co-expression networks were reconstructed from RNA-Seq expression data with the aim of analyzing the time-resolved effects of gene Ly6E in the immune response against the coronavirus responsible for murine hepatitis (MHV). Through the integration of differential expression analyses and reconstructed networks exploration, significant differences in the immune response to virus were observed in Ly6E <math display="inline"> <semantics> <msup> <mrow></mrow> <mrow> <mi>Δ</mi> <mi>H</mi> <mi>S</mi> <mi>C</mi> </mrow> </msup> </semantics> </math> compared to wild type animals. Results show that Ly6E ablation at hematopoietic stem cells (HSCs) leads to a progressive impaired immune response in both liver and spleen. Specifically, depletion of the normal leukocyte mediated immunity and chemokine signaling is observed in the liver of Ly6E <math display="inline"> <semantics> <msup> <mrow></mrow> <mrow> <mi>Δ</mi> <mi>H</mi> <mi>S</mi> <mi>C</mi> </mrow> </msup> </semantics> </math> mice. On the other hand, the immune response in the spleen, which seemed to be mediated by an intense chromatin activity in the normal situation, is replaced by ECM remodeling in Ly6E <math display="inline"> <semantics> <msup> <mrow></mrow> <mrow> <mi>Δ</mi> <mi>H</mi> ...
Keywords	gene co-expression network ; murine coronavirus ; viral infection ; immune response ; data mining ; systems biology ; Genetics ; QH426-470
Subject code	570
Language	English
Publishing date	2020-07-01T00:00:00Z
Publisher	MDPI AG
Document type	Article ; Online
Database	BASE - Bielefeld Academic Search Engine (life sciences selection)

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Article ; Online: Role of a cryptic tRNA gene operon in survival under translational stress.

Santamaría-Gómez, Javier / Rubio, Miguel Ángel / López-Igual, Rocío / Romero-Losada, Ana B / Delgado-Chaves, Fernando M / Bru-Martínez, Roque / Romero-Campero, Francisco J / Herrero, Antonia / Ibba, Michael / Ochoa de Alda, Jesús A G / Luque, Ignacio

Nucleic acids research

2021 Volume 49, Issue 15, Page(s) 8757–8776

Abstract: As compared to eukaryotes, bacteria have a reduced tRNA gene set encoding between 30 and 220 tRNAs. Although in most bacterial phyla tRNA genes are dispersed in the genome, many species from distinct phyla also show genes forming arrays. Here, we show ... ...

Abstract	As compared to eukaryotes, bacteria have a reduced tRNA gene set encoding between 30 and 220 tRNAs. Although in most bacterial phyla tRNA genes are dispersed in the genome, many species from distinct phyla also show genes forming arrays. Here, we show that two types of arrays with distinct evolutionary origins exist. This work focuses on long tRNA gene arrays (L-arrays) that encompass up to 43 genes, which disseminate by horizontal gene transfer and contribute supernumerary tRNA genes to the host. Although in the few cases previously studied these arrays were reported to be poorly transcribed, here we show that the L-array of the model cyanobacterium Anabaena sp. PCC 7120, encoding 23 functional tRNAs, is largely induced upon impairment of the translation machinery. The cellular response to this challenge involves a global reprogramming of the transcriptome in two phases. tRNAs encoded in the array are induced in the second phase of the response, directly contributing to cell survival. Results presented here show that in some bacteria the tRNA gene set may be partitioned between a housekeeping subset, which constantly sustains translation, and an inducible subset that is generally silent but can provide functionality under particular conditions.
MeSH term(s)	Anabaena/genetics ; Anti-Bacterial Agents/pharmacology ; Gene Expression Regulation, Bacterial ; Genes, Bacterial ; Genome, Bacterial ; Microbial Viability/genetics ; Operon ; Protein Biosynthesis ; RNA, Transfer/genetics ; RNA, Transfer/metabolism ; Regulatory Sequences, Nucleic Acid ; Stress, Physiological/genetics
Chemical Substances	Anti-Bacterial Agents ; RNA, Transfer (9014-25-9)
Language	English
Publishing date	2021-08-11
Publishing country	England
Document type	Journal Article ; Research Support, Non-U.S. Gov't ; Research Support, U.S. Gov't, Non-P.H.S.
ZDB-ID	186809-3
ISSN	1362-4962 ; 1362-4954 ; 0301-5610 ; 0305-1048
ISSN (online)	1362-4962 ; 1362-4954
ISSN	0301-5610 ; 0305-1048
DOI	10.1093/nar/gkab661
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Article: Computational Analysis of the Global Effects of Ly6E in the Immune Response to Coronavirus Infection Using Gene Networks

Delgado-Chaves, Fernando M / Gómez-Vela, Francisco / Divina, Federico / García-Torres, Miguel / Rodriguez-Baena, Domingo S

Abstract	Gene networks have arisen as a promising tool in the comprehensive modeling and analysis of complex diseases. Particularly in viral infections, the understanding of the host-pathogen mechanisms, and the immune response to these, is considered a major goal for the rational design of appropriate therapies. For this reason, the use of gene networks may well encourage therapy-associated research in the context of the coronavirus pandemic, orchestrating experimental scrutiny and reducing costs. In this work, gene co-expression networks were reconstructed from RNA-Seq expression data with the aim of analyzing the time-resolved effects of gene Ly6E in the immune response against the coronavirus responsible for murine hepatitis (MHV). Through the integration of differential expression analyses and reconstructed networks exploration, significant differences in the immune response to virus were observed in Ly6E Δ H S C compared to wild type animals. Results show that Ly6E ablation at hematopoietic stem cells (HSCs) leads to a progressive impaired immune response in both liver and spleen. Specifically, depletion of the normal leukocyte mediated immunity and chemokine signaling is observed in the liver of Ly6E Δ H S C mice. On the other hand, the immune response in the spleen, which seemed to be mediated by an intense chromatin activity in the normal situation, is replaced by ECM remodeling in Ly6E Δ H S C mice. These findings, which require further experimental characterization, could be extrapolated to other coronaviruses and motivate the efforts towards novel antiviral approaches.
Keywords	covid19
Publisher	WHO
Document type	Article
Note	WHO #Covidence: #670190
Database	COVID19

