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Moral-Turón C, Asencio-Cortés G, Rodriguez-Diaz F, Rubio A, Navarro AG, Brokate-Llanos AM, Garzón A, Muñoz MJ, Pérez-Pulido AJ. ASACO: Automatic and Serial Analysis of CO-expression to discover gene modifiers with potential use in drug repurposing. Brief Funct Genomics 2024:elae006. [PMID: 38422352 DOI: 10.1093/bfgp/elae006] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/07/2023] [Revised: 01/21/2024] [Accepted: 01/31/2024] [Indexed: 03/02/2024] Open
Abstract
Massive gene expression analyses are widely used to find differentially expressed genes under specific conditions. The results of these experiments are often available in public databases that are undergoing a growth similar to that of molecular sequence databases in the past. This now allows novel secondary computational tools to emerge that use such information to gain new knowledge. If several genes have a similar expression profile across heterogeneous transcriptomics experiments, they could be functionally related. These associations are usually useful for the annotation of uncharacterized genes. In addition, the search for genes with opposite expression profiles is useful for finding negative regulators and proposing inhibitory compounds in drug repurposing projects. Here we present a new web application, Automatic and Serial Analysis of CO-expression (ASACO), which has the potential to discover positive and negative correlator genes to a given query gene, based on thousands of public transcriptomics experiments. In addition, examples of use are presented, comparing with previous contrasted knowledge. The results obtained propose ASACO as a useful tool to improve knowledge about genes associated with human diseases and noncoding genes. ASACO is available at http://www.bioinfocabd.upo.es/asaco/.
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Affiliation(s)
- Cristina Moral-Turón
- Andalusian Centre for Developmental Biology (CABD, UPO-CSIC-JA). Faculty of Experimental Sciences (Genetics Dept.), University Pablo de Olavide, 41013, Seville, Spain
| | | | | | - Alejandro Rubio
- Andalusian Centre for Developmental Biology (CABD, UPO-CSIC-JA). Faculty of Experimental Sciences (Genetics Dept.), University Pablo de Olavide, 41013, Seville, Spain
| | - Alberto G Navarro
- Andalusian Centre for Developmental Biology (CABD, UPO-CSIC-JA). Faculty of Experimental Sciences (Genetics Dept.), University Pablo de Olavide, 41013, Seville, Spain
| | - Ana M Brokate-Llanos
- Andalusian Centre for Developmental Biology (CABD, UPO-CSIC-JA). Faculty of Experimental Sciences (Genetics Dept.), University Pablo de Olavide, 41013, Seville, Spain
| | - Andrés Garzón
- Andalusian Centre for Developmental Biology (CABD, UPO-CSIC-JA). Faculty of Experimental Sciences (Genetics Dept.), University Pablo de Olavide, 41013, Seville, Spain
| | - Manuel J Muñoz
- Andalusian Centre for Developmental Biology (CABD, UPO-CSIC-JA). Faculty of Experimental Sciences (Genetics Dept.), University Pablo de Olavide, 41013, Seville, Spain
| | - Antonio J Pérez-Pulido
- Andalusian Centre for Developmental Biology (CABD, UPO-CSIC-JA). Faculty of Experimental Sciences (Genetics Dept.), University Pablo de Olavide, 41013, Seville, Spain
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Brokate-Llanos AM, Sanchez-Ibañez M, Pérez-Jiménez MM, Monje-Moreno JM, Gómez-Marín C, Caro C, Vivar-Rios C, Moreno-Mateo MA, García-Martín ML, Muñoz MJ, Royo JL. Ribonucleotide reductase inhibition improves the symptoms of a Caenorhabditis elegans model of Alzheimer's Disease. G3 (Bethesda) 2024:jkae040. [PMID: 38412549 DOI: 10.1093/g3journal/jkae040] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Track Full Text] [Subscribe] [Scholar Register] [Received: 12/23/2023] [Revised: 12/23/2023] [Accepted: 01/19/2024] [Indexed: 02/29/2024]
Abstract
Alzheimer's disease is the main cause of aging-associated dementia, for which there is no effective treatment. In this work, we reanalyze the information of a previous Genome Wide Association Study, using a new pipeline design to identify novel potential drugs. With this approach, ribonucleoside-diphosphate reductase gene (RRM2B) emerged as a candidate target and its inhibitor, 2', 2'-difluoro 2'deoxycytidine (Gemcitabine), as a potential pharmaceutical drug against Alzheimer's disease. We functionally verified the effect of inhibiting the RRM2B homologue, rnr-2, in an Alzheimer's model of Caenorhabditis elegans, which accumulates human Aβ1-42 peptide to an irreversible paralysis. RNA interference against rnr-2 and also treatment with 200 ng/ml of Gemcitabine, showed animprovement of the phenotype. Gemcitabine treatment increased the intracellular ATP level 3.03 times, which may point to its mechanism of action. Gemcitabine has been extensively used in humans for cancer treatment but at higher concentration. The 200 ng/ml concentration did not exert a significant effect over cell cycle, or affected cell viability when assayed in microglia N13 cell line. Thus, inhibitory drug of the RRM2B activity could be of potential use to treat Alzheimer's disease and particularly Gemcitabine might be considered as a promising candidate to be repurposed for its treatment.
