Exploring celiac disease candidate pathways by global gene expression profiling and gene network cluster analysis

Banaganapalli, Babajan; Mansour, Haifa; Mohammed, Arif; Alharthi, Arwa Mastoor; Aljuaid, Nada Mohammed; Nasser, Khalidah Khalid; Ahmad, Aftab; Saadah, Omar I.; Al‐Aama, Jumana Y.; Shaik, Noor Ahmad

doi:10.1038/s41598-020-73288-6

Cited by 24 publications

(23 citation statements)

References 61 publications

(74 reference statements)

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“…ApoA-I is a major structural and functional component of HDL, and is considered to play an essential role in reducing CAD risk. 28 ApoB is the main apolipoprotein of chylomicrons and LDL-C, and may contribute to atherogenesis. 29 The ApoB/ApoA-I ratio was found to be associated with CAD risk.…”

Section: Discussionmentioning

confidence: 99%

Apolipoprotein E Gene Polymorphism and Coronary Artery Disease Risk Among Patients in Northwest China

Ma¹,

Ren²,

Zhang³

et al. 2021

PGPM

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Purpose The association between apolipoprotein E (ApoE) gene polymorphisms and the risk of coronary artery disease (CAD) among different populations has been assessed in numerous previous studies, but the results remain inconclusive. The present study aimed to determine the role of ApoE genotypes in CAD risk and the interrelationships between lipid profiles and ApoE alleles and genotypes among the population of northwest China. Patients and Methods This study was performed on 308 patients with CAD and 308 control participants. ApoE gene polymorphism was analysed using the polymerase chain reaction and hybridization. Results The findings indicated that the frequencies of ε3/ε4 genotype and ε4 allele frequency were significantly higher in patients with CAD than in the control participants. ε2 carriers had significantly lower total cholesterol (TC), low-density lipoprotein cholesterol (LDL-C) and triglycerides (TG) levels than did ε3 or ε4 carriers among the control participants. However, our study found no significant differences in plasma lipoprotein levels between ɛ2, ɛ3 and ɛ4 carriers in patients with CAD. Moreover, ε4 carriers had significantly higher ApoB, ApoB/ApoA-I levels and significantly lower ApoE levels in both patients with CAD and control participants. ε4 allele presence was associated with a nearly two-fold higher CAD risk. After adjusting for other established risk factors, ε4 allele was an independent risk factor for CAD. After stratified by age (≤ 60 years and >60 years), ε4 allele was indicated to increase the CAD risk 3.3-fold in elderly patients with CAD, but not in young patients with CAD. After stratified by sex, ε4 allele was not a risk factor in females and males patients with CAD. Conclusion This study provides evidence that the ε4 allele, drinking, smoking, hypertension, and TG and ApoE levels are independent risk factor for CAD among patients in northwest China.

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Section: Discussionmentioning

confidence: 99%

Apolipoprotein E Gene Polymorphism and Coronary Artery Disease Risk Among Patients in Northwest China

Ma¹,

Ren²,

Zhang³

et al. 2021

PGPM

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“…The genome wide gene expression data is a proven resource to identify biological pathways underlying human diseases [ 43 ] [ 44 ], including viral infections [ 45 ]. Few studies have reported gene expression changes in SARS‐CoV‐2 infected clinical samples using in vivo, in vitro or ex vivo approaches [ 46 ] [ 47 ].…”

Section: Discussionmentioning

confidence: 99%

Multilevel systems biology analysis of lung transcriptomics data identifies key miRNAs and potential miRNA target genes for SARS-CoV-2 infection