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Article ; Online: Ensemble and Greedy Approach for the Reconstruction of Large Gene Co-Expression Networks

Francisco Gómez-Vela / Fernando M. Delgado-Chaves / Domingo S. Rodríguez-Baena / Miguel García-Torres / Federico Divina

Entropy, Vol 21, Iss 12, p

2019 Volume 1139

Abstract: Gene networks have become a powerful tool in the comprehensive analysis of gene expression. Due to the increasing amount of available data, computational methods for networks generation must deal with the so-called curse of dimensionality in the quest ... ...

Abstract	Gene networks have become a powerful tool in the comprehensive analysis of gene expression. Due to the increasing amount of available data, computational methods for networks generation must deal with the so-called curse of dimensionality in the quest for the reliability of the obtained results. In this context, ensemble strategies have significantly improved the precision of results by combining different measures or methods. On the other hand, structure optimization techniques are also important in the reduction of the size of the networks, not only improving their topology but also keeping a positive prediction ratio. In this work, we present Ensemble and Greedy networks (EnGNet), a novel two-step method for gene networks inference. First, EnGNet uses an ensemble strategy for co-expression networks generation. Second, a greedy algorithm optimizes both the size and the topological features of the network. Not only do achieved results show that this method is able to obtain reliable networks, but also that it significantly improves topological features. Moreover, the usefulness of the method is proven by an application to a human dataset on post-traumatic stress disorder, revealing an innate immunity-mediated response to this pathology. These results are indicative of the method’s potential in the field of biomarkers discovery and characterization.
Keywords	gene networks ; scale-free networks ; ensemble networks ; graph theory ; computational biology ; mutual information networks ; biomarkers discovery ; Science ; Q ; Astrophysics ; QB460-466 ; Physics ; QC1-999
Subject code	000
Language	English
Publishing date	2019-11-01T00:00:00Z
Publisher	MDPI AG
Document type	Article ; Online
Database	BASE - Bielefeld Academic Search Engine (life sciences selection)

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Article ; Online: Improved blood culture workflow in the time to detection of microorganisms placing incubators systems outside of microbiology laboratory.

Orellana, M Angeles / Chaves, Fernando / Delgado, Rafael

Brazilian journal of microbiology : [publication of the Brazilian Society for Microbiology

2020 Volume 51, Issue 3, Page(s) 1103–1108

Abstract: ... with one BACT/ALERT 3D module located in the microbiology laboratory (ML) (access 8 a.m. to 10 p.m.) and ... with BACT/ALERT VIRTUO. During the 8:00 a.m. to 10:00 p.m. shift, the average ETs were 3.54 ± 5.06 vs 1.59 ... reduction of time during the 10:00 p.m. to 8:00 a.m. shift, where the average ET was 10.52 ± 5.23 vs 1.00 ...

Abstract	Purpose: We analyzed the workflow of the blood culture procedure with one blood culture incubator in the microbiology laboratory, in comparison with the workflow with the incubators systems placing outside, and in a microbiology laboratory without 24-h staffing. Methods: We assessed the elapsed time (ET) and time-to-result (TTR) in the two laboratory workflows during 1 month period in consecutive years. First period with one BACT/ALERT 3D module located in the microbiology laboratory (ML) (access 8 a.m. to 10 p.m.) and second period with three BACT/ALERT VIRTUO modules (one located in ML and two in the core sample laboratory, access 24 h). Results: The mean ET with BACT/ALERT 3D was 7.09 ± 6.15 h and 1.32 ± 3.14 h with BACT/ALERT VIRTUO. During the 8:00 a.m. to 10:00 p.m. shift, the average ETs were 3.54 ± 5.06 vs 1.59 ± 1.29 h for the two time periods, respectively. Since the automated loading of bottles on the BACT/ALERT VIRTUO allows processing of blood cultures during the night shift, there was a significant reduction of time during the 10:00 p.m. to 8:00 a.m. shift, where the average ET was 10.52 ± 5.23 vs 1.00 ± 4.40 h, respectively. The percentage of positivity in the first period was 9.03% and 11.18% in the second (p = 0.0003). The average TTR in the first period was 24.78 ± 15.9 h and 16.85 ± 14.13 h in the second (p < 0.0001). Conclusions: Easy 24-h access to blood culture incubators resulted in significant improvement in the workflow of blood culture, decreasing ET, and therefore decreasing the time to positivity and the efficiency of recovery.
MeSH term(s)	Bacteria/genetics ; Bacteria/growth & development ; Bacteria/isolation & purification ; Bacteriological Techniques/instrumentation ; Bacteriological Techniques/methods ; Blood Culture/instrumentation ; Blood Culture/methods ; Humans ; Incubators ; Laboratories ; Time Factors ; Workflow
Language	English
Publishing date	2020-05-18
Publishing country	Brazil
Document type	Journal Article
ZDB-ID	2017175-4
ISSN	1678-4405 ; 1517-8382
ISSN (online)	1678-4405
ISSN	1517-8382
DOI	10.1007/s42770-020-00298-x
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