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Affiliation(s)
- Ana M Brokate-Llanos
- Centro Andaluz de Biologia del Desarrollo. University Pablo de Olavide-CISC-Junta de Andalucía. Ctra Utrera Km 1. 41013 Sevilla. Spain
| | - Mireya Sanchez-Ibañez
- Department of Surgery, Immunology and Biochemistry. School of Medicine, University of Malaga. Boulevar Louis Pasteur s/n. 29010 Málaga. Spain
| | - Mercedes M Pérez-Jiménez
- Centro Andaluz de Biologia del Desarrollo. University Pablo de Olavide-CISC-Junta de Andalucía. Ctra Utrera Km 1. 41013 Sevilla. Spain
| | - José M Monje-Moreno
- Centro Andaluz de Biologia del Desarrollo. University Pablo de Olavide-CISC-Junta de Andalucía. Ctra Utrera Km 1. 41013 Sevilla. Spain
| | - Carlos Gómez-Marín
- Centro Andaluz de Biologia del Desarrollo. University Pablo de Olavide-CISC-Junta de Andalucía. Ctra Utrera Km 1. 41013 Sevilla. Spain
| | - Carlos Caro
- BIONAND, Andalusian Centre for Nanomedicine and Biotechnology (Junta de Andalucía-Universidad de Málaga), 29590 Málaga, Spain
| | - Carlos Vivar-Rios
- Department of Surgery, Immunology and Biochemistry. School of Medicine, University of Malaga. Boulevar Louis Pasteur s/n. 29010 Málaga. Spain
| | - Miguel A Moreno-Mateo
- Centro Andaluz de Biologia del Desarrollo. University Pablo de Olavide-CISC-Junta de Andalucía. Ctra Utrera Km 1. 41013 Sevilla. Spain
| | - María L García-Martín
- BIONAND, Andalusian Centre for Nanomedicine and Biotechnology (Junta de Andalucía-Universidad de Málaga), 29590 Málaga, Spain
| | - Manuel J Muñoz
- Centro Andaluz de Biologia del Desarrollo. University Pablo de Olavide-CISC-Junta de Andalucía. Ctra Utrera Km 1. 41013 Sevilla. Spain
| | - José L Royo
- Department of Surgery, Immunology and Biochemistry. School of Medicine, University of Malaga. Boulevar Louis Pasteur s/n. 29010 Málaga. Spain
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Pérez-Pulido AJ, Asencio-Cortés G, Brokate-Llanos AM, Brea-Calvo G, Rodríguez-Griñolo R, Garzón A, Muñoz MJ. Serial co-expression analysis of host factors from SARS-CoV viruses highly converges with former high-throughput screenings and proposes key regulators. Brief Bioinform 2021; 22:1038-1052. [PMID: 33458747 PMCID: PMC7929451 DOI: 10.1093/bib/bbaa419] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/14/2020] [Revised: 11/11/2020] [Accepted: 12/19/2020] [Indexed: 11/14/2022] Open
Abstract
The current genomics era is bringing an unprecedented growth in the amount of gene expression data, only comparable to the exponential growth of sequences in databases during the last decades. This data allow the design of secondary analyses that take advantage of this information to create new knowledge. One of these feasible analyses is the evaluation of the expression level for a gene through a series of different conditions or cell types. Based on this idea, we have developed Automatic and Serial Analysis of CO-expression, which performs expression profiles for a given gene along hundreds of heterogeneous and normalized transcriptomics experiments and discover other genes that show either a similar or an inverse behavior. It might help to discover co-regulated genes, and common transcriptional regulators in any biological model. The present severe acute respiratory syndrome coronavirus 2 (SARS-CoV-2) pandemic is an opportunity to test this novel approach due to the wealth of data that are being generated, which could be used for validating results. Thus, we have identified 35 host factors in the literature putatively involved in the infectious cycle of SARS-CoV viruses and searched for genes tightly co-expressed with them. We have found 1899 co-expressed genes whose assigned functions are strongly related to viral cycles. Moreover, this set of genes heavily overlaps with those identified by former laboratory high-throughput screenings (with P-value near 0). Our results reveal a series of common regulators, involved in immune and inflammatory responses that might be key virus targets to induce the coordinated expression of SARS-CoV-2 host factors.
