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Type 2 Diabetes Mellitus and its comorbidity, Alzheimer’s disease: Identifying critical microRNA using machine learning

MicroRNAs (miRNAs) are critical regulators of gene expression in healthy and diseased states, and numerous studies have established their tremendous potential as a tool for improving the diagnosis of Type 2 Diabetes Mellitus (T2D) and its comorbidities. In this regard, we computationally identify no...

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Autores principales: Alamro, Hind, Bajic, Vladan, Macvanin, Mirjana T., Isenovic, Esma R., Gojobori, Takashi, Essack, Magbubah, Gao, Xin
Formato: Online Artículo Texto
Lenguaje:English
Publicado: Frontiers Media S.A. 2023
Materias:
Acceso en línea:https://www.ncbi.nlm.nih.gov/pmc/articles/PMC9893111/
https://www.ncbi.nlm.nih.gov/pubmed/36743910
http://dx.doi.org/10.3389/fendo.2022.1084656
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author Alamro, Hind
Bajic, Vladan
Macvanin, Mirjana T.
Isenovic, Esma R.
Gojobori, Takashi
Essack, Magbubah
Gao, Xin
author_facet Alamro, Hind
Bajic, Vladan
Macvanin, Mirjana T.
Isenovic, Esma R.
Gojobori, Takashi
Essack, Magbubah
Gao, Xin
author_sort Alamro, Hind
collection PubMed
description MicroRNAs (miRNAs) are critical regulators of gene expression in healthy and diseased states, and numerous studies have established their tremendous potential as a tool for improving the diagnosis of Type 2 Diabetes Mellitus (T2D) and its comorbidities. In this regard, we computationally identify novel top-ranked hub miRNAs that might be involved in T2D. We accomplish this via two strategies: 1) by ranking miRNAs based on the number of T2D differentially expressed genes (DEGs) they target, and 2) using only the common DEGs between T2D and its comorbidity, Alzheimer’s disease (AD) to predict and rank miRNA. Then classifier models are built using the DEGs targeted by each miRNA as features. Here, we show the T2D DEGs targeted by hsa-mir-1-3p, hsa-mir-16-5p, hsa-mir-124-3p, hsa-mir-34a-5p, hsa-let-7b-5p, hsa-mir-155-5p, hsa-mir-107, hsa-mir-27a-3p, hsa-mir-129-2-3p, and hsa-mir-146a-5p are capable of distinguishing T2D samples from the controls, which serves as a measure of confidence in the miRNAs’ potential role in T2D progression. Moreover, for the second strategy, we show other critical miRNAs can be made apparent through the disease’s comorbidities, and in this case, overall, the hsa-mir-103a-3p models work well for all the datasets, especially in T2D, while the hsa-mir-124-3p models achieved the best scores for the AD datasets. To the best of our knowledge, this is the first study that used predicted miRNAs to determine the features that can separate the diseased samples (T2D or AD) from the normal ones, instead of using conventional non-biology-based feature selection methods.
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spelling pubmed-98931112023-02-03 Type 2 Diabetes Mellitus and its comorbidity, Alzheimer’s disease: Identifying critical microRNA using machine learning Alamro, Hind Bajic, Vladan Macvanin, Mirjana T. Isenovic, Esma R. Gojobori, Takashi Essack, Magbubah Gao, Xin Front Endocrinol (Lausanne) Endocrinology MicroRNAs (miRNAs) are critical regulators of gene expression in healthy and diseased states, and numerous studies have established their tremendous potential as a tool for improving the diagnosis of Type 2 Diabetes Mellitus (T2D) and its comorbidities. In this regard, we computationally identify novel top-ranked hub miRNAs that might be involved in T2D. We accomplish this via two strategies: 1) by ranking miRNAs based on the number of T2D differentially expressed genes (DEGs) they target, and 2) using only the common DEGs between T2D and its comorbidity, Alzheimer’s disease (AD) to predict and rank miRNA. Then classifier models are built using the DEGs targeted by each miRNA as features. Here, we show the T2D DEGs targeted by hsa-mir-1-3p, hsa-mir-16-5p, hsa-mir-124-3p, hsa-mir-34a-5p, hsa-let-7b-5p, hsa-mir-155-5p, hsa-mir-107, hsa-mir-27a-3p, hsa-mir-129-2-3p, and hsa-mir-146a-5p are capable of distinguishing T2D samples from the controls, which serves as a measure of confidence in the miRNAs’ potential role in T2D progression. Moreover, for the second strategy, we show other critical miRNAs can be made apparent through the disease’s comorbidities, and in this case, overall, the hsa-mir-103a-3p models work well for all the datasets, especially in T2D, while the hsa-mir-124-3p models achieved the best scores for the AD datasets. To the best of our knowledge, this is the first study that used predicted miRNAs to determine the features that can separate the diseased samples (T2D or AD) from the normal ones, instead of using conventional non-biology-based feature selection methods. Frontiers Media S.A. 2023-01-19 /pmc/articles/PMC9893111/ /pubmed/36743910 http://dx.doi.org/10.3389/fendo.2022.1084656 Text en Copyright © 2023 Alamro, Bajic, Macvanin, Isenovic, Gojobori, Essack and Gao https://creativecommons.org/licenses/by/4.0/This is an open-access article distributed under the terms of the Creative Commons Attribution License (CC BY). The use, distribution or reproduction in other forums is permitted, provided the original author(s) and the copyright owner(s) are credited and that the original publication in this journal is cited, in accordance with accepted academic practice. No use, distribution or reproduction is permitted which does not comply with these terms.
spellingShingle Endocrinology
Alamro, Hind
Bajic, Vladan
Macvanin, Mirjana T.
Isenovic, Esma R.
Gojobori, Takashi
Essack, Magbubah
Gao, Xin
Type 2 Diabetes Mellitus and its comorbidity, Alzheimer’s disease: Identifying critical microRNA using machine learning
title Type 2 Diabetes Mellitus and its comorbidity, Alzheimer’s disease: Identifying critical microRNA using machine learning
title_full Type 2 Diabetes Mellitus and its comorbidity, Alzheimer’s disease: Identifying critical microRNA using machine learning
title_fullStr Type 2 Diabetes Mellitus and its comorbidity, Alzheimer’s disease: Identifying critical microRNA using machine learning
title_full_unstemmed Type 2 Diabetes Mellitus and its comorbidity, Alzheimer’s disease: Identifying critical microRNA using machine learning
title_short Type 2 Diabetes Mellitus and its comorbidity, Alzheimer’s disease: Identifying critical microRNA using machine learning
title_sort type 2 diabetes mellitus and its comorbidity, alzheimer’s disease: identifying critical microrna using machine learning
topic Endocrinology
url https://www.ncbi.nlm.nih.gov/pmc/articles/PMC9893111/
https://www.ncbi.nlm.nih.gov/pubmed/36743910
http://dx.doi.org/10.3389/fendo.2022.1084656
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