Abstract
Purpose
Expression microarrays are powerful technology that allows large-scale analysis of RNA profiles in a tissue; these platforms include underexploited detection scores outputs. We developed an algorithm using the detection score, to generate a detection profile of shared elements in retinoblastoma as well as to determine its transcriptomic size and structure.
Methods
We analyzed eight briefly cultured primary retinoblastomas with the Human transcriptome array 2.0 (HTA2.0). Transcripts and genes detection scores were determined using the Detection Above Background algorithm (DABG). We used unsupervised and supervised computational tools to analyze detected and undetected elements; WebGestalt was used to explore functions encoded by genes in relevant clusters and performed experimental validation.
Results
We found a core cluster with 7,513 genes detected and shared by all samples, 4,321 genes in a cluster that was commonly absent, and 7,681 genes variably detected across the samples accounting for tumor heterogeneity. Relevant pathways identified in the core cluster relate to cell cycle, RNA transport, and DNA replication. We performed a kinome analysis of the core cluster and found 4 potential therapeutic kinase targets. Through analysis of the variably detected genes, we discovered 123 differentially expressed transcripts between bilateral and unilateral cases.
Conclusions
This novel analytical approach allowed determining the retinoblastoma transcriptomic size, a shared active transcriptomic core among the samples, potential therapeutic target kinases shared by all samples, transcripts related to inter tumor heterogeneity, and to determine transcriptomic profiles without the need of control tissues. This approach is useful to analyze other cancer or tissue types.
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Acknowledgements
We thank Microarray Core Facility at INMEGEN for experimental support, and Dra. Laura Gómez for valuable technical suggestions.
Funding
This work has been funded by IMSS grant R2015-785-049 and NIH grants CA167833, CA192662, CA98180 (MO) and scholarship by CONACYT to DEAS 407869.
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Contributions
DEAS, HT, algorithm design, programing, analysis, EHL outstanding bioinformatics support. MO clinical design and critical reading of the manuscript; MLCM and SSP tissue procurement and histopathological evaluations; AHA tumor tissue primary cultures; JC and LF validation design and facilities support; MVPC, RNA extraction overall study design, data interpretation, DEAS performed experimental validation, DEAS, HT and MVPC wrote the manuscript. All authors revised and approved the final manuscript.
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Ethics approval and consent to participate
Ethical considerations involved in this study have been addressed according to the Helsinki Declaration 2013. All Samples were obtained after parental informed consent to participate in a larger IRB approved case–control study. This study was approved by Comisión Nacional de Investigación Científica IMSS R2012-785–039 and Comisión de bioética y bioseguridad HIM/2012/054). It includes Rb patients treated at Hospital de Pediatría, at Centro Médico Nacional from Instituto Mexicano del Seguro Social (IMSS) and Hospital Infantil de México Federico Gómez in Mexico City.
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Not applicable.
Availability of data and materials
The data sets are available in NCBI’s Gene Expression Omnibus repository. Accession number GSE141209 https://www.ncbi.nlm.nih.gov/geo/query/acc.cgi?acc=GSE141209.
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The R script is available upon request.
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Alvarez-Suarez, D.E., Tovar, H., Hernández-Lemus, E. et al. Discovery of a transcriptomic core of genes shared in 8 primary retinoblastoma with a novel detection score analysis. J Cancer Res Clin Oncol 146, 2029–2040 (2020). https://doi.org/10.1007/s00432-020-03266-y
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DOI: https://doi.org/10.1007/s00432-020-03266-y