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Affiliation(s)
- Antonio J Pérez-Pulido
- Centro Andaluz de Biologia del Desarrollo (CABD, UPO-CSIC-JA). Facultad de Ciencias Experimentales (Área de Genética), Universidad Pablo de Olavide, 41013, Sevilla, Spain
| | | | - Ana M Brokate-Llanos
- Centro Andaluz de Biologia del Desarrollo (CABD, UPO-CSIC-JA). Facultad de Ciencias Experimentales (Área de Genética), Universidad Pablo de Olavide, 41013, Sevilla, Spain
| | - Gloria Brea-Calvo
- Centro Andaluz de Biología del Desarrollo, Universidad Pablo de Olavide-CSIC-JA, 41013, Sevilla, Spain
- CIBERER, Instituto de Salud Carlos III, 28000, Madrid, Spain
| | - Rosario Rodríguez-Griñolo
- Dpto. de Economía, Métodos Cuantitativos e Historia Económica. Universidad Pablo de Olavide, 41013 Sevilla, Spain
| | - Andrés Garzón
- Centro Andaluz de Biologia del Desarrollo (CABD, UPO-CSIC-JA). Facultad de Ciencias Experimentales (Área de Genética), Universidad Pablo de Olavide, 41013, Sevilla, Spain
| | - Manuel J Muñoz
- Centro Andaluz de Biologia del Desarrollo (CABD, UPO-CSIC-JA). Facultad de Ciencias Experimentales (Área de Genética), Universidad Pablo de Olavide, 41013, Sevilla, Spain
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Casimiro-Soriguer CS, Rigual MM, Brokate-Llanos AM, Muñoz MJ, Garzón A, Pérez-Pulido AJ, Jimenez J. Using AnABlast for intergenic sORF prediction in the Caenorhabditis elegans genome. Bioinformatics 2020; 36:4827-4832. [PMID: 32614398 PMCID: PMC7723330 DOI: 10.1093/bioinformatics/btaa608] [Citation(s) in RCA: 4] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/07/2020] [Revised: 06/21/2020] [Accepted: 06/23/2020] [Indexed: 11/29/2022] Open
Abstract
Motivation Short bioactive peptides encoded by small open reading frames (sORFs) play important roles in eukaryotes. Bioinformatics prediction of ORFs is an early step in a genome sequence analysis, but sORFs encoding short peptides, often using non-AUG initiation codons, are not easily discriminated from false ORFs occurring by chance. Results AnABlast is a computational tool designed to highlight putative protein-coding regions in genomic DNA sequences. This protein-coding finder is independent of ORF length and reading frame shifts, thus making of AnABlast a potentially useful tool to predict sORFs. Using this algorithm, here, we report the identification of 82 putative new intergenic sORFs in the Caenorhabditis elegans genome. Sequence similarity, motif presence, expression data and RNA interference experiments support that the underlined sORFs likely encode functional peptides, encouraging the use of AnABlast as a new approach for the accurate prediction of intergenic sORFs in annotated eukaryotic genomes. Availability and implementation AnABlast is freely available at http://www.bioinfocabd.upo.es/ab/. The C.elegans genome browser with AnABlast results, annotated genes and all data used in this study is available at http://www.bioinfocabd.upo.es/celegans. Supplementary information Supplementary data are available at Bioinformatics online.
