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Identifying General Tumor and Specific Lung Cancer Biomarkers by Transcriptomic Analysis
Indexado
WoS WOS:000833313400001
Scopus SCOPUS_ID:85136254336
DOI 10.3390/BIOLOGY11071082
Año 2022
Tipo artículo de investigación

Citas Totales

Autores Afiliación Chile

Instituciones Chile

% Participación
Internacional

Autores
Afiliación Extranjera

Instituciones
Extranjeras


Abstract



Simple Summary An adequate bioinformatic pipeline is a valuable tool for understanding cancer mechanisms and identifying transcriptomic biomarkers of cancer and specific to lung cancer. The bioinformatic pipeline was applied to analyze multiple transcriptomic studies and to identify an important group of winning transcription factors coexpressed in gene networks of lung cancer, breast cancer and leukemia, capable of forming coregulatory complexes associated with the regulation of genes involved in tumorigenic processes related to the acquisition of the hallmarks of cancer, as well as lung cancer patients survival. The establishment of a general and specific transcriptional regulatory network is essential to develop key molecular tools for prevention, early diagnosis, and treatment aimed at precision personalized medicine of cancer. The bioinformatic pipeline previously developed in our research laboratory is used to identify potential general and specific deregulated tumor genes and transcription factors related to the establishment and progression of tumoral diseases, now comparing lung cancer with other two types of cancer. Twenty microarray datasets were selected and analyzed separately to identify hub differentiated expressed genes and compared to identify all the deregulated genes and transcription factors in common between the three types of cancer and those unique to lung cancer. The winning DEGs analysis allowed to identify an important number of TFs deregulated in the majority of microarray datasets, which can become key biomarkers of general tumors and specific to lung cancer. A coexpression network was constructed for every dataset with all deregulated genes associated with lung cancer, according to DAVID's tool enrichment analysis, and transcription factors capable of regulating them, according to oPOSSUM ' s tool. Several genes and transcription factors are coexpressed in the networks, suggesting that they could be related to the establishment or progression of the tumoral pathology in any tissue and specifically in the lung. The comparison of the coexpression networks of lung cancer and other types of cancer allowed the identification of common connectivity patterns with deregulated genes and transcription factors correlated to important tumoral processes and signaling pathways that have not been studied yet to experimentally validate their role in lung cancer. The Kaplan-Meier estimator determined the association of thirteen deregulated top winning transcription factors with the survival of lung cancer patients. The coregulatory analysis identified two top winning transcription factors networks related to the regulatory control of gene expression in lung and breast cancer. Our transcriptomic analysis suggests that cancer has an important coregulatory network of transcription factors related to the acquisition of the hallmarks of cancer. Moreover, lung cancer has a group of genes and transcription factors unique to pulmonary tissue that are coexpressed during tumorigenesis and must be studied experimentally to fully understand their role in the pathogenesis within its very complex transcriptomic scenario. Therefore, the downstream bioinformatic analysis developed was able to identify a coregulatory metafirm of cancer in general and specific to lung cancer taking into account the great heterogeneity of the tumoral process at cellular and population levels.

Revista



Revista ISSN
Biology 2079-7737

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Disciplinas de Investigación



WOS
Biology
Scopus
Agricultural And Biological Sciences (All)
Biochemistry, Genetics And Molecular Biology (All)
Immunology And Microbiology (All)
SciELO
Sin Disciplinas

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Publicaciones WoS (Ediciones: ISSHP, ISTP, AHCI, SSCI, SCI), Scopus, SciELO Chile.

Colaboración Institucional



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Autores - Afiliación



Ord. Autor Género Institución - País
1 Andrea Otalora-Otalora, Beatriz Mujer UNIV NACL COLOMBIA - Colombia
Universidad Nacional de Colombia, Facultad de Medicina - Colombia
1 Otálora-Otálora, Beatriz Andrea Mujer Universidad Nacional de Colombia, Facultad de Medicina - Colombia
Universidad Nacional de Colombia - Colombia
2 Alejandro Osuna-Garzon, Daniel Hombre UNIV NACL COLOMBIA - Colombia
Universidad Nacional de Colombia - Colombia
3 Steven Carvajal-Parra, Michael Hombre UNIV NACL COLOMBIA - Colombia
Universidad Nacional de Colombia - Colombia
4 CANAS-ARBOLEDA, ALEJANDRA Mujer Pontificia Univ Javeriana - Colombia
Hosp Univ San Ignacio - Colombia
Universidad Javeriana Facultad de Medicina - Colombia
Hospital Universitario San Ignacio - Colombia
5 MONTECINO-LEONARD, MARTIN ALEJANDRO Hombre Universidad Nacional Andrés Bello - Chile
6 Lopez-Kleine, Liliana Mujer UNIV NACL COLOMBIA - Colombia
Universidad Nacional de Colombia - Colombia
7 ROJAS-MORENO, ADRIANA PATRICIA Mujer Pontificia Univ Javeriana - Colombia
Universidad Javeriana Facultad de Medicina - Colombia

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Financiamiento



Fuente
Universidad Nacional de Colombia
National University of Colombia
PUJ ID7687 Pontificia Universidad Javeriana

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Agradecimientos



Agradecimiento
The current article was funded by grant number 41492 from National University of Colombia, and PUJ ID7687 Pontificia Universidad Javeriana.
The current article was funded by grant number 41492 from National University of Colombia, and PUJ ID7687 Pontificia Universidad Javeriana.

Muestra la fuente de financiamiento declarada en la publicación.