Bioinformatics of Brain Diseases

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microarray and RNA-seq technologies on the studied diseases will be pre-

sented in the following sections.

8.5.1

Microarray Studies

Brain tumors have received the most research attention among the diseases

and disorders under study. The prevalence of glioblastoma multiforme (GBM),

the most frequent form of glioma, is rising in many nations as a result of ad-

vancing age, errors in diagnosis, ionizing radiation, polluted air, and other

environmental factors [39]. Mostly tissue microarrays and transcript microar-

rays are used to analyze the gene expression patterns for these cancer types

[40]. For instance, Wang and coworkers performed a comprehensive evaluation

of 34 microarray datasets to identify a diagnostic tool for glioblastoma [41].

Here, they discovered that CBX3 silencing reduces the capacity of cells to pro-

liferate by stopping the cell cycle in the G2/M phase. In another study, Zhang

and coworkers aimed to identify prognostic markers of the disease through the

comparison of GBM microarray datasets, The Cancer Genome Atlas (TCGA),

and Chinese Glioma Genome Atlas (CGGA) [42]. They identified PRKCG,

PRKCB, and CAMK2A as possible prognostic indicators of GBM.

The most frequent primary intracranial neoplasm is meningioma and only

a very small portion of these tumors are malignant (around 1 %). Wede-

meyer and colleagues looked at the differences between specific tumors and

the neighboring normal dura, which is the top layer of the three meninges

that cover and safeguard the brain [43]. They also looked at copy number

variations and epigenetic changes. They performed whole-exome sequencing,

single-nucleotide polymorphism (SNP) and methylation array and identified

dysregulation of FOXC1. In another study Menghi and coworkers identified

CKS2 and LEPR as potential biomarkers of the disease performing DNA mi-

croarray on tumor tissues and blood samples of individuals with meningioma

[44].

Central nervous system lymphoma (CNSL) is a rare and incredibly ag-

gressive disease that appears in the white blood cells of the brain or spinal

cord. Villa and coworkers performed tissue microarray for primary CNSL with

diffuse large B-cell lymphoma [45]. Their population-based analysis demon-

strated that key molecular characteristics of primary CNSL are distinct from

those of systemic diffuse large B-cell lymphoma. In another study Takashima

and colleagues used total RNA extracted from tumor tissue of patients with

primary CNSL to identify distinct expression patterns of miRNAs [46]. Their

findings showed that miR-101/548b/554/1202, which are linked to cancer im-

munity, can serve as an effective predictive marker in PCNSL that may aid

in our understanding of the target pathways for PCNSL therapy.

Currently the most extensively studied neurodegenerative condition is

Alzheimer’s disease (AD). This is due to the unclear pathophysiology of the

condition and lack of a currently available treatment. Increases in life ex-

pectancy and the diagnosis of AD patients will have a significant negative