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Affiliation(s)
- C S Casimiro-Soriguer
- Centro Andaluz de Biología del Desarrollo (CABD, UPO-CSIC), Universidad Pablo de Olavide, 41013 Sevilla, Spain
| | - M M Rigual
- Centro Andaluz de Biología del Desarrollo (CABD, UPO-CSIC), Universidad Pablo de Olavide, 41013 Sevilla, Spain
| | - A M Brokate-Llanos
- Centro Andaluz de Biología del Desarrollo (CABD, UPO-CSIC), Universidad Pablo de Olavide, 41013 Sevilla, Spain
| | - M J Muñoz
- Centro Andaluz de Biología del Desarrollo (CABD, UPO-CSIC), Universidad Pablo de Olavide, 41013 Sevilla, Spain
| | - A Garzón
- Centro Andaluz de Biología del Desarrollo (CABD, UPO-CSIC), Universidad Pablo de Olavide, 41013 Sevilla, Spain
| | - A J Pérez-Pulido
- Centro Andaluz de Biología del Desarrollo (CABD, UPO-CSIC), Universidad Pablo de Olavide, 41013 Sevilla, Spain
| | - J Jimenez
- Centro Andaluz de Biología del Desarrollo (CABD, UPO-CSIC), Universidad Pablo de Olavide, 41013 Sevilla, Spain
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Pérez-Pulido AJ, Asencio-Cortés G, Brokate-Llanos AM, Brea-Calvo G, Rodríguez-Griñolo R, Garzón A, Muñoz MJ. Serial co-expression analysis of host factors from SARS-CoV viruses highly converges with former high-throughput screenings and proposes key regulators and co-option of cellular pathways. bioRxiv 2020:2020.07.28.225078. [PMID: 34013266 PMCID: PMC8132222 DOI: 10.1101/2020.07.28.225078] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Abstract] [Track Full Text] [Download PDF] [Subscribe] [Scholar Register] [Indexed: 11/25/2022]
Abstract
The current genomics era is bringing an unprecedented growth in the amount of gene expression data, only comparable to the exponential growth of sequences in databases during the last decades. This data now allows the design of secondary analyses that take advantage of this information to create new knowledge through specific computational approaches. One of these feasible analyses is the evaluation of the expression level for a gene through a series of different conditions or cell types. Based on this idea, we have developed ASACO, Automatic and Serial Analysis of CO-expression, which performs expression profiles for a given gene along hundreds of normalized and heterogeneous transcriptomics experiments and discover other genes that show either a similar or an inverse behavior. It might help to discover co-regulated genes, and even common transcriptional regulators in any biological model, including human diseases or microbial infections. The present SARS-CoV-2 pandemic is an opportunity to test this novel approach due to the wealth of data that is being generated, which could be used for validating results. In addition, new cell mechanisms identified could become new therapeutic targets. Thus, we have identified 35 host factors in the literature putatively involved in the infectious cycle of SARS-CoV and/or SARS-CoV-2 and searched for genes tightly co-expressed with them. We have found around 1900 co-expressed genes whose assigned functions are strongly related to viral cycles. Moreover, this set of genes heavily overlap with those identified by former laboratory high-throughput screenings (with p-value near 0). Some of these genes aim to cellular structures such as the stress granules, which could be essential for the virus replication and thereby could constitute potential targets in the current fight against the virus. Additionally, our results reveal a series of common transcription regulators, involved in immune and inflammatory responses, that might be key virus targets to induce the coordinated expression of SARS-CoV-2 host factors. All of this proves that ASACO can discover gene co-regulation networks with potential for proposing new genes, pathways and regulators participating in particular biological systems. Highlights ASACO identifies regulatory associations of genes using public transcriptomics data.ASACO highlights new cell functions likely involved in the infection of coronavirus.Comparison with high-throughput screenings validates candidates proposed by ASACO.Genes co-expressed with host's genes used by SARS-CoV-2 are related to stress granules.
