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Vicencio E, Nuñez-Belmar J, Cardenas JP, Cortés BI, Martin AJM, Maracaja-Coutinho V, Rojas A, Cafferata EA, González-Osuna L, Vernal R, Cortez C. Transcriptional Signatures and Network-Based Approaches Identified Master Regulators Transcription Factors Involved in Experimental Periodontitis Pathogenesis. Int J Mol Sci 2023; 24:14835. [PMID: 37834287 PMCID: PMC10573220 DOI: 10.3390/ijms241914835] [Citation(s) in RCA: 1] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/31/2023] [Revised: 09/26/2023] [Accepted: 09/28/2023] [Indexed: 10/15/2023] Open
Abstract
Periodontitis is a chronic inflammatory disease characterized by the progressive and irreversible destruction of the periodontium. Its aetiopathogenesis lies in the constant challenge of the dysbiotic biofilm, which triggers a deregulated immune response responsible for the disease phenotype. Although the molecular mechanisms underlying periodontitis have been extensively studied, the regulatory mechanisms at the transcriptional level remain unclear. To generate transcriptomic data, we performed RNA shotgun sequencing of the oral mucosa of periodontitis-affected mice. Since genes are not expressed in isolation during pathological processes, we disclose here the complete repertoire of differentially expressed genes (DEG) and co-expressed modules to build Gene Regulatory Networks (GRNs) and identify the Master Transcriptional Regulators of periodontitis. The transcriptional changes revealed 366 protein-coding genes and 42 non-coding genes differentially expressed and enriched in the immune response. Furthermore, we found 13 co-expression modules with different representation degrees and gene expression levels. Our GRN comprises genes from 12 gene clusters, 166 nodes, of which 33 encode Transcription Factors, and 201 connections. Finally, using these strategies, 26 master regulators of periodontitis were identified. In conclusion, combining the transcriptomic analyses with the regulatory network construction represents a powerful and efficient strategy for identifying potential periodontitis-therapeutic targets.
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Affiliation(s)
- Emiliano Vicencio
- Escuela de Tecnología Médica, Facultad de Ciencias, Pontificia Universidad Católica de Valparaíso, Valparaíso 2373223, Chile;
| | - Josefa Nuñez-Belmar
- Centro de Genómica y Bioinformática, Facultad de Ciencias, Ingeniería y Tecnología, Universidad Mayor, Santiago 8580745, Chile; (J.N.-B.); (J.P.C.)
| | - Juan P. Cardenas
- Centro de Genómica y Bioinformática, Facultad de Ciencias, Ingeniería y Tecnología, Universidad Mayor, Santiago 8580745, Chile; (J.N.-B.); (J.P.C.)
- Escuela de Biotecnología, Facultad de Ciencias, Ingeniería y Tecnología, Universidad Mayor, Santiago 8580745, Chile
| | - Bastian I. Cortés
- Departamento de Biología Celular y Molecular, Facultad de Ciencias Biológicas, Pontificia Universidad Católica de Chile, Santiago 8331150, Chile
| | - Alberto J. M. Martin
- Laboratorio de Redes Biológicas, Centro Científico y Tecnológico de Excelencia Ciencia & Vida, Fundación Ciencia & Vida, Santiago 7780272, Chile;
- Escuela de Ingeniería, Facultad de Ingeniería, Arquitectura y Diseño, Universidad San Sebastián, Santiago 8420524, Chile
| | - Vinicius Maracaja-Coutinho
- Centro de Modelamiento Molecular, Biofísica y Bioinformática, Facultad de Ciencias Químicas y Farmacéuticas, Universidad de Chile, Santiago 8380492, Chile; (V.M.-C.); (A.R.)
- Advanced Center for Chronic Diseases—ACCDiS, Facultad de Ciencias Químicas y Farmacéuticas, Universidad de Chile, Santiago 8380492, Chile
| | - Adolfo Rojas
- Centro de Modelamiento Molecular, Biofísica y Bioinformática, Facultad de Ciencias Químicas y Farmacéuticas, Universidad de Chile, Santiago 8380492, Chile; (V.M.-C.); (A.R.)
| | - Emilio A. Cafferata
- Laboratorio de Biología Periodontal, Facultad de Odontología, Universidad de Chile, Santiago 8380492, Chile; (E.A.C.); (L.G.-O.); (R.V.)
| | - Luis González-Osuna
- Laboratorio de Biología Periodontal, Facultad de Odontología, Universidad de Chile, Santiago 8380492, Chile; (E.A.C.); (L.G.-O.); (R.V.)
