Determination of molecular signatures and pathways common to brain tissues of autism spectrum disorder: Insights from comprehensive bioinformatics approach

Bristy, Sadia Afrin; Islam, Aminul; Andalib, K.M. Salim; Khan, Umama; Awal, Md. Abdul; Rahman, Habibur

doi:10.1016/j.imu.2022.100871

Cited by 13 publications

(3 citation statements)

References 99 publications

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“…The present results are aligned with reports that mutations in Suz12 have been associated with MIA-related autism spectrum disorder phenotypes [ 64 ]. The association of many differentially expressed genes to TCF7L1 is supported by a meta-analysis of transcriptome experiments that associated this transcription factor with autism spectrum disorder [ 65 ].…”

Section: Discussionmentioning

confidence: 99%

Prenatal and postnatal challenges affect the hypothalamic molecular pathways that regulate hormonal levels

Rodriguez-Zas,

Southey,

Rund

et al. 2023

PLoS ONE

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This study aimed to improve our understanding of how the hypothalamus mediates the effects of prenatal and postnatal challenges on behavior and sensitivity to stimuli. A pig model of virally initiated maternal immune activation (MIA) was used to investigate potential interactions of the prenatal challenge both with sex and with postnatal nursing withdrawal. The hypothalami of 72 females and males were profiled for the effects of MIA and nursing withdrawal using RNA-sequencing. Significant differential expression (FDR-adjusted p value < 0.05) was detected in the profile of 222 genes. Genes involved in the Gene Ontology biological process of regulation of hormone levels tended to be over-expressed in individuals exposed to both challenges relative to individuals exposed to either one challenge, and most of these genes were over-expressed in MIA females relative to males across nursing levels. Differentially expressed genes included Fshb, Ttr, Agrp, Gata3, Foxa2, Tfap2b, Gh1, En2, Cga, Msx1, and Npy. The study also found that prenatal and postnatal challenges, as well as sex, impacted the regulation of neurotransmitter activity and immune effector processes in the hypothalamus. In particular, the olfactory transduction pathway genes were over-expressed in weaned MIA males, and several transcription factors were potentially found to target the differentially expressed genes. Overall, these results highlight how multiple environmental challenges can interact and affect the molecular mechanisms of the hypothalamus, including hormonal, immune response, and neurotransmitter processes.

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Section: Discussionmentioning

confidence: 99%

Prenatal and postnatal challenges affect the hypothalamic molecular pathways that regulate hormonal levels

Rodriguez-Zas,

Southey,

Rund

et al. 2023

PLoS ONE

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“…Gene set enrichment analysis identifies DEGs from a large set of genes linked to disease symptoms using a number of statistical approaches. 29 , 30 Figure 1 visualizes the steps involved in data acquisition and identifying DEGs also shows the analytical approaches in a nutshell. GSE64810 and GSE95343 shared a total of 162 common genes, whereas 106 genes were up-regulated and 56 genes were down-regulated.…”

Section: Materials and Methodologymentioning

confidence: 99%

A Comprehensive Bioinformatics Approach to Identify Molecular Signatures and Key Pathways for the Huntington Disease

Meem,

Khan,

Mredul

et al. 2023

Bioinform Biol Insights

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Huntington disease (HD) is a degenerative brain disease caused by the expansion of CAG (cytosine-adenine-guanine) repeats, which is inherited as a dominant trait and progressively worsens over time possessing threat. Although HD is monogenetic, the specific pathophysiology and biomarkers are yet unknown specifically, also, complex to diagnose at an early stage, and identification is restricted in accuracy and precision. This study combined bioinformatics analysis and network-based system biology approaches to discover the biomarker, pathways, and drug targets related to molecular mechanism of HD etiology. The gene expression profile data sets GSE64810 and GSE95343 were analyzed to predict the molecular markers in HD where 162 mutual differentially expressed genes (DEGs) were detected. Ten hub genes among them ( DUSP1, NKX2-5, GLI1, KLF4, SCNN1B, NPHS1, SGK2, PITX2, S100A4, and MSX1) were identified from protein-protein interaction (PPI) network which were mostly expressed as down-regulated. Following that, transcription factors (TFs)-DEGs interactions (FOXC1, GATA2, etc), TF-microRNA (miRNA) interactions (hsa-miR-340, hsa-miR-34a, etc), protein-drug interactions, and disorders associated with DEGs were predicted. Furthermore, we used gene set enrichment analysis (GSEA) to emphasize relevant gene ontology terms (eg, TF activity, sequence-specific DNA binding) linked to DEGs in HD. Disease interactions revealed the diseases that are linked to HD, and the prospective small drug molecules like cytarabine and arsenite was predicted against HD. This study reveals molecular biomarkers at the RNA and protein levels that may be beneficial to improve the understanding of molecular mechanisms, early diagnosis, as well as prospective pharmacologic targets for designing beneficial HD treatment.

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“…PPIs regulate a vast variety of biological activities, and physiological activities notably tissue connectivity as well as developmental management [ 43 ]. To build the PPI network and identify the associated genes or protein databases, we utilized a well-known search program STRING ( http://string-db.org ).…”

Section: Methodsmentioning

confidence: 99%

An integrated complete-genome sequencing and systems biology approach to predict antimicrobial resistance genes in the virulent bacterial strains of Moraxella catarrhalis

Bristy¹,

Hossain

Hasan

et al. 2023

Briefings in Functional Genomics

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Moraxella catarrhalis is a symbiotic as well as mucosal infection-causing bacterium unique to humans. Currently, it is considered as one of the leading factors of acute middle ear infection in children. As M. catarrhalis is resistant to multiple drugs, the treatment is unsuccessful; therefore, innovative and forward-thinking approaches are required to combat the problem of antimicrobial resistance (AMR). To better comprehend the numerous processes that lead to antibiotic resistance in M. catarrhalis, we have adopted a computational method in this study. From the NCBI-Genome database, we investigated 12 strains of M. catarrhalis. We explored the interaction network comprising 74 antimicrobial-resistant genes found by analyzing M. catarrhalis bacterial strains. Moreover, to elucidate the molecular mechanism of the AMR system, clustering and the functional enrichment analysis were assessed employing AMR gene interactions networks. According to the findings of our assessment, the majority of the genes in the network were involved in antibiotic inactivation; antibiotic target replacement, alteration and antibiotic efflux pump processes. They exhibit resistance to several antibiotics, such as isoniazid, ethionamide, cycloserine, fosfomycin, triclosan, etc. Additionally, rpoB, atpA, fusA, groEL and rpoL have the highest frequency of relevant interactors in the interaction network and are therefore regarded as the hub nodes. These genes can be exploited to create novel medications by serving as possible therapeutic targets. Finally, we believe that our findings could be useful to advance knowledge of the AMR system present in M. catarrhalis.

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Determination of molecular signatures and pathways common to brain tissues of autism spectrum disorder: Insights from comprehensive bioinformatics approach

Cited by 13 publications

References 99 publications

Prenatal and postnatal challenges affect the hypothalamic molecular pathways that regulate hormonal levels

Prenatal and postnatal challenges affect the hypothalamic molecular pathways that regulate hormonal levels

A Comprehensive Bioinformatics Approach to Identify Molecular Signatures and Key Pathways for the Huntington Disease

An integrated complete-genome sequencing and systems biology approach to predict antimicrobial resistance genes in the virulent bacterial strains of Moraxella catarrhalis

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