Strategies for activity analysis of single nucleotide polymorphisms associated with human diseases

Ren, Naixia; Dai, Shang-Kun; Ma, Shumin; Yang, Fengtang

doi:10.1111/cge.14282

Cited by 3 publications

(4 citation statements)

References 117 publications

(210 reference statements)

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“…In the introduction, we discussed the advantages of using SNPs as IVs for MR. On the one hand, SNPs exist before acquired exposure, ensuring that causal estimations are unaffected by reverse causality. Furthermore, SNPs are inherited separately from other features and are unaffected by other confounding variables [ 14 ]. As a result, we used the most recent and comprehensive population genetic variation data from publicly accessible sources for MR analysis.…”

Section: Methodsmentioning

confidence: 99%

“…MR uses SNPs to infer causal relationships between exposures and outcomes. Its benefit is that SNPs exist before acquired exposure, and the correlation with the outcome follows a causal, temporal relationship and is unaffected by acquired environmental, social, and other confounding factors [ 14 ]. Independent sample MR, two-sample MR, multivariate MR, and bidirectional MR extensively investigate the causal association between risk factors and diseases [ 15 , 16 , 17 ].…”

Section: Introductionmentioning

confidence: 99%

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Identifying Proteins and Amino Acids Associated with Liver Cancer Risk: A Study Utilizing Mendelian Randomization and Bulk RNA Sequencing Analysis

Ma,

Tang,

Yao

et al. 2024

JPM

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Background: Primary liver cancer (PLC) ranks third in terms of fatality rate among all malignant tumors worldwide. Proteomics and metabolomics have become widely utilized in identifying causes and diagnostic indicators of PLC. Nevertheless, in studies aiming to identify proteins/metabolites that experienced significant changes before PLC, the potential impact of reverse causation and confounding variables still needs to be fully addressed. Methods: This study thoroughly investigated the causal relationship between 4719 blood proteins, 21 amino acids, and the risk of PLC using the Mendelian randomization (MR) method. In addition, through a comprehensive analysis of the TCGA-LIHC cohort and GEO databases, we evaluated the differentially expressed genes (DEGs) related to serine metabolism in diagnosing and predicting the prognosis of patients with PLC. Results: A total of 63 proteins have been identified as connected to the risk of PLC. Additionally, there has been confirmation of a positive cause–effect between PLC and the concentration of serine. The integration of findings from both MR analyses determined that the protein associated with PLC risk exhibited a significant correlation with serine metabolism. Upon careful analysis of the TCGA-LIHC cohort, it was found that eight DEGs are linked to serine metabolism. After thoroughly validating the GEO database, two DEGs, TDO2 and MICB, emerged as potential biomarkers for diagnosing PLC. Conclusions: Two proteins involved in serine metabolism, MICB and TDO2, are causally linked to the risk of PLC and could potentially be used as diagnostic indicators.

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Section: Methodsmentioning

confidence: 99%

Section: Introductionmentioning

confidence: 99%

Identifying Proteins and Amino Acids Associated with Liver Cancer Risk: A Study Utilizing Mendelian Randomization and Bulk RNA Sequencing Analysis

Ma,

Tang,

Yao

et al. 2024

JPM

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“…Nevertheless, the pathogenic effects of such molecular markers can be eliminated by changing lifestyle [48], breaking unhealthy habits [49], using low-molecular inhibitors of proteins encoded by the corresponding genes as medicines against excess of these proteins [50], using exogenous recombinant human proteins to compensate for the lack of these proteins caused by the corresponding SNPs [51] and using short antisense oligonucleotides as pharmacotherapy treatment of SNP-promoted misregulation of human gene expression [52]. That is why regulatory SNP markers are becoming more and more in focus as personalized medicine progresses [53].…”

Section: Introductionmentioning

confidence: 99%

Candidate SNP Markers Significantly Altering the Affinity of TATA-Binding Protein for the Promoters of Human Hub Genes for Atherogenesis, Atherosclerosis and Atheroprotection