| | - Rolando Vernal
- Laboratorio de Biología Periodontal, Facultad de Odontología, Universidad de Chile, Santiago 8380492, Chile; (E.A.C.); (L.G.-O.); (R.V.)
| | - Cristian Cortez
- Escuela de Tecnología Médica, Facultad de Ciencias, Pontificia Universidad Católica de Valparaíso, Valparaíso 2373223, Chile;
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2
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Romero L, Contreras-Riquelme S, Lira M, Martin AJM, Perez-Rueda E. Homology-based reconstruction of regulatory networks for bacterial and archaeal genomes. Front Microbiol 2022; 13:923105. [PMID: 35928164 PMCID: PMC9344073 DOI: 10.3389/fmicb.2022.923105] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/18/2022] [Accepted: 06/27/2022] [Indexed: 12/04/2022] Open
Abstract
Gene regulation is a key process for all microorganisms, as it allows them to adapt to different environmental stimuli. However, despite the relevance of gene expression control, for only a handful of organisms is there related information about genome regulation. In this work, we inferred the gene regulatory networks (GRNs) of bacterial and archaeal genomes by comparisons with six organisms with well-known regulatory interactions. The references we used are: Escherichia coli K-12 MG1655, Bacillus subtilis 168, Mycobacterium tuberculosis, Pseudomonas aeruginosa PAO1, Salmonella enterica subsp. enterica serovar typhimurium LT2, and Staphylococcus aureus N315. To this end, the inferences were achieved in two steps. First, the six model organisms were contrasted in an all-vs-all comparison of known interactions based on Transcription Factor (TF)-Target Gene (TG) orthology relationships and Transcription Unit (TU) assignments. In the second step, we used a guilt-by-association approach to infer the GRNs for 12,230 bacterial and 649 archaeal genomes based on TF-TG orthology relationships of the six bacterial models determined in the first step. Finally, we discuss examples to show the most relevant results obtained from these inferences. A web server with all the predicted GRNs is available at https://regulatorynetworks.unam.mx/ or http://132.247.46.6/.
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Affiliation(s)
- Luis Romero
- Licenciatura en Ciencias Genomicas, Universidad Nacional Autonoma de Mexico, Cuernavaca, Mexico
| | - Sebastian Contreras-Riquelme
- Laboratorio de Biología de Redes, Centro de Genómica y Bioinformática, Facultad Ciencias, Ingeniería y Tecnología, Universidad Mayor, Santiago, Chile
| | - Manuel Lira
- Cómputo Académico, Facultad de Ciencias - UMDI-Sisal, Sede Parque Científico y Tecnológico de Yucatán, Universidad Nacional Autónoma de México, Mérida, Mexico
| | - Alberto J. M. Martin
- Laboratorio de Biología de Redes, Centro de Genómica y Bioinformática, Facultad Ciencias, Ingeniería y Tecnología, Universidad Mayor, Santiago, Chile
- Alberto J. M. Martin,
| | - Ernesto Perez-Rueda
- Instituto de Investigaciones en Matemáticas Aplicadas y en Sistemas, Universidad Nacional Autónoma de México, Unidad Académica Yucatán, Mérida, Mexico
- *Correspondence: Ernesto Perez-Rueda,
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Huang CH, Zaenudin E, Tsai JJ, Kurubanjerdjit N, Ng KL. Network subgraph-based approach for analyzing and comparing molecular networks. PeerJ 2022; 10:e13137. [PMID: 35529499 PMCID: PMC9074881 DOI: 10.7717/peerj.13137] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/19/2021] [Accepted: 02/28/2022] [Indexed: 01/12/2023] Open
Abstract
Molecular networks are built up from genetic elements that exhibit feedback interactions. Here, we studied the problem of measuring the similarity of directed networks by proposing a novel alignment-free approach: the network subgraph-based approach. Our approach does not make use of randomized networks to determine modular patterns embedded in a network, and this method differs from the network motif and graphlet methods. Network similarity was quantified by gauging the difference between the subgraph frequency distributions of two networks using Jensen-Shannon entropy. We applied the subgraph approach to study three types of molecular networks, i.e., cancer networks, signal transduction networks, and cellular process networks, which exhibit diverse molecular functions. We compared the performance of our subgraph detection algorithm with other algorithms, and the results were consistent, but other algorithms could not address the issue of subgraphs/motifs embedded within a subgraph/motif. To evaluate the effectiveness of the subgraph-based method, we applied the method along with the Jensen-Shannon entropy to classify six network models, and it achieves a 100% accuracy of classification. The proposed information-theoretic approach allows us to determine the structural similarity of two networks regardless of node identity and network size. We demonstrated the effectiveness of the subgraph approach to cluster molecular networks that exhibit similar regulatory interaction topologies. As an illustration, our method can identify (i) common subgraph-mediated signal transduction and/or cellular processes in AML and pancreatic cancer, and (ii) scaffold proteins in gastric cancer and hepatocellular carcinoma; thus, the results suggested that there are common regulation modules for cancer formation. We also found that the underlying substructures of the molecular networks are dominated by irreducible subgraphs; this feature is valid for the three classes of molecular networks we studied. The subgraph-based approach provides a systematic scenario for analyzing, compare and classifying molecular networks with diverse functionalities.