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Brokate-Llanos AM, Monje JM, Murdoch PDS, Muñoz MJ. Developmental defects in a Caenorhabditis elegans model for type III galactosemia. Genetics 2014; 198:1559-69. [PMID: 25298520 PMCID: PMC4256771 DOI: 10.1534/genetics.114.170084] [Citation(s) in RCA: 19] [Impact Index Per Article: 1.9] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/21/2014] [Accepted: 10/01/2014] [Indexed: 12/21/2022] Open
Abstract
Type III galactosemia is a metabolic disorder caused by reduced activity of UDP-galactose-4-epimerase, which participates in galactose metabolism and the generation of various UDP-sugar species. We characterized gale-1 in Caenorhabditis elegans and found that a complete loss-of-function mutation is lethal, as has been hypothesized for humans, whereas a nonlethal partial loss-of-function allele causes a variety of developmental abnormalities, likely resulting from the impairment of the glycosylation process. We also observed that gale-1 mutants are hypersensitive to galactose as well as to infections. Interestingly, we found interactions between gale-1 and the unfolded protein response.
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Affiliation(s)
- Ana M Brokate-Llanos
- Centro Andaluz de Biología del Desarrollo, Consejo Superior de Investigaciones Científicas-Universidad Pablo de Olavide-Junta de Andalucía, 41013 Seville, Spain
| | - José M Monje
- Centro Andaluz de Biología del Desarrollo, Consejo Superior de Investigaciones Científicas-Universidad Pablo de Olavide-Junta de Andalucía, 41013 Seville, Spain
| | - Piedad Del Socorro Murdoch
- Departamento de Bioquímica y Biología Molecular, Facultad de Biología, Universidad de Sevilla, 41012 Seville, Spain
| | - Manuel J Muñoz
- Centro Andaluz de Biología del Desarrollo, Consejo Superior de Investigaciones Científicas-Universidad Pablo de Olavide-Junta de Andalucía, 41013 Seville, Spain
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Monje JM, Brokate-Llanos AM, Pérez-Jiménez MM, Fidalgo MA, Muñoz MJ. pkc-1 regulates daf-2 insulin/IGF signalling-dependent control of dauer formation in Caenorhabditis elegans. Aging Cell 2011; 10:1021-31. [PMID: 21933341 DOI: 10.1111/j.1474-9726.2011.00747.x] [Citation(s) in RCA: 7] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/27/2022] Open
Abstract
In Caenorhabditis elegans, the insulin/IGF pathway participates in the decision to initiate dauer development. Dauer is a diapause stage that is triggered by environmental stresses, such as a lack of nutrients. Insulin/IGF receptor mutants arrest constitutively in dauer, an effect that can be suppressed by mutations in other elements of the insulin/IGF pathway or by a reduction in the activity of the nuclear hormone receptor daf-12. We have isolated a pkc-1 mutant that acts as a novel suppressor of the dauer phenotypes caused by insulin/IGF receptor mutations. Interactions between insulin/IGF mutants and the pkc-1 suppressor mutant are similar to those described for daf-12 or the DAF-12 coregulator din-1. Moreover, we show that the expression of the DAF-12 target daf-9, which is normally elevated upon a reduction in insulin/IGF receptor activity, is suppressed in a pkc-1 mutant background, suggesting that pkc-1 could link the daf-12 and insulin/IGF pathways. pkc-1 has been implicated in the regulation of peptide neurosecretion in C. elegans. Although we demonstrate that pkc-1 expression in the nervous system regulates dauer formation, our results suggest that the requirement for pkc-1 in neurosecretion is independent of its role in modulating insulin/IGF signalling. pkc-1 belongs to the novel protein kinase C (nPKC) family, members of which have been implicated in insulin resistance and diabetes in mammals, suggesting a conserved role for pkc-1 in the regulation of the insulin/IGF pathway.
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Affiliation(s)
- José M Monje
- Centro Andaluz de Biología del Desarrollo (CABD), CSIC/Universidad Pablo de Olavide, Seville, Spain
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