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Identification of potential microRNAs regulating metabolic plasticity and cellular phenotypes in glioblastoma

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Abstract

MicroRNAs (miRNAs) play important role in regulating cellular metabolism, and are currently being explored in cancer. As metabolic reprogramming in cancer is a major mediator of phenotypic plasticity, understanding miRNA-regulated metabolism will provide opportunities to identify miRNA targets that can regulate oncogenic phenotypes by taking control of cellular metabolism. In the present work, we studied the effect of differentially expressed miRNAs on metabolism, and associated oncogenic phenotypes in glioblastoma (GBM) using patient-derived data. Networks of differentially expressed miRNAs and metabolic genes were created and analyzed to identify important miRNAs that regulate major metabolism in GBM. Graph network-based approaches like network diffusion, backbone extraction, and different centrality measures were used to analyze these networks for identification of potential miRNA targets. Important metabolic processes and cellular phenotypes were annotated to trace the functional responses associated with these miRNA-regulated metabolic genes and associated phenotype networks. miRNA-regulated metabolic gene subnetworks of cellular phenotypes were extracted, and important miRNAs regulating these phenotypes were identified. The most important outcome of the study is the target miRNA combinations predicted for five different oncogenic phenotypes that can be tested experimentally for miRNA-based therapeutic design in GBM. Strategies implemented in the study can be used to generate testable hypotheses in other cancer types as well, and design context-specific miRNA-based therapy for individual patient. Their usability can be further extended to other gene regulatory networks in cancer and other genetic diseases.

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Acknowledgements

RB acknowledges Council of Scientific & Industrial Research (CSIR) for the Senior Research Fellowship (CSIR File No.: 31/011(1047)/2018-EMR-I dated 26-04-2018). RRS acknowledges CSIR-National Chemical Laboratory for funding support (MLP038826) to carry out this work.

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  1. Chemical Engineering and Process Development Division, CSIR-National Chemical Laboratory, Pune, Maharashtra, 411008, India

    Rupa Bhowmick & Ram Rup Sarkar

  2. Academy of Scientific and Innovative Research (AcSIR), Ghaziabad, 201002, India

    Rupa Bhowmick & Ram Rup Sarkar

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  1. Rupa Bhowmick
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RRS conceived and conceptualized the work. RB designed the methodologies, wrote and executed the computer programs and performed the simulations and analyses. RB wrote the original manuscript. RRS supervised the work, reviewed and edited the manuscript.

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Correspondence to Ram Rup Sarkar.

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Bhowmick, R., Sarkar, R.R. Identification of potential microRNAs regulating metabolic plasticity and cellular phenotypes in glioblastoma. Mol Genet Genomics 298, 161–181 (2023). https://doi.org/10.1007/s00438-022-01966-3

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