Bogomolov

Filonov

Chadaeva

et al. 2023

IJMS

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Atherosclerosis is a systemic disease in which focal lesions in arteries promote the build-up of lipoproteins and cholesterol they are transporting. The development of atheroma (atherogenesis) narrows blood vessels, reduces the blood supply and leads to cardiovascular diseases. According to the World Health Organization (WHO), cardiovascular diseases are the leading cause of death, which has been especially boosted since the COVID-19 pandemic. There is a variety of contributors to atherosclerosis, including lifestyle factors and genetic predisposition. Antioxidant diets and recreational exercises act as atheroprotectors and can retard atherogenesis. The search for molecular markers of atherogenesis and atheroprotection for predictive, preventive and personalized medicine appears to be the most promising direction for the study of atherosclerosis. In this work, we have analyzed 1068 human genes associated with atherogenesis, atherosclerosis and atheroprotection. The hub genes regulating these processes have been found to be the most ancient. In silico analysis of all 5112 SNPs in their promoters has revealed 330 candidate SNP markers, which statistically significantly change the affinity of the TATA-binding protein (TBP) for these promoters. These molecular markers have made us confident that natural selection acts against underexpression of the hub genes for atherogenesis, atherosclerosis and atheroprotection. At the same time, upregulation of the one for atheroprotection promotes human health.

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“…A review reported that MIR215, MIR487A , and MIR502 are diagnostic and prognostic biomarkers in stable CAD [18]. SNPs are the most common type of genetic variation in human genomes which are mostly located in non-coding regions [19]. MiR-SNPs change the levels of miRNA expression, which increases one’s vulnerability to a number of diseases [20].…”

Section: Introductionmentioning

confidence: 99%

The potential impact of microRNA-related functional polymorphisms in the pathogenesis of coronary heart disease

Haq,

Ali,

Rehman

et al. 2023

Preprint

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MicroRNAs (miRNA) are important post-transcriptional gene regulators. Various populations have experienced a marked rise in the risk of coronary heart disease (CHD) due to multiple miRNA variations. The current case-control study (150 cases and 150 healthy controls) was designed to determine the potential role of five miRNA functional variants (rs2292832, rs3746444, rs11614913, rs1044165, and rs767649) as risk factors for CHD in the Pakistani population using TaqMan Real-time PCR Assay. It was observed that the single nucleotide polymorphism (SNP) rs3746444 was significantly associated with the risk of CHD using the co-dominant model [χ2 =79.51; P = 0.0001], dominant model (GG vs AA+AG) [OR = 9.333 (5.180-16.82); P = 0.0001], heterozygous model (AG vs AA+GG) [OR = 0.1241 (0.065-0.234); P = 0.0001] and additive model [A vs G; OR = 0.3440 (0.2468-0.4795); P = 0.0001] respectively. Furthermore, rs11614913 was also linked with CHD when analyzed using a co-dominant model [χ2 =16.24; P = 0.0003], dominant model (CC vs CT+TT) [OR = 1.918 (1.210-3.042); P = 0.0075], recessive model (TT vs CT+CC) [OR = 0.2754 (0.1369-0.5540); P = 0.0002], and additive model [OR = 2.033 (1.445-2.861); P = 0.0001]. It was also found that rs767649 is connected to CHD using a co-dominant model [χ2 =114.9; P = 0.0001], dominant model (AA vs AT+TT) [OR = 7.851 (3.554-17.34); P = 0.0001], recessive model (TT vs AT+AA) [OR = 0.04956 (0.026-0.092); P = 0.0001], heterozygous model (AT vs AA+TT) [OR = 4.495 (2.737-7.382); P = 0.0001], and inheritance additive model [A vs T; OR=7.154 (4.902-10.44); P = 0.0001] respectively. The SNP rs1044165 revealed a strong correlation with CHD using the heterozygous inheritance model (AG vs GG+AA) [OR = 0.3442 (0.1308-0.9055); P = 0.0276]. No statistically significant association (P ˃ 0.05) of rs2292832 SNP with CHD was found using all five inheritance models.

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Strategies for activity analysis of single nucleotide polymorphisms associated with human diseases

Cited by 3 publications

References 117 publications

Identifying Proteins and Amino Acids Associated with Liver Cancer Risk: A Study Utilizing Mendelian Randomization and Bulk RNA Sequencing Analysis

Identifying Proteins and Amino Acids Associated with Liver Cancer Risk: A Study Utilizing Mendelian Randomization and Bulk RNA Sequencing Analysis

Candidate SNP Markers Significantly Altering the Affinity of TATA-Binding Protein for the Promoters of Human Hub Genes for Atherogenesis, Atherosclerosis and Atheroprotection

The potential impact of microRNA-related functional polymorphisms in the pathogenesis of coronary heart disease

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