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Affiliation(s)
- Chien-Hung Huang
- Department of Computer Science and Information Engineering, National Formosa University, Yun-Lin, Taiwan
| | - Efendi Zaenudin
- National Research and Innovation Agency, Bandung, Jawa Barat, Republic of Indonesia,Department of Bioinformatics and Medical Engineering, Asia University, Taichung, Taiwan
| | - Jeffrey J.P. Tsai
- Department of Bioinformatics and Medical Engineering, Asia University, Taichung, Taiwan
| | | | - Ka-Lok Ng
- Department of Bioinformatics and Medical Engineering, Asia University, Taichung, Taiwan,Center for Artificial Intelligence and Precision Medicine Research, Asia University, Taichung, Taiwan,Department of Medical Research, China Medical University Hospital, China Medical University, Taichung, Taiwan
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Network-Based Approaches Reveal Potential Therapeutic Targets for Host-Directed Antileishmanial Therapy Driving Drug Repurposing. Microbiol Spectr 2021; 9:e0101821. [PMID: 34668739 PMCID: PMC8528132 DOI: 10.1128/spectrum.01018-21] [Citation(s) in RCA: 4] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/28/2023] Open
Abstract
Leishmania parasites are the causal agent of leishmaniasis, an endemic disease in more than 90 countries worldwide. Over the years, traditional approaches focused on the parasite when developing treatments against leishmaniasis. Despite numerous attempts, there is not yet a universal treatment, and those available have allowed for the appearance of resistance. Here, we propose and follow a host-directed approach that aims to overcome the current lack of treatment. Our approach identifies potential therapeutic targets in the host cell and proposes known drug interactions aiming to improve the immune response and to block the host machinery necessary for the survival of the parasite. We started analyzing transcription factor regulatory networks of macrophages infected with Leishmania major. Next, based on the regulatory dynamics of the infection and available gene expression profiles, we selected potential therapeutic target proteins. The function of these proteins was then analyzed following a multilayered network scheme in which we combined information on metabolic pathways with known drugs that have a direct connection with the activity carried out by these proteins. Using our approach, we were able to identify five host protein-coding gene products that are potential therapeutic targets for treating leishmaniasis. Moreover, from the 11 drugs known to interact with the function performed by these proteins, 3 have already been tested against this parasite, verifying in this way our novel methodology. More importantly, the remaining eight drugs previously employed to treat other diseases, remain as promising yet-untested antileishmanial therapies. IMPORTANCE This work opens a new path to fight parasites by targeting host molecular functions by repurposing available and approved drugs. We created a novel approach to identify key proteins involved in any biological process by combining gene regulatory networks and expression profiles. Once proteins have been selected, our approach employs a multilayered network methodology that relates proteins to functions to drugs that alter these functions. By applying our novel approach to macrophages during the Leishmania infection process, we both validated our work and found eight drugs already approved for use in humans that to the best of our knowledge were never employed to treat leishmaniasis, rendering our work as a new tool in the box available to the scientific community fighting parasites.
