A system biology approach to determine therapeutic targets by identifying molecular mechanisms and key pathways for type 2 diabetes that are linked to the development of tuberculosis and rheumatoid arthritis

Hasan, Md. Imran; Hossain, Md. Sanower; Bhuiyan, Piplu; Miah, Md Sipon; Rahman, Md. Habibur

doi:10.1016/j.lfs.2022.120483

Cited by 15 publications

(6 citation statements)

References 89 publications

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“…Interestingly some of these transcription factors have been identified as playing a role in adipose tissue development and/or diabetes. For example, it has been shown that GATA2 plays an important role in diabetes development and associated diseases ( 55 ). It has been described that hyperinsulinemia, observed during Type 2 diabetes, can activate NR2F2 which can induce development of different diseases ( 56 ).…”

Section: Discussionmentioning

confidence: 99%

Anthocyanin-rich extract from black beans exerts anti-diabetic effects in rats through a multi-genomic mode of action in adipose tissue

Damián-Medina¹,

Milenković²,

Salinas-Moreno³

et al. 2022

Front. Nutr.

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Black beans (BB) are an important source of a range of plant bioactive compounds including polyphenols, particularly anthocyanins. Several studies support that consumption of BB is associated with health benefits, including prevention of type 2 diabetes mellitus (T2DM). However, molecular mechanisms underlying the potential health properties of BB on adipose tissue (AT) are still largely unknown. The purpose of this study was to investigate multi-genomic effects of BB intake and identify regulatory networks potentially mediating T2DM on AT. Male Wistar diabetic rats consumed an anthocyanin-rich black bean extract for 5 weeks. Global gene expression from AT, protein coding and non-coding RNA profiles were determined using RNAseq. Biological function analyses were performed using a variety of bioinformatic tools. The evaluation of global gene expression profiles exhibited significant change following BB consumption with 406 significantly differentially expressed genes, 33 miRNA and 39 lncRNA and 3 snRNA. Functional analyses indicated that these genes play an important role in regulation of PI3K signaling, NIN/NF-kB signaling, insulin secretion, and endoplasmic reticulum (ER) organization. Interestingly, transcription factors such as GATA2, or POU2AF1 demonstrated to modulate their activity by BB extract by direct interaction with polyphenol metabolites, or by interactions with cell signaling proteins, like PKB, AKT or PI3K, that could control transcription factor activity and as a result impact on adipogenesis regulation. Therefore, the constant consumption of an anthocyanin-rich black bean extract may have anti-diabetic protective effects by modulating gene expression, resulting in a promising alternative for T2DM patients.

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Section: Discussionmentioning

confidence: 99%

Anthocyanin-rich extract from black beans exerts anti-diabetic effects in rats through a multi-genomic mode of action in adipose tissue

Damián-Medina¹,

Milenković²,

Salinas-Moreno³

et al. 2022

Front. Nutr.

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“…Studying protein–drug interactions is essential to comprehending the structural requirements for ligand affinity. 45,46 The DrugBank 47 dataset is also used to construct protein-drug interactions. We used this (version 1.0) 48 database to find potential medications that significantly interact with genes.…”

Section: Methodsmentioning

confidence: 99%

Molecular Biomarker Identification Using a Network-Based Bioinformatics Approach That Links COVID-19 With Smoking

Rahman

Amin

Yeasmin

et al. 2023

Bioinform Biol Insights

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The COVID-19 coronavirus, which primarily affects the lungs, is the source of the disease known as SARS-CoV-2. According to “Smoking and COVID-19: a scoping review,” about 32% of smokers had a severe case of COVID-19 pneumonia at their admission time and 15% of non-smokers had this case of COVID-19 pneumonia. We were able to determine which genes were expressed differently in each group by comparing the expression of gene transcriptomic datasets of COVID-19 patients, smokers, and healthy controls. In all, 37 dysregulated genes are common in COVID-19 patients and smokers, according to our analysis. We have applied all important methods namely protein-protein interaction, hub-protein interaction, drug-protein interaction, tf-gene interaction, and gene-MiRNA interaction of bioinformatics to analyze to understand deeply the connection between both smoking and COVID-19 severity. We have also analyzed Pathways and Gene Ontology where 5 significant signaling pathways were validated with previous literature. Also, we verified 7 hub-proteins, and finally, we validated a total of 7 drugs with the previous study.

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“…MAL2 gene expression was found to be upregulated in the subcutaneous adipose tissue of Huntington's disease patients [56]. A computational analysis of transcriptomic data showed MAL2 to be one of the strongest hub genes involved in signaling pathways in diabetes type 2 connected to tuberculosis and rheumatoid arthritis, although the contribution (if any) of MAL2 to the disease is unknown [57]. Altered PLLP expression has been related to a number of neurological diseases (e.g., schizophrenia, depressive disorder, and Alzheimer's disease), diabetes type 2, cornea degeneration, lung sarcoidosis, and hyperalphalipoproteinemia [40].…”

Section: Association With Non-cancerous Diseasesmentioning

confidence: 99%

The MAL Family of Proteins: Normal Function, Expression in Cancer, and Potential Use as Cancer Biomarkers

Labat-de-Hoz

Rubio-Ramos

Correas

et al. 2023

Cancers

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The MAL family of integral membrane proteins consists of MAL, MAL2, MALL, PLLP, CMTM8, MYADM, and MYADML2. The best characterized members are elements of the machinery that controls specialized pathways of membrane traffic and cell signaling. This review aims to help answer the following questions about the MAL-family genes: (i) is their expression regulated in cancer and, if so, how? (ii) What role do they play in cancer? (iii) Might they have biomedical applications? Analysis of large-scale gene expression datasets indicated altered levels of MAL-family transcripts in specific cancer types. A comprehensive literature search provides evidence of MAL-family gene dysregulation and protein function repurposing in cancer. For MAL, and probably for other genes of the family, dysregulation is primarily a consequence of gene methylation, although copy number alterations also contribute to varying degrees. The scrutiny of the two sources of information, datasets and published studies, reveals potential prognostic applications of MAL-family members as cancer biomarkers—for instance, MAL2 in breast cancer, MAL2 and MALL in pancreatic cancer, and MAL and MYADM in lung cancer—and other biomedical uses. The availability of validated antibodies to some MAL-family proteins sanctions their use as cancer biomarkers in routine clinical practice.

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A system biology approach to determine therapeutic targets by identifying molecular mechanisms and key pathways for type 2 diabetes that are linked to the development of tuberculosis and rheumatoid arthritis

Cited by 15 publications

References 89 publications

Anthocyanin-rich extract from black beans exerts anti-diabetic effects in rats through a multi-genomic mode of action in adipose tissue

Anthocyanin-rich extract from black beans exerts anti-diabetic effects in rats through a multi-genomic mode of action in adipose tissue

Molecular Biomarker Identification Using a Network-Based Bioinformatics Approach That Links COVID-19 With Smoking

The MAL Family of Proteins: Normal Function, Expression in Cancer, and Potential Use as Cancer Biomarkers

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