Banaganapalli

Alrayes²,

Awan

et al. 2021

Computers in Biology and Medicine

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Background The spread of a novel severe acute respiratory syndrome corona virus 2 (SARS-CoV-2) has affected both the public health and the global economy. The current study was aimed at analysing the genetic sequence of this highly contagious corona virus from an evolutionary perspective, comparing the genetic variation features of different geographic strains, and identifying the key miRNAs as well as their gene targets from the transcriptome data of viral infected lung tissues. Methods A multilevel robust computational analysis was undertaken for viral genetic sequence alignment, phylogram construction, genome-wide transcriptome data interpretation of virus-infected lung tissues, miRNA mapping, and functional biology networking. Results Our findings show both genetic similarities as well as notable differences in the S protein length among SARS-CoV-1, SARS-CoV-2 and MERS viruses. All SARS-CoV-2 strains showed a high genetic similarity with the parent Wuhan strain, but Saudi Arabian, South African, USA, Russia and New Zealand strains carry 3 additional genetic variations like P333L (RNA -dependant RNA polymerase), D614G (spike), and P4715L (ORF1ab). The infected lung tissues demonstrated the upregulation of 282 (56.51%) antiviral defensive response pathway genes and downregulation of 217 (43.48%) genes involved in autophagy and lung repair pathways. By miRNA mapping, 4 key miRNAs ( hsa-miR-342-5p, hsa-miR-432-5p, hsa-miR-98-5p and hsa-miR-17-5p ), targeting multiple host genes ( MYC, IL6, ICAM1 and VEGFA ) as well as SARS-CoV2 gene ( ORF1ab ) were identified. Conclusion Systems biology methods offer a new perspective in understanding the molecular reasons underlying the faster spread of SARS-CoV-2 infection. The antiviral miRNAs identified in this study may aid in the ongoing search for novel personalized therapeutic avenues for COVID patients.

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“…These pathways have been associated with villous atrophy and a high level of intraepithelial lymphocytes (IELs). All this information could provide important data in the future regarding the discovery of biomarkers useful in the prognosis, diagnosis and treatment of CD [8,9]. The role of the Wnt pathway in the gastrointestinal tract is to preserve the self-renewal capacity of epithelial stem cells.…”

Section: Introductionmentioning

confidence: 99%

Expression of Selected Genes and Circulating microRNAs in Patients with Celiac Disease

et al. 2022

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Background and Objectives: Celiac disease (CD) is an immune-mediated enteropathy with characteristic intestinal alterations. CD occurs as a chronic inflammation secondary to gluten sensitivity in genetically susceptible individuals. Until now, the exact cause of the disease has not been established, which is why new studies have appeared that address the involvement of various genes and microRNAs (miRNAs) in the pathogenesis. The aim of the study is to describe the expression of selected genes (Wnt family member 3, WNT3; Wnt family member 11, WNT11; tumor necrosis factor alpha, TNFα; mitogen-activated protein kinase 1, MAPK1; AKT serine/threonine kinase 3, AKT3; phosphatidylinositol-4,5-bisphosphate 3-kinase catalytic subunit alpha, PIK3CA; and cyclin D1, CCND1) and miRNAs (miR-192-5p, miR-194-5p, miR-449a and miR-638) in adult patients with CD. Materials and Methods: In total, 15 patients with CD at diagnosis (newly diagnosed), 33 patients on a gluten-free diet (GFD) for at least 1 year and 10 controls (control) were prospectively included. Blood samples were evaluated by quantitative real-time polymerase chain reaction (qRT-PCR). Results: The results show that TNFα, MAPK1 and CCND1 were significantly overexpressed (p = 0.0249, p = 0.0019 and p = 0.0275, respectively) when comparing the newly diagnosed group to the controls. The other genes studied in CD patients were mostly with high values compared to controls, without reaching statistical significance. Among the miRNAs, the closest to a statistically significant value was miR-194-5p when the newly diagnosed group versus control (p = 0.0510) and GFD group versus control (p = 0.0671) were compared. The DIANA and miRNet databases identified significant functional activity for miR-449a and miR-192-5p and an interconnection of miR-194-5p and miR-449a with CCND1. Conclusions: In conclusion, genes and circulating miRNAs require further studies as they could represent important biomarkers in clinical practice.

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Exploring celiac disease candidate pathways by global gene expression profiling and gene network cluster analysis

Cited by 24 publications

References 61 publications

Apolipoprotein E Gene Polymorphism and Coronary Artery Disease Risk Among Patients in Northwest China

Apolipoprotein E Gene Polymorphism and Coronary Artery Disease Risk Among Patients in Northwest China

Multilevel systems biology analysis of lung transcriptomics data identifies key miRNAs and potential miRNA target genes for SARS-CoV-2 infection

Expression of Selected Genes and Circulating microRNAs in Patients with Celiac Disease

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