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Melkus G, Rucevskis P, Celms E, Čerāns K, Freivalds K, Kikusts P, Lace L, Opmanis M, Rituma D, Viksna J. Network motif-based analysis of regulatory patterns in paralogous gene pairs. J Bioinform Comput Biol 2021; 18:2040008. [PMID: 32698721 DOI: 10.1142/s0219720020400089] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.7] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/02/2023]
Abstract
Current high-throughput experimental techniques make it feasible to infer gene regulatory interactions at the whole-genome level with reasonably good accuracy. Such experimentally inferred regulatory networks have become available for a number of simpler model organisms such as S. cerevisiae, and others. The availability of such networks provides an opportunity to compare gene regulatory processes at the whole genome level, and in particular, to assess similarity of regulatory interactions for homologous gene pairs either from the same or from different species. We present here a new technique for analyzing the regulatory interaction neighborhoods of paralogous gene pairs. Our central focus is the analysis of S. cerevisiae gene interaction graphs, which are of particular interest due to the ancestral whole-genome duplication (WGD) that allows to distinguish between paralogous transcription factors that are traceable to this duplication event and other paralogues. Similar analysis is also applied to E. coli and C. elegans networks. We compare paralogous gene pairs according to the presence and size of bi-fan arrays, classically associated in the literature with gene duplication, within other network motifs. We further extend this framework beyond transcription factor comparison to obtain topology-based similarity metrics based on the overlap of interaction neighborhoods applicable to most genes in a given organism. We observe that our network divergence metrics show considerably larger similarity between paralogues, especially those traceable to WGD. This is the case for both yeast and C. elegans, but not for E. coli regulatory network. While there is no obvious cross-species link between metrics, different classes of paralogues show notable differences in interaction overlap, with traceable duplications tending toward higher overlap compared to genes with shared protein families. Our findings indicate that divergence in paralogous interaction networks reflects a shared genetic origin, and that our approach may be useful for investigating structural similarity in the interaction networks of paralogous genes.
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Affiliation(s)
- Gatis Melkus
- Institute of Mathematics and Computer Science, University of Latvia, Rainis blvd. 29, Riga, LV-1459, Latvia
| | - Peteris Rucevskis
- Institute of Mathematics and Computer Science, University of Latvia, Rainis blvd. 29, Riga, LV-1459, Latvia
| | - Edgars Celms
- Institute of Mathematics and Computer Science, University of Latvia, Rainis blvd. 29, Riga, LV-1459, Latvia
| | - Kārlis Čerāns
- Institute of Mathematics and Computer Science, University of Latvia, Rainis blvd. 29, Riga, LV-1459, Latvia
| | - Karlis Freivalds
- Institute of Mathematics and Computer Science, University of Latvia, Rainis blvd. 29, Riga, LV-1459, Latvia
| | - Paulis Kikusts
- Institute of Mathematics and Computer Science, University of Latvia, Rainis blvd. 29, Riga, LV-1459, Latvia
| | - Lelde Lace
- Institute of Mathematics and Computer Science, University of Latvia, Rainis blvd. 29, Riga, LV-1459, Latvia
| | - Mārtiņš Opmanis
- Institute of Mathematics and Computer Science, University of Latvia, Rainis blvd. 29, Riga, LV-1459, Latvia
| | - Darta Rituma
- Institute of Mathematics and Computer Science, University of Latvia, Rainis blvd. 29, Riga, LV-1459, Latvia
| | - Juris Viksna
- Institute of Mathematics and Computer Science, University of Latvia, Rainis blvd. 29, Riga, LV-1459, Latvia
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6
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Murgas L, Contreras-Riquelme S, Martínez-Hernandez JE, Villaman C, Santibáñez R, Martin AJM. Automated generation of context-specific gene regulatory networks with a weighted approach in Drosophila melanogaster. Interface Focus 2021; 11:20200076. [PMID: 34123358 PMCID: PMC8193463 DOI: 10.1098/rsfs.2020.0076] [Citation(s) in RCA: 3] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Accepted: 04/21/2021] [Indexed: 01/22/2023] Open
Abstract
The regulation of gene expression is a key factor in the development and maintenance of life in all organisms. Even so, little is known at whole genome scale for most genes and contexts. We propose a method, Tool for Weighted Epigenomic Networks in Drosophila melanogaster (Fly T-WEoN), to generate context-specific gene regulatory networks starting from a reference network that contains all known gene regulations in the fly. Unlikely regulations are removed by applying a series of knowledge-based filters. Each of these filters is implemented as an independent module that considers a type of experimental evidence, including DNA methylation, chromatin accessibility, histone modifications and gene expression. Fly T-WEoN is based on heuristic rules that reflect current knowledge on gene regulation in D. melanogaster obtained from the literature. Experimental data files can be generated with several standard procedures and used solely when and if available. Fly T-WEoN is available as a Cytoscape application that permits integration with other tools and facilitates downstream network analysis. In this work, we first demonstrate the reliability of our method to then provide a relevant application case of our tool: early development of D. melanogaster. Fly T-WEoN together with its step-by-step guide is available at https://weon.readthedocs.io.
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Affiliation(s)
- Leandro Murgas
- Laboratorio de Biología de Redes, Centro de Genónica y Bioinformática, Facultad de Ciencias, Universidad Mayor, Santiago 8580745, Chile.,Programa de Doctorado en Genómica Integrativa, Vicerrectoría de Investigación, Universidad Mayor, Santiago, Chile
| | - Sebastian Contreras-Riquelme
- Laboratorio de Biología de Redes, Centro de Genónica y Bioinformática, Facultad de Ciencias, Universidad Mayor, Santiago 8580745, Chile.,Facultad de Ciencias de la Vida, Universidad Andres Bello, Santiago 8370146, Chile
| | - J Eduardo Martínez-Hernandez
- Laboratorio de Biología de Redes, Centro de Genónica y Bioinformática, Facultad de Ciencias, Universidad Mayor, Santiago 8580745, Chile.,Centro de Modelamiento Molecular, Biofísica y Bioinformática-CM2B2, Facultad de Ciencias Químicas y Farmaceuticas, Universidad de Chile, Santiago 8380492, Chile.,Programa de Doctorado en Genómica Integrativa, Vicerrectoría de Investigación, Universidad Mayor, Santiago, Chile
| | - Camilo Villaman
- Laboratorio de Biología de Redes, Centro de Genónica y Bioinformática, Facultad de Ciencias, Universidad Mayor, Santiago 8580745, Chile.,Programa de Doctorado en Genómica Integrativa, Vicerrectoría de Investigación, Universidad Mayor, Santiago, Chile
| | - Rodrigo Santibáñez
- Laboratorio de Biología de Redes, Centro de Genónica y Bioinformática, Facultad de Ciencias, Universidad Mayor, Santiago 8580745, Chile
| | - Alberto J M Martin
- Laboratorio de Biología de Redes, Centro de Genónica y Bioinformática, Facultad de Ciencias, Universidad Mayor, Santiago 8580745, Chile
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Huang CH, Zaenudin E, Tsai JJP, Kurubanjerdjit N, Dessie EY, Ng KL. Dissecting molecular network structures using a network subgraph approach. PeerJ 2020; 8:e9556. [PMID: 33005483 PMCID: PMC7512139 DOI: 10.7717/peerj.9556] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/08/2020] [Accepted: 06/25/2020] [Indexed: 11/20/2022] Open
Abstract
Biological processes are based on molecular networks, which exhibit biological functions through interactions of genetic elements or proteins. This study presents a graph-based method to characterize molecular networks by decomposing the networks into directed multigraphs: network subgraphs. Spectral graph theory, reciprocity and complexity measures were used to quantify the network subgraphs. Graph energy, reciprocity and cyclomatic complexity can optimally specify network subgraphs with some degree of degeneracy. Seventy-one molecular networks were analyzed from three network types: cancer networks, signal transduction networks, and cellular processes. Molecular networks are built from a finite number of subgraph patterns and subgraphs with large graph energies are not present, which implies a graph energy cutoff. In addition, certain subgraph patterns are absent from the three network types. Thus, the Shannon entropy of the subgraph frequency distribution is not maximal. Furthermore, frequently-observed subgraphs are irreducible graphs. These novel findings warrant further investigation and may lead to important applications. Finally, we observed that cancer-related cellular processes are enriched with subgraph-associated driver genes. Our study provides a systematic approach for dissecting biological networks and supports the conclusion that there are organizational principles underlying molecular networks.
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Affiliation(s)
- Chien-Hung Huang
- Department of Computer Science and Information Engineering, National Formosa University, Yunlin, Taiwan
| | - Efendi Zaenudin
- Department of Bioinformatics and Medical Engineering, Asia University, Taichung, Taiwan.,Research Center for Informatics, Indonesian Institute of Sciences, Bandung, Indonesia
| | - Jeffrey J P Tsai
- Department of Bioinformatics and Medical Engineering, Asia University, Taichung, Taiwan
| | | | - Eskezeia Y Dessie
- Department of Bioinformatics and Medical Engineering, Asia University, Taichung, Taiwan
| | - Ka-Lok Ng
- Department of Bioinformatics and Medical Engineering, Asia University, Taichung, Taiwan.,Department of Medical Research, China Medical University Hospital, China Medical University, Taichung, Taiwan
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